y*g
2 楼
一小朋友问一富翁说，叔叔你为什么这么有钱？富翁摸摸小朋友的头说，小时候我爸给
了我一个苹果，我卖掉它有了两个苹果，后来我又赚了四个苹果。小朋友若有所思地说
，哦…叔叔，我好像懂了。富翁说：“你懂你妹啊，后来我爸死了，我继承了他的财产
……”
给创业者提个醒，不要痴迷于从阅读成功人士的传记中需找经验，这些书大部分经
过了精致的包装，很多重要的事实都不会告诉你。
例如，盖茨的书不会告诉你他母亲是ＩＢＭ董事，是她给儿子促成了第一单大生意
，巴菲特的书只会告诉你他８岁就知道去参观纽交所，但不会告诉你他国会议员的父亲
带他去的，是高盛的董事接待的。
了我一个苹果，我卖掉它有了两个苹果，后来我又赚了四个苹果。小朋友若有所思地说
，哦…叔叔，我好像懂了。富翁说：“你懂你妹啊，后来我爸死了，我继承了他的财产
……”
给创业者提个醒，不要痴迷于从阅读成功人士的传记中需找经验，这些书大部分经
过了精致的包装，很多重要的事实都不会告诉你。
例如，盖茨的书不会告诉你他母亲是ＩＢＭ董事，是她给儿子促成了第一单大生意
，巴菲特的书只会告诉你他８岁就知道去参观纽交所，但不会告诉你他国会议员的父亲
带他去的，是高盛的董事接待的。
m*g
3 楼
本来在开始读PhD的时候，就打算要广泛阅读主流学术杂志，比如Nature, Science,
PNAS, Plos genetics等等，但是自己总是拖拖拉拉，偶尔有心血来潮就一口气读很久
，没兴趣／时间的话就个把月都不翻一下。
就好比动漫监督需要看其他畅销动漫（暴露兴趣了，太不学术了），我们也应该多多看
看生物的杂志，以增强自己对整个领域的理解，并且了解一些文献的逻辑、方法和写法
。所以我打算开这个贴说说每周最喜欢的几篇文章什么的，每周一更（日期不定），以
监督自己，防止自己不读文献。如果没有做到，请大家不要用砖头砸，把好吃的狠狠地
砸过来就好了，然后再狠狠地鄙视我就好。
我是学遗传进化方向的，做实验和编程都做一点（但是为什么现在还这么菜呢，果然是
因为我太懒惰了），总之看看文献没有坏处，也欢迎相似方向的大家一起来贴贴推荐的
本周的文献吧（当然，如果不是本周也OK的）。
今天是星期一，就从这周开始啦。格式啥的都无所谓，可以发些critical的评论什么的
（不过至少应该写出标题^_^）。好像没看到这个论坛有类似的帖子（可能是我的“近
视度”太高，没注意到）。总之，大家多多支持，一起交流努力啦。
PNAS, Plos genetics等等，但是自己总是拖拖拉拉，偶尔有心血来潮就一口气读很久
，没兴趣／时间的话就个把月都不翻一下。
就好比动漫监督需要看其他畅销动漫（暴露兴趣了，太不学术了），我们也应该多多看
看生物的杂志，以增强自己对整个领域的理解，并且了解一些文献的逻辑、方法和写法
。所以我打算开这个贴说说每周最喜欢的几篇文章什么的，每周一更（日期不定），以
监督自己，防止自己不读文献。如果没有做到，请大家不要用砖头砸，把好吃的狠狠地
砸过来就好了，然后再狠狠地鄙视我就好。
我是学遗传进化方向的，做实验和编程都做一点（但是为什么现在还这么菜呢，果然是
因为我太懒惰了），总之看看文献没有坏处，也欢迎相似方向的大家一起来贴贴推荐的
本周的文献吧（当然，如果不是本周也OK的）。
今天是星期一，就从这周开始啦。格式啥的都无所谓，可以发些critical的评论什么的
（不过至少应该写出标题^_^）。好像没看到这个论坛有类似的帖子（可能是我的“近
视度”太高，没注意到）。总之，大家多多支持，一起交流努力啦。
P*t
4 楼
贵!!!
【在 w***u 的大作中提到】
: 感觉挺贵，一般多少钱比较合适？
: 另外预防针可以让自己的家庭医生打，保险COVER吗？
T*U
5 楼
我真的不懂，被忽悠了。
b*s
6 楼
支持。虽然我不是做这个方向的。但是对这个方向一直很有兴趣。
【在 m******g 的大作中提到】
: 本来在开始读PhD的时候，就打算要广泛阅读主流学术杂志，比如Nature, Science,
: PNAS, Plos genetics等等，但是自己总是拖拖拉拉，偶尔有心血来潮就一口气读很久
: ，没兴趣／时间的话就个把月都不翻一下。
: 就好比动漫监督需要看其他畅销动漫（暴露兴趣了，太不学术了），我们也应该多多看
: 看生物的杂志，以增强自己对整个领域的理解，并且了解一些文献的逻辑、方法和写法
: 。所以我打算开这个贴说说每周最喜欢的几篇文章什么的，每周一更（日期不定），以
: 监督自己，防止自己不读文献。如果没有做到，请大家不要用砖头砸，把好吃的狠狠地
: 砸过来就好了，然后再狠狠地鄙视我就好。
: 我是学遗传进化方向的，做实验和编程都做一点（但是为什么现在还这么菜呢，果然是
: 因为我太懒惰了），总之看看文献没有坏处，也欢迎相似方向的大家一起来贴贴推荐的
【在 m******g 的大作中提到】
: 本来在开始读PhD的时候，就打算要广泛阅读主流学术杂志，比如Nature, Science,
: PNAS, Plos genetics等等，但是自己总是拖拖拉拉，偶尔有心血来潮就一口气读很久
: ，没兴趣／时间的话就个把月都不翻一下。
: 就好比动漫监督需要看其他畅销动漫（暴露兴趣了，太不学术了），我们也应该多多看
: 看生物的杂志，以增强自己对整个领域的理解，并且了解一些文献的逻辑、方法和写法
: 。所以我打算开这个贴说说每周最喜欢的几篇文章什么的，每周一更（日期不定），以
: 监督自己，防止自己不读文献。如果没有做到，请大家不要用砖头砸，把好吃的狠狠地
: 砸过来就好了，然后再狠狠地鄙视我就好。
: 我是学遗传进化方向的，做实验和编程都做一点（但是为什么现在还这么菜呢，果然是
: 因为我太懒惰了），总之看看文献没有坏处，也欢迎相似方向的大家一起来贴贴推荐的
n*3
7 楼
太贵了
s*s
8 楼
不错
e*o
9 楼
支持，最好将通俗一些。让俺这转行的也能看懂。
w*u
10 楼
那一般体检加两针，应该多少钱
【在 P*****t 的大作中提到】
:
: 贵!!!
【在 P*****t 的大作中提到】
:
: 贵!!!
c*7
11 楼
=。=原来都是富二代啊。。。
s*y
12 楼
支持。我也喜欢看相关文章，可是我也特别懒。你能讲讲一些最新进展那可是最好不过
了。
【在 m******g 的大作中提到】
: 本来在开始读PhD的时候，就打算要广泛阅读主流学术杂志，比如Nature, Science,
: PNAS, Plos genetics等等，但是自己总是拖拖拉拉，偶尔有心血来潮就一口气读很久
: ，没兴趣／时间的话就个把月都不翻一下。
: 就好比动漫监督需要看其他畅销动漫（暴露兴趣了，太不学术了），我们也应该多多看
: 看生物的杂志，以增强自己对整个领域的理解，并且了解一些文献的逻辑、方法和写法
: 。所以我打算开这个贴说说每周最喜欢的几篇文章什么的，每周一更（日期不定），以
: 监督自己，防止自己不读文献。如果没有做到，请大家不要用砖头砸，把好吃的狠狠地
: 砸过来就好了，然后再狠狠地鄙视我就好。
: 我是学遗传进化方向的，做实验和编程都做一点（但是为什么现在还这么菜呢，果然是
: 因为我太懒惰了），总之看看文献没有坏处，也欢迎相似方向的大家一起来贴贴推荐的
了。
【在 m******g 的大作中提到】
: 本来在开始读PhD的时候，就打算要广泛阅读主流学术杂志，比如Nature, Science,
: PNAS, Plos genetics等等，但是自己总是拖拖拉拉，偶尔有心血来潮就一口气读很久
: ，没兴趣／时间的话就个把月都不翻一下。
: 就好比动漫监督需要看其他畅销动漫（暴露兴趣了，太不学术了），我们也应该多多看
: 看生物的杂志，以增强自己对整个领域的理解，并且了解一些文献的逻辑、方法和写法
: 。所以我打算开这个贴说说每周最喜欢的几篇文章什么的，每周一更（日期不定），以
: 监督自己，防止自己不读文献。如果没有做到，请大家不要用砖头砸，把好吃的狠狠地
: 砸过来就好了，然后再狠狠地鄙视我就好。
: 我是学遗传进化方向的，做实验和编程都做一点（但是为什么现在还这么菜呢，果然是
: 因为我太懒惰了），总之看看文献没有坏处，也欢迎相似方向的大家一起来贴贴推荐的
m*c
13 楼
It is ridiculous and too expensive. but the price varies from regions to
regions. your city must be a big city.
I just did it and was fooled by the doctor and nurse, although I thought I
prepared well and they should be
honest. They lied and said my negative result actually might be a positive
result. They did not follow the
procedures, and asked me to take Chest X ray for TB, which cost 30 dollars,
plus basic 50 dollar physical
examination fee, 80 dollar total.
For 预防针 you can get most records from your previous university or
employer in USA, if no records, usually
they will provide free vaccine. then bring records go there. some time, you
need updated vaccine, the
doctors and nurses always try to find the expired one and ask you to pay for
a new vaccine.
you d better read pijiang's article in wenxuecity, esp TB test, and read 683
instruction and download 683
form to have a look to know what you will have to have.
If you prepare well, I think you only need to pay the basic physical
examination fee.
before go there, you should know very well what is required, and how much
each vaccine cost, and whether
you need the updated vaccine, like tetanus vaccine which is expired after 10
years.
today i went there, i recorded all the conversation which showed they
fabricate the result deliberately and
did not follow the procedures.
if i want to accuse them, they will have big trouble, however, really don't
want to spend another 50 dollar to
get a 2nd result, and spend time to report these ugly doctors and staffs to
USCIS.
【在 w***u 的大作中提到】
: 感觉挺贵，一般多少钱比较合适？
: 另外预防针可以让自己的家庭医生打，保险COVER吗？
regions. your city must be a big city.
I just did it and was fooled by the doctor and nurse, although I thought I
prepared well and they should be
honest. They lied and said my negative result actually might be a positive
result. They did not follow the
procedures, and asked me to take Chest X ray for TB, which cost 30 dollars,
plus basic 50 dollar physical
examination fee, 80 dollar total.
For 预防针 you can get most records from your previous university or
employer in USA, if no records, usually
they will provide free vaccine. then bring records go there. some time, you
need updated vaccine, the
doctors and nurses always try to find the expired one and ask you to pay for
a new vaccine.
you d better read pijiang's article in wenxuecity, esp TB test, and read 683
instruction and download 683
form to have a look to know what you will have to have.
If you prepare well, I think you only need to pay the basic physical
examination fee.
before go there, you should know very well what is required, and how much
each vaccine cost, and whether
you need the updated vaccine, like tetanus vaccine which is expired after 10
years.
today i went there, i recorded all the conversation which showed they
fabricate the result deliberately and
did not follow the procedures.
if i want to accuse them, they will have big trouble, however, really don't
want to spend another 50 dollar to
get a 2nd result, and spend time to report these ugly doctors and staffs to
USCIS.
【在 w***u 的大作中提到】
: 感觉挺贵，一般多少钱比较合适？
: 另外预防针可以让自己的家庭医生打，保险COVER吗？
x*e
14 楼
问题是学术杂志没有新番导读哇
【在 m******g 的大作中提到】
: 本来在开始读PhD的时候，就打算要广泛阅读主流学术杂志，比如Nature, Science,
: PNAS, Plos genetics等等，但是自己总是拖拖拉拉，偶尔有心血来潮就一口气读很久
: ，没兴趣／时间的话就个把月都不翻一下。
: 就好比动漫监督需要看其他畅销动漫（暴露兴趣了，太不学术了），我们也应该多多看
: 看生物的杂志，以增强自己对整个领域的理解，并且了解一些文献的逻辑、方法和写法
: 。所以我打算开这个贴说说每周最喜欢的几篇文章什么的，每周一更（日期不定），以
: 监督自己，防止自己不读文献。如果没有做到，请大家不要用砖头砸，把好吃的狠狠地
: 砸过来就好了，然后再狠狠地鄙视我就好。
: 我是学遗传进化方向的，做实验和编程都做一点（但是为什么现在还这么菜呢，果然是
: 因为我太懒惰了），总之看看文献没有坏处，也欢迎相似方向的大家一起来贴贴推荐的
【在 m******g 的大作中提到】
: 本来在开始读PhD的时候，就打算要广泛阅读主流学术杂志，比如Nature, Science,
: PNAS, Plos genetics等等，但是自己总是拖拖拉拉，偶尔有心血来潮就一口气读很久
: ，没兴趣／时间的话就个把月都不翻一下。
: 就好比动漫监督需要看其他畅销动漫（暴露兴趣了，太不学术了），我们也应该多多看
: 看生物的杂志，以增强自己对整个领域的理解，并且了解一些文献的逻辑、方法和写法
: 。所以我打算开这个贴说说每周最喜欢的几篇文章什么的，每周一更（日期不定），以
: 监督自己，防止自己不读文献。如果没有做到，请大家不要用砖头砸，把好吃的狠狠地
: 砸过来就好了，然后再狠狠地鄙视我就好。
: 我是学遗传进化方向的，做实验和编程都做一点（但是为什么现在还这么菜呢，果然是
: 因为我太懒惰了），总之看看文献没有坏处，也欢迎相似方向的大家一起来贴贴推荐的
G*0
15 楼
China town $200 全包
【在 w***u 的大作中提到】
: 感觉挺贵，一般多少钱比较合适？
: 另外预防针可以让自己的家庭医生打，保险COVER吗？
【在 w***u 的大作中提到】
: 感觉挺贵，一般多少钱比较合适？
: 另外预防针可以让自己的家庭医生打，保险COVER吗？
w*r
16 楼
做生物贵在精深，广博并非没有用处，但往往得不偿失
大多成为pi的人都是心灵手巧，吃苦耐劳的类型
【在 m******g 的大作中提到】
: 本来在开始读PhD的时候，就打算要广泛阅读主流学术杂志，比如Nature, Science,
: PNAS, Plos genetics等等，但是自己总是拖拖拉拉，偶尔有心血来潮就一口气读很久
: ，没兴趣／时间的话就个把月都不翻一下。
: 就好比动漫监督需要看其他畅销动漫（暴露兴趣了，太不学术了），我们也应该多多看
: 看生物的杂志，以增强自己对整个领域的理解，并且了解一些文献的逻辑、方法和写法
: 。所以我打算开这个贴说说每周最喜欢的几篇文章什么的，每周一更（日期不定），以
: 监督自己，防止自己不读文献。如果没有做到，请大家不要用砖头砸，把好吃的狠狠地
: 砸过来就好了，然后再狠狠地鄙视我就好。
: 我是学遗传进化方向的，做实验和编程都做一点（但是为什么现在还这么菜呢，果然是
: 因为我太懒惰了），总之看看文献没有坏处，也欢迎相似方向的大家一起来贴贴推荐的
大多成为pi的人都是心灵手巧，吃苦耐劳的类型
【在 m******g 的大作中提到】
: 本来在开始读PhD的时候，就打算要广泛阅读主流学术杂志，比如Nature, Science,
: PNAS, Plos genetics等等，但是自己总是拖拖拉拉，偶尔有心血来潮就一口气读很久
: ，没兴趣／时间的话就个把月都不翻一下。
: 就好比动漫监督需要看其他畅销动漫（暴露兴趣了，太不学术了），我们也应该多多看
: 看生物的杂志，以增强自己对整个领域的理解，并且了解一些文献的逻辑、方法和写法
: 。所以我打算开这个贴说说每周最喜欢的几篇文章什么的，每周一更（日期不定），以
: 监督自己，防止自己不读文献。如果没有做到，请大家不要用砖头砸，把好吃的狠狠地
: 砸过来就好了，然后再狠狠地鄙视我就好。
: 我是学遗传进化方向的，做实验和编程都做一点（但是为什么现在还这么菜呢，果然是
: 因为我太懒惰了），总之看看文献没有坏处，也欢迎相似方向的大家一起来贴贴推荐的
f*s
17 楼
问你体检医生办公室的小蜜 他们billing的那些service的code是什么 CPT code（？
记不太清了） 然后打电话给你保险公司说要查一些service是不是包括 给他们那些
code
偶的全都包 关键不在保险公司 而在体检的地方会不会用code
【在 w***u 的大作中提到】
: 感觉挺贵，一般多少钱比较合适？
: 另外预防针可以让自己的家庭医生打，保险COVER吗？
记不太清了） 然后打电话给你保险公司说要查一些service是不是包括 给他们那些
code
偶的全都包 关键不在保险公司 而在体检的地方会不会用code
【在 w***u 的大作中提到】
: 感觉挺贵，一般多少钱比较合适？
: 另外预防针可以让自己的家庭医生打，保险COVER吗？
l*1
18 楼
Just follow Twitter
https://twitter.com/evoldir
conference msg,
for example,
http://sitemaker.umich.edu/ecss2014/home
or
https://twitter.com/evoldir/status/400911676511621120
next google invited speaker her/his new publications..
【在 x********e 的大作中提到】
: 问题是学术杂志没有新番导读哇
https://twitter.com/evoldir
conference msg,
for example,
http://sitemaker.umich.edu/ecss2014/home
or
https://twitter.com/evoldir/status/400911676511621120
next google invited speaker her/his new publications..
【在 x********e 的大作中提到】
: 问题是学术杂志没有新番导读哇
Y*1
19 楼
NND,我们当时也是画的这么多钱。还不如去中国城，又快又便宜。
D*a
20 楼
生物谷等 和twitter 和podcast嘛
还有RSS
【在 x********e 的大作中提到】
: 问题是学术杂志没有新番导读哇
还有RSS
【在 x********e 的大作中提到】
: 问题是学术杂志没有新番导读哇
Y*n
21 楼
是的。
【在 Y*******1 的大作中提到】
: NND,我们当时也是画的这么多钱。还不如去中国城，又快又便宜。
【在 Y*******1 的大作中提到】
: NND,我们当时也是画的这么多钱。还不如去中国城，又快又便宜。
z*t
22 楼
精深当然不可少，但做出真正成就的往往要广博
【在 w***r 的大作中提到】
: 做生物贵在精深，广博并非没有用处，但往往得不偿失
: 大多成为pi的人都是心灵手巧，吃苦耐劳的类型
【在 w***r 的大作中提到】
: 做生物贵在精深，广博并非没有用处，但往往得不偿失
: 大多成为pi的人都是心灵手巧，吃苦耐劳的类型
y*e
23 楼
我们这一针都没打，还收了54+175＝229呢，xray啥的还没算
感觉挺贵，一般多少钱比较合适？
另外预防针可以让自己的家庭医生打，保险COVER吗？
【在 w***u 的大作中提到】
: 感觉挺贵，一般多少钱比较合适？
: 另外预防针可以让自己的家庭医生打，保险COVER吗？
感觉挺贵，一般多少钱比较合适？
另外预防针可以让自己的家庭医生打，保险COVER吗？
【在 w***u 的大作中提到】
: 感觉挺贵，一般多少钱比较合适？
: 另外预防针可以让自己的家庭医生打，保险COVER吗？
p*r
24 楼
好也。我最近也在这个领域打了个酱油，和朋友合作发了篇PNAS.
你对GWAS怎么看呢，我感觉是不是还有2-3年好日子也就到头了？
【在 m******g 的大作中提到】
: 本来在开始读PhD的时候，就打算要广泛阅读主流学术杂志，比如Nature, Science,
: PNAS, Plos genetics等等，但是自己总是拖拖拉拉，偶尔有心血来潮就一口气读很久
: ，没兴趣／时间的话就个把月都不翻一下。
: 就好比动漫监督需要看其他畅销动漫（暴露兴趣了，太不学术了），我们也应该多多看
: 看生物的杂志，以增强自己对整个领域的理解，并且了解一些文献的逻辑、方法和写法
: 。所以我打算开这个贴说说每周最喜欢的几篇文章什么的，每周一更（日期不定），以
: 监督自己，防止自己不读文献。如果没有做到，请大家不要用砖头砸，把好吃的狠狠地
: 砸过来就好了，然后再狠狠地鄙视我就好。
: 我是学遗传进化方向的，做实验和编程都做一点（但是为什么现在还这么菜呢，果然是
: 因为我太懒惰了），总之看看文献没有坏处，也欢迎相似方向的大家一起来贴贴推荐的
你对GWAS怎么看呢，我感觉是不是还有2-3年好日子也就到头了？
【在 m******g 的大作中提到】
: 本来在开始读PhD的时候，就打算要广泛阅读主流学术杂志，比如Nature, Science,
: PNAS, Plos genetics等等，但是自己总是拖拖拉拉，偶尔有心血来潮就一口气读很久
: ，没兴趣／时间的话就个把月都不翻一下。
: 就好比动漫监督需要看其他畅销动漫（暴露兴趣了，太不学术了），我们也应该多多看
: 看生物的杂志，以增强自己对整个领域的理解，并且了解一些文献的逻辑、方法和写法
: 。所以我打算开这个贴说说每周最喜欢的几篇文章什么的，每周一更（日期不定），以
: 监督自己，防止自己不读文献。如果没有做到，请大家不要用砖头砸，把好吃的狠狠地
: 砸过来就好了，然后再狠狠地鄙视我就好。
: 我是学遗传进化方向的，做实验和编程都做一点（但是为什么现在还这么菜呢，果然是
: 因为我太懒惰了），总之看看文献没有坏处，也欢迎相似方向的大家一起来贴贴推荐的
m*g
25 楼
Science 13.11.15 (包含Editor's Choice等推荐的其他杂志的文章，之后省略这句话)
推荐：
1. Dosage compensation via transposable element mediated rewiring of a
regulatory network
D. miranda在1 my前出现neo-X chromosome, TE-mediated rewiring of regulatory
network (domestication, amplification, and fine-tuning) followed by erosion
of nonfunctional parts of the transposon
idea挺有趣的.
2. Long-term dynamics of adaptation in asexual populations
Power law model fits/predicts the data better than Hyperbolic model with an
asymptote.
Fitness似乎在不断增长，并没有出现渐进靠近最大值的情况
稍微了解一下：
1. Genetic and neural modularity underlie the evolution of schooling
behavior in threespine sticklebacks
定位了影响tendency to school和body position的基因，在不同的区域（个人挺喜欢
这种定位决定行为的基因的文章，比如之前有篇map掘洞基因的）
2. 有Richard Lenski的访谈（50,000代的long-term evolution of E.coli）！！！
并附有一个report: Long-Term Dynamics of Adaptation in Asexual Populations
脑残粉们不要错过哇！一个实验做20多年，一直发paper什么的太伟大了！
小知识：
因为全球变暖，大雨会越来越频繁
狗的驯化是起源于欧洲（对古代犬的线粒体序列分析得出结论）
推荐：
1. Dosage compensation via transposable element mediated rewiring of a
regulatory network
D. miranda在1 my前出现neo-X chromosome, TE-mediated rewiring of regulatory
network (domestication, amplification, and fine-tuning) followed by erosion
of nonfunctional parts of the transposon
idea挺有趣的.
2. Long-term dynamics of adaptation in asexual populations
Power law model fits/predicts the data better than Hyperbolic model with an
asymptote.
Fitness似乎在不断增长，并没有出现渐进靠近最大值的情况
稍微了解一下：
1. Genetic and neural modularity underlie the evolution of schooling
behavior in threespine sticklebacks
定位了影响tendency to school和body position的基因，在不同的区域（个人挺喜欢
这种定位决定行为的基因的文章，比如之前有篇map掘洞基因的）
2. 有Richard Lenski的访谈（50,000代的long-term evolution of E.coli）！！！
并附有一个report: Long-Term Dynamics of Adaptation in Asexual Populations
脑残粉们不要错过哇！一个实验做20多年，一直发paper什么的太伟大了！
小知识：
因为全球变暖，大雨会越来越频繁
狗的驯化是起源于欧洲（对古代犬的线粒体序列分析得出结论）
m*g
26 楼
只是我瞎说说个人看法。我觉得GWAS对于研究决定common disease的common variant的
correlation很直观有效，以后如果新生儿测序提上日程，再加上完备的医疗记录，
GWAS应该会变的很routine（目前GWAS的几大缺陷也可以得到有效解决，比如
publication bias, population structure之类的），就像现在的测序一样常见，估计
就很难像几年前那样发容易文章了，个人幻想应该会像现在查基因序列一样，十年之后
可以查到各种疾病、性状的对应major SNPs。
【在 p*******r 的大作中提到】
: 好也。我最近也在这个领域打了个酱油，和朋友合作发了篇PNAS.
: 你对GWAS怎么看呢，我感觉是不是还有2-3年好日子也就到头了？
correlation很直观有效，以后如果新生儿测序提上日程，再加上完备的医疗记录，
GWAS应该会变的很routine（目前GWAS的几大缺陷也可以得到有效解决，比如
publication bias, population structure之类的），就像现在的测序一样常见，估计
就很难像几年前那样发容易文章了，个人幻想应该会像现在查基因序列一样，十年之后
可以查到各种疾病、性状的对应major SNPs。
【在 p*******r 的大作中提到】
: 好也。我最近也在这个领域打了个酱油，和朋友合作发了篇PNAS.
: 你对GWAS怎么看呢，我感觉是不是还有2-3年好日子也就到头了？
g*l
27 楼
我感觉现在都不太提common variant对common disease的影响了，因为实在太小。业界
对missing heritability的解释也是没太多亮点，总之GWAS基本上就是留给后人做实验
验证的，真要说应用于临床，恐怕还差得远，即使可行。
NGS倒是发展迅猛，但也就单基因疾病方面比较成功，这个以后必然是新生儿、乃至产
前筛查的范围。但就复杂疾病来讲，NGS找出的rare variants仍然没太大作用，至少在
牛皮癣里是这样（参见http://www.ncbi.nlm.nih.gov/pubmed/24212883）。
我悲观地认为，复杂疾病的genetics将来的前途十分不明朗，毕竟环境因素太大、太难
以评估。我甚至怀疑想用genetics解释复杂疾病，本身带有很大的机会主义成分，或受
到利益集团的操纵（Illumina、Affymetrix、ABI。。。）
欢迎讨论
【在 m******g 的大作中提到】
: 只是我瞎说说个人看法。我觉得GWAS对于研究决定common disease的common variant的
: correlation很直观有效，以后如果新生儿测序提上日程，再加上完备的医疗记录，
: GWAS应该会变的很routine（目前GWAS的几大缺陷也可以得到有效解决，比如
: publication bias, population structure之类的），就像现在的测序一样常见，估计
: 就很难像几年前那样发容易文章了，个人幻想应该会像现在查基因序列一样，十年之后
: 可以查到各种疾病、性状的对应major SNPs。
对missing heritability的解释也是没太多亮点，总之GWAS基本上就是留给后人做实验
验证的，真要说应用于临床，恐怕还差得远，即使可行。
NGS倒是发展迅猛，但也就单基因疾病方面比较成功，这个以后必然是新生儿、乃至产
前筛查的范围。但就复杂疾病来讲，NGS找出的rare variants仍然没太大作用，至少在
牛皮癣里是这样（参见http://www.ncbi.nlm.nih.gov/pubmed/24212883）。
我悲观地认为，复杂疾病的genetics将来的前途十分不明朗，毕竟环境因素太大、太难
以评估。我甚至怀疑想用genetics解释复杂疾病，本身带有很大的机会主义成分，或受
到利益集团的操纵（Illumina、Affymetrix、ABI。。。）
欢迎讨论
【在 m******g 的大作中提到】
: 只是我瞎说说个人看法。我觉得GWAS对于研究决定common disease的common variant的
: correlation很直观有效，以后如果新生儿测序提上日程，再加上完备的医疗记录，
: GWAS应该会变的很routine（目前GWAS的几大缺陷也可以得到有效解决，比如
: publication bias, population structure之类的），就像现在的测序一样常见，估计
: 就很难像几年前那样发容易文章了，个人幻想应该会像现在查基因序列一样，十年之后
: 可以查到各种疾病、性状的对应major SNPs。
w*r
28 楼
这想法嫩得都出水了
【在 z*t 的大作中提到】
: 精深当然不可少，但做出真正成就的往往要广博
【在 z*t 的大作中提到】
: 精深当然不可少，但做出真正成就的往往要广博
z*t
29 楼
您看来老得没什么水了：）
我倒是年方二八，正是嫩的出水的时节
【在 w***r 的大作中提到】
: 这想法嫩得都出水了
我倒是年方二八，正是嫩的出水的时节
【在 w***r 的大作中提到】
: 这想法嫩得都出水了
x*e
30 楼
RSS 过一段时间,看不过来就放弃了
去面壁一下
【在 D*a 的大作中提到】
: 生物谷等 和twitter 和podcast嘛
: 还有RSS
去面壁一下
【在 D*a 的大作中提到】
: 生物谷等 和twitter 和podcast嘛
: 还有RSS
D*a
31 楼
16岁就博士啦？
:)
【在 z*t 的大作中提到】
: 您看来老得没什么水了：）
: 我倒是年方二八，正是嫩的出水的时节
:)
【在 z*t 的大作中提到】
: 您看来老得没什么水了：）
: 我倒是年方二八，正是嫩的出水的时节
l*1
32 楼
That guy did topological Hopf link
Pls check,
http://en.wikipedia.org/wiki/Skein_relation
not your times calculation..
Btw,
it is relative to DNA topology/Computing
knot theory,
http://www2.imperial.ac.uk/~dbuck/Hiring.html
or
http://en.wikipedia.org/wiki/Tangle_(mathematics)
【在 D*a 的大作中提到】
: 16岁就博士啦？
: :)
Pls check,
http://en.wikipedia.org/wiki/Skein_relation
not your times calculation..
Btw,
it is relative to DNA topology/Computing
knot theory,
http://www2.imperial.ac.uk/~dbuck/Hiring.html
or
http://en.wikipedia.org/wiki/Tangle_(mathematics)
【在 D*a 的大作中提到】
: 16岁就博士啦？
: :)
p*r
33 楼
你觉得再往下应该做什么呢？
【在 m******g 的大作中提到】
: 只是我瞎说说个人看法。我觉得GWAS对于研究决定common disease的common variant的
: correlation很直观有效，以后如果新生儿测序提上日程，再加上完备的医疗记录，
: GWAS应该会变的很routine（目前GWAS的几大缺陷也可以得到有效解决，比如
: publication bias, population structure之类的），就像现在的测序一样常见，估计
: 就很难像几年前那样发容易文章了，个人幻想应该会像现在查基因序列一样，十年之后
: 可以查到各种疾病、性状的对应major SNPs。
【在 m******g 的大作中提到】
: 只是我瞎说说个人看法。我觉得GWAS对于研究决定common disease的common variant的
: correlation很直观有效，以后如果新生儿测序提上日程，再加上完备的医疗记录，
: GWAS应该会变的很routine（目前GWAS的几大缺陷也可以得到有效解决，比如
: publication bias, population structure之类的），就像现在的测序一样常见，估计
: 就很难像几年前那样发容易文章了，个人幻想应该会像现在查基因序列一样，十年之后
: 可以查到各种疾病、性状的对应major SNPs。
p*r
34 楼
我觉得看什么disease, 我比较熟悉neural 相关 disease。 昨天和鲁白讨论的时候，
他提到
Alzhimer应该是十个左右gene这个级别，autism几十个，depression就多了。
所以我觉得现阶段最exiciting的应该是几十这个级别的disease吧。
【在 g*******l 的大作中提到】
: 我感觉现在都不太提common variant对common disease的影响了，因为实在太小。业界
: 对missing heritability的解释也是没太多亮点，总之GWAS基本上就是留给后人做实验
: 验证的，真要说应用于临床，恐怕还差得远，即使可行。
: NGS倒是发展迅猛，但也就单基因疾病方面比较成功，这个以后必然是新生儿、乃至产
: 前筛查的范围。但就复杂疾病来讲，NGS找出的rare variants仍然没太大作用，至少在
: 牛皮癣里是这样（参见http://www.ncbi.nlm.nih.gov/pubmed/24212883）。
: 我悲观地认为，复杂疾病的genetics将来的前途十分不明朗，毕竟环境因素太大、太难
: 以评估。我甚至怀疑想用genetics解释复杂疾病，本身带有很大的机会主义成分，或受
: 到利益集团的操纵（Illumina、Affymetrix、ABI。。。）
: 欢迎讨论
他提到
Alzhimer应该是十个左右gene这个级别，autism几十个，depression就多了。
所以我觉得现阶段最exiciting的应该是几十这个级别的disease吧。
【在 g*******l 的大作中提到】
: 我感觉现在都不太提common variant对common disease的影响了，因为实在太小。业界
: 对missing heritability的解释也是没太多亮点，总之GWAS基本上就是留给后人做实验
: 验证的，真要说应用于临床，恐怕还差得远，即使可行。
: NGS倒是发展迅猛，但也就单基因疾病方面比较成功，这个以后必然是新生儿、乃至产
: 前筛查的范围。但就复杂疾病来讲，NGS找出的rare variants仍然没太大作用，至少在
: 牛皮癣里是这样（参见http://www.ncbi.nlm.nih.gov/pubmed/24212883）。
: 我悲观地认为，复杂疾病的genetics将来的前途十分不明朗，毕竟环境因素太大、太难
: 以评估。我甚至怀疑想用genetics解释复杂疾病，本身带有很大的机会主义成分，或受
: 到利益集团的操纵（Illumina、Affymetrix、ABI。。。）
: 欢迎讨论
l*1
35 楼
Molecular Phenome from below flow chat figure noted >2/3 are Hu You Fundings
items,
cited from 2012 one Book one chapter,
full PDF link:
http://www.mitbbs.com/article_t/Biology/31855315.html
【在 g*******l 的大作中提到】
: 我感觉现在都不太提common variant对common disease的影响了，因为实在太小。业界
: 对missing heritability的解释也是没太多亮点，总之GWAS基本上就是留给后人做实验
: 验证的，真要说应用于临床，恐怕还差得远，即使可行。
: NGS倒是发展迅猛，但也就单基因疾病方面比较成功，这个以后必然是新生儿、乃至产
: 前筛查的范围。但就复杂疾病来讲，NGS找出的rare variants仍然没太大作用，至少在
: 牛皮癣里是这样（参见http://www.ncbi.nlm.nih.gov/pubmed/24212883）。
: 我悲观地认为，复杂疾病的genetics将来的前途十分不明朗，毕竟环境因素太大、太难
: 以评估。我甚至怀疑想用genetics解释复杂疾病，本身带有很大的机会主义成分，或受
: 到利益集团的操纵（Illumina、Affymetrix、ABI。。。）
: 欢迎讨论
items,
cited from 2012 one Book one chapter,
full PDF link:
http://www.mitbbs.com/article_t/Biology/31855315.html
【在 g*******l 的大作中提到】
: 我感觉现在都不太提common variant对common disease的影响了，因为实在太小。业界
: 对missing heritability的解释也是没太多亮点，总之GWAS基本上就是留给后人做实验
: 验证的，真要说应用于临床，恐怕还差得远，即使可行。
: NGS倒是发展迅猛，但也就单基因疾病方面比较成功，这个以后必然是新生儿、乃至产
: 前筛查的范围。但就复杂疾病来讲，NGS找出的rare variants仍然没太大作用，至少在
: 牛皮癣里是这样（参见http://www.ncbi.nlm.nih.gov/pubmed/24212883）。
: 我悲观地认为，复杂疾病的genetics将来的前途十分不明朗，毕竟环境因素太大、太难
: 以评估。我甚至怀疑想用genetics解释复杂疾病，本身带有很大的机会主义成分，或受
: 到利益集团的操纵（Illumina、Affymetrix、ABI。。。）
: 欢迎讨论
s*y
36 楼
哦呵呵呵呵，突然发现我研究的东西在那个表里的一个节点上。
【在 l**********1 的大作中提到】
: Molecular Phenome from below flow chat figure noted >2/3 are Hu You Fundings
: items,
: cited from 2012 one Book one chapter,
: full PDF link:
: http://www.mitbbs.com/article_t/Biology/31855315.html
【在 l**********1 的大作中提到】
: Molecular Phenome from below flow chat figure noted >2/3 are Hu You Fundings
: items,
: cited from 2012 one Book one chapter,
: full PDF link:
: http://www.mitbbs.com/article_t/Biology/31855315.html
l*1
37 楼
Shall we Hu You stuff funding from that flow chat another nod/s later ?
【在 s******y 的大作中提到】
: 哦呵呵呵呵，突然发现我研究的东西在那个表里的一个节点上。
【在 s******y 的大作中提到】
: 哦呵呵呵呵，突然发现我研究的东西在那个表里的一个节点上。
m*g
38 楼
Nature 13.11.14
推荐：
1. A high-resolution map of the three-dimensional chromatin interactome in
human cells
3C方法（你知道4C,5C等等吗）determined over one million long-range chromatin
interactions at 5-10kb resolution.
知道有这么个资源就好，好像有不少类似产数据的paper,但是感觉physically close离
function还是有很长的距离要走（特别是本来就是连锁在一起的gene），加油~
稍微了解一下：
1. Dedifferentiation of committed epithelial cells into stem cells in vivo
看一下标题，知道有这件事情就好啦
2. RNA catalyses nuclear pre-mRNA splicing
The spliceosome is shown to catalyse splicing through the RNA and not the
protein components of the spliceosome; pre-messenger RNA splicing requires
U6 snRNA acting by a mechanism similar to that used by group II self-
splicing introns.以前学过两类RNAmechanism还记得吗，呵呵。These findings
indicate that group II introns and the spliceosome share common catalytic
mechanisms and probably common evolutionary origins. Our results demonstrate
that RNA mediates catalysis within the spliceosome.不过我一直以为都是RNA
catalyse,只是一种需要蛋白辅助，一种是只有RNA而已，可能这个只是提供了实验证据
吧。
小知识：
针对HIV和malaria，非洲采取了大规模预防措施，一些concern与achievements
肠道细菌Prevotella copri与人的关节炎有强correlation，第一次精确到种
NIH的funding：Large NIH projects cut
推荐：
1. A high-resolution map of the three-dimensional chromatin interactome in
human cells
3C方法（你知道4C,5C等等吗）determined over one million long-range chromatin
interactions at 5-10kb resolution.
知道有这么个资源就好，好像有不少类似产数据的paper,但是感觉physically close离
function还是有很长的距离要走（特别是本来就是连锁在一起的gene），加油~
稍微了解一下：
1. Dedifferentiation of committed epithelial cells into stem cells in vivo
看一下标题，知道有这件事情就好啦
2. RNA catalyses nuclear pre-mRNA splicing
The spliceosome is shown to catalyse splicing through the RNA and not the
protein components of the spliceosome; pre-messenger RNA splicing requires
U6 snRNA acting by a mechanism similar to that used by group II self-
splicing introns.以前学过两类RNAmechanism还记得吗，呵呵。These findings
indicate that group II introns and the spliceosome share common catalytic
mechanisms and probably common evolutionary origins. Our results demonstrate
that RNA mediates catalysis within the spliceosome.不过我一直以为都是RNA
catalyse,只是一种需要蛋白辅助，一种是只有RNA而已，可能这个只是提供了实验证据
吧。
小知识：
针对HIV和malaria，非洲采取了大规模预防措施，一些concern与achievements
肠道细菌Prevotella copri与人的关节炎有强correlation，第一次精确到种
NIH的funding：Large NIH projects cut
x*e
39 楼
赞这次的推荐
chromatin
【在 m******g 的大作中提到】
: Nature 13.11.14
: 推荐：
: 1. A high-resolution map of the three-dimensional chromatin interactome in
: human cells
: 3C方法（你知道4C,5C等等吗）determined over one million long-range chromatin
: interactions at 5-10kb resolution.
: 知道有这么个资源就好，好像有不少类似产数据的paper,但是感觉physically close离
: function还是有很长的距离要走（特别是本来就是连锁在一起的gene），加油~
: 稍微了解一下：
: 1. Dedifferentiation of committed epithelial cells into stem cells in vivo
chromatin
【在 m******g 的大作中提到】
: Nature 13.11.14
: 推荐：
: 1. A high-resolution map of the three-dimensional chromatin interactome in
: human cells
: 3C方法（你知道4C,5C等等吗）determined over one million long-range chromatin
: interactions at 5-10kb resolution.
: 知道有这么个资源就好，好像有不少类似产数据的paper,但是感觉physically close离
: function还是有很长的距离要走（特别是本来就是连锁在一起的gene），加油~
: 稍微了解一下：
: 1. Dedifferentiation of committed epithelial cells into stem cells in vivo
l*1
40 楼
Plus PMID 23953117 Lim [email protected] new Cell paper:
Coyle SM, et al., (2013).
Exploitation of latent allostery enables the evolution of new modes of MAP
kinase regulation.
Cell. 154: 875-87.
n.b. MAPK 变构反应 原来是为了进化潜规则 中 起到调控另外的pathway/s 开关作用
的...
>Abstract
ignored stuff
>The magnitude of this latent allosteric potential drifts widely among pre-
Ste5 MAP kinases, providing a
pool of hidden phenotypic diversity that, when revealed by new activators,
could lead to functional divergence and to the evolution of distinct
signaling behaviors
http://www.ncbi.nlm.nih.gov/pubmed/23953117
PDF link:
HTTP dot//limlab.ucsf.edu/papers/pdfs/smc_2013.pdf
plus last figure one part of this Cell paper.
or
RE 谁知道他老人家最近在琢磨啥大问题？好久没看到他的牛文了
By XBaldwin ID on
2012-01-20 22:45:
来自: 99.
18th floor
http://ipv6.weiming.info/zhuti/Biology/31627573/
Wendell LIM一直是我膜拜的牛人之一，他的东西看起来很性感，每一篇文章都当做圣
经一样
但感觉他的东西在概念上可能更重要：understand by building。可是真去看他做
MAPKpathway，还是没有解决这个pathway的根本问题：specificity。
谁知道他老人家最近在琢磨啥大问题？好久没看到他的牛文了
chromatin
【在 m******g 的大作中提到】
: Nature 13.11.14
: 推荐：
: 1. A high-resolution map of the three-dimensional chromatin interactome in
: human cells
: 3C方法（你知道4C,5C等等吗）determined over one million long-range chromatin
: interactions at 5-10kb resolution.
: 知道有这么个资源就好，好像有不少类似产数据的paper,但是感觉physically close离
: function还是有很长的距离要走（特别是本来就是连锁在一起的gene），加油~
: 稍微了解一下：
: 1. Dedifferentiation of committed epithelial cells into stem cells in vivo
Coyle SM, et al., (2013).
Exploitation of latent allostery enables the evolution of new modes of MAP
kinase regulation.
Cell. 154: 875-87.
n.b. MAPK 变构反应 原来是为了进化潜规则 中 起到调控另外的pathway/s 开关作用
的...
>Abstract
ignored stuff
>The magnitude of this latent allosteric potential drifts widely among pre-
Ste5 MAP kinases, providing a
pool of hidden phenotypic diversity that, when revealed by new activators,
could lead to functional divergence and to the evolution of distinct
signaling behaviors
http://www.ncbi.nlm.nih.gov/pubmed/23953117
PDF link:
HTTP dot//limlab.ucsf.edu/papers/pdfs/smc_2013.pdf
plus last figure one part of this Cell paper.
or
RE 谁知道他老人家最近在琢磨啥大问题？好久没看到他的牛文了
By XBaldwin ID on
2012-01-20 22:45:
来自: 99.
18th floor
http://ipv6.weiming.info/zhuti/Biology/31627573/
Wendell LIM一直是我膜拜的牛人之一，他的东西看起来很性感，每一篇文章都当做圣
经一样
但感觉他的东西在概念上可能更重要：understand by building。可是真去看他做
MAPKpathway，还是没有解决这个pathway的根本问题：specificity。
谁知道他老人家最近在琢磨啥大问题？好久没看到他的牛文了
chromatin
【在 m******g 的大作中提到】
: Nature 13.11.14
: 推荐：
: 1. A high-resolution map of the three-dimensional chromatin interactome in
: human cells
: 3C方法（你知道4C,5C等等吗）determined over one million long-range chromatin
: interactions at 5-10kb resolution.
: 知道有这么个资源就好，好像有不少类似产数据的paper,但是感觉physically close离
: function还是有很长的距离要走（特别是本来就是连锁在一起的gene），加油~
: 稍微了解一下：
: 1. Dedifferentiation of committed epithelial cells into stem cells in vivo
m*g
41 楼
PNAS 13.11.19
推荐：
Computational evaluation of cellular metabolic costs successfully predicts
genes whose expression is deleterious
稍微了解有这么件事情
1. miRNA and mRNA cancer signatures determined by analysis of expression
levels in large cohors of patients
2. Subnuclear relocalization and silencing of a chromosomal region by an
ectopic ribosomal DNA repeat
有趣的小知识
Honey bees selectively avoid difficult choices
推荐：
Computational evaluation of cellular metabolic costs successfully predicts
genes whose expression is deleterious
稍微了解有这么件事情
1. miRNA and mRNA cancer signatures determined by analysis of expression
levels in large cohors of patients
2. Subnuclear relocalization and silencing of a chromosomal region by an
ectopic ribosomal DNA repeat
有趣的小知识
Honey bees selectively avoid difficult choices
s*y
42 楼
RNA splicing 那个很有意思。
chromatin
【在 m******g 的大作中提到】
: Nature 13.11.14
: 推荐：
: 1. A high-resolution map of the three-dimensional chromatin interactome in
: human cells
: 3C方法（你知道4C,5C等等吗）determined over one million long-range chromatin
: interactions at 5-10kb resolution.
: 知道有这么个资源就好，好像有不少类似产数据的paper,但是感觉physically close离
: function还是有很长的距离要走（特别是本来就是连锁在一起的gene），加油~
: 稍微了解一下：
: 1. Dedifferentiation of committed epithelial cells into stem cells in vivo
chromatin
【在 m******g 的大作中提到】
: Nature 13.11.14
: 推荐：
: 1. A high-resolution map of the three-dimensional chromatin interactome in
: human cells
: 3C方法（你知道4C,5C等等吗）determined over one million long-range chromatin
: interactions at 5-10kb resolution.
: 知道有这么个资源就好，好像有不少类似产数据的paper,但是感觉physically close离
: function还是有很长的距离要走（特别是本来就是连锁在一起的gene），加油~
: 稍微了解一下：
: 1. Dedifferentiation of committed epithelial cells into stem cells in vivo
x*e
43 楼
版上有做splicing的吗 最近对alternative splicing感兴趣
【在 s******y 的大作中提到】
: RNA splicing 那个很有意思。
:
: chromatin
【在 s******y 的大作中提到】
: RNA splicing 那个很有意思。
:
: chromatin
l*1
44 楼
Before NGS 2.0 or 3.0 Illumina platform can read enough longer different
isoforms within Exome sequencing and systems biology aspect,
it is still elusive to answer the linkage between SNP2.0 or 3.0 alternative
splicing with
syndromic disease...
Pls check,
>Although previously described in TS, no CACNA1C mutations have been
reported for
>non-syndromic LQTS. With our functional studies confirming Cav1.2 gain-of-
function as the cellular basis for the CACNA1C mutation-positive patient’s
LQTS phenotype,
a paradox has
emerged. Namely, how can some gain-of-function mutations, like Gly406Arg in
the alternatively spliced exon 8A, result in the multi-organ system
phenotype of
TS while other
missense mutations, like Pro857Arg, yield a cardiac-only phenotype of
autosomal dominant
LQTS? With this being a new discovery, it is not surprising that the answer
is elusive
cited from PMID 23677916
Boczek NJ et al., (2013).
Exome sequencing and systems biology converge to identify novel mutations in
the L-type calcium channel, CACNA1C, linked to autosomal dominant long QT
syndrome.
Circ Cardiovasc Genet. 6: 279-89.
http://www.ncbi.nlm.nih.gov/pubmed/23677916
PDF link,
HTTP double dot//circgenetics.ahajournals.org/content/early/2013/05/15/
CIRCGENETICS.113.000138.full.pdf
its pp20
or
http://www.mitbbs.com/article_t/Biology/31855831.html
7th floor
【在 x********e 的大作中提到】
: 版上有做splicing的吗 最近对alternative splicing感兴趣
isoforms within Exome sequencing and systems biology aspect,
it is still elusive to answer the linkage between SNP2.0 or 3.0 alternative
splicing with
syndromic disease...
Pls check,
>Although previously described in TS, no CACNA1C mutations have been
reported for
>non-syndromic LQTS. With our functional studies confirming Cav1.2 gain-of-
function as the cellular basis for the CACNA1C mutation-positive patient’s
LQTS phenotype,
a paradox has
emerged. Namely, how can some gain-of-function mutations, like Gly406Arg in
the alternatively spliced exon 8A, result in the multi-organ system
phenotype of
TS while other
missense mutations, like Pro857Arg, yield a cardiac-only phenotype of
autosomal dominant
LQTS? With this being a new discovery, it is not surprising that the answer
is elusive
cited from PMID 23677916
Boczek NJ et al., (2013).
Exome sequencing and systems biology converge to identify novel mutations in
the L-type calcium channel, CACNA1C, linked to autosomal dominant long QT
syndrome.
Circ Cardiovasc Genet. 6: 279-89.
http://www.ncbi.nlm.nih.gov/pubmed/23677916
PDF link,
HTTP double dot//circgenetics.ahajournals.org/content/early/2013/05/15/
CIRCGENETICS.113.000138.full.pdf
its pp20
or
http://www.mitbbs.com/article_t/Biology/31855831.html
7th floor
【在 x********e 的大作中提到】
: 版上有做splicing的吗 最近对alternative splicing感兴趣
E*g
45 楼
Rama Ranganathan的SCA方法算不算遗传/进化方向的？
单个氨基酸是如何改变蛋白功能的？
蛋白进化的单位是什么？
进化也是一个动力学过程吗？
为什么会有共进化？
别构调节是共进化的结果吗？
Halabi, N.*, Rivoire, O.*, S. Leibler, and R. Ranganathan. Protein Sectors:
Evolutionary Units of Three-Dimensional Structure. (2009) Cell, 138: 774-786
K.A. Reynolds, R.N. McLaughlin. R. Ranganathan. Hotspots for Allosteric
Regulation on Protein Surfaces. (2011) Cell, 147: 1564-1575
R.N. McLaughlin, F.J. Poelwijk, A. Raman, W.S. Gosal, and R. Ranganathan.
The Spatial Architecture of Protein Function and Adaptation. (2012) Nature
O. Rivoire Elements of coevolution in biological sequences. (2013) Phys.
Rev. Lett. 110 : 178102
单个氨基酸是如何改变蛋白功能的？
蛋白进化的单位是什么？
进化也是一个动力学过程吗？
为什么会有共进化？
别构调节是共进化的结果吗？
Halabi, N.*, Rivoire, O.*, S. Leibler, and R. Ranganathan. Protein Sectors:
Evolutionary Units of Three-Dimensional Structure. (2009) Cell, 138: 774-786
K.A. Reynolds, R.N. McLaughlin. R. Ranganathan. Hotspots for Allosteric
Regulation on Protein Surfaces. (2011) Cell, 147: 1564-1575
R.N. McLaughlin, F.J. Poelwijk, A. Raman, W.S. Gosal, and R. Ranganathan.
The Spatial Architecture of Protein Function and Adaptation. (2012) Nature
O. Rivoire Elements of coevolution in biological sequences. (2013) Phys.
Rev. Lett. 110 : 178102
b*r
46 楼
mark一个
不过我觉得这些3C 4C或者其他DNA RNA 调控的 高级结构，在我们职业发展阶段都变不
了真金白银，最多靠忽悠点funding，日子稍微过好一点
遗传学的真金白银最近这些年基本只在cancer genetics里，又能拿funding，搞不好还
能像IT业那样有大量的startup机会
不过我觉得这些3C 4C或者其他DNA RNA 调控的 高级结构，在我们职业发展阶段都变不
了真金白银，最多靠忽悠点funding，日子稍微过好一点
遗传学的真金白银最近这些年基本只在cancer genetics里，又能拿funding，搞不好还
能像IT业那样有大量的startup机会
n*k
47 楼
比较好奇，比较感兴趣： 不知道这些十个，几十个等的具体含义，而这中间预测的依
据又在哪里？
【在 p*******r 的大作中提到】
: 我觉得看什么disease, 我比较熟悉neural 相关 disease。 昨天和鲁白讨论的时候，
: 他提到
: Alzhimer应该是十个左右gene这个级别，autism几十个，depression就多了。
: 所以我觉得现阶段最exiciting的应该是几十这个级别的disease吧。
据又在哪里？
【在 p*******r 的大作中提到】
: 我觉得看什么disease, 我比较熟悉neural 相关 disease。 昨天和鲁白讨论的时候，
: 他提到
: Alzhimer应该是十个左右gene这个级别，autism几十个，depression就多了。
: 所以我觉得现阶段最exiciting的应该是几十这个级别的disease吧。
v*r
48 楼
co-ask. this seems an interesting question.
【在 n********k 的大作中提到】
: 比较好奇，比较感兴趣： 不知道这些十个，几十个等的具体含义，而这中间预测的依
: 据又在哪里？
【在 n********k 的大作中提到】
: 比较好奇，比较感兴趣： 不知道这些十个，几十个等的具体含义，而这中间预测的依
: 据又在哪里？
v*r
49 楼
it could be more helpful if more details are summarized.
话)
erosion
an
【在 m******g 的大作中提到】
: Science 13.11.15 (包含Editor's Choice等推荐的其他杂志的文章，之后省略这句话)
: 推荐：
: 1. Dosage compensation via transposable element mediated rewiring of a
: regulatory network
: D. miranda在1 my前出现neo-X chromosome, TE-mediated rewiring of regulatory
: network (domestication, amplification, and fine-tuning) followed by erosion
: of nonfunctional parts of the transposon
: idea挺有趣的.
: 2. Long-term dynamics of adaptation in asexual populations
: Power law model fits/predicts the data better than Hyperbolic model with an
话)
erosion
an
【在 m******g 的大作中提到】
: Science 13.11.15 (包含Editor's Choice等推荐的其他杂志的文章，之后省略这句话)
: 推荐：
: 1. Dosage compensation via transposable element mediated rewiring of a
: regulatory network
: D. miranda在1 my前出现neo-X chromosome, TE-mediated rewiring of regulatory
: network (domestication, amplification, and fine-tuning) followed by erosion
: of nonfunctional parts of the transposon
: idea挺有趣的.
: 2. Long-term dynamics of adaptation in asexual populations
: Power law model fits/predicts the data better than Hyperbolic model with an
H*g
50 楼
通过mapping就可以定位了，只不过在人身上做起来限制比较多
【在 v***r 的大作中提到】
: co-ask. this seems an interesting question.
【在 v***r 的大作中提到】
: co-ask. this seems an interesting question.
m*g
51 楼
主要是为了监督自己看文献，所以有点懒得打字（只写成自己看到能够联想到的程度）
，我以后会尽量多写一点的，呵呵。也可以直接去下载那篇文献呀，其实abstract就比
较detailed了
【在 v***r 的大作中提到】
: it could be more helpful if more details are summarized.
:
: 话)
: erosion
: an
，我以后会尽量多写一点的，呵呵。也可以直接去下载那篇文献呀，其实abstract就比
较detailed了
【在 v***r 的大作中提到】
: it could be more helpful if more details are summarized.
:
: 话)
: erosion
: an
m*g
52 楼
楼主我最近申请了统计学双学位硕士（终于下定决心这么做了，开心！）
因为上周忙申请，所以基本没有更新。
Nature 13.11.21
推荐：
1. DNMT1-interacting RNAs block gene-specific DNA methylation
基因表达调节甲基化程度，对具体机制也有研究。
稍微了解一下：
1.Group size determines cultural complexity (引文)
正文：Experimental evidence for the influence of group size on cultural
complexity
实验室内的人的行为学研究，分为2，4， 8， 16人／组，完成简单和复杂的电脑任务
并判定完成的复杂度。
如果群体太小，复杂任务的质量会下降
（感觉做的很有意思，虽然结果是非常as expected.）
有趣的小知识：
1. Biology tool uncloaks folk-tale evolution
用进化树的方法研究童话的起源
2. Fish babies bigger in toxic waters
当然后代数量会减少，个体大以解毒硫化物
3. The risks of the replication drive
我们该不该花钱请专业公司来复制我们的结果呢？作者Argue againt this idea （可
行性，可靠性，打击积极性）
4. Killing the survivors
发现了当和其他抗生素混用时，可以杀死休眠细菌（persister）的新小分子 ADEP4
（个人挺喜欢和persister相关的一些研究）
因为上周忙申请，所以基本没有更新。
Nature 13.11.21
推荐：
1. DNMT1-interacting RNAs block gene-specific DNA methylation
基因表达调节甲基化程度，对具体机制也有研究。
稍微了解一下：
1.Group size determines cultural complexity (引文)
正文：Experimental evidence for the influence of group size on cultural
complexity
实验室内的人的行为学研究，分为2，4， 8， 16人／组，完成简单和复杂的电脑任务
并判定完成的复杂度。
如果群体太小，复杂任务的质量会下降
（感觉做的很有意思，虽然结果是非常as expected.）
有趣的小知识：
1. Biology tool uncloaks folk-tale evolution
用进化树的方法研究童话的起源
2. Fish babies bigger in toxic waters
当然后代数量会减少，个体大以解毒硫化物
3. The risks of the replication drive
我们该不该花钱请专业公司来复制我们的结果呢？作者Argue againt this idea （可
行性，可靠性，打击积极性）
4. Killing the survivors
发现了当和其他抗生素混用时，可以杀死休眠细菌（persister）的新小分子 ADEP4
（个人挺喜欢和persister相关的一些研究）
m*g
53 楼
自己吐槽一下，虽然对于看过文献的研究系统／漂亮的图什么的记得比较清楚
但是作者什么的老是不太记得
有时候看到有的人可以一堆一堆地数出来，感觉好厉害啊！
觉得这期science比较有趣，虽然没有那种看得超感动的文章，但是还是有不少很值得
一看的paper的。
Science 13.11.22
推荐：
1. Organization of the Mitotic Chromosome
用5C和Hi-C, 发现分裂中期结构是与位点无关的均质，并用polymer模拟
“A simple, robust model explains higher-order organization of mammalian
chromosomes.”
（最近这类文章真多，好像周周都有？感觉个人不是那么感兴趣了～～～）
2. Two Y Genes Can Replace the Entire Y Chromosome for Assisted Reproduction
in the Mouse
testis determinant factor Sry
spermatogonial proliferation factor Eif2s3y
稍微了解一下：
1. Defining Stem Cell Dynamics in Models of Intestinal Tumor Initiation
癌变了可以快速分裂的细胞就一定有优势吗？有的话又有多少？
本文告诉你这是一个相当随机的过程（有一定bias）
（喜欢肠道小窝这几个干细胞随机性成为主导的系统，之前也出过一些有趣的文章）
2. Substitutions Near the Receptor Binding Site Determine Major Antigenic
Change During Influenza Virus Evolution
小知识：
1. Commensal Bacteria Control Cancer Response to Therapy by Modulating the
Tumor Microenvironment
肠道菌群对于肿瘤治疗是有益的
In antibiotics-treated or germ-free mice, tumor-infiltrating myeloid-derived
cells responded poorly to therapy
以及类似文章一篇
The Intestinal Microbiota Modulates the Anticancer Immune Effects of
Cyclophosphamide
2. Beyond Stem Cells: Self-Renewal of Differentiated Macrophages
These findings suggest that macrophages are mature differentiated cells that
may have a self-renewal potential similar to that of stem cells.
但是作者什么的老是不太记得
有时候看到有的人可以一堆一堆地数出来，感觉好厉害啊！
觉得这期science比较有趣，虽然没有那种看得超感动的文章，但是还是有不少很值得
一看的paper的。
Science 13.11.22
推荐：
1. Organization of the Mitotic Chromosome
用5C和Hi-C, 发现分裂中期结构是与位点无关的均质，并用polymer模拟
“A simple, robust model explains higher-order organization of mammalian
chromosomes.”
（最近这类文章真多，好像周周都有？感觉个人不是那么感兴趣了～～～）
2. Two Y Genes Can Replace the Entire Y Chromosome for Assisted Reproduction
in the Mouse
testis determinant factor Sry
spermatogonial proliferation factor Eif2s3y
稍微了解一下：
1. Defining Stem Cell Dynamics in Models of Intestinal Tumor Initiation
癌变了可以快速分裂的细胞就一定有优势吗？有的话又有多少？
本文告诉你这是一个相当随机的过程（有一定bias）
（喜欢肠道小窝这几个干细胞随机性成为主导的系统，之前也出过一些有趣的文章）
2. Substitutions Near the Receptor Binding Site Determine Major Antigenic
Change During Influenza Virus Evolution
小知识：
1. Commensal Bacteria Control Cancer Response to Therapy by Modulating the
Tumor Microenvironment
肠道菌群对于肿瘤治疗是有益的
In antibiotics-treated or germ-free mice, tumor-infiltrating myeloid-derived
cells responded poorly to therapy
以及类似文章一篇
The Intestinal Microbiota Modulates the Anticancer Immune Effects of
Cyclophosphamide
2. Beyond Stem Cells: Self-Renewal of Differentiated Macrophages
These findings suggest that macrophages are mature differentiated cells that
may have a self-renewal potential similar to that of stem cells.
l*1
54 楼
Chip-seq doesn't need?
pls refer,
>gene profiling and chromatin immunoprecipitation followed >by massive
parallel sequencing (ChIP-seq) in intact animal models of Alzheimer disease
are being used to assess IEG controlled signaling pathways.
http://koldamovalefterovlab.pitt.edu/
http://koldamovalefterovlab.pitt.edu/publications.html
or dPeak NGS 2.0 tool,
http://www.ncbi.nlm.nih.gov/pubmed/24146601
【在 H*********g 的大作中提到】
: 通过mapping就可以定位了，只不过在人身上做起来限制比较多
pls refer,
>gene profiling and chromatin immunoprecipitation followed >by massive
parallel sequencing (ChIP-seq) in intact animal models of Alzheimer disease
are being used to assess IEG controlled signaling pathways.
http://koldamovalefterovlab.pitt.edu/
http://koldamovalefterovlab.pitt.edu/publications.html
or dPeak NGS 2.0 tool,
http://www.ncbi.nlm.nih.gov/pubmed/24146601
【在 H*********g 的大作中提到】
: 通过mapping就可以定位了，只不过在人身上做起来限制比较多
m*g
55 楼
祝大家新年快乐！
我果然坑了，呵呵，这个帖子好久没更新。
圣诞节期间在忙别的没用的事情去了
以后求不坑，呵呵……
PNAS 13.11.26
推荐：
1. Gene amplification and microsatellite polymorphism underlie a recent
insect host shift
Model: polyphagous aphid
Host shift to feed on tobacco
expression level of CYP6CY3
expansion of dinucleotide microsatellite in promoter and a recent gene
amplification
稍微了解一下：
1. Intrinsic karyotype stability and gene copy number variations may have
laid the foundation for tetraploid wheat formation
allopolyploidy of tetraploid wheat
immediate and persistent karyotype stability is intrinsic to newly formed
allotetraploid wheat
小知识：
1. Similarity increases altruistic punishment in humans
Homophily: humans attracted to similar others
perceived similarity increases altruistic punishment
2. Pathogen selection drives nonoverlapping associations between HLA loci
exceptional polymorphism of HLA gene cluster
pathogen-meiated selection promotes nonrandom association
我果然坑了，呵呵，这个帖子好久没更新。
圣诞节期间在忙别的没用的事情去了
以后求不坑，呵呵……
PNAS 13.11.26
推荐：
1. Gene amplification and microsatellite polymorphism underlie a recent
insect host shift
Model: polyphagous aphid
Host shift to feed on tobacco
expression level of CYP6CY3
expansion of dinucleotide microsatellite in promoter and a recent gene
amplification
稍微了解一下：
1. Intrinsic karyotype stability and gene copy number variations may have
laid the foundation for tetraploid wheat formation
allopolyploidy of tetraploid wheat
immediate and persistent karyotype stability is intrinsic to newly formed
allotetraploid wheat
小知识：
1. Similarity increases altruistic punishment in humans
Homophily: humans attracted to similar others
perceived similarity increases altruistic punishment
2. Pathogen selection drives nonoverlapping associations between HLA loci
exceptional polymorphism of HLA gene cluster
pathogen-meiated selection promotes nonrandom association
m*g
56 楼
基本上就是题目+bulletin point的形式吧，不要纠结我对paper的品味，呵呵。新年快
乐！
PNAS 13.12.03
推荐：
1. Reintroducing domesticated wild mice to sociality induces adaptive
transgenerational effects on MUP expression
promiscuous / monogamous-line
higher MUP (pheromone) expression in pros-line
Male become more attractive
Difference in Mup promoter methylation level
2. High-throughput DNA sequencing errors are reduced by orders of magnitude
using circle sequencing
Previously ~0.1-1x10^-2
Unique library preparation strategy
Copied multiple times in tandem with a rolling circle polymerase
Error rate 7.6x1-^-6 per base
Higher efficiency and lower cost than existing barcode schemes
稍微了解一下：
1. Distribution, evolution, and diversity of retrotransposons at the
flamenco locus reflect the regulatory properties of piRNA clusters
piRNA-RNA producing locus
control transposable elment
trap for TEs coming from horizontal transfer from other Drosophila species
2. Bacterial natural transformation by highly fragmented and damaged DNA
molecule > 20 bp that may contain basic sites, cross-links can be acquired
uptake DNA from a 43,000y wooly mammoth bone
DNA recombination if RecA recombinase independent
3. Genome rearrangements caused by interstitial telomeric sequences in yeast
Interstitial telomeric sequences are associated with genome instabilities
and disease in human
yeast telomeric (Ytel) repeats
formation of dsDNA break within Ytel sequences
promote deletion, duplication, inversion and translocation
乐！
PNAS 13.12.03
推荐：
1. Reintroducing domesticated wild mice to sociality induces adaptive
transgenerational effects on MUP expression
promiscuous / monogamous-line
higher MUP (pheromone) expression in pros-line
Male become more attractive
Difference in Mup promoter methylation level
2. High-throughput DNA sequencing errors are reduced by orders of magnitude
using circle sequencing
Previously ~0.1-1x10^-2
Unique library preparation strategy
Copied multiple times in tandem with a rolling circle polymerase
Error rate 7.6x1-^-6 per base
Higher efficiency and lower cost than existing barcode schemes
稍微了解一下：
1. Distribution, evolution, and diversity of retrotransposons at the
flamenco locus reflect the regulatory properties of piRNA clusters
piRNA-RNA producing locus
control transposable elment
trap for TEs coming from horizontal transfer from other Drosophila species
2. Bacterial natural transformation by highly fragmented and damaged DNA
molecule > 20 bp that may contain basic sites, cross-links can be acquired
uptake DNA from a 43,000y wooly mammoth bone
DNA recombination if RecA recombinase independent
3. Genome rearrangements caused by interstitial telomeric sequences in yeast
Interstitial telomeric sequences are associated with genome instabilities
and disease in human
yeast telomeric (Ytel) repeats
formation of dsDNA break within Ytel sequences
promote deletion, duplication, inversion and translocation
m*g
57 楼
祝想学好生物的大家在新的一年收到实验女神的眷顾，想转行的快点换行！
想拿funding的拿到funding，天天开心！
PNAS 13.12.10
极力推荐：
1. Limitations of inclusive fitness
从11年开始就非常支持作者对inclusive fitness的反对，^_^
稍微了解一下：
1. Broad-scale phylogenomics provides insights into retrovirus–host
evolution
Large endogenous retrovirus
Horizontal transmission between different host species
90,000 ERVs from 60 vertebrate host genomes
Designation, host distribution, origin and tranmission
2. Chemical map of Schizosaccharomyces pombe reveals species-specific
features in nucleosome positioning
Genome-wide map at base pair resolution
Linker length of 10n + 4/5bp
A/T-rich sequences are enriched in S. pombe nucleosomes
3. Genome-scale metabolic reconstructions of multiple Escherichia coli
strains highlight strain-specific adaptations to nutritional environments
Genome-scale models of metabolism
Analyze growth growth capabilities in more than 650 different growth
conditions
Test 12 GEMs in 6 differentiating nutrients
想拿funding的拿到funding，天天开心！
PNAS 13.12.10
极力推荐：
1. Limitations of inclusive fitness
从11年开始就非常支持作者对inclusive fitness的反对，^_^
稍微了解一下：
1. Broad-scale phylogenomics provides insights into retrovirus–host
evolution
Large endogenous retrovirus
Horizontal transmission between different host species
90,000 ERVs from 60 vertebrate host genomes
Designation, host distribution, origin and tranmission
2. Chemical map of Schizosaccharomyces pombe reveals species-specific
features in nucleosome positioning
Genome-wide map at base pair resolution
Linker length of 10n + 4/5bp
A/T-rich sequences are enriched in S. pombe nucleosomes
3. Genome-scale metabolic reconstructions of multiple Escherichia coli
strains highlight strain-specific adaptations to nutritional environments
Genome-scale models of metabolism
Analyze growth growth capabilities in more than 650 different growth
conditions
Test 12 GEMs in 6 differentiating nutrients
m*g
58 楼
虽然看了，但是没来得及整理一下，整理贴出来，顺便复习一下，呵呵。
交流群：342148521 （开心读文献贵在坚持，加群请输入最喜欢的科学家、杂志或领域
的名称或者其他什么，无附加信息不予通过，希望大家一起参与呢）
Nature 13.11.28
推荐：
1. Memory and modularity in cell-fate decision making
Bacillus subtilis
Motile state and sessile state
Microfluidic device consisting of several channels
Visualize switching in real time
Memoryless motility and timed chaining
评论： 见How bacteria choose a lifestyle
稍微了解一下：
1. Accelerated growth in the absence of DNA replication origins
Bacteria and some archaea: single origin
Eukaryote and most archaea: multiple origin
Some virus: homologous recombination
Delete individual origins: reduce growth
Delete all origins: grow significantly faster
Initiate at dispersed site
小知识：
1. Antibiotic re-frames decoding
Ketolide antibiotics induce a ribosomal frameshift
Expression of defense gene ON
交流群：342148521 （开心读文献贵在坚持，加群请输入最喜欢的科学家、杂志或领域
的名称或者其他什么，无附加信息不予通过，希望大家一起参与呢）
Nature 13.11.28
推荐：
1. Memory and modularity in cell-fate decision making
Bacillus subtilis
Motile state and sessile state
Microfluidic device consisting of several channels
Visualize switching in real time
Memoryless motility and timed chaining
评论： 见How bacteria choose a lifestyle
稍微了解一下：
1. Accelerated growth in the absence of DNA replication origins
Bacteria and some archaea: single origin
Eukaryote and most archaea: multiple origin
Some virus: homologous recombination
Delete individual origins: reduce growth
Delete all origins: grow significantly faster
Initiate at dispersed site
小知识：
1. Antibiotic re-frames decoding
Ketolide antibiotics induce a ribosomal frameshift
Expression of defense gene ON
z*9
59 楼
好帖，支持，
m*g
60 楼
哇，拖了好多……最近会补上的，不会坑掉。
交流群：342148521 （开心读文献贵在坚持，加群请输入最喜欢的科学家、杂志或领域
的名称或者其他什么，无附加信息不予通过，希望大家一起参与呢）
Science 13.11.29
推荐：
1. Primate transcript and protein expression levels evolve under
compensatory selection pressures
概述文：Protein Expression Under Pressure
Protein level more conserved than mRNA
基本是as expected，不过能够measure一下是很重要的
自问：有没有可能是方法本身的精确性
导致了信号的压缩呢
自答：应该不会
因为看mRNA浓度跨度是3-4个数量级
而蛋白的浓度是4-6个数量级
2. The Innate Growth Bistability and Fitness Landscapes of Antibiotic-
Resistant Bacteria
Translation-inhibiting antibiotics
Bulk and single-cell measurements
Growing and nongrowing states for isogenic cells
Correct modeling of fitness landscape
稍微了解一下：
1. Genomes from Metagenomics (Perspective)
Binning methods for time-series or multiple samples
Single cell sequencing
小知识：
1. Protecting Self-Replicating RNA?
RNA as primordial catalysis
Problem: requires high level of Mg
Mg incompatible with fatty acid vesible integrity
Several chelator (citrate, isocitrate) would stabilize and protect RNA
2. Pattern sensing
Synthetic system with fluorescent
Self-segulated system
Reaction-diffusion model
交流群：342148521 （开心读文献贵在坚持，加群请输入最喜欢的科学家、杂志或领域
的名称或者其他什么，无附加信息不予通过，希望大家一起参与呢）
Science 13.11.29
推荐：
1. Primate transcript and protein expression levels evolve under
compensatory selection pressures
概述文：Protein Expression Under Pressure
Protein level more conserved than mRNA
基本是as expected，不过能够measure一下是很重要的
自问：有没有可能是方法本身的精确性
导致了信号的压缩呢
自答：应该不会
因为看mRNA浓度跨度是3-4个数量级
而蛋白的浓度是4-6个数量级
2. The Innate Growth Bistability and Fitness Landscapes of Antibiotic-
Resistant Bacteria
Translation-inhibiting antibiotics
Bulk and single-cell measurements
Growing and nongrowing states for isogenic cells
Correct modeling of fitness landscape
稍微了解一下：
1. Genomes from Metagenomics (Perspective)
Binning methods for time-series or multiple samples
Single cell sequencing
小知识：
1. Protecting Self-Replicating RNA?
RNA as primordial catalysis
Problem: requires high level of Mg
Mg incompatible with fatty acid vesible integrity
Several chelator (citrate, isocitrate) would stabilize and protect RNA
2. Pattern sensing
Synthetic system with fluorescent
Self-segulated system
Reaction-diffusion model
m*g
61 楼
Nature 13.12.05
推荐：
1. Genetic incompatibilities are widespread within species
Drosophila melanogaster recombinant inbred lines
Mendelian proportions among unlinked alleles
Genotype ratio distortion
Estimate: 1.15 pairs of epistatic alleles for any two genome
稍微了解一下：
1. RNAs leave yeast poised for action
Long ncRNAs accelerate activation of protein-coding gene
GAL genes released from repression
Long ncRNA speed upGAL expression
By recruiting a key enzyme needed
小知识：
1. Hormone boosts attractiveness
Nasal puffs of oxytocin
Improves rating for their partner over unfamiliar/familiar woman
呵呵，大家知道应该怎么留住他/她了吧
推荐：
1. Genetic incompatibilities are widespread within species
Drosophila melanogaster recombinant inbred lines
Mendelian proportions among unlinked alleles
Genotype ratio distortion
Estimate: 1.15 pairs of epistatic alleles for any two genome
稍微了解一下：
1. RNAs leave yeast poised for action
Long ncRNAs accelerate activation of protein-coding gene
GAL genes released from repression
Long ncRNA speed upGAL expression
By recruiting a key enzyme needed
小知识：
1. Hormone boosts attractiveness
Nasal puffs of oxytocin
Improves rating for their partner over unfamiliar/familiar woman
呵呵，大家知道应该怎么留住他/她了吧
m*g
62 楼
开学了，突然变得很有效率，脱离了颓废的圣诞假期感觉真好！
发布顺序有点乱，不过大概还是按照时间顺序的。
Science 13.12.06
推荐：
1. Genetic determinants and cellular constraints in noisy gene expression
Evidences for gene-specific v.s. genome-wide regulation
Mainly focused on yeast and E. coli
2. Functional Roles of Pulsing in Genetic Circuits
两篇都是Review, 不是我最喜欢的那类Review, 有点罗列的感觉
稍微了解一下：
1. Single-Cell Metabolomics: Analytical and Biological Perspectives
也是review，主要讲方法
小知识：
1. Playing Kissy with the Relatives
Who to select for cooperate
Surface receptor spot relatedness
Less-related cell as a stopgap if needed
2. Direct and Reversible Hydrogenation of CO2 to Formate by a Bacterial
Carbon Dioxide Reductase
Enzymes from anaerobic bacteria
Catalyze the storage of hydrogen
In the form of formic acid
诶，感觉从我的文件复制粘贴过来之后格式就变得很奇怪……
发布顺序有点乱，不过大概还是按照时间顺序的。
Science 13.12.06
推荐：
1. Genetic determinants and cellular constraints in noisy gene expression
Evidences for gene-specific v.s. genome-wide regulation
Mainly focused on yeast and E. coli
2. Functional Roles of Pulsing in Genetic Circuits
两篇都是Review, 不是我最喜欢的那类Review, 有点罗列的感觉
稍微了解一下：
1. Single-Cell Metabolomics: Analytical and Biological Perspectives
也是review，主要讲方法
小知识：
1. Playing Kissy with the Relatives
Who to select for cooperate
Surface receptor spot relatedness
Less-related cell as a stopgap if needed
2. Direct and Reversible Hydrogenation of CO2 to Formate by a Bacterial
Carbon Dioxide Reductase
Enzymes from anaerobic bacteria
Catalyze the storage of hydrogen
In the form of formic acid
诶，感觉从我的文件复制粘贴过来之后格式就变得很奇怪……
m*g
63 楼
都没有人回帖的样子呢~孤单的猫箱
Nature 13.12.12
推荐：
1. Chromatin connectivity maps reveal dynamic promoter–enhancer long-range
associations
Transcriptional interactome
Antibody recognizes preinitiation complexes
Three types of stem cells in mouse
40,000 long-range interaction
稍微了解一下：
1. An archaeal origin of eukaryotes supports only two primary domains of
life
Evidence for eocyte hypothesis
Archaea is a paraphyletic group
小知识：
果然学生物的最原始的动力就是这些小实验呢
1. Baboons know when to be noisy
The experimenters stood facing the animals with their eyes either open or
closed, or turned away from the animals
More begging hand gestures when experimenters had their eyes open
Make noisy banging actions in the other cases
Adjust their mode of communication according to the level of an observer's
attention
2. Bees are better for strawberries
heavier, redder, and had a longer shelf life and a more desirable sugar-to-
acid ratio
A permeable plastic to eliminate wind and bee pollination, or fine-mesh bags
to exclude just bees
3. CRISPR corrects genetic disease
Correct the mutated Crygc gene in fertilized mouse eggs
CRISPR还是挺有前途的呢！
Nature 13.12.12
推荐：
1. Chromatin connectivity maps reveal dynamic promoter–enhancer long-range
associations
Transcriptional interactome
Antibody recognizes preinitiation complexes
Three types of stem cells in mouse
40,000 long-range interaction
稍微了解一下：
1. An archaeal origin of eukaryotes supports only two primary domains of
life
Evidence for eocyte hypothesis
Archaea is a paraphyletic group
小知识：
果然学生物的最原始的动力就是这些小实验呢
1. Baboons know when to be noisy
The experimenters stood facing the animals with their eyes either open or
closed, or turned away from the animals
More begging hand gestures when experimenters had their eyes open
Make noisy banging actions in the other cases
Adjust their mode of communication according to the level of an observer's
attention
2. Bees are better for strawberries
heavier, redder, and had a longer shelf life and a more desirable sugar-to-
acid ratio
A permeable plastic to eliminate wind and bee pollination, or fine-mesh bags
to exclude just bees
3. CRISPR corrects genetic disease
Correct the mutated Crygc gene in fertilized mouse eggs
CRISPR还是挺有前途的呢！
m*g
64 楼
今天去找导师汇报，本来觉得自己的内容太少，会被批评的，结果导师还鼓励了我，我
一定要加倍努力呀！感动ing。希望以后也能成为我导师那样的好导师！
Science 13.12.13
推荐：
1. Exonic Transcription Factor Binding Directs Codon Choice and Affects
Protein Evolution
概要：Long-Term Dynamics of Adaptation in Asexual Populations
Mean fitness seems to have no upper bound
Power law better than hyperbolic model
2. The Hidden Codes That Shape Protein Evolution
TF binding code
Human genome in 81 cell types
Constraining codes
~14% codons within 86.9% of genes are occupied by TFs
3. Cavefish Study Supports Controversial Evolutionary Mechanism
Mexican tetra
HSP90 as capacitor
Similar case for drosophila eye development
稍微了解一下：
1. Finding the Right Partner in a 3D Genome
Architecture of nucleus in real time
high-throughput time-lapse imaging
Translocation after DSB induction
一定要加倍努力呀！感动ing。希望以后也能成为我导师那样的好导师！
Science 13.12.13
推荐：
1. Exonic Transcription Factor Binding Directs Codon Choice and Affects
Protein Evolution
概要：Long-Term Dynamics of Adaptation in Asexual Populations
Mean fitness seems to have no upper bound
Power law better than hyperbolic model
2. The Hidden Codes That Shape Protein Evolution
TF binding code
Human genome in 81 cell types
Constraining codes
~14% codons within 86.9% of genes are occupied by TFs
3. Cavefish Study Supports Controversial Evolutionary Mechanism
Mexican tetra
HSP90 as capacitor
Similar case for drosophila eye development
稍微了解一下：
1. Finding the Right Partner in a 3D Genome
Architecture of nucleus in real time
high-throughput time-lapse imaging
Translocation after DSB induction
t*z
65 楼
顶下楼主的执着热情。我也是做进化的，来学习下。
m*g
66 楼
唔，今天似乎有点偷懒……没有做实验……
Nature 13.12.19
推荐： Solutions to the Public Goods Dilemma in Bacterial Biofilms
我自己特别喜欢cheater的defense mechanism, cooperation的形成之类的
评论： Biofilms block bacterial cheaters
Cheaters do not thrive as well as enzyme producers when they are grown in
communities called biofilms
小知识：
1. Microbes meddle with microRNA
Infection with Listeria monocytogenes
Reduced expression of six microRNAs after the infection in normal mice
No decrease for five of them in mice without gut microbes
Nature 13.12.19
推荐： Solutions to the Public Goods Dilemma in Bacterial Biofilms
我自己特别喜欢cheater的defense mechanism, cooperation的形成之类的
评论： Biofilms block bacterial cheaters
Cheaters do not thrive as well as enzyme producers when they are grown in
communities called biofilms
小知识：
1. Microbes meddle with microRNA
Infection with Listeria monocytogenes
Reduced expression of six microRNAs after the infection in normal mice
No decrease for five of them in mice without gut microbes
m*g
67 楼
Nature 14.01.02
稍微了解一下：
1. N6-methyladenosine-dependent regulation of messenger RNA stability
m6A: most prevalent internal modification in mRNA
Recognized by human YTH domain family
From translatable to mRNA decay
小知识：
1. Low investment in sexual reproduction threatens plants adapted to
phosphorus limitation
2. Upper Palaeolithic Siberian genome reveals dual ancestry of Native
Americans
3. The complete genome sequence of a Neanderthal from the Altai Mountains
稍微了解一下：
1. N6-methyladenosine-dependent regulation of messenger RNA stability
m6A: most prevalent internal modification in mRNA
Recognized by human YTH domain family
From translatable to mRNA decay
小知识：
1. Low investment in sexual reproduction threatens plants adapted to
phosphorus limitation
2. Upper Palaeolithic Siberian genome reveals dual ancestry of Native
Americans
3. The complete genome sequence of a Neanderthal from the Altai Mountains
m*g
68 楼
哦。谢谢！觉得自己有时候懒死了，不想做实验，就去看看文献什么的。
【在 t*****z 的大作中提到】
: 顶下楼主的执着热情。我也是做进化的，来学习下。
【在 t*****z 的大作中提到】
: 顶下楼主的执着热情。我也是做进化的，来学习下。
m*g
69 楼
Science 13.12.20
稍微了解一下：
1. Genomic Clues to the Ancestral Flowering Plant
Mt and nuclear genes sequenced
Single sister species to all other extant angiosperms
Mt: Horizontal Transfer of Entire Genomes via Mitochondrial Fusion in the
AngiospermAmborella
Horizontal gene transfer
75% fortein mt protein genes are pseudogenes
Genome: The Amborella Genome and the Evolution of Flowering Plants
小知识：
1. Brood Parasitism and the Evolution of Cooperative Breeding in Birds
Cooperative breeders related to brood parasites
Brood parasites get better care
Cooperate breeders defend better against brood parasites
2. No Barriers to Cellulose Breakdown
Balteria enzyme CelA
Breaks down cellulose and hemicellulose
稍微了解一下：
1. Genomic Clues to the Ancestral Flowering Plant
Mt and nuclear genes sequenced
Single sister species to all other extant angiosperms
Mt: Horizontal Transfer of Entire Genomes via Mitochondrial Fusion in the
AngiospermAmborella
Horizontal gene transfer
75% fortein mt protein genes are pseudogenes
Genome: The Amborella Genome and the Evolution of Flowering Plants
小知识：
1. Brood Parasitism and the Evolution of Cooperative Breeding in Birds
Cooperative breeders related to brood parasites
Brood parasites get better care
Cooperate breeders defend better against brood parasites
2. No Barriers to Cellulose Breakdown
Balteria enzyme CelA
Breaks down cellulose and hemicellulose
m*g
70 楼
PNAS 13.12.17
本周似乎没有碰到那种令人眼前一亮的文章，下面几篇可以稍微看一下。
1. Codon 104 variation of p53 gene provides adaptive apoptotic responses to
extreme environments in mammals of the Tibet plateau
2. Repeated elevational transitions in hemoglobin function during the
evolution of Andean hummingbirds
3. The Burmese python genome reveals the molecular basis for extreme
adaptation in snakes
4. The king cobra genome reveals dynamic gene evolution and adaptation in
the snake venom system
本周似乎没有碰到那种令人眼前一亮的文章，下面几篇可以稍微看一下。
1. Codon 104 variation of p53 gene provides adaptive apoptotic responses to
extreme environments in mammals of the Tibet plateau
2. Repeated elevational transitions in hemoglobin function during the
evolution of Andean hummingbirds
3. The Burmese python genome reveals the molecular basis for extreme
adaptation in snakes
4. The king cobra genome reveals dynamic gene evolution and adaptation in
the snake venom system
m*g
71 楼
呼呼，下一个post终于要进入2014年了，感觉我写的内容越来越少了~~~
PNAS 13.12.24
稍微了解一下：
1. Mutational effects on stability are largely conserved during protein
evolution
Influenza nucleoprotein
Measure mutational effects on stability
In diverged homologs
Largely conserved
Simulated protein evolution is similar
小知识：
1. Genetic mapping of adaptation reveals fitness tradeoffs in Arabidopsis
thaliana
2. Visible light alters yeast metabolic rhythms by inhibiting respiration
3. Stepwise artificial evolution of a plant disease resistance gene
4. A fully defined and scalable 3D culture system for human pluripotent stem
cell expansion and differentiation
PNAS 13.12.24
稍微了解一下：
1. Mutational effects on stability are largely conserved during protein
evolution
Influenza nucleoprotein
Measure mutational effects on stability
In diverged homologs
Largely conserved
Simulated protein evolution is similar
小知识：
1. Genetic mapping of adaptation reveals fitness tradeoffs in Arabidopsis
thaliana
2. Visible light alters yeast metabolic rhythms by inhibiting respiration
3. Stepwise artificial evolution of a plant disease resistance gene
4. A fully defined and scalable 3D culture system for human pluripotent stem
cell expansion and differentiation
m*g
72 楼
Science 14.01.03
新年快乐！P.S. 这周又没有遇到“推荐”的paper。
稍微了解一下：
1. Two Y Genes Can Replace the Entire Y Chromosome for Assisted Reproduction
in the Mouse
另外，
complex and multilayered palindromic structure of the Y chromosome
may facilitate internal pairing of nucleotide bases
2. Break-Induced Replication Repair of Damaged Forks Induces Genomic
Duplications in Human Cells
小知识：
1. A Cascade of Histone Modifications Induces Chromatin Condensation in
Mitosis
2. A Neural Mechanism Underlying Mating Preferences for Familiar Individuals
in Medaka Fish
新年快乐！P.S. 这周又没有遇到“推荐”的paper。
稍微了解一下：
1. Two Y Genes Can Replace the Entire Y Chromosome for Assisted Reproduction
in the Mouse
另外，
complex and multilayered palindromic structure of the Y chromosome
may facilitate internal pairing of nucleotide bases
2. Break-Induced Replication Repair of Damaged Forks Induces Genomic
Duplications in Human Cells
小知识：
1. A Cascade of Histone Modifications Induces Chromatin Condensation in
Mitosis
2. A Neural Mechanism Underlying Mating Preferences for Familiar Individuals
in Medaka Fish
m*g
73 楼
最近被导师说了，觉得我被distracted了，我自己也这么觉得，不过可能真的心智不够
成熟吧，感觉与自己以及导师的预期差了不少。我会努力的！
新年快乐！
Nature 14.01.09
推荐：
原文两篇见science
1. Genome-Scale CRISPR-Cas9 Knockout Screening in Human Cells
评论： CRISPR screen identifies genes
A library of 64,751 guide RNA sequences
Target 18,080 genes in human cells
Genes that are required by cancer and stem cells to survive
稍微了解一下：
1. The effects of genetic variation on gene expression dynamics during
development
2. Diversity of ageing across the tree of life
小知识：
1. Serial Femtosecond Crystallography of G Protein–Coupled Receptors
Room-temperature free-electron-laser approach may better capture the protein
's conformation in its native environment
成熟吧，感觉与自己以及导师的预期差了不少。我会努力的！
新年快乐！
Nature 14.01.09
推荐：
原文两篇见science
1. Genome-Scale CRISPR-Cas9 Knockout Screening in Human Cells
评论： CRISPR screen identifies genes
A library of 64,751 guide RNA sequences
Target 18,080 genes in human cells
Genes that are required by cancer and stem cells to survive
稍微了解一下：
1. The effects of genetic variation on gene expression dynamics during
development
2. Diversity of ageing across the tree of life
小知识：
1. Serial Femtosecond Crystallography of G Protein–Coupled Receptors
Room-temperature free-electron-laser approach may better capture the protein
's conformation in its native environment
m*g
74 楼
最近面临着4个deadline，果然我是那种喜欢冲击deadline的拖延症患者。
希望能够顺利完成呢（应该说非完成不可）！加油！
Science 14.01.10
推荐：
1. Single-Cell RNA-Seq Reveals Dynamic, Random Monoallelic Gene Expression
in Mammalian Cells
Single cell expression of mouse of mixed background
Abundant monoallelic expression
2. Genetic Screens in Human Cells Using the CRISPR-Cas9 System
Pooled, LOF genetic screening approach
Genome-scale lentival sgRNA library
Generate knockout collections
3. Genome-Scale CRISPR-Cas9 Knockout Screening in Human Cells
稍微了解一下：
1. Mutational Analysis Reveals the Origin and Therapy-Driven Evolution of
Recurrent Glioma
小知识：
1. Studies Suggest Two-Way Street for Science Majors
里面包含STEM专业的专业率和肄业率，以及转专业后的方向，有兴趣可以了解一下。
2. Bacterial Vesicles in Marine Ecosystems
简介： Bacterial Vesicles in the Ocean
3. Status and Ecological Effects of the World's Largest Carnivores
希望能够顺利完成呢（应该说非完成不可）！加油！
Science 14.01.10
推荐：
1. Single-Cell RNA-Seq Reveals Dynamic, Random Monoallelic Gene Expression
in Mammalian Cells
Single cell expression of mouse of mixed background
Abundant monoallelic expression
2. Genetic Screens in Human Cells Using the CRISPR-Cas9 System
Pooled, LOF genetic screening approach
Genome-scale lentival sgRNA library
Generate knockout collections
3. Genome-Scale CRISPR-Cas9 Knockout Screening in Human Cells
稍微了解一下：
1. Mutational Analysis Reveals the Origin and Therapy-Driven Evolution of
Recurrent Glioma
小知识：
1. Studies Suggest Two-Way Street for Science Majors
里面包含STEM专业的专业率和肄业率，以及转专业后的方向，有兴趣可以了解一下。
2. Bacterial Vesicles in Marine Ecosystems
简介： Bacterial Vesicles in the Ocean
3. Status and Ecological Effects of the World's Largest Carnivores
m*u
75 楼
感觉你只是为自己有动力才更新帖子的。若真想讨论东西，为什么不概括总结一下这些
文章内容呢？不必完全摘用摘要或summary的东西，重要的是你觉得这文章有什么新的
东西促使你罗列或highlight它！
谢谢。
文章内容呢？不必完全摘用摘要或summary的东西，重要的是你觉得这文章有什么新的
东西促使你罗列或highlight它！
谢谢。
m*g
76 楼
谢谢你的建议。我确实是只为了监督自己才开的这个帖子呢。而且这样开组会找paper
就变得很简单，只要扫一眼这个帖子，就能找出自己最喜欢的文献用于讨论了。
不列出想法和理由的原因是，我觉得即使列出各种用于讨论的东西，列出10次，也不一
定有人回复1次，基本上是有去无回的，所以心里想想就好了，highlight一篇文章当然
是有自己的理由的^_^，个人觉得每周的推荐阅读大概都是有值得讨论的paper呢。不过
列出来就太长了……我比较懒，不好意思哈。
如果您有什么想要讨论的paper欢迎列出，我应该会回复的呢。也欢迎您开一个类似的
帖子，做个榜样，那样子也许我也会更有动力，嘻嘻。新年快乐！
【在 m******u 的大作中提到】
: 感觉你只是为自己有动力才更新帖子的。若真想讨论东西，为什么不概括总结一下这些
: 文章内容呢？不必完全摘用摘要或summary的东西，重要的是你觉得这文章有什么新的
: 东西促使你罗列或highlight它！
: 谢谢。
就变得很简单，只要扫一眼这个帖子，就能找出自己最喜欢的文献用于讨论了。
不列出想法和理由的原因是，我觉得即使列出各种用于讨论的东西，列出10次，也不一
定有人回复1次，基本上是有去无回的，所以心里想想就好了，highlight一篇文章当然
是有自己的理由的^_^，个人觉得每周的推荐阅读大概都是有值得讨论的paper呢。不过
列出来就太长了……我比较懒，不好意思哈。
如果您有什么想要讨论的paper欢迎列出，我应该会回复的呢。也欢迎您开一个类似的
帖子，做个榜样，那样子也许我也会更有动力，嘻嘻。新年快乐！
【在 m******u 的大作中提到】
: 感觉你只是为自己有动力才更新帖子的。若真想讨论东西，为什么不概括总结一下这些
: 文章内容呢？不必完全摘用摘要或summary的东西，重要的是你觉得这文章有什么新的
: 东西促使你罗列或highlight它！
: 谢谢。
b*s
77 楼
你能坚持这么久已经很了不起了。请继续。
没有回复，不是没人看，而是大部分不是这个领域的。但是开卷有益，读过多少总是有
收获的。
paper
【在 m******g 的大作中提到】
: 谢谢你的建议。我确实是只为了监督自己才开的这个帖子呢。而且这样开组会找paper
: 就变得很简单，只要扫一眼这个帖子，就能找出自己最喜欢的文献用于讨论了。
: 不列出想法和理由的原因是，我觉得即使列出各种用于讨论的东西，列出10次，也不一
: 定有人回复1次，基本上是有去无回的，所以心里想想就好了，highlight一篇文章当然
: 是有自己的理由的^_^，个人觉得每周的推荐阅读大概都是有值得讨论的paper呢。不过
: 列出来就太长了……我比较懒，不好意思哈。
: 如果您有什么想要讨论的paper欢迎列出，我应该会回复的呢。也欢迎您开一个类似的
: 帖子，做个榜样，那样子也许我也会更有动力，嘻嘻。新年快乐！
没有回复，不是没人看，而是大部分不是这个领域的。但是开卷有益，读过多少总是有
收获的。
paper
【在 m******g 的大作中提到】
: 谢谢你的建议。我确实是只为了监督自己才开的这个帖子呢。而且这样开组会找paper
: 就变得很简单，只要扫一眼这个帖子，就能找出自己最喜欢的文献用于讨论了。
: 不列出想法和理由的原因是，我觉得即使列出各种用于讨论的东西，列出10次，也不一
: 定有人回复1次，基本上是有去无回的，所以心里想想就好了，highlight一篇文章当然
: 是有自己的理由的^_^，个人觉得每周的推荐阅读大概都是有值得讨论的paper呢。不过
: 列出来就太长了……我比较懒，不好意思哈。
: 如果您有什么想要讨论的paper欢迎列出，我应该会回复的呢。也欢迎您开一个类似的
: 帖子，做个榜样，那样子也许我也会更有动力，嘻嘻。新年快乐！
l*1
78 楼
One ask,
from your cited >100 papers from CNS or N sisiter what relevant to 遗传进化
方向, could you eteact at least >two proposals? i mean for your K99/R00 in
the soon future..
paper
【在 m******g 的大作中提到】
: 谢谢你的建议。我确实是只为了监督自己才开的这个帖子呢。而且这样开组会找paper
: 就变得很简单，只要扫一眼这个帖子，就能找出自己最喜欢的文献用于讨论了。
: 不列出想法和理由的原因是，我觉得即使列出各种用于讨论的东西，列出10次，也不一
: 定有人回复1次，基本上是有去无回的，所以心里想想就好了，highlight一篇文章当然
: 是有自己的理由的^_^，个人觉得每周的推荐阅读大概都是有值得讨论的paper呢。不过
: 列出来就太长了……我比较懒，不好意思哈。
: 如果您有什么想要讨论的paper欢迎列出，我应该会回复的呢。也欢迎您开一个类似的
: 帖子，做个榜样，那样子也许我也会更有动力，嘻嘻。新年快乐！
from your cited >100 papers from CNS or N sisiter what relevant to 遗传进化
方向, could you eteact at least >two proposals? i mean for your K99/R00 in
the soon future..
paper
【在 m******g 的大作中提到】
: 谢谢你的建议。我确实是只为了监督自己才开的这个帖子呢。而且这样开组会找paper
: 就变得很简单，只要扫一眼这个帖子，就能找出自己最喜欢的文献用于讨论了。
: 不列出想法和理由的原因是，我觉得即使列出各种用于讨论的东西，列出10次，也不一
: 定有人回复1次，基本上是有去无回的，所以心里想想就好了，highlight一篇文章当然
: 是有自己的理由的^_^，个人觉得每周的推荐阅读大概都是有值得讨论的paper呢。不过
: 列出来就太长了……我比较懒，不好意思哈。
: 如果您有什么想要讨论的paper欢迎列出，我应该会回复的呢。也欢迎您开一个类似的
: 帖子，做个榜样，那样子也许我也会更有动力，嘻嘻。新年快乐！
m*g
79 楼
没太懂问题啊。是不是说看多少文献，可以提取多少proposal?
个人觉得这个问题就跟“看多少小说可以写出一部小说”和“做多少习题可以考95分以
上”是一样的，因人而异，但是如果不看小说，不做习题，肯定是没办法写出小说和考
95分以上的（大天才除外），哈哈。感觉看了之后对于自己理解、设计、写作都很有帮
助。
感觉文献挺有意思的啊。就像看小说一样，不需要有太功利的目的嘛。
【在 l**********1 的大作中提到】
: One ask,
: from your cited >100 papers from CNS or N sisiter what relevant to 遗传进化
: 方向, could you eteact at least >two proposals? i mean for your K99/R00 in
: the soon future..
:
: paper
个人觉得这个问题就跟“看多少小说可以写出一部小说”和“做多少习题可以考95分以
上”是一样的，因人而异，但是如果不看小说，不做习题，肯定是没办法写出小说和考
95分以上的（大天才除外），哈哈。感觉看了之后对于自己理解、设计、写作都很有帮
助。
感觉文献挺有意思的啊。就像看小说一样，不需要有太功利的目的嘛。
【在 l**********1 的大作中提到】
: One ask,
: from your cited >100 papers from CNS or N sisiter what relevant to 遗传进化
: 方向, could you eteact at least >two proposals? i mean for your K99/R00 in
: the soon future..
:
: paper
m*g
80 楼
555，不好意思，我觉得好难用自己的话一一列举为什么要罗列某篇文章啊，那还是就
这么贴出来吧。
PNAS 14.01.07
推荐：
1. Ohnologs are overrepresented in pathogenic copy number mutations
Ohnolog: retained after WGD
Overrepresented in pathogenic SNV
2. Contribution of phenotypic heterogeneity to adaptive antibiotic
resistance
Some due to mutation, some due to heterogeneity
Different responses after non-selective response
I think the result is expected, but still a nice story
稍微了解一下：
1. Drastic neofunctionalization associated with evolution of the timezyme
AANAT 500 Mya
小知识：
1. A unique covalent bond in basement membrane is a primordial innovation
for tissue evolution
2. Policing of reproduction by hidden threats in a cooperative mammal
selection to evade the threat of infanticide by dominant females
explain the evolution of remarkable birth synchrony
有一些奇怪的联想……
这么贴出来吧。
PNAS 14.01.07
推荐：
1. Ohnologs are overrepresented in pathogenic copy number mutations
Ohnolog: retained after WGD
Overrepresented in pathogenic SNV
2. Contribution of phenotypic heterogeneity to adaptive antibiotic
resistance
Some due to mutation, some due to heterogeneity
Different responses after non-selective response
I think the result is expected, but still a nice story
稍微了解一下：
1. Drastic neofunctionalization associated with evolution of the timezyme
AANAT 500 Mya
小知识：
1. A unique covalent bond in basement membrane is a primordial innovation
for tissue evolution
2. Policing of reproduction by hidden threats in a cooperative mammal
selection to evade the threat of infanticide by dominant females
explain the evolution of remarkable birth synchrony
有一些奇怪的联想……
m*g
81 楼
这周好累，连续三天晚上1点爬起来工作到5点(自作自受)，以后争取不要再这么抢着
deadline做
事了。
感觉冲deadline玩的就是心跳，而且对不住导师。
Nature 14.1.16
推荐：
1. RNA retrieved from intact tissue
原文： Transcriptome in vivo analysis (TIVA) of spatially defined single
cells in live tissue
小知识：
1. Starfish eyes see the light
deadline做
事了。
感觉冲deadline玩的就是心跳，而且对不住导师。
Nature 14.1.16
推荐：
1. RNA retrieved from intact tissue
原文： Transcriptome in vivo analysis (TIVA) of spatially defined single
cells in live tissue
小知识：
1. Starfish eyes see the light
l*1
82 楼
Proposal to Reference (P and R) can be taken as Main and sub relationship!
To initiative, first title and key words might be from R or previously got
result
> more direct or indirect relevant R
>P modified
>more R
>P modi again
>more R or preli result
>Final draft of P
Just two cents.
【在 m******g 的大作中提到】
: 没太懂问题啊。是不是说看多少文献，可以提取多少proposal?
: 个人觉得这个问题就跟“看多少小说可以写出一部小说”和“做多少习题可以考95分以
: 上”是一样的，因人而异，但是如果不看小说，不做习题，肯定是没办法写出小说和考
: 95分以上的（大天才除外），哈哈。感觉看了之后对于自己理解、设计、写作都很有帮
: 助。
: 感觉文献挺有意思的啊。就像看小说一样，不需要有太功利的目的嘛。
To initiative, first title and key words might be from R or previously got
result
> more direct or indirect relevant R
>P modified
>more R
>P modi again
>more R or preli result
>Final draft of P
Just two cents.
【在 m******g 的大作中提到】
: 没太懂问题啊。是不是说看多少文献，可以提取多少proposal?
: 个人觉得这个问题就跟“看多少小说可以写出一部小说”和“做多少习题可以考95分以
: 上”是一样的，因人而异，但是如果不看小说，不做习题，肯定是没办法写出小说和考
: 95分以上的（大天才除外），哈哈。感觉看了之后对于自己理解、设计、写作都很有帮
: 助。
: 感觉文献挺有意思的啊。就像看小说一样，不需要有太功利的目的嘛。
m*u
83 楼
我认为：就是某篇文章文笔很好都可以是你想列它的原因。我自己也有某段时间不喜某
篇文章，过一段时间又会觉得它很好。对其内容的理解也随之不同。
发信人: maoxiang (白水), 信区: Biology
标 题: Re: 大家一起来读主流杂志吧［遗传进化方向］希望每周更新
发信站: BBS 未名空间站 (Fri Feb 7 17:34:00 2014, 美东)
555，不好意思，我觉得好难用自己的话一一列举为什么要罗列某篇文章啊，那还是就
这么贴出来吧。
篇文章，过一段时间又会觉得它很好。对其内容的理解也随之不同。
发信人: maoxiang (白水), 信区: Biology
标 题: Re: 大家一起来读主流杂志吧［遗传进化方向］希望每周更新
发信站: BBS 未名空间站 (Fri Feb 7 17:34:00 2014, 美东)
555，不好意思，我觉得好难用自己的话一一列举为什么要罗列某篇文章啊，那还是就
这么贴出来吧。
m*g
84 楼
我这个月对这个topic很感兴趣呢。
读了一些文献。
有什么具体问题可以讨论一下啊
【在 x********e 的大作中提到】
: 版上有做splicing的吗 最近对alternative splicing感兴趣
读了一些文献。
有什么具体问题可以讨论一下啊
【在 x********e 的大作中提到】
: 版上有做splicing的吗 最近对alternative splicing感兴趣
m*g
85 楼
补番中……
PNAS 14.1.14
推荐：
1. Neutral genomic regions refine models of recent rapid human population
growth
Population growth or purifying selection contributes to rare alleles
Sequence genetic variants far from genes (neutral)
3.4% per generation over the last 3,000–4,000 y
稍微了解一下：
1. Harnessing evolutionary fitness in Plasmodium falciparum for drug
discovery and suppressing resistance
只是描述现象：混用某两种inhibitor可防止其产生耐药性
因为我比较喜欢耐药性方面的东西，所以还是列一下好了
小知识：
1. Spontaneous slow replication fork progression elicits mitosis alterations
in homologous recombination-deficient mammalian cells
2. Systems analysis of sex differences reveals an immunosuppressive role for
testosterone in the response to influenza vaccination
PNAS 14.1.14
推荐：
1. Neutral genomic regions refine models of recent rapid human population
growth
Population growth or purifying selection contributes to rare alleles
Sequence genetic variants far from genes (neutral)
3.4% per generation over the last 3,000–4,000 y
稍微了解一下：
1. Harnessing evolutionary fitness in Plasmodium falciparum for drug
discovery and suppressing resistance
只是描述现象：混用某两种inhibitor可防止其产生耐药性
因为我比较喜欢耐药性方面的东西，所以还是列一下好了
小知识：
1. Spontaneous slow replication fork progression elicits mitosis alterations
in homologous recombination-deficient mammalian cells
2. Systems analysis of sex differences reveals an immunosuppressive role for
testosterone in the response to influenza vaccination
m*g
86 楼
最近感觉要做的事情超多，时间刷的一下就过去了。
Science 14.1.17
推荐：
1. Direct in Vivo RNAi Screen Unveils Myosin IIa as a Tumor Suppressor of
Squamous Cell Carcinomas
稍微了解一下：
1. Ribose—An Internal Threat to DNA
小知识：
1. Many Paths to the Origin of Life
2. Conserved Class of Queen Pheromones Stops Social Insect Workers from
Reproducing
Science 14.1.17
推荐：
1. Direct in Vivo RNAi Screen Unveils Myosin IIa as a Tumor Suppressor of
Squamous Cell Carcinomas
稍微了解一下：
1. Ribose—An Internal Threat to DNA
小知识：
1. Many Paths to the Origin of Life
2. Conserved Class of Queen Pheromones Stops Social Insect Workers from
Reproducing
m*g
87 楼
求提高效率！求上帝保佑（非基督徒）！
Nature 14.01.23
稍微了解一下：
1. Diet rapidly and reproducibly alters the human gut microbiome
2. Discovery and saturation analysis of cancer genes across 21 tumour types
Nature 14.01.23
稍微了解一下：
1. Diet rapidly and reproducibly alters the human gut microbiome
2. Discovery and saturation analysis of cancer genes across 21 tumour types
m*g
88 楼
最近感觉自己太懒惰了，很容易就distracted，很多事情都一拖再拖，踩着deadline，
一定要改正。
PNAS 14.1.21
很推荐：
1. Genetic drift opposes mutualism during spatial population expansion
方法很有趣，系统很喜欢
稍微了解一下：
1. Sympatric incipient speciation of spiny mice Acomys at "Evolution Canyon,
" Israel
2. Information transfer by leaky, heterogeneous, protein kinase signaling
systems
小知识：
1. Perfect genetic correlation between number of offspring and
grandoffspring in an industrialized human population
一定要改正。
PNAS 14.1.21
很推荐：
1. Genetic drift opposes mutualism during spatial population expansion
方法很有趣，系统很喜欢
稍微了解一下：
1. Sympatric incipient speciation of spiny mice Acomys at "Evolution Canyon,
" Israel
2. Information transfer by leaky, heterogeneous, protein kinase signaling
systems
小知识：
1. Perfect genetic correlation between number of offspring and
grandoffspring in an industrialized human population
n*k
89 楼
看了一圈，这个要强挺一下！绝对是牛人的搞法，牛人的路子！只要坚持好，把握机会
，最好把本版几年前有几个强人的帖子好好读读，包括DRBIOLOGY和另外一个在
SINGAPORE的FACULTY写的一些关于职业规划设计的帖子好好读一读，把握机会，前途不
可限量！任何时候，机会都是自己可以创造和把握的，真正的牛人是没有机会也创造出
机会！聪明人很多，但牛人很少！你可能已经具备了一些成为牛人的素质哈；贵在坚持
，聪明的坚持，智慧的前行！
最后，以你的目前状态，不会有太糟糕的运气；万一的话，只要我能在学术界立足，随
时欢迎你这种人来我实验室哈--只要不是那种只动脑不动手的哈：））。
【在 m******g 的大作中提到】
: 最近感觉要做的事情超多，时间刷的一下就过去了。
: Science 14.1.17
: 推荐：
: 1. Direct in Vivo RNAi Screen Unveils Myosin IIa as a Tumor Suppressor of
: Squamous Cell Carcinomas
: 稍微了解一下：
: 1. Ribose—An Internal Threat to DNA
: 小知识：
: 1. Many Paths to the Origin of Life
: 2. Conserved Class of Queen Pheromones Stops Social Insect Workers from
，最好把本版几年前有几个强人的帖子好好读读，包括DRBIOLOGY和另外一个在
SINGAPORE的FACULTY写的一些关于职业规划设计的帖子好好读一读，把握机会，前途不
可限量！任何时候，机会都是自己可以创造和把握的，真正的牛人是没有机会也创造出
机会！聪明人很多，但牛人很少！你可能已经具备了一些成为牛人的素质哈；贵在坚持
，聪明的坚持，智慧的前行！
最后，以你的目前状态，不会有太糟糕的运气；万一的话，只要我能在学术界立足，随
时欢迎你这种人来我实验室哈--只要不是那种只动脑不动手的哈：））。
【在 m******g 的大作中提到】
: 最近感觉要做的事情超多，时间刷的一下就过去了。
: Science 14.1.17
: 推荐：
: 1. Direct in Vivo RNAi Screen Unveils Myosin IIa as a Tumor Suppressor of
: Squamous Cell Carcinomas
: 稍微了解一下：
: 1. Ribose—An Internal Threat to DNA
: 小知识：
: 1. Many Paths to the Origin of Life
: 2. Conserved Class of Queen Pheromones Stops Social Insect Workers from
l*1
90 楼
本版台柱美女PKU PI 也得时常回这 找潜力高俊(high EQ and IQ both) 徒弟 哈;
不然就只看着本版前四大牛人 找(high EQ and IQ)美徒妹 ?
【在 n********k 的大作中提到】
: 看了一圈，这个要强挺一下！绝对是牛人的搞法，牛人的路子！只要坚持好，把握机会
: ，最好把本版几年前有几个强人的帖子好好读读，包括DRBIOLOGY和另外一个在
: SINGAPORE的FACULTY写的一些关于职业规划设计的帖子好好读一读，把握机会，前途不
: 可限量！任何时候，机会都是自己可以创造和把握的，真正的牛人是没有机会也创造出
: 机会！聪明人很多，但牛人很少！你可能已经具备了一些成为牛人的素质哈；贵在坚持
: ，聪明的坚持，智慧的前行！
: 最后，以你的目前状态，不会有太糟糕的运气；万一的话，只要我能在学术界立足，随
: 时欢迎你这种人来我实验室哈--只要不是那种只动脑不动手的哈：））。
不然就只看着本版前四大牛人 找(high EQ and IQ)美徒妹 ?
【在 n********k 的大作中提到】
: 看了一圈，这个要强挺一下！绝对是牛人的搞法，牛人的路子！只要坚持好，把握机会
: ，最好把本版几年前有几个强人的帖子好好读读，包括DRBIOLOGY和另外一个在
: SINGAPORE的FACULTY写的一些关于职业规划设计的帖子好好读一读，把握机会，前途不
: 可限量！任何时候，机会都是自己可以创造和把握的，真正的牛人是没有机会也创造出
: 机会！聪明人很多，但牛人很少！你可能已经具备了一些成为牛人的素质哈；贵在坚持
: ，聪明的坚持，智慧的前行！
: 最后，以你的目前状态，不会有太糟糕的运气；万一的话，只要我能在学术界立足，随
: 时欢迎你这种人来我实验室哈--只要不是那种只动脑不动手的哈：））。
m*g
91 楼
谢谢楼上两位的建议，我有时间会去看看学习一下的。
Science 14.1.24
推荐：
1. The Epigenetics Heretic
算是科学家背后的故事，看起来有点意思
发现abnormalties caused by pesticide persists for generations
2. An Ancient Dog in the Modern World
About a transmissible cancer in dog
稍微了解一下：
1. A Paleogenomic Perspective on Evolution and Gene Function: New insights
from Ancient DNA
A well written review for progresses in ancient DNA studies
小知识：
1. Extraordinary Color Vision
Color vision in mantis shrimp
12 spectral receptors
Science 14.1.24
推荐：
1. The Epigenetics Heretic
算是科学家背后的故事，看起来有点意思
发现abnormalties caused by pesticide persists for generations
2. An Ancient Dog in the Modern World
About a transmissible cancer in dog
稍微了解一下：
1. A Paleogenomic Perspective on Evolution and Gene Function: New insights
from Ancient DNA
A well written review for progresses in ancient DNA studies
小知识：
1. Extraordinary Color Vision
Color vision in mantis shrimp
12 spectral receptors
m*g
92 楼
这期Nature好赞！
Nature 14.1.30
非常推荐：
1. Molecular biology: A second layer of information in RNA
1) In vivo genome-wide profiling of RNA secondary structure reveals novel
regulatory features
2) Genome-wide probing of RNA structure reveals active unfolding of mRNA
structures in vivo
3) Landscape and variation of RNA secondary structure across the human
transcriptome
2. Cell biology: Potency unchained
Mildly acidic conditions triggers potential for a new cell state with
diverse potentials
1) Bidirectional developmental potential in reprogrammed cells with acquired
pluripotency
2) Stimulus-triggered fate conversion of somatic cells into pluripotency
http://www.nature.com/news/acid-bath-stem-cell-study-under-inve
据说真实性受到挑战？
3. The evolution of lncRNA repertoires and expression patterns in tetrapods
4. Mutational and fitness landscapes of an RNA virus revealed through
population sequencing
非常推荐读一读这一篇
Great methodology: sequencing rate终于降到mutation rate之下了
稍微了解一下：
1. Evolution and transmission of drug-resistant tuberculosis in a Russian
population
2. Genome-wide dissection of the quorum sensing signalling pathway in
Trypanosoma brucei
小知识：
1. Immobile bacteria hitchhike on rafts
Intereting story about attract and use another species as transport
原文： Surface-motility induction, attraction and hitchhiking between
bacterial species promote dispersal on solid surfaces
2. Mother's fatty diet hurts offspring
3. Poor diet boosts innate immunity
特指缺少Vitamin A
4. River dolphin found
5. Evolutionary biology: Brotherly love benefits females
原文： Within-group male relatedness reduces harm to females in Drosophila
Fruit flies alter their behaviour among kin
Brothers being less aggressive
Females reproducing for longer as a result
Nature 14.1.30
非常推荐：
1. Molecular biology: A second layer of information in RNA
1) In vivo genome-wide profiling of RNA secondary structure reveals novel
regulatory features
2) Genome-wide probing of RNA structure reveals active unfolding of mRNA
structures in vivo
3) Landscape and variation of RNA secondary structure across the human
transcriptome
2. Cell biology: Potency unchained
Mildly acidic conditions triggers potential for a new cell state with
diverse potentials
1) Bidirectional developmental potential in reprogrammed cells with acquired
pluripotency
2) Stimulus-triggered fate conversion of somatic cells into pluripotency
http://www.nature.com/news/acid-bath-stem-cell-study-under-inve
据说真实性受到挑战？
3. The evolution of lncRNA repertoires and expression patterns in tetrapods
4. Mutational and fitness landscapes of an RNA virus revealed through
population sequencing
非常推荐读一读这一篇
Great methodology: sequencing rate终于降到mutation rate之下了
稍微了解一下：
1. Evolution and transmission of drug-resistant tuberculosis in a Russian
population
2. Genome-wide dissection of the quorum sensing signalling pathway in
Trypanosoma brucei
小知识：
1. Immobile bacteria hitchhike on rafts
Intereting story about attract and use another species as transport
原文： Surface-motility induction, attraction and hitchhiking between
bacterial species promote dispersal on solid surfaces
2. Mother's fatty diet hurts offspring
3. Poor diet boosts innate immunity
特指缺少Vitamin A
4. River dolphin found
5. Evolutionary biology: Brotherly love benefits females
原文： Within-group male relatedness reduces harm to females in Drosophila
Fruit flies alter their behaviour among kin
Brothers being less aggressive
Females reproducing for longer as a result
m*g
93 楼
本来在开始读PhD的时候，就打算要广泛阅读主流学术杂志，比如Nature, Science,
PNAS, Plos genetics等等，但是自己总是拖拖拉拉，偶尔有心血来潮就一口气读很久
，没兴趣／时间的话就个把月都不翻一下。
就好比动漫监督需要看其他畅销动漫（暴露兴趣了，太不学术了），我们也应该多多看
看生物的杂志，以增强自己对整个领域的理解，并且了解一些文献的逻辑、方法和写法
。所以我打算开这个贴说说每周最喜欢的几篇文章什么的，每周一更（日期不定），以
监督自己，防止自己不读文献。如果没有做到，请大家不要用砖头砸，把好吃的狠狠地
砸过来就好了，然后再狠狠地鄙视我就好。
我是学遗传进化方向的，做实验和编程都做一点（但是为什么现在还这么菜呢，果然是
因为我太懒惰了），总之看看文献没有坏处，也欢迎相似方向的大家一起来贴贴推荐的
本周的文献吧（当然，如果不是本周也OK的）。
今天是星期一，就从这周开始啦。格式啥的都无所谓，可以发些critical的评论什么的
（不过至少应该写出标题^_^）。好像没看到这个论坛有类似的帖子（可能是我的“近
视度”太高，没注意到）。总之，大家多多支持，一起交流努力啦。
交流群：342148521 （开心读文献贵在坚持，加群请输入最喜欢的科学家、杂志或领域
的名称或者其他什么，无附加信息不予通过，希望大家一起参与呢）
PNAS, Plos genetics等等，但是自己总是拖拖拉拉，偶尔有心血来潮就一口气读很久
，没兴趣／时间的话就个把月都不翻一下。
就好比动漫监督需要看其他畅销动漫（暴露兴趣了，太不学术了），我们也应该多多看
看生物的杂志，以增强自己对整个领域的理解，并且了解一些文献的逻辑、方法和写法
。所以我打算开这个贴说说每周最喜欢的几篇文章什么的，每周一更（日期不定），以
监督自己，防止自己不读文献。如果没有做到，请大家不要用砖头砸，把好吃的狠狠地
砸过来就好了，然后再狠狠地鄙视我就好。
我是学遗传进化方向的，做实验和编程都做一点（但是为什么现在还这么菜呢，果然是
因为我太懒惰了），总之看看文献没有坏处，也欢迎相似方向的大家一起来贴贴推荐的
本周的文献吧（当然，如果不是本周也OK的）。
今天是星期一，就从这周开始啦。格式啥的都无所谓，可以发些critical的评论什么的
（不过至少应该写出标题^_^）。好像没看到这个论坛有类似的帖子（可能是我的“近
视度”太高，没注意到）。总之，大家多多支持，一起交流努力啦。
交流群：342148521 （开心读文献贵在坚持，加群请输入最喜欢的科学家、杂志或领域
的名称或者其他什么，无附加信息不予通过，希望大家一起参与呢）
b*s
94 楼
支持。虽然我不是做这个方向的。但是对这个方向一直很有兴趣。
【在 m******g 的大作中提到】
: 本来在开始读PhD的时候，就打算要广泛阅读主流学术杂志，比如Nature, Science,
: PNAS, Plos genetics等等，但是自己总是拖拖拉拉，偶尔有心血来潮就一口气读很久
: ，没兴趣／时间的话就个把月都不翻一下。
: 就好比动漫监督需要看其他畅销动漫（暴露兴趣了，太不学术了），我们也应该多多看
: 看生物的杂志，以增强自己对整个领域的理解，并且了解一些文献的逻辑、方法和写法
: 。所以我打算开这个贴说说每周最喜欢的几篇文章什么的，每周一更（日期不定），以
: 监督自己，防止自己不读文献。如果没有做到，请大家不要用砖头砸，把好吃的狠狠地
: 砸过来就好了，然后再狠狠地鄙视我就好。
: 我是学遗传进化方向的，做实验和编程都做一点（但是为什么现在还这么菜呢，果然是
: 因为我太懒惰了），总之看看文献没有坏处，也欢迎相似方向的大家一起来贴贴推荐的
【在 m******g 的大作中提到】
: 本来在开始读PhD的时候，就打算要广泛阅读主流学术杂志，比如Nature, Science,
: PNAS, Plos genetics等等，但是自己总是拖拖拉拉，偶尔有心血来潮就一口气读很久
: ，没兴趣／时间的话就个把月都不翻一下。
: 就好比动漫监督需要看其他畅销动漫（暴露兴趣了，太不学术了），我们也应该多多看
: 看生物的杂志，以增强自己对整个领域的理解，并且了解一些文献的逻辑、方法和写法
: 。所以我打算开这个贴说说每周最喜欢的几篇文章什么的，每周一更（日期不定），以
: 监督自己，防止自己不读文献。如果没有做到，请大家不要用砖头砸，把好吃的狠狠地
: 砸过来就好了，然后再狠狠地鄙视我就好。
: 我是学遗传进化方向的，做实验和编程都做一点（但是为什么现在还这么菜呢，果然是
: 因为我太懒惰了），总之看看文献没有坏处，也欢迎相似方向的大家一起来贴贴推荐的
e*o
95 楼
支持，最好将通俗一些。让俺这转行的也能看懂。
s*y
96 楼
支持。我也喜欢看相关文章，可是我也特别懒。你能讲讲一些最新进展那可是最好不过
了。
【在 m******g 的大作中提到】
: 本来在开始读PhD的时候，就打算要广泛阅读主流学术杂志，比如Nature, Science,
: PNAS, Plos genetics等等，但是自己总是拖拖拉拉，偶尔有心血来潮就一口气读很久
: ，没兴趣／时间的话就个把月都不翻一下。
: 就好比动漫监督需要看其他畅销动漫（暴露兴趣了，太不学术了），我们也应该多多看
: 看生物的杂志，以增强自己对整个领域的理解，并且了解一些文献的逻辑、方法和写法
: 。所以我打算开这个贴说说每周最喜欢的几篇文章什么的，每周一更（日期不定），以
: 监督自己，防止自己不读文献。如果没有做到，请大家不要用砖头砸，把好吃的狠狠地
: 砸过来就好了，然后再狠狠地鄙视我就好。
: 我是学遗传进化方向的，做实验和编程都做一点（但是为什么现在还这么菜呢，果然是
: 因为我太懒惰了），总之看看文献没有坏处，也欢迎相似方向的大家一起来贴贴推荐的
了。
【在 m******g 的大作中提到】
: 本来在开始读PhD的时候，就打算要广泛阅读主流学术杂志，比如Nature, Science,
: PNAS, Plos genetics等等，但是自己总是拖拖拉拉，偶尔有心血来潮就一口气读很久
: ，没兴趣／时间的话就个把月都不翻一下。
: 就好比动漫监督需要看其他畅销动漫（暴露兴趣了，太不学术了），我们也应该多多看
: 看生物的杂志，以增强自己对整个领域的理解，并且了解一些文献的逻辑、方法和写法
: 。所以我打算开这个贴说说每周最喜欢的几篇文章什么的，每周一更（日期不定），以
: 监督自己，防止自己不读文献。如果没有做到，请大家不要用砖头砸，把好吃的狠狠地
: 砸过来就好了，然后再狠狠地鄙视我就好。
: 我是学遗传进化方向的，做实验和编程都做一点（但是为什么现在还这么菜呢，果然是
: 因为我太懒惰了），总之看看文献没有坏处，也欢迎相似方向的大家一起来贴贴推荐的
x*e
97 楼
问题是学术杂志没有新番导读哇
【在 m******g 的大作中提到】
: 本来在开始读PhD的时候，就打算要广泛阅读主流学术杂志，比如Nature, Science,
: PNAS, Plos genetics等等，但是自己总是拖拖拉拉，偶尔有心血来潮就一口气读很久
: ，没兴趣／时间的话就个把月都不翻一下。
: 就好比动漫监督需要看其他畅销动漫（暴露兴趣了，太不学术了），我们也应该多多看
: 看生物的杂志，以增强自己对整个领域的理解，并且了解一些文献的逻辑、方法和写法
: 。所以我打算开这个贴说说每周最喜欢的几篇文章什么的，每周一更（日期不定），以
: 监督自己，防止自己不读文献。如果没有做到，请大家不要用砖头砸，把好吃的狠狠地
: 砸过来就好了，然后再狠狠地鄙视我就好。
: 我是学遗传进化方向的，做实验和编程都做一点（但是为什么现在还这么菜呢，果然是
: 因为我太懒惰了），总之看看文献没有坏处，也欢迎相似方向的大家一起来贴贴推荐的
【在 m******g 的大作中提到】
: 本来在开始读PhD的时候，就打算要广泛阅读主流学术杂志，比如Nature, Science,
: PNAS, Plos genetics等等，但是自己总是拖拖拉拉，偶尔有心血来潮就一口气读很久
: ，没兴趣／时间的话就个把月都不翻一下。
: 就好比动漫监督需要看其他畅销动漫（暴露兴趣了，太不学术了），我们也应该多多看
: 看生物的杂志，以增强自己对整个领域的理解，并且了解一些文献的逻辑、方法和写法
: 。所以我打算开这个贴说说每周最喜欢的几篇文章什么的，每周一更（日期不定），以
: 监督自己，防止自己不读文献。如果没有做到，请大家不要用砖头砸，把好吃的狠狠地
: 砸过来就好了，然后再狠狠地鄙视我就好。
: 我是学遗传进化方向的，做实验和编程都做一点（但是为什么现在还这么菜呢，果然是
: 因为我太懒惰了），总之看看文献没有坏处，也欢迎相似方向的大家一起来贴贴推荐的
w*r
98 楼
做生物贵在精深，广博并非没有用处，但往往得不偿失
大多成为pi的人都是心灵手巧，吃苦耐劳的类型
【在 m******g 的大作中提到】
: 本来在开始读PhD的时候，就打算要广泛阅读主流学术杂志，比如Nature, Science,
: PNAS, Plos genetics等等，但是自己总是拖拖拉拉，偶尔有心血来潮就一口气读很久
: ，没兴趣／时间的话就个把月都不翻一下。
: 就好比动漫监督需要看其他畅销动漫（暴露兴趣了，太不学术了），我们也应该多多看
: 看生物的杂志，以增强自己对整个领域的理解，并且了解一些文献的逻辑、方法和写法
: 。所以我打算开这个贴说说每周最喜欢的几篇文章什么的，每周一更（日期不定），以
: 监督自己，防止自己不读文献。如果没有做到，请大家不要用砖头砸，把好吃的狠狠地
: 砸过来就好了，然后再狠狠地鄙视我就好。
: 我是学遗传进化方向的，做实验和编程都做一点（但是为什么现在还这么菜呢，果然是
: 因为我太懒惰了），总之看看文献没有坏处，也欢迎相似方向的大家一起来贴贴推荐的
大多成为pi的人都是心灵手巧，吃苦耐劳的类型
【在 m******g 的大作中提到】
: 本来在开始读PhD的时候，就打算要广泛阅读主流学术杂志，比如Nature, Science,
: PNAS, Plos genetics等等，但是自己总是拖拖拉拉，偶尔有心血来潮就一口气读很久
: ，没兴趣／时间的话就个把月都不翻一下。
: 就好比动漫监督需要看其他畅销动漫（暴露兴趣了，太不学术了），我们也应该多多看
: 看生物的杂志，以增强自己对整个领域的理解，并且了解一些文献的逻辑、方法和写法
: 。所以我打算开这个贴说说每周最喜欢的几篇文章什么的，每周一更（日期不定），以
: 监督自己，防止自己不读文献。如果没有做到，请大家不要用砖头砸，把好吃的狠狠地
: 砸过来就好了，然后再狠狠地鄙视我就好。
: 我是学遗传进化方向的，做实验和编程都做一点（但是为什么现在还这么菜呢，果然是
: 因为我太懒惰了），总之看看文献没有坏处，也欢迎相似方向的大家一起来贴贴推荐的
l*1
99 楼
Just follow Twitter
https://twitter.com/evoldir
conference msg,
for example,
http://sitemaker.umich.edu/ecss2014/home
or
https://twitter.com/evoldir/status/400911676511621120
next google invited speaker her/his new publications..
【在 x********e 的大作中提到】
: 问题是学术杂志没有新番导读哇
https://twitter.com/evoldir
conference msg,
for example,
http://sitemaker.umich.edu/ecss2014/home
or
https://twitter.com/evoldir/status/400911676511621120
next google invited speaker her/his new publications..
【在 x********e 的大作中提到】
: 问题是学术杂志没有新番导读哇
D*a
100 楼
生物谷等 和twitter 和podcast嘛
还有RSS
【在 x********e 的大作中提到】
: 问题是学术杂志没有新番导读哇
还有RSS
【在 x********e 的大作中提到】
: 问题是学术杂志没有新番导读哇
z*t
101 楼
精深当然不可少，但做出真正成就的往往要广博
【在 w***r 的大作中提到】
: 做生物贵在精深，广博并非没有用处，但往往得不偿失
: 大多成为pi的人都是心灵手巧，吃苦耐劳的类型
【在 w***r 的大作中提到】
: 做生物贵在精深，广博并非没有用处，但往往得不偿失
: 大多成为pi的人都是心灵手巧，吃苦耐劳的类型
p*r
102 楼
好也。我最近也在这个领域打了个酱油，和朋友合作发了篇PNAS.
你对GWAS怎么看呢，我感觉是不是还有2-3年好日子也就到头了？
【在 m******g 的大作中提到】
: 本来在开始读PhD的时候，就打算要广泛阅读主流学术杂志，比如Nature, Science,
: PNAS, Plos genetics等等，但是自己总是拖拖拉拉，偶尔有心血来潮就一口气读很久
: ，没兴趣／时间的话就个把月都不翻一下。
: 就好比动漫监督需要看其他畅销动漫（暴露兴趣了，太不学术了），我们也应该多多看
: 看生物的杂志，以增强自己对整个领域的理解，并且了解一些文献的逻辑、方法和写法
: 。所以我打算开这个贴说说每周最喜欢的几篇文章什么的，每周一更（日期不定），以
: 监督自己，防止自己不读文献。如果没有做到，请大家不要用砖头砸，把好吃的狠狠地
: 砸过来就好了，然后再狠狠地鄙视我就好。
: 我是学遗传进化方向的，做实验和编程都做一点（但是为什么现在还这么菜呢，果然是
: 因为我太懒惰了），总之看看文献没有坏处，也欢迎相似方向的大家一起来贴贴推荐的
你对GWAS怎么看呢，我感觉是不是还有2-3年好日子也就到头了？
【在 m******g 的大作中提到】
: 本来在开始读PhD的时候，就打算要广泛阅读主流学术杂志，比如Nature, Science,
: PNAS, Plos genetics等等，但是自己总是拖拖拉拉，偶尔有心血来潮就一口气读很久
: ，没兴趣／时间的话就个把月都不翻一下。
: 就好比动漫监督需要看其他畅销动漫（暴露兴趣了，太不学术了），我们也应该多多看
: 看生物的杂志，以增强自己对整个领域的理解，并且了解一些文献的逻辑、方法和写法
: 。所以我打算开这个贴说说每周最喜欢的几篇文章什么的，每周一更（日期不定），以
: 监督自己，防止自己不读文献。如果没有做到，请大家不要用砖头砸，把好吃的狠狠地
: 砸过来就好了，然后再狠狠地鄙视我就好。
: 我是学遗传进化方向的，做实验和编程都做一点（但是为什么现在还这么菜呢，果然是
: 因为我太懒惰了），总之看看文献没有坏处，也欢迎相似方向的大家一起来贴贴推荐的
m*g
103 楼
Science 13.11.15 (包含Editor's Choice等推荐的其他杂志的文章，之后省略这句话)
推荐：
1. Dosage compensation via transposable element mediated rewiring of a
regulatory network
D. miranda在1 my前出现neo-X chromosome, TE-mediated rewiring of regulatory
network (domestication, amplification, and fine-tuning) followed by erosion
of nonfunctional parts of the transposon
idea挺有趣的.
2. Long-term dynamics of adaptation in asexual populations
Power law model fits/predicts the data better than Hyperbolic model with an
asymptote.
Fitness似乎在不断增长，并没有出现渐进靠近最大值的情况
稍微了解一下：
1. Genetic and neural modularity underlie the evolution of schooling
behavior in threespine sticklebacks
定位了影响tendency to school和body position的基因，在不同的区域（个人挺喜欢
这种定位决定行为的基因的文章，比如之前有篇map掘洞基因的）
2. 有Richard Lenski的访谈（50,000代的long-term evolution of E.coli）！！！
并附有一个report: Long-Term Dynamics of Adaptation in Asexual Populations
脑残粉们不要错过哇！一个实验做20多年，一直发paper什么的太伟大了！
小知识：
因为全球变暖，大雨会越来越频繁
狗的驯化是起源于欧洲（对古代犬的线粒体序列分析得出结论）
推荐：
1. Dosage compensation via transposable element mediated rewiring of a
regulatory network
D. miranda在1 my前出现neo-X chromosome, TE-mediated rewiring of regulatory
network (domestication, amplification, and fine-tuning) followed by erosion
of nonfunctional parts of the transposon
idea挺有趣的.
2. Long-term dynamics of adaptation in asexual populations
Power law model fits/predicts the data better than Hyperbolic model with an
asymptote.
Fitness似乎在不断增长，并没有出现渐进靠近最大值的情况
稍微了解一下：
1. Genetic and neural modularity underlie the evolution of schooling
behavior in threespine sticklebacks
定位了影响tendency to school和body position的基因，在不同的区域（个人挺喜欢
这种定位决定行为的基因的文章，比如之前有篇map掘洞基因的）
2. 有Richard Lenski的访谈（50,000代的long-term evolution of E.coli）！！！
并附有一个report: Long-Term Dynamics of Adaptation in Asexual Populations
脑残粉们不要错过哇！一个实验做20多年，一直发paper什么的太伟大了！
小知识：
因为全球变暖，大雨会越来越频繁
狗的驯化是起源于欧洲（对古代犬的线粒体序列分析得出结论）
m*g
104 楼
只是我瞎说说个人看法。我觉得GWAS对于研究决定common disease的common variant的
correlation很直观有效，以后如果新生儿测序提上日程，再加上完备的医疗记录，
GWAS应该会变的很routine（目前GWAS的几大缺陷也可以得到有效解决，比如
publication bias, population structure之类的），就像现在的测序一样常见，估计
就很难像几年前那样发容易文章了，个人幻想应该会像现在查基因序列一样，十年之后
可以查到各种疾病、性状的对应major SNPs。
【在 p*******r 的大作中提到】
: 好也。我最近也在这个领域打了个酱油，和朋友合作发了篇PNAS.
: 你对GWAS怎么看呢，我感觉是不是还有2-3年好日子也就到头了？
correlation很直观有效，以后如果新生儿测序提上日程，再加上完备的医疗记录，
GWAS应该会变的很routine（目前GWAS的几大缺陷也可以得到有效解决，比如
publication bias, population structure之类的），就像现在的测序一样常见，估计
就很难像几年前那样发容易文章了，个人幻想应该会像现在查基因序列一样，十年之后
可以查到各种疾病、性状的对应major SNPs。
【在 p*******r 的大作中提到】
: 好也。我最近也在这个领域打了个酱油，和朋友合作发了篇PNAS.
: 你对GWAS怎么看呢，我感觉是不是还有2-3年好日子也就到头了？
g*l
105 楼
我感觉现在都不太提common variant对common disease的影响了，因为实在太小。业界
对missing heritability的解释也是没太多亮点，总之GWAS基本上就是留给后人做实验
验证的，真要说应用于临床，恐怕还差得远，即使可行。
NGS倒是发展迅猛，但也就单基因疾病方面比较成功，这个以后必然是新生儿、乃至产
前筛查的范围。但就复杂疾病来讲，NGS找出的rare variants仍然没太大作用，至少在
牛皮癣里是这样（参见http://www.ncbi.nlm.nih.gov/pubmed/24212883）。
我悲观地认为，复杂疾病的genetics将来的前途十分不明朗，毕竟环境因素太大、太难
以评估。我甚至怀疑想用genetics解释复杂疾病，本身带有很大的机会主义成分，或受
到利益集团的操纵（Illumina、Affymetrix、ABI。。。）
欢迎讨论
【在 m******g 的大作中提到】
: 只是我瞎说说个人看法。我觉得GWAS对于研究决定common disease的common variant的
: correlation很直观有效，以后如果新生儿测序提上日程，再加上完备的医疗记录，
: GWAS应该会变的很routine（目前GWAS的几大缺陷也可以得到有效解决，比如
: publication bias, population structure之类的），就像现在的测序一样常见，估计
: 就很难像几年前那样发容易文章了，个人幻想应该会像现在查基因序列一样，十年之后
: 可以查到各种疾病、性状的对应major SNPs。
对missing heritability的解释也是没太多亮点，总之GWAS基本上就是留给后人做实验
验证的，真要说应用于临床，恐怕还差得远，即使可行。
NGS倒是发展迅猛，但也就单基因疾病方面比较成功，这个以后必然是新生儿、乃至产
前筛查的范围。但就复杂疾病来讲，NGS找出的rare variants仍然没太大作用，至少在
牛皮癣里是这样（参见http://www.ncbi.nlm.nih.gov/pubmed/24212883）。
我悲观地认为，复杂疾病的genetics将来的前途十分不明朗，毕竟环境因素太大、太难
以评估。我甚至怀疑想用genetics解释复杂疾病，本身带有很大的机会主义成分，或受
到利益集团的操纵（Illumina、Affymetrix、ABI。。。）
欢迎讨论
【在 m******g 的大作中提到】
: 只是我瞎说说个人看法。我觉得GWAS对于研究决定common disease的common variant的
: correlation很直观有效，以后如果新生儿测序提上日程，再加上完备的医疗记录，
: GWAS应该会变的很routine（目前GWAS的几大缺陷也可以得到有效解决，比如
: publication bias, population structure之类的），就像现在的测序一样常见，估计
: 就很难像几年前那样发容易文章了，个人幻想应该会像现在查基因序列一样，十年之后
: 可以查到各种疾病、性状的对应major SNPs。
w*r
106 楼
这想法嫩得都出水了
【在 z*t 的大作中提到】
: 精深当然不可少，但做出真正成就的往往要广博
【在 z*t 的大作中提到】
: 精深当然不可少，但做出真正成就的往往要广博
z*t
107 楼
您看来老得没什么水了：）
我倒是年方二八，正是嫩的出水的时节
【在 w***r 的大作中提到】
: 这想法嫩得都出水了
我倒是年方二八，正是嫩的出水的时节
【在 w***r 的大作中提到】
: 这想法嫩得都出水了
x*e
108 楼
RSS 过一段时间,看不过来就放弃了
去面壁一下
【在 D*a 的大作中提到】
: 生物谷等 和twitter 和podcast嘛
: 还有RSS
去面壁一下
【在 D*a 的大作中提到】
: 生物谷等 和twitter 和podcast嘛
: 还有RSS
D*a
109 楼
16岁就博士啦？
:)
【在 z*t 的大作中提到】
: 您看来老得没什么水了：）
: 我倒是年方二八，正是嫩的出水的时节
:)
【在 z*t 的大作中提到】
: 您看来老得没什么水了：）
: 我倒是年方二八，正是嫩的出水的时节
l*1
110 楼
That guy did topological Hopf link
Pls check,
http://en.wikipedia.org/wiki/Skein_relation
not your times calculation..
Btw,
it is relative to DNA topology/Computing
knot theory,
http://www2.imperial.ac.uk/~dbuck/Hiring.html
or
http://en.wikipedia.org/wiki/Tangle_(mathematics)
【在 D*a 的大作中提到】
: 16岁就博士啦？
: :)
Pls check,
http://en.wikipedia.org/wiki/Skein_relation
not your times calculation..
Btw,
it is relative to DNA topology/Computing
knot theory,
http://www2.imperial.ac.uk/~dbuck/Hiring.html
or
http://en.wikipedia.org/wiki/Tangle_(mathematics)
【在 D*a 的大作中提到】
: 16岁就博士啦？
: :)
p*r
111 楼
你觉得再往下应该做什么呢？
【在 m******g 的大作中提到】
: 只是我瞎说说个人看法。我觉得GWAS对于研究决定common disease的common variant的
: correlation很直观有效，以后如果新生儿测序提上日程，再加上完备的医疗记录，
: GWAS应该会变的很routine（目前GWAS的几大缺陷也可以得到有效解决，比如
: publication bias, population structure之类的），就像现在的测序一样常见，估计
: 就很难像几年前那样发容易文章了，个人幻想应该会像现在查基因序列一样，十年之后
: 可以查到各种疾病、性状的对应major SNPs。
【在 m******g 的大作中提到】
: 只是我瞎说说个人看法。我觉得GWAS对于研究决定common disease的common variant的
: correlation很直观有效，以后如果新生儿测序提上日程，再加上完备的医疗记录，
: GWAS应该会变的很routine（目前GWAS的几大缺陷也可以得到有效解决，比如
: publication bias, population structure之类的），就像现在的测序一样常见，估计
: 就很难像几年前那样发容易文章了，个人幻想应该会像现在查基因序列一样，十年之后
: 可以查到各种疾病、性状的对应major SNPs。
p*r
112 楼
我觉得看什么disease, 我比较熟悉neural 相关 disease。 昨天和鲁白讨论的时候，
他提到
Alzhimer应该是十个左右gene这个级别，autism几十个，depression就多了。
所以我觉得现阶段最exiciting的应该是几十这个级别的disease吧。
【在 g*******l 的大作中提到】
: 我感觉现在都不太提common variant对common disease的影响了，因为实在太小。业界
: 对missing heritability的解释也是没太多亮点，总之GWAS基本上就是留给后人做实验
: 验证的，真要说应用于临床，恐怕还差得远，即使可行。
: NGS倒是发展迅猛，但也就单基因疾病方面比较成功，这个以后必然是新生儿、乃至产
: 前筛查的范围。但就复杂疾病来讲，NGS找出的rare variants仍然没太大作用，至少在
: 牛皮癣里是这样（参见http://www.ncbi.nlm.nih.gov/pubmed/24212883）。
: 我悲观地认为，复杂疾病的genetics将来的前途十分不明朗，毕竟环境因素太大、太难
: 以评估。我甚至怀疑想用genetics解释复杂疾病，本身带有很大的机会主义成分，或受
: 到利益集团的操纵（Illumina、Affymetrix、ABI。。。）
: 欢迎讨论
他提到
Alzhimer应该是十个左右gene这个级别，autism几十个，depression就多了。
所以我觉得现阶段最exiciting的应该是几十这个级别的disease吧。
【在 g*******l 的大作中提到】
: 我感觉现在都不太提common variant对common disease的影响了，因为实在太小。业界
: 对missing heritability的解释也是没太多亮点，总之GWAS基本上就是留给后人做实验
: 验证的，真要说应用于临床，恐怕还差得远，即使可行。
: NGS倒是发展迅猛，但也就单基因疾病方面比较成功，这个以后必然是新生儿、乃至产
: 前筛查的范围。但就复杂疾病来讲，NGS找出的rare variants仍然没太大作用，至少在
: 牛皮癣里是这样（参见http://www.ncbi.nlm.nih.gov/pubmed/24212883）。
: 我悲观地认为，复杂疾病的genetics将来的前途十分不明朗，毕竟环境因素太大、太难
: 以评估。我甚至怀疑想用genetics解释复杂疾病，本身带有很大的机会主义成分，或受
: 到利益集团的操纵（Illumina、Affymetrix、ABI。。。）
: 欢迎讨论
l*1
113 楼
Molecular Phenome from below flow chat figure noted >2/3 are Hu You Fundings
items,
cited from 2012 one Book one chapter,
full PDF link:
http://www.mitbbs.com/article_t/Biology/31855315.html
【在 g*******l 的大作中提到】
: 我感觉现在都不太提common variant对common disease的影响了，因为实在太小。业界
: 对missing heritability的解释也是没太多亮点，总之GWAS基本上就是留给后人做实验
: 验证的，真要说应用于临床，恐怕还差得远，即使可行。
: NGS倒是发展迅猛，但也就单基因疾病方面比较成功，这个以后必然是新生儿、乃至产
: 前筛查的范围。但就复杂疾病来讲，NGS找出的rare variants仍然没太大作用，至少在
: 牛皮癣里是这样（参见http://www.ncbi.nlm.nih.gov/pubmed/24212883）。
: 我悲观地认为，复杂疾病的genetics将来的前途十分不明朗，毕竟环境因素太大、太难
: 以评估。我甚至怀疑想用genetics解释复杂疾病，本身带有很大的机会主义成分，或受
: 到利益集团的操纵（Illumina、Affymetrix、ABI。。。）
: 欢迎讨论
items,
cited from 2012 one Book one chapter,
full PDF link:
http://www.mitbbs.com/article_t/Biology/31855315.html
【在 g*******l 的大作中提到】
: 我感觉现在都不太提common variant对common disease的影响了，因为实在太小。业界
: 对missing heritability的解释也是没太多亮点，总之GWAS基本上就是留给后人做实验
: 验证的，真要说应用于临床，恐怕还差得远，即使可行。
: NGS倒是发展迅猛，但也就单基因疾病方面比较成功，这个以后必然是新生儿、乃至产
: 前筛查的范围。但就复杂疾病来讲，NGS找出的rare variants仍然没太大作用，至少在
: 牛皮癣里是这样（参见http://www.ncbi.nlm.nih.gov/pubmed/24212883）。
: 我悲观地认为，复杂疾病的genetics将来的前途十分不明朗，毕竟环境因素太大、太难
: 以评估。我甚至怀疑想用genetics解释复杂疾病，本身带有很大的机会主义成分，或受
: 到利益集团的操纵（Illumina、Affymetrix、ABI。。。）
: 欢迎讨论
s*y
114 楼
哦呵呵呵呵，突然发现我研究的东西在那个表里的一个节点上。
【在 l**********1 的大作中提到】
: Molecular Phenome from below flow chat figure noted >2/3 are Hu You Fundings
: items,
: cited from 2012 one Book one chapter,
: full PDF link:
: http://www.mitbbs.com/article_t/Biology/31855315.html
【在 l**********1 的大作中提到】
: Molecular Phenome from below flow chat figure noted >2/3 are Hu You Fundings
: items,
: cited from 2012 one Book one chapter,
: full PDF link:
: http://www.mitbbs.com/article_t/Biology/31855315.html
l*1
115 楼
Shall we Hu You stuff funding from that flow chat another nod/s later ?
【在 s******y 的大作中提到】
: 哦呵呵呵呵，突然发现我研究的东西在那个表里的一个节点上。
【在 s******y 的大作中提到】
: 哦呵呵呵呵，突然发现我研究的东西在那个表里的一个节点上。
m*g
116 楼
Nature 13.11.14
推荐：
1. A high-resolution map of the three-dimensional chromatin interactome in
human cells
3C方法（你知道4C,5C等等吗）determined over one million long-range chromatin
interactions at 5-10kb resolution.
知道有这么个资源就好，好像有不少类似产数据的paper,但是感觉physically close离
function还是有很长的距离要走（特别是本来就是连锁在一起的gene），加油~
稍微了解一下：
1. Dedifferentiation of committed epithelial cells into stem cells in vivo
看一下标题，知道有这件事情就好啦
2. RNA catalyses nuclear pre-mRNA splicing
The spliceosome is shown to catalyse splicing through the RNA and not the
protein components of the spliceosome; pre-messenger RNA splicing requires
U6 snRNA acting by a mechanism similar to that used by group II self-
splicing introns.以前学过两类RNAmechanism还记得吗，呵呵。These findings
indicate that group II introns and the spliceosome share common catalytic
mechanisms and probably common evolutionary origins. Our results demonstrate
that RNA mediates catalysis within the spliceosome.不过我一直以为都是RNA
catalyse,只是一种需要蛋白辅助，一种是只有RNA而已，可能这个只是提供了实验证据
吧。
小知识：
针对HIV和malaria，非洲采取了大规模预防措施，一些concern与achievements
肠道细菌Prevotella copri与人的关节炎有强correlation，第一次精确到种
NIH的funding：Large NIH projects cut
推荐：
1. A high-resolution map of the three-dimensional chromatin interactome in
human cells
3C方法（你知道4C,5C等等吗）determined over one million long-range chromatin
interactions at 5-10kb resolution.
知道有这么个资源就好，好像有不少类似产数据的paper,但是感觉physically close离
function还是有很长的距离要走（特别是本来就是连锁在一起的gene），加油~
稍微了解一下：
1. Dedifferentiation of committed epithelial cells into stem cells in vivo
看一下标题，知道有这件事情就好啦
2. RNA catalyses nuclear pre-mRNA splicing
The spliceosome is shown to catalyse splicing through the RNA and not the
protein components of the spliceosome; pre-messenger RNA splicing requires
U6 snRNA acting by a mechanism similar to that used by group II self-
splicing introns.以前学过两类RNAmechanism还记得吗，呵呵。These findings
indicate that group II introns and the spliceosome share common catalytic
mechanisms and probably common evolutionary origins. Our results demonstrate
that RNA mediates catalysis within the spliceosome.不过我一直以为都是RNA
catalyse,只是一种需要蛋白辅助，一种是只有RNA而已，可能这个只是提供了实验证据
吧。
小知识：
针对HIV和malaria，非洲采取了大规模预防措施，一些concern与achievements
肠道细菌Prevotella copri与人的关节炎有强correlation，第一次精确到种
NIH的funding：Large NIH projects cut
x*e
117 楼
赞这次的推荐
chromatin
【在 m******g 的大作中提到】
: Nature 13.11.14
: 推荐：
: 1. A high-resolution map of the three-dimensional chromatin interactome in
: human cells
: 3C方法（你知道4C,5C等等吗）determined over one million long-range chromatin
: interactions at 5-10kb resolution.
: 知道有这么个资源就好，好像有不少类似产数据的paper,但是感觉physically close离
: function还是有很长的距离要走（特别是本来就是连锁在一起的gene），加油~
: 稍微了解一下：
: 1. Dedifferentiation of committed epithelial cells into stem cells in vivo
chromatin
【在 m******g 的大作中提到】
: Nature 13.11.14
: 推荐：
: 1. A high-resolution map of the three-dimensional chromatin interactome in
: human cells
: 3C方法（你知道4C,5C等等吗）determined over one million long-range chromatin
: interactions at 5-10kb resolution.
: 知道有这么个资源就好，好像有不少类似产数据的paper,但是感觉physically close离
: function还是有很长的距离要走（特别是本来就是连锁在一起的gene），加油~
: 稍微了解一下：
: 1. Dedifferentiation of committed epithelial cells into stem cells in vivo
l*1
118 楼
Plus PMID 23953117 Lim [email protected] new Cell paper:
Coyle SM, et al., (2013).
Exploitation of latent allostery enables the evolution of new modes of MAP
kinase regulation.
Cell. 154: 875-87.
n.b. MAPK 变构反应 原来是为了进化潜规则 中 起到调控另外的pathway/s 开关作用
的...
>Abstract
ignored stuff
>The magnitude of this latent allosteric potential drifts widely among pre-
Ste5 MAP kinases, providing a
pool of hidden phenotypic diversity that, when revealed by new activators,
could lead to functional divergence and to the evolution of distinct
signaling behaviors
http://www.ncbi.nlm.nih.gov/pubmed/23953117
PDF link:
HTTP dot//limlab.ucsf.edu/papers/pdfs/smc_2013.pdf
plus last figure one part of this Cell paper.
or
RE 谁知道他老人家最近在琢磨啥大问题？好久没看到他的牛文了
By XBaldwin ID on
2012-01-20 22:45:
来自: 99.
18th floor
http://ipv6.weiming.info/zhuti/Biology/31627573/
Wendell LIM一直是我膜拜的牛人之一，他的东西看起来很性感，每一篇文章都当做圣
经一样
但感觉他的东西在概念上可能更重要：understand by building。可是真去看他做
MAPKpathway，还是没有解决这个pathway的根本问题：specificity。
谁知道他老人家最近在琢磨啥大问题？好久没看到他的牛文了
chromatin
【在 m******g 的大作中提到】
: Nature 13.11.14
: 推荐：
: 1. A high-resolution map of the three-dimensional chromatin interactome in
: human cells
: 3C方法（你知道4C,5C等等吗）determined over one million long-range chromatin
: interactions at 5-10kb resolution.
: 知道有这么个资源就好，好像有不少类似产数据的paper,但是感觉physically close离
: function还是有很长的距离要走（特别是本来就是连锁在一起的gene），加油~
: 稍微了解一下：
: 1. Dedifferentiation of committed epithelial cells into stem cells in vivo
Coyle SM, et al., (2013).
Exploitation of latent allostery enables the evolution of new modes of MAP
kinase regulation.
Cell. 154: 875-87.
n.b. MAPK 变构反应 原来是为了进化潜规则 中 起到调控另外的pathway/s 开关作用
的...
>Abstract
ignored stuff
>The magnitude of this latent allosteric potential drifts widely among pre-
Ste5 MAP kinases, providing a
pool of hidden phenotypic diversity that, when revealed by new activators,
could lead to functional divergence and to the evolution of distinct
signaling behaviors
http://www.ncbi.nlm.nih.gov/pubmed/23953117
PDF link:
HTTP dot//limlab.ucsf.edu/papers/pdfs/smc_2013.pdf
plus last figure one part of this Cell paper.
or
RE 谁知道他老人家最近在琢磨啥大问题？好久没看到他的牛文了
By XBaldwin ID on
2012-01-20 22:45:
来自: 99.
18th floor
http://ipv6.weiming.info/zhuti/Biology/31627573/
Wendell LIM一直是我膜拜的牛人之一，他的东西看起来很性感，每一篇文章都当做圣
经一样
但感觉他的东西在概念上可能更重要：understand by building。可是真去看他做
MAPKpathway，还是没有解决这个pathway的根本问题：specificity。
谁知道他老人家最近在琢磨啥大问题？好久没看到他的牛文了
chromatin
【在 m******g 的大作中提到】
: Nature 13.11.14
: 推荐：
: 1. A high-resolution map of the three-dimensional chromatin interactome in
: human cells
: 3C方法（你知道4C,5C等等吗）determined over one million long-range chromatin
: interactions at 5-10kb resolution.
: 知道有这么个资源就好，好像有不少类似产数据的paper,但是感觉physically close离
: function还是有很长的距离要走（特别是本来就是连锁在一起的gene），加油~
: 稍微了解一下：
: 1. Dedifferentiation of committed epithelial cells into stem cells in vivo
m*g
119 楼
PNAS 13.11.19
推荐：
Computational evaluation of cellular metabolic costs successfully predicts
genes whose expression is deleterious
稍微了解有这么件事情
1. miRNA and mRNA cancer signatures determined by analysis of expression
levels in large cohors of patients
2. Subnuclear relocalization and silencing of a chromosomal region by an
ectopic ribosomal DNA repeat
有趣的小知识
Honey bees selectively avoid difficult choices
推荐：
Computational evaluation of cellular metabolic costs successfully predicts
genes whose expression is deleterious
稍微了解有这么件事情
1. miRNA and mRNA cancer signatures determined by analysis of expression
levels in large cohors of patients
2. Subnuclear relocalization and silencing of a chromosomal region by an
ectopic ribosomal DNA repeat
有趣的小知识
Honey bees selectively avoid difficult choices
s*y
120 楼
RNA splicing 那个很有意思。
chromatin
【在 m******g 的大作中提到】
: Nature 13.11.14
: 推荐：
: 1. A high-resolution map of the three-dimensional chromatin interactome in
: human cells
: 3C方法（你知道4C,5C等等吗）determined over one million long-range chromatin
: interactions at 5-10kb resolution.
: 知道有这么个资源就好，好像有不少类似产数据的paper,但是感觉physically close离
: function还是有很长的距离要走（特别是本来就是连锁在一起的gene），加油~
: 稍微了解一下：
: 1. Dedifferentiation of committed epithelial cells into stem cells in vivo
chromatin
【在 m******g 的大作中提到】
: Nature 13.11.14
: 推荐：
: 1. A high-resolution map of the three-dimensional chromatin interactome in
: human cells
: 3C方法（你知道4C,5C等等吗）determined over one million long-range chromatin
: interactions at 5-10kb resolution.
: 知道有这么个资源就好，好像有不少类似产数据的paper,但是感觉physically close离
: function还是有很长的距离要走（特别是本来就是连锁在一起的gene），加油~
: 稍微了解一下：
: 1. Dedifferentiation of committed epithelial cells into stem cells in vivo
x*e
121 楼
版上有做splicing的吗 最近对alternative splicing感兴趣
【在 s******y 的大作中提到】
: RNA splicing 那个很有意思。
:
: chromatin
【在 s******y 的大作中提到】
: RNA splicing 那个很有意思。
:
: chromatin
l*1
122 楼
Before NGS 2.0 or 3.0 Illumina platform can read enough longer different
isoforms within Exome sequencing and systems biology aspect,
it is still elusive to answer the linkage between SNP2.0 or 3.0 alternative
splicing with
syndromic disease...
Pls check,
>Although previously described in TS, no CACNA1C mutations have been
reported for
>non-syndromic LQTS. With our functional studies confirming Cav1.2 gain-of-
function as the cellular basis for the CACNA1C mutation-positive patient’s
LQTS phenotype,
a paradox has
emerged. Namely, how can some gain-of-function mutations, like Gly406Arg in
the alternatively spliced exon 8A, result in the multi-organ system
phenotype of
TS while other
missense mutations, like Pro857Arg, yield a cardiac-only phenotype of
autosomal dominant
LQTS? With this being a new discovery, it is not surprising that the answer
is elusive
cited from PMID 23677916
Boczek NJ et al., (2013).
Exome sequencing and systems biology converge to identify novel mutations in
the L-type calcium channel, CACNA1C, linked to autosomal dominant long QT
syndrome.
Circ Cardiovasc Genet. 6: 279-89.
http://www.ncbi.nlm.nih.gov/pubmed/23677916
PDF link,
HTTP double dot//circgenetics.ahajournals.org/content/early/2013/05/15/
CIRCGENETICS.113.000138.full.pdf
its pp20
or
http://www.mitbbs.com/article_t/Biology/31855831.html
7th floor
【在 x********e 的大作中提到】
: 版上有做splicing的吗 最近对alternative splicing感兴趣
isoforms within Exome sequencing and systems biology aspect,
it is still elusive to answer the linkage between SNP2.0 or 3.0 alternative
splicing with
syndromic disease...
Pls check,
>Although previously described in TS, no CACNA1C mutations have been
reported for
>non-syndromic LQTS. With our functional studies confirming Cav1.2 gain-of-
function as the cellular basis for the CACNA1C mutation-positive patient’s
LQTS phenotype,
a paradox has
emerged. Namely, how can some gain-of-function mutations, like Gly406Arg in
the alternatively spliced exon 8A, result in the multi-organ system
phenotype of
TS while other
missense mutations, like Pro857Arg, yield a cardiac-only phenotype of
autosomal dominant
LQTS? With this being a new discovery, it is not surprising that the answer
is elusive
cited from PMID 23677916
Boczek NJ et al., (2013).
Exome sequencing and systems biology converge to identify novel mutations in
the L-type calcium channel, CACNA1C, linked to autosomal dominant long QT
syndrome.
Circ Cardiovasc Genet. 6: 279-89.
http://www.ncbi.nlm.nih.gov/pubmed/23677916
PDF link,
HTTP double dot//circgenetics.ahajournals.org/content/early/2013/05/15/
CIRCGENETICS.113.000138.full.pdf
its pp20
or
http://www.mitbbs.com/article_t/Biology/31855831.html
7th floor
【在 x********e 的大作中提到】
: 版上有做splicing的吗 最近对alternative splicing感兴趣
E*g
123 楼
Rama Ranganathan的SCA方法算不算遗传/进化方向的？
单个氨基酸是如何改变蛋白功能的？
蛋白进化的单位是什么？
进化也是一个动力学过程吗？
为什么会有共进化？
别构调节是共进化的结果吗？
Halabi, N.*, Rivoire, O.*, S. Leibler, and R. Ranganathan. Protein Sectors:
Evolutionary Units of Three-Dimensional Structure. (2009) Cell, 138: 774-786
K.A. Reynolds, R.N. McLaughlin. R. Ranganathan. Hotspots for Allosteric
Regulation on Protein Surfaces. (2011) Cell, 147: 1564-1575
R.N. McLaughlin, F.J. Poelwijk, A. Raman, W.S. Gosal, and R. Ranganathan.
The Spatial Architecture of Protein Function and Adaptation. (2012) Nature
O. Rivoire Elements of coevolution in biological sequences. (2013) Phys.
Rev. Lett. 110 : 178102
单个氨基酸是如何改变蛋白功能的？
蛋白进化的单位是什么？
进化也是一个动力学过程吗？
为什么会有共进化？
别构调节是共进化的结果吗？
Halabi, N.*, Rivoire, O.*, S. Leibler, and R. Ranganathan. Protein Sectors:
Evolutionary Units of Three-Dimensional Structure. (2009) Cell, 138: 774-786
K.A. Reynolds, R.N. McLaughlin. R. Ranganathan. Hotspots for Allosteric
Regulation on Protein Surfaces. (2011) Cell, 147: 1564-1575
R.N. McLaughlin, F.J. Poelwijk, A. Raman, W.S. Gosal, and R. Ranganathan.
The Spatial Architecture of Protein Function and Adaptation. (2012) Nature
O. Rivoire Elements of coevolution in biological sequences. (2013) Phys.
Rev. Lett. 110 : 178102
b*r
124 楼
mark一个
不过我觉得这些3C 4C或者其他DNA RNA 调控的 高级结构，在我们职业发展阶段都变不
了真金白银，最多靠忽悠点funding，日子稍微过好一点
遗传学的真金白银最近这些年基本只在cancer genetics里，又能拿funding，搞不好还
能像IT业那样有大量的startup机会
不过我觉得这些3C 4C或者其他DNA RNA 调控的 高级结构，在我们职业发展阶段都变不
了真金白银，最多靠忽悠点funding，日子稍微过好一点
遗传学的真金白银最近这些年基本只在cancer genetics里，又能拿funding，搞不好还
能像IT业那样有大量的startup机会
n*k
125 楼
比较好奇，比较感兴趣： 不知道这些十个，几十个等的具体含义，而这中间预测的依
据又在哪里？
【在 p*******r 的大作中提到】
: 我觉得看什么disease, 我比较熟悉neural 相关 disease。 昨天和鲁白讨论的时候，
: 他提到
: Alzhimer应该是十个左右gene这个级别，autism几十个，depression就多了。
: 所以我觉得现阶段最exiciting的应该是几十这个级别的disease吧。
据又在哪里？
【在 p*******r 的大作中提到】
: 我觉得看什么disease, 我比较熟悉neural 相关 disease。 昨天和鲁白讨论的时候，
: 他提到
: Alzhimer应该是十个左右gene这个级别，autism几十个，depression就多了。
: 所以我觉得现阶段最exiciting的应该是几十这个级别的disease吧。
v*r
126 楼
co-ask. this seems an interesting question.
【在 n********k 的大作中提到】
: 比较好奇，比较感兴趣： 不知道这些十个，几十个等的具体含义，而这中间预测的依
: 据又在哪里？
【在 n********k 的大作中提到】
: 比较好奇，比较感兴趣： 不知道这些十个，几十个等的具体含义，而这中间预测的依
: 据又在哪里？
v*r
127 楼
it could be more helpful if more details are summarized.
话)
erosion
an
【在 m******g 的大作中提到】
: Science 13.11.15 (包含Editor's Choice等推荐的其他杂志的文章，之后省略这句话)
: 推荐：
: 1. Dosage compensation via transposable element mediated rewiring of a
: regulatory network
: D. miranda在1 my前出现neo-X chromosome, TE-mediated rewiring of regulatory
: network (domestication, amplification, and fine-tuning) followed by erosion
: of nonfunctional parts of the transposon
: idea挺有趣的.
: 2. Long-term dynamics of adaptation in asexual populations
: Power law model fits/predicts the data better than Hyperbolic model with an
话)
erosion
an
【在 m******g 的大作中提到】
: Science 13.11.15 (包含Editor's Choice等推荐的其他杂志的文章，之后省略这句话)
: 推荐：
: 1. Dosage compensation via transposable element mediated rewiring of a
: regulatory network
: D. miranda在1 my前出现neo-X chromosome, TE-mediated rewiring of regulatory
: network (domestication, amplification, and fine-tuning) followed by erosion
: of nonfunctional parts of the transposon
: idea挺有趣的.
: 2. Long-term dynamics of adaptation in asexual populations
: Power law model fits/predicts the data better than Hyperbolic model with an
H*g
128 楼
通过mapping就可以定位了，只不过在人身上做起来限制比较多
【在 v***r 的大作中提到】
: co-ask. this seems an interesting question.
【在 v***r 的大作中提到】
: co-ask. this seems an interesting question.
m*g
129 楼
主要是为了监督自己看文献，所以有点懒得打字（只写成自己看到能够联想到的程度）
，我以后会尽量多写一点的，呵呵。也可以直接去下载那篇文献呀，其实abstract就比
较detailed了
【在 v***r 的大作中提到】
: it could be more helpful if more details are summarized.
:
: 话)
: erosion
: an
，我以后会尽量多写一点的，呵呵。也可以直接去下载那篇文献呀，其实abstract就比
较detailed了
【在 v***r 的大作中提到】
: it could be more helpful if more details are summarized.
:
: 话)
: erosion
: an
m*g
130 楼
楼主我最近申请了统计学双学位硕士（终于下定决心这么做了，开心！）
因为上周忙申请，所以基本没有更新。
Nature 13.11.21
推荐：
1. DNMT1-interacting RNAs block gene-specific DNA methylation
基因表达调节甲基化程度，对具体机制也有研究。
稍微了解一下：
1.Group size determines cultural complexity (引文)
正文：Experimental evidence for the influence of group size on cultural
complexity
实验室内的人的行为学研究，分为2，4， 8， 16人／组，完成简单和复杂的电脑任务
并判定完成的复杂度。
如果群体太小，复杂任务的质量会下降
（感觉做的很有意思，虽然结果是非常as expected.）
有趣的小知识：
1. Biology tool uncloaks folk-tale evolution
用进化树的方法研究童话的起源
2. Fish babies bigger in toxic waters
当然后代数量会减少，个体大以解毒硫化物
3. The risks of the replication drive
我们该不该花钱请专业公司来复制我们的结果呢？作者Argue againt this idea （可
行性，可靠性，打击积极性）
4. Killing the survivors
发现了当和其他抗生素混用时，可以杀死休眠细菌（persister）的新小分子 ADEP4
（个人挺喜欢和persister相关的一些研究）
因为上周忙申请，所以基本没有更新。
Nature 13.11.21
推荐：
1. DNMT1-interacting RNAs block gene-specific DNA methylation
基因表达调节甲基化程度，对具体机制也有研究。
稍微了解一下：
1.Group size determines cultural complexity (引文)
正文：Experimental evidence for the influence of group size on cultural
complexity
实验室内的人的行为学研究，分为2，4， 8， 16人／组，完成简单和复杂的电脑任务
并判定完成的复杂度。
如果群体太小，复杂任务的质量会下降
（感觉做的很有意思，虽然结果是非常as expected.）
有趣的小知识：
1. Biology tool uncloaks folk-tale evolution
用进化树的方法研究童话的起源
2. Fish babies bigger in toxic waters
当然后代数量会减少，个体大以解毒硫化物
3. The risks of the replication drive
我们该不该花钱请专业公司来复制我们的结果呢？作者Argue againt this idea （可
行性，可靠性，打击积极性）
4. Killing the survivors
发现了当和其他抗生素混用时，可以杀死休眠细菌（persister）的新小分子 ADEP4
（个人挺喜欢和persister相关的一些研究）
m*g
131 楼
自己吐槽一下，虽然对于看过文献的研究系统／漂亮的图什么的记得比较清楚
但是作者什么的老是不太记得
有时候看到有的人可以一堆一堆地数出来，感觉好厉害啊！
觉得这期science比较有趣，虽然没有那种看得超感动的文章，但是还是有不少很值得
一看的paper的。
Science 13.11.22
推荐：
1. Organization of the Mitotic Chromosome
用5C和Hi-C, 发现分裂中期结构是与位点无关的均质，并用polymer模拟
“A simple, robust model explains higher-order organization of mammalian
chromosomes.”
（最近这类文章真多，好像周周都有？感觉个人不是那么感兴趣了～～～）
2. Two Y Genes Can Replace the Entire Y Chromosome for Assisted Reproduction
in the Mouse
testis determinant factor Sry
spermatogonial proliferation factor Eif2s3y
稍微了解一下：
1. Defining Stem Cell Dynamics in Models of Intestinal Tumor Initiation
癌变了可以快速分裂的细胞就一定有优势吗？有的话又有多少？
本文告诉你这是一个相当随机的过程（有一定bias）
（喜欢肠道小窝这几个干细胞随机性成为主导的系统，之前也出过一些有趣的文章）
2. Substitutions Near the Receptor Binding Site Determine Major Antigenic
Change During Influenza Virus Evolution
小知识：
1. Commensal Bacteria Control Cancer Response to Therapy by Modulating the
Tumor Microenvironment
肠道菌群对于肿瘤治疗是有益的
In antibiotics-treated or germ-free mice, tumor-infiltrating myeloid-derived
cells responded poorly to therapy
以及类似文章一篇
The Intestinal Microbiota Modulates the Anticancer Immune Effects of
Cyclophosphamide
2. Beyond Stem Cells: Self-Renewal of Differentiated Macrophages
These findings suggest that macrophages are mature differentiated cells that
may have a self-renewal potential similar to that of stem cells.
但是作者什么的老是不太记得
有时候看到有的人可以一堆一堆地数出来，感觉好厉害啊！
觉得这期science比较有趣，虽然没有那种看得超感动的文章，但是还是有不少很值得
一看的paper的。
Science 13.11.22
推荐：
1. Organization of the Mitotic Chromosome
用5C和Hi-C, 发现分裂中期结构是与位点无关的均质，并用polymer模拟
“A simple, robust model explains higher-order organization of mammalian
chromosomes.”
（最近这类文章真多，好像周周都有？感觉个人不是那么感兴趣了～～～）
2. Two Y Genes Can Replace the Entire Y Chromosome for Assisted Reproduction
in the Mouse
testis determinant factor Sry
spermatogonial proliferation factor Eif2s3y
稍微了解一下：
1. Defining Stem Cell Dynamics in Models of Intestinal Tumor Initiation
癌变了可以快速分裂的细胞就一定有优势吗？有的话又有多少？
本文告诉你这是一个相当随机的过程（有一定bias）
（喜欢肠道小窝这几个干细胞随机性成为主导的系统，之前也出过一些有趣的文章）
2. Substitutions Near the Receptor Binding Site Determine Major Antigenic
Change During Influenza Virus Evolution
小知识：
1. Commensal Bacteria Control Cancer Response to Therapy by Modulating the
Tumor Microenvironment
肠道菌群对于肿瘤治疗是有益的
In antibiotics-treated or germ-free mice, tumor-infiltrating myeloid-derived
cells responded poorly to therapy
以及类似文章一篇
The Intestinal Microbiota Modulates the Anticancer Immune Effects of
Cyclophosphamide
2. Beyond Stem Cells: Self-Renewal of Differentiated Macrophages
These findings suggest that macrophages are mature differentiated cells that
may have a self-renewal potential similar to that of stem cells.
l*1
132 楼
Chip-seq doesn't need?
pls refer,
>gene profiling and chromatin immunoprecipitation followed >by massive
parallel sequencing (ChIP-seq) in intact animal models of Alzheimer disease
are being used to assess IEG controlled signaling pathways.
http://koldamovalefterovlab.pitt.edu/
http://koldamovalefterovlab.pitt.edu/publications.html
or dPeak NGS 2.0 tool,
http://www.ncbi.nlm.nih.gov/pubmed/24146601
【在 H*********g 的大作中提到】
: 通过mapping就可以定位了，只不过在人身上做起来限制比较多
pls refer,
>gene profiling and chromatin immunoprecipitation followed >by massive
parallel sequencing (ChIP-seq) in intact animal models of Alzheimer disease
are being used to assess IEG controlled signaling pathways.
http://koldamovalefterovlab.pitt.edu/
http://koldamovalefterovlab.pitt.edu/publications.html
or dPeak NGS 2.0 tool,
http://www.ncbi.nlm.nih.gov/pubmed/24146601
【在 H*********g 的大作中提到】
: 通过mapping就可以定位了，只不过在人身上做起来限制比较多
m*g
133 楼
祝大家新年快乐！
我果然坑了，呵呵，这个帖子好久没更新。
圣诞节期间在忙别的没用的事情去了
以后求不坑，呵呵……
PNAS 13.11.26
推荐：
1. Gene amplification and microsatellite polymorphism underlie a recent
insect host shift
Model: polyphagous aphid
Host shift to feed on tobacco
expression level of CYP6CY3
expansion of dinucleotide microsatellite in promoter and a recent gene
amplification
稍微了解一下：
1. Intrinsic karyotype stability and gene copy number variations may have
laid the foundation for tetraploid wheat formation
allopolyploidy of tetraploid wheat
immediate and persistent karyotype stability is intrinsic to newly formed
allotetraploid wheat
小知识：
1. Similarity increases altruistic punishment in humans
Homophily: humans attracted to similar others
perceived similarity increases altruistic punishment
2. Pathogen selection drives nonoverlapping associations between HLA loci
exceptional polymorphism of HLA gene cluster
pathogen-meiated selection promotes nonrandom association
我果然坑了，呵呵，这个帖子好久没更新。
圣诞节期间在忙别的没用的事情去了
以后求不坑，呵呵……
PNAS 13.11.26
推荐：
1. Gene amplification and microsatellite polymorphism underlie a recent
insect host shift
Model: polyphagous aphid
Host shift to feed on tobacco
expression level of CYP6CY3
expansion of dinucleotide microsatellite in promoter and a recent gene
amplification
稍微了解一下：
1. Intrinsic karyotype stability and gene copy number variations may have
laid the foundation for tetraploid wheat formation
allopolyploidy of tetraploid wheat
immediate and persistent karyotype stability is intrinsic to newly formed
allotetraploid wheat
小知识：
1. Similarity increases altruistic punishment in humans
Homophily: humans attracted to similar others
perceived similarity increases altruistic punishment
2. Pathogen selection drives nonoverlapping associations between HLA loci
exceptional polymorphism of HLA gene cluster
pathogen-meiated selection promotes nonrandom association
m*g
134 楼
基本上就是题目+bulletin point的形式吧，不要纠结我对paper的品味，呵呵。新年快
乐！
PNAS 13.12.03
推荐：
1. Reintroducing domesticated wild mice to sociality induces adaptive
transgenerational effects on MUP expression
promiscuous / monogamous-line
higher MUP (pheromone) expression in pros-line
Male become more attractive
Difference in Mup promoter methylation level
2. High-throughput DNA sequencing errors are reduced by orders of magnitude
using circle sequencing
Previously ~0.1-1x10^-2
Unique library preparation strategy
Copied multiple times in tandem with a rolling circle polymerase
Error rate 7.6x1-^-6 per base
Higher efficiency and lower cost than existing barcode schemes
稍微了解一下：
1. Distribution, evolution, and diversity of retrotransposons at the
flamenco locus reflect the regulatory properties of piRNA clusters
piRNA-RNA producing locus
control transposable elment
trap for TEs coming from horizontal transfer from other Drosophila species
2. Bacterial natural transformation by highly fragmented and damaged DNA
molecule > 20 bp that may contain basic sites, cross-links can be acquired
uptake DNA from a 43,000y wooly mammoth bone
DNA recombination if RecA recombinase independent
3. Genome rearrangements caused by interstitial telomeric sequences in yeast
Interstitial telomeric sequences are associated with genome instabilities
and disease in human
yeast telomeric (Ytel) repeats
formation of dsDNA break within Ytel sequences
promote deletion, duplication, inversion and translocation
乐！
PNAS 13.12.03
推荐：
1. Reintroducing domesticated wild mice to sociality induces adaptive
transgenerational effects on MUP expression
promiscuous / monogamous-line
higher MUP (pheromone) expression in pros-line
Male become more attractive
Difference in Mup promoter methylation level
2. High-throughput DNA sequencing errors are reduced by orders of magnitude
using circle sequencing
Previously ~0.1-1x10^-2
Unique library preparation strategy
Copied multiple times in tandem with a rolling circle polymerase
Error rate 7.6x1-^-6 per base
Higher efficiency and lower cost than existing barcode schemes
稍微了解一下：
1. Distribution, evolution, and diversity of retrotransposons at the
flamenco locus reflect the regulatory properties of piRNA clusters
piRNA-RNA producing locus
control transposable elment
trap for TEs coming from horizontal transfer from other Drosophila species
2. Bacterial natural transformation by highly fragmented and damaged DNA
molecule > 20 bp that may contain basic sites, cross-links can be acquired
uptake DNA from a 43,000y wooly mammoth bone
DNA recombination if RecA recombinase independent
3. Genome rearrangements caused by interstitial telomeric sequences in yeast
Interstitial telomeric sequences are associated with genome instabilities
and disease in human
yeast telomeric (Ytel) repeats
formation of dsDNA break within Ytel sequences
promote deletion, duplication, inversion and translocation
m*g
135 楼
祝想学好生物的大家在新的一年收到实验女神的眷顾，想转行的快点换行！
想拿funding的拿到funding，天天开心！
PNAS 13.12.10
极力推荐：
1. Limitations of inclusive fitness
从11年开始就非常支持作者对inclusive fitness的反对，^_^
稍微了解一下：
1. Broad-scale phylogenomics provides insights into retrovirus–host
evolution
Large endogenous retrovirus
Horizontal transmission between different host species
90,000 ERVs from 60 vertebrate host genomes
Designation, host distribution, origin and tranmission
2. Chemical map of Schizosaccharomyces pombe reveals species-specific
features in nucleosome positioning
Genome-wide map at base pair resolution
Linker length of 10n + 4/5bp
A/T-rich sequences are enriched in S. pombe nucleosomes
3. Genome-scale metabolic reconstructions of multiple Escherichia coli
strains highlight strain-specific adaptations to nutritional environments
Genome-scale models of metabolism
Analyze growth growth capabilities in more than 650 different growth
conditions
Test 12 GEMs in 6 differentiating nutrients
想拿funding的拿到funding，天天开心！
PNAS 13.12.10
极力推荐：
1. Limitations of inclusive fitness
从11年开始就非常支持作者对inclusive fitness的反对，^_^
稍微了解一下：
1. Broad-scale phylogenomics provides insights into retrovirus–host
evolution
Large endogenous retrovirus
Horizontal transmission between different host species
90,000 ERVs from 60 vertebrate host genomes
Designation, host distribution, origin and tranmission
2. Chemical map of Schizosaccharomyces pombe reveals species-specific
features in nucleosome positioning
Genome-wide map at base pair resolution
Linker length of 10n + 4/5bp
A/T-rich sequences are enriched in S. pombe nucleosomes
3. Genome-scale metabolic reconstructions of multiple Escherichia coli
strains highlight strain-specific adaptations to nutritional environments
Genome-scale models of metabolism
Analyze growth growth capabilities in more than 650 different growth
conditions
Test 12 GEMs in 6 differentiating nutrients
m*g
136 楼
虽然看了，但是没来得及整理一下，整理贴出来，顺便复习一下，呵呵。
交流群：342148521 （开心读文献贵在坚持，加群请输入最喜欢的科学家、杂志或领域
的名称或者其他什么，无附加信息不予通过，希望大家一起参与呢）
Nature 13.11.28
推荐：
1. Memory and modularity in cell-fate decision making
Bacillus subtilis
Motile state and sessile state
Microfluidic device consisting of several channels
Visualize switching in real time
Memoryless motility and timed chaining
评论： 见How bacteria choose a lifestyle
稍微了解一下：
1. Accelerated growth in the absence of DNA replication origins
Bacteria and some archaea: single origin
Eukaryote and most archaea: multiple origin
Some virus: homologous recombination
Delete individual origins: reduce growth
Delete all origins: grow significantly faster
Initiate at dispersed site
小知识：
1. Antibiotic re-frames decoding
Ketolide antibiotics induce a ribosomal frameshift
Expression of defense gene ON
交流群：342148521 （开心读文献贵在坚持，加群请输入最喜欢的科学家、杂志或领域
的名称或者其他什么，无附加信息不予通过，希望大家一起参与呢）
Nature 13.11.28
推荐：
1. Memory and modularity in cell-fate decision making
Bacillus subtilis
Motile state and sessile state
Microfluidic device consisting of several channels
Visualize switching in real time
Memoryless motility and timed chaining
评论： 见How bacteria choose a lifestyle
稍微了解一下：
1. Accelerated growth in the absence of DNA replication origins
Bacteria and some archaea: single origin
Eukaryote and most archaea: multiple origin
Some virus: homologous recombination
Delete individual origins: reduce growth
Delete all origins: grow significantly faster
Initiate at dispersed site
小知识：
1. Antibiotic re-frames decoding
Ketolide antibiotics induce a ribosomal frameshift
Expression of defense gene ON
z*9
137 楼
好帖，支持，
m*g
138 楼
哇，拖了好多……最近会补上的，不会坑掉。
交流群：342148521 （开心读文献贵在坚持，加群请输入最喜欢的科学家、杂志或领域
的名称或者其他什么，无附加信息不予通过，希望大家一起参与呢）
Science 13.11.29
推荐：
1. Primate transcript and protein expression levels evolve under
compensatory selection pressures
概述文：Protein Expression Under Pressure
Protein level more conserved than mRNA
基本是as expected，不过能够measure一下是很重要的
自问：有没有可能是方法本身的精确性
导致了信号的压缩呢
自答：应该不会
因为看mRNA浓度跨度是3-4个数量级
而蛋白的浓度是4-6个数量级
2. The Innate Growth Bistability and Fitness Landscapes of Antibiotic-
Resistant Bacteria
Translation-inhibiting antibiotics
Bulk and single-cell measurements
Growing and nongrowing states for isogenic cells
Correct modeling of fitness landscape
稍微了解一下：
1. Genomes from Metagenomics (Perspective)
Binning methods for time-series or multiple samples
Single cell sequencing
小知识：
1. Protecting Self-Replicating RNA?
RNA as primordial catalysis
Problem: requires high level of Mg
Mg incompatible with fatty acid vesible integrity
Several chelator (citrate, isocitrate) would stabilize and protect RNA
2. Pattern sensing
Synthetic system with fluorescent
Self-segulated system
Reaction-diffusion model
交流群：342148521 （开心读文献贵在坚持，加群请输入最喜欢的科学家、杂志或领域
的名称或者其他什么，无附加信息不予通过，希望大家一起参与呢）
Science 13.11.29
推荐：
1. Primate transcript and protein expression levels evolve under
compensatory selection pressures
概述文：Protein Expression Under Pressure
Protein level more conserved than mRNA
基本是as expected，不过能够measure一下是很重要的
自问：有没有可能是方法本身的精确性
导致了信号的压缩呢
自答：应该不会
因为看mRNA浓度跨度是3-4个数量级
而蛋白的浓度是4-6个数量级
2. The Innate Growth Bistability and Fitness Landscapes of Antibiotic-
Resistant Bacteria
Translation-inhibiting antibiotics
Bulk and single-cell measurements
Growing and nongrowing states for isogenic cells
Correct modeling of fitness landscape
稍微了解一下：
1. Genomes from Metagenomics (Perspective)
Binning methods for time-series or multiple samples
Single cell sequencing
小知识：
1. Protecting Self-Replicating RNA?
RNA as primordial catalysis
Problem: requires high level of Mg
Mg incompatible with fatty acid vesible integrity
Several chelator (citrate, isocitrate) would stabilize and protect RNA
2. Pattern sensing
Synthetic system with fluorescent
Self-segulated system
Reaction-diffusion model
m*g
139 楼
Nature 13.12.05
推荐：
1. Genetic incompatibilities are widespread within species
Drosophila melanogaster recombinant inbred lines
Mendelian proportions among unlinked alleles
Genotype ratio distortion
Estimate: 1.15 pairs of epistatic alleles for any two genome
稍微了解一下：
1. RNAs leave yeast poised for action
Long ncRNAs accelerate activation of protein-coding gene
GAL genes released from repression
Long ncRNA speed upGAL expression
By recruiting a key enzyme needed
小知识：
1. Hormone boosts attractiveness
Nasal puffs of oxytocin
Improves rating for their partner over unfamiliar/familiar woman
呵呵，大家知道应该怎么留住他/她了吧
推荐：
1. Genetic incompatibilities are widespread within species
Drosophila melanogaster recombinant inbred lines
Mendelian proportions among unlinked alleles
Genotype ratio distortion
Estimate: 1.15 pairs of epistatic alleles for any two genome
稍微了解一下：
1. RNAs leave yeast poised for action
Long ncRNAs accelerate activation of protein-coding gene
GAL genes released from repression
Long ncRNA speed upGAL expression
By recruiting a key enzyme needed
小知识：
1. Hormone boosts attractiveness
Nasal puffs of oxytocin
Improves rating for their partner over unfamiliar/familiar woman
呵呵，大家知道应该怎么留住他/她了吧
m*g
140 楼
开学了，突然变得很有效率，脱离了颓废的圣诞假期感觉真好！
发布顺序有点乱，不过大概还是按照时间顺序的。
Science 13.12.06
推荐：
1. Genetic determinants and cellular constraints in noisy gene expression
Evidences for gene-specific v.s. genome-wide regulation
Mainly focused on yeast and E. coli
2. Functional Roles of Pulsing in Genetic Circuits
两篇都是Review, 不是我最喜欢的那类Review, 有点罗列的感觉
稍微了解一下：
1. Single-Cell Metabolomics: Analytical and Biological Perspectives
也是review，主要讲方法
小知识：
1. Playing Kissy with the Relatives
Who to select for cooperate
Surface receptor spot relatedness
Less-related cell as a stopgap if needed
2. Direct and Reversible Hydrogenation of CO2 to Formate by a Bacterial
Carbon Dioxide Reductase
Enzymes from anaerobic bacteria
Catalyze the storage of hydrogen
In the form of formic acid
诶，感觉从我的文件复制粘贴过来之后格式就变得很奇怪……
发布顺序有点乱，不过大概还是按照时间顺序的。
Science 13.12.06
推荐：
1. Genetic determinants and cellular constraints in noisy gene expression
Evidences for gene-specific v.s. genome-wide regulation
Mainly focused on yeast and E. coli
2. Functional Roles of Pulsing in Genetic Circuits
两篇都是Review, 不是我最喜欢的那类Review, 有点罗列的感觉
稍微了解一下：
1. Single-Cell Metabolomics: Analytical and Biological Perspectives
也是review，主要讲方法
小知识：
1. Playing Kissy with the Relatives
Who to select for cooperate
Surface receptor spot relatedness
Less-related cell as a stopgap if needed
2. Direct and Reversible Hydrogenation of CO2 to Formate by a Bacterial
Carbon Dioxide Reductase
Enzymes from anaerobic bacteria
Catalyze the storage of hydrogen
In the form of formic acid
诶，感觉从我的文件复制粘贴过来之后格式就变得很奇怪……
m*g
141 楼
都没有人回帖的样子呢~孤单的猫箱
Nature 13.12.12
推荐：
1. Chromatin connectivity maps reveal dynamic promoter–enhancer long-range
associations
Transcriptional interactome
Antibody recognizes preinitiation complexes
Three types of stem cells in mouse
40,000 long-range interaction
稍微了解一下：
1. An archaeal origin of eukaryotes supports only two primary domains of
life
Evidence for eocyte hypothesis
Archaea is a paraphyletic group
小知识：
果然学生物的最原始的动力就是这些小实验呢
1. Baboons know when to be noisy
The experimenters stood facing the animals with their eyes either open or
closed, or turned away from the animals
More begging hand gestures when experimenters had their eyes open
Make noisy banging actions in the other cases
Adjust their mode of communication according to the level of an observer's
attention
2. Bees are better for strawberries
heavier, redder, and had a longer shelf life and a more desirable sugar-to-
acid ratio
A permeable plastic to eliminate wind and bee pollination, or fine-mesh bags
to exclude just bees
3. CRISPR corrects genetic disease
Correct the mutated Crygc gene in fertilized mouse eggs
CRISPR还是挺有前途的呢！
Nature 13.12.12
推荐：
1. Chromatin connectivity maps reveal dynamic promoter–enhancer long-range
associations
Transcriptional interactome
Antibody recognizes preinitiation complexes
Three types of stem cells in mouse
40,000 long-range interaction
稍微了解一下：
1. An archaeal origin of eukaryotes supports only two primary domains of
life
Evidence for eocyte hypothesis
Archaea is a paraphyletic group
小知识：
果然学生物的最原始的动力就是这些小实验呢
1. Baboons know when to be noisy
The experimenters stood facing the animals with their eyes either open or
closed, or turned away from the animals
More begging hand gestures when experimenters had their eyes open
Make noisy banging actions in the other cases
Adjust their mode of communication according to the level of an observer's
attention
2. Bees are better for strawberries
heavier, redder, and had a longer shelf life and a more desirable sugar-to-
acid ratio
A permeable plastic to eliminate wind and bee pollination, or fine-mesh bags
to exclude just bees
3. CRISPR corrects genetic disease
Correct the mutated Crygc gene in fertilized mouse eggs
CRISPR还是挺有前途的呢！
m*g
142 楼
今天去找导师汇报，本来觉得自己的内容太少，会被批评的，结果导师还鼓励了我，我
一定要加倍努力呀！感动ing。希望以后也能成为我导师那样的好导师！
Science 13.12.13
推荐：
1. Exonic Transcription Factor Binding Directs Codon Choice and Affects
Protein Evolution
概要：Long-Term Dynamics of Adaptation in Asexual Populations
Mean fitness seems to have no upper bound
Power law better than hyperbolic model
2. The Hidden Codes That Shape Protein Evolution
TF binding code
Human genome in 81 cell types
Constraining codes
~14% codons within 86.9% of genes are occupied by TFs
3. Cavefish Study Supports Controversial Evolutionary Mechanism
Mexican tetra
HSP90 as capacitor
Similar case for drosophila eye development
稍微了解一下：
1. Finding the Right Partner in a 3D Genome
Architecture of nucleus in real time
high-throughput time-lapse imaging
Translocation after DSB induction
一定要加倍努力呀！感动ing。希望以后也能成为我导师那样的好导师！
Science 13.12.13
推荐：
1. Exonic Transcription Factor Binding Directs Codon Choice and Affects
Protein Evolution
概要：Long-Term Dynamics of Adaptation in Asexual Populations
Mean fitness seems to have no upper bound
Power law better than hyperbolic model
2. The Hidden Codes That Shape Protein Evolution
TF binding code
Human genome in 81 cell types
Constraining codes
~14% codons within 86.9% of genes are occupied by TFs
3. Cavefish Study Supports Controversial Evolutionary Mechanism
Mexican tetra
HSP90 as capacitor
Similar case for drosophila eye development
稍微了解一下：
1. Finding the Right Partner in a 3D Genome
Architecture of nucleus in real time
high-throughput time-lapse imaging
Translocation after DSB induction
t*z
143 楼
顶下楼主的执着热情。我也是做进化的，来学习下。
m*g
144 楼
唔，今天似乎有点偷懒……没有做实验……
Nature 13.12.19
推荐： Solutions to the Public Goods Dilemma in Bacterial Biofilms
我自己特别喜欢cheater的defense mechanism, cooperation的形成之类的
评论： Biofilms block bacterial cheaters
Cheaters do not thrive as well as enzyme producers when they are grown in
communities called biofilms
小知识：
1. Microbes meddle with microRNA
Infection with Listeria monocytogenes
Reduced expression of six microRNAs after the infection in normal mice
No decrease for five of them in mice without gut microbes
Nature 13.12.19
推荐： Solutions to the Public Goods Dilemma in Bacterial Biofilms
我自己特别喜欢cheater的defense mechanism, cooperation的形成之类的
评论： Biofilms block bacterial cheaters
Cheaters do not thrive as well as enzyme producers when they are grown in
communities called biofilms
小知识：
1. Microbes meddle with microRNA
Infection with Listeria monocytogenes
Reduced expression of six microRNAs after the infection in normal mice
No decrease for five of them in mice without gut microbes
m*g
145 楼
Nature 14.01.02
稍微了解一下：
1. N6-methyladenosine-dependent regulation of messenger RNA stability
m6A: most prevalent internal modification in mRNA
Recognized by human YTH domain family
From translatable to mRNA decay
小知识：
1. Low investment in sexual reproduction threatens plants adapted to
phosphorus limitation
2. Upper Palaeolithic Siberian genome reveals dual ancestry of Native
Americans
3. The complete genome sequence of a Neanderthal from the Altai Mountains
稍微了解一下：
1. N6-methyladenosine-dependent regulation of messenger RNA stability
m6A: most prevalent internal modification in mRNA
Recognized by human YTH domain family
From translatable to mRNA decay
小知识：
1. Low investment in sexual reproduction threatens plants adapted to
phosphorus limitation
2. Upper Palaeolithic Siberian genome reveals dual ancestry of Native
Americans
3. The complete genome sequence of a Neanderthal from the Altai Mountains
m*g
146 楼
哦。谢谢！觉得自己有时候懒死了，不想做实验，就去看看文献什么的。
【在 t*****z 的大作中提到】
: 顶下楼主的执着热情。我也是做进化的，来学习下。
【在 t*****z 的大作中提到】
: 顶下楼主的执着热情。我也是做进化的，来学习下。
m*g
147 楼
Science 13.12.20
稍微了解一下：
1. Genomic Clues to the Ancestral Flowering Plant
Mt and nuclear genes sequenced
Single sister species to all other extant angiosperms
Mt: Horizontal Transfer of Entire Genomes via Mitochondrial Fusion in the
AngiospermAmborella
Horizontal gene transfer
75% fortein mt protein genes are pseudogenes
Genome: The Amborella Genome and the Evolution of Flowering Plants
小知识：
1. Brood Parasitism and the Evolution of Cooperative Breeding in Birds
Cooperative breeders related to brood parasites
Brood parasites get better care
Cooperate breeders defend better against brood parasites
2. No Barriers to Cellulose Breakdown
Balteria enzyme CelA
Breaks down cellulose and hemicellulose
稍微了解一下：
1. Genomic Clues to the Ancestral Flowering Plant
Mt and nuclear genes sequenced
Single sister species to all other extant angiosperms
Mt: Horizontal Transfer of Entire Genomes via Mitochondrial Fusion in the
AngiospermAmborella
Horizontal gene transfer
75% fortein mt protein genes are pseudogenes
Genome: The Amborella Genome and the Evolution of Flowering Plants
小知识：
1. Brood Parasitism and the Evolution of Cooperative Breeding in Birds
Cooperative breeders related to brood parasites
Brood parasites get better care
Cooperate breeders defend better against brood parasites
2. No Barriers to Cellulose Breakdown
Balteria enzyme CelA
Breaks down cellulose and hemicellulose
m*g
148 楼
PNAS 13.12.17
本周似乎没有碰到那种令人眼前一亮的文章，下面几篇可以稍微看一下。
1. Codon 104 variation of p53 gene provides adaptive apoptotic responses to
extreme environments in mammals of the Tibet plateau
2. Repeated elevational transitions in hemoglobin function during the
evolution of Andean hummingbirds
3. The Burmese python genome reveals the molecular basis for extreme
adaptation in snakes
4. The king cobra genome reveals dynamic gene evolution and adaptation in
the snake venom system
本周似乎没有碰到那种令人眼前一亮的文章，下面几篇可以稍微看一下。
1. Codon 104 variation of p53 gene provides adaptive apoptotic responses to
extreme environments in mammals of the Tibet plateau
2. Repeated elevational transitions in hemoglobin function during the
evolution of Andean hummingbirds
3. The Burmese python genome reveals the molecular basis for extreme
adaptation in snakes
4. The king cobra genome reveals dynamic gene evolution and adaptation in
the snake venom system
m*g
149 楼
呼呼，下一个post终于要进入2014年了，感觉我写的内容越来越少了~~~
PNAS 13.12.24
稍微了解一下：
1. Mutational effects on stability are largely conserved during protein
evolution
Influenza nucleoprotein
Measure mutational effects on stability
In diverged homologs
Largely conserved
Simulated protein evolution is similar
小知识：
1. Genetic mapping of adaptation reveals fitness tradeoffs in Arabidopsis
thaliana
2. Visible light alters yeast metabolic rhythms by inhibiting respiration
3. Stepwise artificial evolution of a plant disease resistance gene
4. A fully defined and scalable 3D culture system for human pluripotent stem
cell expansion and differentiation
PNAS 13.12.24
稍微了解一下：
1. Mutational effects on stability are largely conserved during protein
evolution
Influenza nucleoprotein
Measure mutational effects on stability
In diverged homologs
Largely conserved
Simulated protein evolution is similar
小知识：
1. Genetic mapping of adaptation reveals fitness tradeoffs in Arabidopsis
thaliana
2. Visible light alters yeast metabolic rhythms by inhibiting respiration
3. Stepwise artificial evolution of a plant disease resistance gene
4. A fully defined and scalable 3D culture system for human pluripotent stem
cell expansion and differentiation
m*g
150 楼
Science 14.01.03
新年快乐！P.S. 这周又没有遇到“推荐”的paper。
稍微了解一下：
1. Two Y Genes Can Replace the Entire Y Chromosome for Assisted Reproduction
in the Mouse
另外，
complex and multilayered palindromic structure of the Y chromosome
may facilitate internal pairing of nucleotide bases
2. Break-Induced Replication Repair of Damaged Forks Induces Genomic
Duplications in Human Cells
小知识：
1. A Cascade of Histone Modifications Induces Chromatin Condensation in
Mitosis
2. A Neural Mechanism Underlying Mating Preferences for Familiar Individuals
in Medaka Fish
新年快乐！P.S. 这周又没有遇到“推荐”的paper。
稍微了解一下：
1. Two Y Genes Can Replace the Entire Y Chromosome for Assisted Reproduction
in the Mouse
另外，
complex and multilayered palindromic structure of the Y chromosome
may facilitate internal pairing of nucleotide bases
2. Break-Induced Replication Repair of Damaged Forks Induces Genomic
Duplications in Human Cells
小知识：
1. A Cascade of Histone Modifications Induces Chromatin Condensation in
Mitosis
2. A Neural Mechanism Underlying Mating Preferences for Familiar Individuals
in Medaka Fish
m*g
151 楼
最近被导师说了，觉得我被distracted了，我自己也这么觉得，不过可能真的心智不够
成熟吧，感觉与自己以及导师的预期差了不少。我会努力的！
新年快乐！
Nature 14.01.09
推荐：
原文两篇见science
1. Genome-Scale CRISPR-Cas9 Knockout Screening in Human Cells
评论： CRISPR screen identifies genes
A library of 64,751 guide RNA sequences
Target 18,080 genes in human cells
Genes that are required by cancer and stem cells to survive
稍微了解一下：
1. The effects of genetic variation on gene expression dynamics during
development
2. Diversity of ageing across the tree of life
小知识：
1. Serial Femtosecond Crystallography of G Protein–Coupled Receptors
Room-temperature free-electron-laser approach may better capture the protein
's conformation in its native environment
成熟吧，感觉与自己以及导师的预期差了不少。我会努力的！
新年快乐！
Nature 14.01.09
推荐：
原文两篇见science
1. Genome-Scale CRISPR-Cas9 Knockout Screening in Human Cells
评论： CRISPR screen identifies genes
A library of 64,751 guide RNA sequences
Target 18,080 genes in human cells
Genes that are required by cancer and stem cells to survive
稍微了解一下：
1. The effects of genetic variation on gene expression dynamics during
development
2. Diversity of ageing across the tree of life
小知识：
1. Serial Femtosecond Crystallography of G Protein–Coupled Receptors
Room-temperature free-electron-laser approach may better capture the protein
's conformation in its native environment
m*g
152 楼
最近面临着4个deadline，果然我是那种喜欢冲击deadline的拖延症患者。
希望能够顺利完成呢（应该说非完成不可）！加油！
Science 14.01.10
推荐：
1. Single-Cell RNA-Seq Reveals Dynamic, Random Monoallelic Gene Expression
in Mammalian Cells
Single cell expression of mouse of mixed background
Abundant monoallelic expression
2. Genetic Screens in Human Cells Using the CRISPR-Cas9 System
Pooled, LOF genetic screening approach
Genome-scale lentival sgRNA library
Generate knockout collections
3. Genome-Scale CRISPR-Cas9 Knockout Screening in Human Cells
稍微了解一下：
1. Mutational Analysis Reveals the Origin and Therapy-Driven Evolution of
Recurrent Glioma
小知识：
1. Studies Suggest Two-Way Street for Science Majors
里面包含STEM专业的专业率和肄业率，以及转专业后的方向，有兴趣可以了解一下。
2. Bacterial Vesicles in Marine Ecosystems
简介： Bacterial Vesicles in the Ocean
3. Status and Ecological Effects of the World's Largest Carnivores
希望能够顺利完成呢（应该说非完成不可）！加油！
Science 14.01.10
推荐：
1. Single-Cell RNA-Seq Reveals Dynamic, Random Monoallelic Gene Expression
in Mammalian Cells
Single cell expression of mouse of mixed background
Abundant monoallelic expression
2. Genetic Screens in Human Cells Using the CRISPR-Cas9 System
Pooled, LOF genetic screening approach
Genome-scale lentival sgRNA library
Generate knockout collections
3. Genome-Scale CRISPR-Cas9 Knockout Screening in Human Cells
稍微了解一下：
1. Mutational Analysis Reveals the Origin and Therapy-Driven Evolution of
Recurrent Glioma
小知识：
1. Studies Suggest Two-Way Street for Science Majors
里面包含STEM专业的专业率和肄业率，以及转专业后的方向，有兴趣可以了解一下。
2. Bacterial Vesicles in Marine Ecosystems
简介： Bacterial Vesicles in the Ocean
3. Status and Ecological Effects of the World's Largest Carnivores
m*u
153 楼
感觉你只是为自己有动力才更新帖子的。若真想讨论东西，为什么不概括总结一下这些
文章内容呢？不必完全摘用摘要或summary的东西，重要的是你觉得这文章有什么新的
东西促使你罗列或highlight它！
谢谢。
文章内容呢？不必完全摘用摘要或summary的东西，重要的是你觉得这文章有什么新的
东西促使你罗列或highlight它！
谢谢。
m*g
154 楼
谢谢你的建议。我确实是只为了监督自己才开的这个帖子呢。而且这样开组会找paper
就变得很简单，只要扫一眼这个帖子，就能找出自己最喜欢的文献用于讨论了。
不列出想法和理由的原因是，我觉得即使列出各种用于讨论的东西，列出10次，也不一
定有人回复1次，基本上是有去无回的，所以心里想想就好了，highlight一篇文章当然
是有自己的理由的^_^，个人觉得每周的推荐阅读大概都是有值得讨论的paper呢。不过
列出来就太长了……我比较懒，不好意思哈。
如果您有什么想要讨论的paper欢迎列出，我应该会回复的呢。也欢迎您开一个类似的
帖子，做个榜样，那样子也许我也会更有动力，嘻嘻。新年快乐！
【在 m******u 的大作中提到】
: 感觉你只是为自己有动力才更新帖子的。若真想讨论东西，为什么不概括总结一下这些
: 文章内容呢？不必完全摘用摘要或summary的东西，重要的是你觉得这文章有什么新的
: 东西促使你罗列或highlight它！
: 谢谢。
就变得很简单，只要扫一眼这个帖子，就能找出自己最喜欢的文献用于讨论了。
不列出想法和理由的原因是，我觉得即使列出各种用于讨论的东西，列出10次，也不一
定有人回复1次，基本上是有去无回的，所以心里想想就好了，highlight一篇文章当然
是有自己的理由的^_^，个人觉得每周的推荐阅读大概都是有值得讨论的paper呢。不过
列出来就太长了……我比较懒，不好意思哈。
如果您有什么想要讨论的paper欢迎列出，我应该会回复的呢。也欢迎您开一个类似的
帖子，做个榜样，那样子也许我也会更有动力，嘻嘻。新年快乐！
【在 m******u 的大作中提到】
: 感觉你只是为自己有动力才更新帖子的。若真想讨论东西，为什么不概括总结一下这些
: 文章内容呢？不必完全摘用摘要或summary的东西，重要的是你觉得这文章有什么新的
: 东西促使你罗列或highlight它！
: 谢谢。
b*s
155 楼
你能坚持这么久已经很了不起了。请继续。
没有回复，不是没人看，而是大部分不是这个领域的。但是开卷有益，读过多少总是有
收获的。
paper
【在 m******g 的大作中提到】
: 谢谢你的建议。我确实是只为了监督自己才开的这个帖子呢。而且这样开组会找paper
: 就变得很简单，只要扫一眼这个帖子，就能找出自己最喜欢的文献用于讨论了。
: 不列出想法和理由的原因是，我觉得即使列出各种用于讨论的东西，列出10次，也不一
: 定有人回复1次，基本上是有去无回的，所以心里想想就好了，highlight一篇文章当然
: 是有自己的理由的^_^，个人觉得每周的推荐阅读大概都是有值得讨论的paper呢。不过
: 列出来就太长了……我比较懒，不好意思哈。
: 如果您有什么想要讨论的paper欢迎列出，我应该会回复的呢。也欢迎您开一个类似的
: 帖子，做个榜样，那样子也许我也会更有动力，嘻嘻。新年快乐！
没有回复，不是没人看，而是大部分不是这个领域的。但是开卷有益，读过多少总是有
收获的。
paper
【在 m******g 的大作中提到】
: 谢谢你的建议。我确实是只为了监督自己才开的这个帖子呢。而且这样开组会找paper
: 就变得很简单，只要扫一眼这个帖子，就能找出自己最喜欢的文献用于讨论了。
: 不列出想法和理由的原因是，我觉得即使列出各种用于讨论的东西，列出10次，也不一
: 定有人回复1次，基本上是有去无回的，所以心里想想就好了，highlight一篇文章当然
: 是有自己的理由的^_^，个人觉得每周的推荐阅读大概都是有值得讨论的paper呢。不过
: 列出来就太长了……我比较懒，不好意思哈。
: 如果您有什么想要讨论的paper欢迎列出，我应该会回复的呢。也欢迎您开一个类似的
: 帖子，做个榜样，那样子也许我也会更有动力，嘻嘻。新年快乐！
l*1
156 楼
One ask,
from your cited >100 papers from CNS or N sisiter what relevant to 遗传进化
方向, could you eteact at least >two proposals? i mean for your K99/R00 in
the soon future..
paper
【在 m******g 的大作中提到】
: 谢谢你的建议。我确实是只为了监督自己才开的这个帖子呢。而且这样开组会找paper
: 就变得很简单，只要扫一眼这个帖子，就能找出自己最喜欢的文献用于讨论了。
: 不列出想法和理由的原因是，我觉得即使列出各种用于讨论的东西，列出10次，也不一
: 定有人回复1次，基本上是有去无回的，所以心里想想就好了，highlight一篇文章当然
: 是有自己的理由的^_^，个人觉得每周的推荐阅读大概都是有值得讨论的paper呢。不过
: 列出来就太长了……我比较懒，不好意思哈。
: 如果您有什么想要讨论的paper欢迎列出，我应该会回复的呢。也欢迎您开一个类似的
: 帖子，做个榜样，那样子也许我也会更有动力，嘻嘻。新年快乐！
from your cited >100 papers from CNS or N sisiter what relevant to 遗传进化
方向, could you eteact at least >two proposals? i mean for your K99/R00 in
the soon future..
paper
【在 m******g 的大作中提到】
: 谢谢你的建议。我确实是只为了监督自己才开的这个帖子呢。而且这样开组会找paper
: 就变得很简单，只要扫一眼这个帖子，就能找出自己最喜欢的文献用于讨论了。
: 不列出想法和理由的原因是，我觉得即使列出各种用于讨论的东西，列出10次，也不一
: 定有人回复1次，基本上是有去无回的，所以心里想想就好了，highlight一篇文章当然
: 是有自己的理由的^_^，个人觉得每周的推荐阅读大概都是有值得讨论的paper呢。不过
: 列出来就太长了……我比较懒，不好意思哈。
: 如果您有什么想要讨论的paper欢迎列出，我应该会回复的呢。也欢迎您开一个类似的
: 帖子，做个榜样，那样子也许我也会更有动力，嘻嘻。新年快乐！
m*g
157 楼
555，不好意思，我觉得好难用自己的话一一列举为什么要罗列某篇文章啊，那还是就
这么贴出来吧。
PNAS 14.01.07
推荐：
1. Ohnologs are overrepresented in pathogenic copy number mutations
Ohnolog: retained after WGD
Overrepresented in pathogenic SNV
2. Contribution of phenotypic heterogeneity to adaptive antibiotic
resistance
Some due to mutation, some due to heterogeneity
Different responses after non-selective response
I think the result is expected, but still a nice story
稍微了解一下：
1. Drastic neofunctionalization associated with evolution of the timezyme
AANAT 500 Mya
小知识：
1. A unique covalent bond in basement membrane is a primordial innovation
for tissue evolution
2. Policing of reproduction by hidden threats in a cooperative mammal
selection to evade the threat of infanticide by dominant females
explain the evolution of remarkable birth synchrony
有一些奇怪的联想……
这么贴出来吧。
PNAS 14.01.07
推荐：
1. Ohnologs are overrepresented in pathogenic copy number mutations
Ohnolog: retained after WGD
Overrepresented in pathogenic SNV
2. Contribution of phenotypic heterogeneity to adaptive antibiotic
resistance
Some due to mutation, some due to heterogeneity
Different responses after non-selective response
I think the result is expected, but still a nice story
稍微了解一下：
1. Drastic neofunctionalization associated with evolution of the timezyme
AANAT 500 Mya
小知识：
1. A unique covalent bond in basement membrane is a primordial innovation
for tissue evolution
2. Policing of reproduction by hidden threats in a cooperative mammal
selection to evade the threat of infanticide by dominant females
explain the evolution of remarkable birth synchrony
有一些奇怪的联想……
m*g
158 楼
这周好累，连续三天晚上1点爬起来工作到5点(自作自受)，以后争取不要再这么抢着
deadline做
事了。
感觉冲deadline玩的就是心跳，而且对不住导师。
Nature 14.1.16
推荐：
1. RNA retrieved from intact tissue
原文： Transcriptome in vivo analysis (TIVA) of spatially defined single
cells in live tissue
小知识：
1. Starfish eyes see the light
deadline做
事了。
感觉冲deadline玩的就是心跳，而且对不住导师。
Nature 14.1.16
推荐：
1. RNA retrieved from intact tissue
原文： Transcriptome in vivo analysis (TIVA) of spatially defined single
cells in live tissue
小知识：
1. Starfish eyes see the light
l*1
159 楼
Proposal to Reference (P and R) can be taken as Main and sub relationship!
To initiative, first title and key words might be from R or previously got
result
> more direct or indirect relevant R
>P modified
>more R
>P modi again
>more R or preli result
>Final draft of P
Just two cents.
【在 m******g 的大作中提到】
: 没太懂问题啊。是不是说看多少文献，可以提取多少proposal?
: 个人觉得这个问题就跟“看多少小说可以写出一部小说”和“做多少习题可以考95分以
: 上”是一样的，因人而异，但是如果不看小说，不做习题，肯定是没办法写出小说和考
: 95分以上的（大天才除外），哈哈。感觉看了之后对于自己理解、设计、写作都很有帮
: 助。
: 感觉文献挺有意思的啊。就像看小说一样，不需要有太功利的目的嘛。
To initiative, first title and key words might be from R or previously got
result
> more direct or indirect relevant R
>P modified
>more R
>P modi again
>more R or preli result
>Final draft of P
Just two cents.
【在 m******g 的大作中提到】
: 没太懂问题啊。是不是说看多少文献，可以提取多少proposal?
: 个人觉得这个问题就跟“看多少小说可以写出一部小说”和“做多少习题可以考95分以
: 上”是一样的，因人而异，但是如果不看小说，不做习题，肯定是没办法写出小说和考
: 95分以上的（大天才除外），哈哈。感觉看了之后对于自己理解、设计、写作都很有帮
: 助。
: 感觉文献挺有意思的啊。就像看小说一样，不需要有太功利的目的嘛。
m*u
160 楼
我认为：就是某篇文章文笔很好都可以是你想列它的原因。我自己也有某段时间不喜某
篇文章，过一段时间又会觉得它很好。对其内容的理解也随之不同。
发信人: maoxiang (白水), 信区: Biology
标 题: Re: 大家一起来读主流杂志吧［遗传进化方向］希望每周更新
发信站: BBS 未名空间站 (Fri Feb 7 17:34:00 2014, 美东)
555，不好意思，我觉得好难用自己的话一一列举为什么要罗列某篇文章啊，那还是就
这么贴出来吧。
篇文章，过一段时间又会觉得它很好。对其内容的理解也随之不同。
发信人: maoxiang (白水), 信区: Biology
标 题: Re: 大家一起来读主流杂志吧［遗传进化方向］希望每周更新
发信站: BBS 未名空间站 (Fri Feb 7 17:34:00 2014, 美东)
555，不好意思，我觉得好难用自己的话一一列举为什么要罗列某篇文章啊，那还是就
这么贴出来吧。
m*g
161 楼
我这个月对这个topic很感兴趣呢。
读了一些文献。
有什么具体问题可以讨论一下啊
【在 x********e 的大作中提到】
: 版上有做splicing的吗 最近对alternative splicing感兴趣
读了一些文献。
有什么具体问题可以讨论一下啊
【在 x********e 的大作中提到】
: 版上有做splicing的吗 最近对alternative splicing感兴趣
m*g
162 楼
补番中……
PNAS 14.1.14
推荐：
1. Neutral genomic regions refine models of recent rapid human population
growth
Population growth or purifying selection contributes to rare alleles
Sequence genetic variants far from genes (neutral)
3.4% per generation over the last 3,000–4,000 y
稍微了解一下：
1. Harnessing evolutionary fitness in Plasmodium falciparum for drug
discovery and suppressing resistance
只是描述现象：混用某两种inhibitor可防止其产生耐药性
因为我比较喜欢耐药性方面的东西，所以还是列一下好了
小知识：
1. Spontaneous slow replication fork progression elicits mitosis alterations
in homologous recombination-deficient mammalian cells
2. Systems analysis of sex differences reveals an immunosuppressive role for
testosterone in the response to influenza vaccination
PNAS 14.1.14
推荐：
1. Neutral genomic regions refine models of recent rapid human population
growth
Population growth or purifying selection contributes to rare alleles
Sequence genetic variants far from genes (neutral)
3.4% per generation over the last 3,000–4,000 y
稍微了解一下：
1. Harnessing evolutionary fitness in Plasmodium falciparum for drug
discovery and suppressing resistance
只是描述现象：混用某两种inhibitor可防止其产生耐药性
因为我比较喜欢耐药性方面的东西，所以还是列一下好了
小知识：
1. Spontaneous slow replication fork progression elicits mitosis alterations
in homologous recombination-deficient mammalian cells
2. Systems analysis of sex differences reveals an immunosuppressive role for
testosterone in the response to influenza vaccination
m*g
163 楼
最近感觉要做的事情超多，时间刷的一下就过去了。
Science 14.1.17
推荐：
1. Direct in Vivo RNAi Screen Unveils Myosin IIa as a Tumor Suppressor of
Squamous Cell Carcinomas
稍微了解一下：
1. Ribose—An Internal Threat to DNA
小知识：
1. Many Paths to the Origin of Life
2. Conserved Class of Queen Pheromones Stops Social Insect Workers from
Reproducing
Science 14.1.17
推荐：
1. Direct in Vivo RNAi Screen Unveils Myosin IIa as a Tumor Suppressor of
Squamous Cell Carcinomas
稍微了解一下：
1. Ribose—An Internal Threat to DNA
小知识：
1. Many Paths to the Origin of Life
2. Conserved Class of Queen Pheromones Stops Social Insect Workers from
Reproducing
m*g
164 楼
求提高效率！求上帝保佑（非基督徒）！
Nature 14.01.23
稍微了解一下：
1. Diet rapidly and reproducibly alters the human gut microbiome
2. Discovery and saturation analysis of cancer genes across 21 tumour types
Nature 14.01.23
稍微了解一下：
1. Diet rapidly and reproducibly alters the human gut microbiome
2. Discovery and saturation analysis of cancer genes across 21 tumour types
m*g
165 楼
最近感觉自己太懒惰了，很容易就distracted，很多事情都一拖再拖，踩着deadline，
一定要改正。
PNAS 14.1.21
很推荐：
1. Genetic drift opposes mutualism during spatial population expansion
方法很有趣，系统很喜欢
稍微了解一下：
1. Sympatric incipient speciation of spiny mice Acomys at "Evolution Canyon,
" Israel
2. Information transfer by leaky, heterogeneous, protein kinase signaling
systems
小知识：
1. Perfect genetic correlation between number of offspring and
grandoffspring in an industrialized human population
一定要改正。
PNAS 14.1.21
很推荐：
1. Genetic drift opposes mutualism during spatial population expansion
方法很有趣，系统很喜欢
稍微了解一下：
1. Sympatric incipient speciation of spiny mice Acomys at "Evolution Canyon,
" Israel
2. Information transfer by leaky, heterogeneous, protein kinase signaling
systems
小知识：
1. Perfect genetic correlation between number of offspring and
grandoffspring in an industrialized human population
n*k
166 楼
看了一圈，这个要强挺一下！绝对是牛人的搞法，牛人的路子！只要坚持好，把握机会
，最好把本版几年前有几个强人的帖子好好读读，包括DRBIOLOGY和另外一个在
SINGAPORE的FACULTY写的一些关于职业规划设计的帖子好好读一读，把握机会，前途不
可限量！任何时候，机会都是自己可以创造和把握的，真正的牛人是没有机会也创造出
机会！聪明人很多，但牛人很少！你可能已经具备了一些成为牛人的素质哈；贵在坚持
，聪明的坚持，智慧的前行！
最后，以你的目前状态，不会有太糟糕的运气；万一的话，只要我能在学术界立足，随
时欢迎你这种人来我实验室哈--只要不是那种只动脑不动手的哈：））。
【在 m******g 的大作中提到】
: 最近感觉要做的事情超多，时间刷的一下就过去了。
: Science 14.1.17
: 推荐：
: 1. Direct in Vivo RNAi Screen Unveils Myosin IIa as a Tumor Suppressor of
: Squamous Cell Carcinomas
: 稍微了解一下：
: 1. Ribose—An Internal Threat to DNA
: 小知识：
: 1. Many Paths to the Origin of Life
: 2. Conserved Class of Queen Pheromones Stops Social Insect Workers from
，最好把本版几年前有几个强人的帖子好好读读，包括DRBIOLOGY和另外一个在
SINGAPORE的FACULTY写的一些关于职业规划设计的帖子好好读一读，把握机会，前途不
可限量！任何时候，机会都是自己可以创造和把握的，真正的牛人是没有机会也创造出
机会！聪明人很多，但牛人很少！你可能已经具备了一些成为牛人的素质哈；贵在坚持
，聪明的坚持，智慧的前行！
最后，以你的目前状态，不会有太糟糕的运气；万一的话，只要我能在学术界立足，随
时欢迎你这种人来我实验室哈--只要不是那种只动脑不动手的哈：））。
【在 m******g 的大作中提到】
: 最近感觉要做的事情超多，时间刷的一下就过去了。
: Science 14.1.17
: 推荐：
: 1. Direct in Vivo RNAi Screen Unveils Myosin IIa as a Tumor Suppressor of
: Squamous Cell Carcinomas
: 稍微了解一下：
: 1. Ribose—An Internal Threat to DNA
: 小知识：
: 1. Many Paths to the Origin of Life
: 2. Conserved Class of Queen Pheromones Stops Social Insect Workers from
l*1
167 楼
本版台柱美女PKU PI 也得时常回这 找潜力高俊(high EQ and IQ both) 徒弟 哈;
不然就只看着本版前四大牛人 找(high EQ and IQ)美徒妹 ?
【在 n********k 的大作中提到】
: 看了一圈，这个要强挺一下！绝对是牛人的搞法，牛人的路子！只要坚持好，把握机会
: ，最好把本版几年前有几个强人的帖子好好读读，包括DRBIOLOGY和另外一个在
: SINGAPORE的FACULTY写的一些关于职业规划设计的帖子好好读一读，把握机会，前途不
: 可限量！任何时候，机会都是自己可以创造和把握的，真正的牛人是没有机会也创造出
: 机会！聪明人很多，但牛人很少！你可能已经具备了一些成为牛人的素质哈；贵在坚持
: ，聪明的坚持，智慧的前行！
: 最后，以你的目前状态，不会有太糟糕的运气；万一的话，只要我能在学术界立足，随
: 时欢迎你这种人来我实验室哈--只要不是那种只动脑不动手的哈：））。
不然就只看着本版前四大牛人 找(high EQ and IQ)美徒妹 ?
【在 n********k 的大作中提到】
: 看了一圈，这个要强挺一下！绝对是牛人的搞法，牛人的路子！只要坚持好，把握机会
: ，最好把本版几年前有几个强人的帖子好好读读，包括DRBIOLOGY和另外一个在
: SINGAPORE的FACULTY写的一些关于职业规划设计的帖子好好读一读，把握机会，前途不
: 可限量！任何时候，机会都是自己可以创造和把握的，真正的牛人是没有机会也创造出
: 机会！聪明人很多，但牛人很少！你可能已经具备了一些成为牛人的素质哈；贵在坚持
: ，聪明的坚持，智慧的前行！
: 最后，以你的目前状态，不会有太糟糕的运气；万一的话，只要我能在学术界立足，随
: 时欢迎你这种人来我实验室哈--只要不是那种只动脑不动手的哈：））。
m*g
168 楼
谢谢楼上两位的建议，我有时间会去看看学习一下的。
Science 14.1.24
推荐：
1. The Epigenetics Heretic
算是科学家背后的故事，看起来有点意思
发现abnormalties caused by pesticide persists for generations
2. An Ancient Dog in the Modern World
About a transmissible cancer in dog
稍微了解一下：
1. A Paleogenomic Perspective on Evolution and Gene Function: New insights
from Ancient DNA
A well written review for progresses in ancient DNA studies
小知识：
1. Extraordinary Color Vision
Color vision in mantis shrimp
12 spectral receptors
Science 14.1.24
推荐：
1. The Epigenetics Heretic
算是科学家背后的故事，看起来有点意思
发现abnormalties caused by pesticide persists for generations
2. An Ancient Dog in the Modern World
About a transmissible cancer in dog
稍微了解一下：
1. A Paleogenomic Perspective on Evolution and Gene Function: New insights
from Ancient DNA
A well written review for progresses in ancient DNA studies
小知识：
1. Extraordinary Color Vision
Color vision in mantis shrimp
12 spectral receptors
m*g
169 楼
这期Nature好赞！
Nature 14.1.30
非常推荐：
1. Molecular biology: A second layer of information in RNA
1) In vivo genome-wide profiling of RNA secondary structure reveals novel
regulatory features
2) Genome-wide probing of RNA structure reveals active unfolding of mRNA
structures in vivo
3) Landscape and variation of RNA secondary structure across the human
transcriptome
2. Cell biology: Potency unchained
Mildly acidic conditions triggers potential for a new cell state with
diverse potentials
1) Bidirectional developmental potential in reprogrammed cells with acquired
pluripotency
2) Stimulus-triggered fate conversion of somatic cells into pluripotency
http://www.nature.com/news/acid-bath-stem-cell-study-under-inve
据说真实性受到挑战？
3. The evolution of lncRNA repertoires and expression patterns in tetrapods
4. Mutational and fitness landscapes of an RNA virus revealed through
population sequencing
非常推荐读一读这一篇
Great methodology: sequencing rate终于降到mutation rate之下了
稍微了解一下：
1. Evolution and transmission of drug-resistant tuberculosis in a Russian
population
2. Genome-wide dissection of the quorum sensing signalling pathway in
Trypanosoma brucei
小知识：
1. Immobile bacteria hitchhike on rafts
Intereting story about attract and use another species as transport
原文： Surface-motility induction, attraction and hitchhiking between
bacterial species promote dispersal on solid surfaces
2. Mother's fatty diet hurts offspring
3. Poor diet boosts innate immunity
特指缺少Vitamin A
4. River dolphin found
5. Evolutionary biology: Brotherly love benefits females
原文： Within-group male relatedness reduces harm to females in Drosophila
Fruit flies alter their behaviour among kin
Brothers being less aggressive
Females reproducing for longer as a result
Nature 14.1.30
非常推荐：
1. Molecular biology: A second layer of information in RNA
1) In vivo genome-wide profiling of RNA secondary structure reveals novel
regulatory features
2) Genome-wide probing of RNA structure reveals active unfolding of mRNA
structures in vivo
3) Landscape and variation of RNA secondary structure across the human
transcriptome
2. Cell biology: Potency unchained
Mildly acidic conditions triggers potential for a new cell state with
diverse potentials
1) Bidirectional developmental potential in reprogrammed cells with acquired
pluripotency
2) Stimulus-triggered fate conversion of somatic cells into pluripotency
http://www.nature.com/news/acid-bath-stem-cell-study-under-inve
据说真实性受到挑战？
3. The evolution of lncRNA repertoires and expression patterns in tetrapods
4. Mutational and fitness landscapes of an RNA virus revealed through
population sequencing
非常推荐读一读这一篇
Great methodology: sequencing rate终于降到mutation rate之下了
稍微了解一下：
1. Evolution and transmission of drug-resistant tuberculosis in a Russian
population
2. Genome-wide dissection of the quorum sensing signalling pathway in
Trypanosoma brucei
小知识：
1. Immobile bacteria hitchhike on rafts
Intereting story about attract and use another species as transport
原文： Surface-motility induction, attraction and hitchhiking between
bacterial species promote dispersal on solid surfaces
2. Mother's fatty diet hurts offspring
3. Poor diet boosts innate immunity
特指缺少Vitamin A
4. River dolphin found
5. Evolutionary biology: Brotherly love benefits females
原文： Within-group male relatedness reduces harm to females in Drosophila
Fruit flies alter their behaviour among kin
Brothers being less aggressive
Females reproducing for longer as a result
m*g
170 楼
说好的希望每周更新呢？不过是“希望”嘛，很快补上。
Science 14.1.31
小知识：
1. Neandertals and Moderns Made Imperfect Mates
Two papers with different methodology
(whether or not use Neandertal's reference genome)
Lower fertility in hybrids
Regions determined (desert in X chromosome & traits related)
2. Online Video Game Plugs Players Into Remote-Controlled Biochemistry Lab
3. Editing of Targeted Genes Proved Possible in Monkeys
Using CRISPR in primates
4. Chemical Warfare in the Battle of the Sexes
In D. melanogaster and C. elegans
解释好牵强，因为食物也有类似的影响啊，总没有antagonistic coevolution吧
1) Mating Induces Shrinking and Death in Caenorhabditis mothers
2) Males Shorten the Life Span of C. elegans Hermaphrodites via Secreted
Compounds
3) Drosophila Life Span and Physiology Are Modulated by Sexual Perception
and Reward
Science 14.1.31
小知识：
1. Neandertals and Moderns Made Imperfect Mates
Two papers with different methodology
(whether or not use Neandertal's reference genome)
Lower fertility in hybrids
Regions determined (desert in X chromosome & traits related)
2. Online Video Game Plugs Players Into Remote-Controlled Biochemistry Lab
3. Editing of Targeted Genes Proved Possible in Monkeys
Using CRISPR in primates
4. Chemical Warfare in the Battle of the Sexes
In D. melanogaster and C. elegans
解释好牵强，因为食物也有类似的影响啊，总没有antagonistic coevolution吧
1) Mating Induces Shrinking and Death in Caenorhabditis mothers
2) Males Shorten the Life Span of C. elegans Hermaphrodites via Secreted
Compounds
3) Drosophila Life Span and Physiology Are Modulated by Sexual Perception
and Reward
x*e
171 楼
最后一个, diet和sex behavior是有很大关联的。metabolism/hormone 跟性行为相互
反馈
【在 m******g 的大作中提到】
: 说好的希望每周更新呢？不过是“希望”嘛，很快补上。
: Science 14.1.31
: 小知识：
: 1. Neandertals and Moderns Made Imperfect Mates
: Two papers with different methodology
: (whether or not use Neandertal's reference genome)
: Lower fertility in hybrids
: Regions determined (desert in X chromosome & traits related)
: 2. Online Video Game Plugs Players Into Remote-Controlled Biochemistry Lab
: 3. Editing of Targeted Genes Proved Possible in Monkeys
反馈
【在 m******g 的大作中提到】
: 说好的希望每周更新呢？不过是“希望”嘛，很快补上。
: Science 14.1.31
: 小知识：
: 1. Neandertals and Moderns Made Imperfect Mates
: Two papers with different methodology
: (whether or not use Neandertal's reference genome)
: Lower fertility in hybrids
: Regions determined (desert in X chromosome & traits related)
: 2. Online Video Game Plugs Players Into Remote-Controlled Biochemistry Lab
: 3. Editing of Targeted Genes Proved Possible in Monkeys
m*g
172 楼
PNAS 14.1.28
稍微了解一下：
1. Searching for missing heritability: Designing rare variant association
studies
2. Transcriptional occlusion caused by overlapping promoters
小知识：
1. Deletion of conserved protein phosphatases reverses defects associated
with mitochondrial DNA damage in Saccharomyces cerevisiae
2. Estrogen receptor α polymorphism in a species with alternative
behavioral phenotypes
3. Evolutionary genetics and implications of small size and twinning in
callitrichine primates
4. In vitro selection with artificial expanded genetic information systems
5. Primate energy expenditure and life history
Lower total energy expenditure might explain slow rate of growth,
reproduction and aging
稍微了解一下：
1. Searching for missing heritability: Designing rare variant association
studies
2. Transcriptional occlusion caused by overlapping promoters
小知识：
1. Deletion of conserved protein phosphatases reverses defects associated
with mitochondrial DNA damage in Saccharomyces cerevisiae
2. Estrogen receptor α polymorphism in a species with alternative
behavioral phenotypes
3. Evolutionary genetics and implications of small size and twinning in
callitrichine primates
4. In vitro selection with artificial expanded genetic information systems
5. Primate energy expenditure and life history
Lower total energy expenditure might explain slow rate of growth,
reproduction and aging
m*g
173 楼
Science 14.2.7
推荐：
1. A Promiscuous Intermediate Underlies the Evolution of LEAFY DNA Binding
Specificity
稍微了解一下：
1.Interchromosomal Communication Coordinates Intrinsically Stochastic
Expression Between Alleles
推荐：
1. A Promiscuous Intermediate Underlies the Evolution of LEAFY DNA Binding
Specificity
稍微了解一下：
1.Interchromosomal Communication Coordinates Intrinsically Stochastic
Expression Between Alleles
x*e
174 楼
哈哈 一看第二篇的标题就知道是他的文章
不过没听说他最近文章被science接收啊
【在 m******g 的大作中提到】
: Science 14.2.7
: 推荐：
: 1. A Promiscuous Intermediate Underlies the Evolution of LEAFY DNA Binding
: Specificity
: 稍微了解一下：
: 1.Interchromosomal Communication Coordinates Intrinsically Stochastic
: Expression Between Alleles
不过没听说他最近文章被science接收啊
【在 m******g 的大作中提到】
: Science 14.2.7
: 推荐：
: 1. A Promiscuous Intermediate Underlies the Evolution of LEAFY DNA Binding
: Specificity
: 稍微了解一下：
: 1.Interchromosomal Communication Coordinates Intrinsically Stochastic
: Expression Between Alleles
m*g
175 楼
PNAS 14.2.4
稍微了解一下：
1. Mutational landscape of yeast mutator strains
2. Lineage-specific expansions of TET/JBP genes and a new class of DNA
transposons shape fungal genomic and epigenetic landscapes
稍微了解一下：
1. Mutational landscape of yeast mutator strains
2. Lineage-specific expansions of TET/JBP genes and a new class of DNA
transposons shape fungal genomic and epigenetic landscapes
m*g
176 楼
Nature 14.2.6
小知识：
1. CRISPR makes modified monkeys
2. Prion strings pictured on cells
3. Lizards socialize to thrive
4. Tiny cracks toughen up glass
Similar to tooth enamel and nacre in mollusc shells
小知识：
1. CRISPR makes modified monkeys
2. Prion strings pictured on cells
3. Lizards socialize to thrive
4. Tiny cracks toughen up glass
Similar to tooth enamel and nacre in mollusc shells
a*a
177 楼
我也报个名。我要求参加。督促自己学习新知识！
【在 m******g 的大作中提到】
: 本来在开始读PhD的时候，就打算要广泛阅读主流学术杂志，比如Nature, Science,
: PNAS, Plos genetics等等，但是自己总是拖拖拉拉，偶尔有心血来潮就一口气读很久
: ，没兴趣／时间的话就个把月都不翻一下。
: 就好比动漫监督需要看其他畅销动漫（暴露兴趣了，太不学术了），我们也应该多多看
: 看生物的杂志，以增强自己对整个领域的理解，并且了解一些文献的逻辑、方法和写法
: 。所以我打算开这个贴说说每周最喜欢的几篇文章什么的，每周一更（日期不定），以
: 监督自己，防止自己不读文献。如果没有做到，请大家不要用砖头砸，把好吃的狠狠地
: 砸过来就好了，然后再狠狠地鄙视我就好。
: 我是学遗传进化方向的，做实验和编程都做一点（但是为什么现在还这么菜呢，果然是
: 因为我太懒惰了），总之看看文献没有坏处，也欢迎相似方向的大家一起来贴贴推荐的
【在 m******g 的大作中提到】
: 本来在开始读PhD的时候，就打算要广泛阅读主流学术杂志，比如Nature, Science,
: PNAS, Plos genetics等等，但是自己总是拖拖拉拉，偶尔有心血来潮就一口气读很久
: ，没兴趣／时间的话就个把月都不翻一下。
: 就好比动漫监督需要看其他畅销动漫（暴露兴趣了，太不学术了），我们也应该多多看
: 看生物的杂志，以增强自己对整个领域的理解，并且了解一些文献的逻辑、方法和写法
: 。所以我打算开这个贴说说每周最喜欢的几篇文章什么的，每周一更（日期不定），以
: 监督自己，防止自己不读文献。如果没有做到，请大家不要用砖头砸，把好吃的狠狠地
: 砸过来就好了，然后再狠狠地鄙视我就好。
: 我是学遗传进化方向的，做实验和编程都做一点（但是为什么现在还这么菜呢，果然是
: 因为我太懒惰了），总之看看文献没有坏处，也欢迎相似方向的大家一起来贴贴推荐的
m*g
178 楼
Nature 14.02.13
稍微了解一下：
1. STATISTICAL ERRORS
About the overuse and misuse of p-values
Introduce about some alternatives
2. Webcraft 101
How to design an eye pleasing website for your lab
小知识：
1. Glowing probe reveals infection
2. CRISPR takes out bacterial species
3. Genetic roots of the first Americans
稍微了解一下：
1. STATISTICAL ERRORS
About the overuse and misuse of p-values
Introduce about some alternatives
2. Webcraft 101
How to design an eye pleasing website for your lab
小知识：
1. Glowing probe reveals infection
2. CRISPR takes out bacterial species
3. Genetic roots of the first Americans
m*g
179 楼
PNAS 14.2.11
推荐：
1. Recursive genomewide recombination and sequencing reveals a key
refinement step in the evolution of a metabolic innovation in Escherichia
coli
稍微了解一下：
1. Separating endogenous ancient DNA from modern day contamination in a
Siberian Neandertal
2. Stability-activity tradeoffs constrain the adaptive evolution of RubisCO
推荐：
1. Recursive genomewide recombination and sequencing reveals a key
refinement step in the evolution of a metabolic innovation in Escherichia
coli
稍微了解一下：
1. Separating endogenous ancient DNA from modern day contamination in a
Siberian Neandertal
2. Stability-activity tradeoffs constrain the adaptive evolution of RubisCO
m*g
180 楼
Science 14.2.14
稍微了解一下：
1. Leaf Shape Evolution Through Duplication, Regulatory Diversification, and
Loss of a Homeobox Gene
2. Designing Collective Behavior in a Termite-Inspired Robot Construction
Team
小知识：
1. Oil Is Bad for the Heart
Crude oil is cardiotoxic to fish embryos
2. A Genetic Atlas of Human Admixture History
3. Limb Regeneration
Anthropods use commited progenitor cells to regenerated
Unlike flat worms, similar to vertebrate
4. Designing Collective Behavior in a Termite-Inspired Robot Construction
Team
I like the podcast^_^
5. Predicting the Next Generation
Hybrid root biomass predicted by metabolites
稍微了解一下：
1. Leaf Shape Evolution Through Duplication, Regulatory Diversification, and
Loss of a Homeobox Gene
2. Designing Collective Behavior in a Termite-Inspired Robot Construction
Team
小知识：
1. Oil Is Bad for the Heart
Crude oil is cardiotoxic to fish embryos
2. A Genetic Atlas of Human Admixture History
3. Limb Regeneration
Anthropods use commited progenitor cells to regenerated
Unlike flat worms, similar to vertebrate
4. Designing Collective Behavior in a Termite-Inspired Robot Construction
Team
I like the podcast^_^
5. Predicting the Next Generation
Hybrid root biomass predicted by metabolites
b*r
181 楼
autism怎么都不止几十个，已知有autistic表型的都不止几十，别说未知的了
我觉得geneics能解决的是一些cancer的新问题。单基因病的诊断和预防是已经在解决
这个不必说了
【在 p*******r 的大作中提到】
: 我觉得看什么disease, 我比较熟悉neural 相关 disease。 昨天和鲁白讨论的时候，
: 他提到
: Alzhimer应该是十个左右gene这个级别，autism几十个，depression就多了。
: 所以我觉得现阶段最exiciting的应该是几十这个级别的disease吧。
我觉得geneics能解决的是一些cancer的新问题。单基因病的诊断和预防是已经在解决
这个不必说了
【在 p*******r 的大作中提到】
: 我觉得看什么disease, 我比较熟悉neural 相关 disease。 昨天和鲁白讨论的时候，
: 他提到
: Alzhimer应该是十个左右gene这个级别，autism几十个，depression就多了。
: 所以我觉得现阶段最exiciting的应该是几十这个级别的disease吧。
m*g
182 楼
PNAS 14.2.18
稍微了解一下：
1. Ancient west Eurasian ancestry in southern and eastern Africa
Two admixture events
Some ancestry related to Europeans and Middle Easterners
2. Population genomics of the honey bee reveals strong signatures of
positive selection on worker traits
稍微了解一下：
1. Ancient west Eurasian ancestry in southern and eastern Africa
Two admixture events
Some ancestry related to Europeans and Middle Easterners
2. Population genomics of the honey bee reveals strong signatures of
positive selection on worker traits
m*g
183 楼
PNAS 14.2.18
稍微了解一下：
1. Ancient west Eurasian ancestry in southern and eastern Africa
Two admixture events
Some ancentry related to Europeans and Middle Easterners
2. Population genomics of the honey bee reveals strong signatures of
positive selection on worker traits
稍微了解一下：
1. Ancient west Eurasian ancestry in southern and eastern Africa
Two admixture events
Some ancentry related to Europeans and Middle Easterners
2. Population genomics of the honey bee reveals strong signatures of
positive selection on worker traits
t*z
184 楼
继续支持楼主！
m*g
185 楼
Science 14.02.21
推荐：
1. The Robustness and Evolvability of Transcription Factor Binding Sites
Yeast and mice
More connected TF Binding Sites also bind more TF
小知识：
1. FDA Considers Trials of ‘Three-Parent Embryos’
mitochondrial DNA replacement
2. DNA Sequencers Still Waiting for The Nanopore Revolution
3. Eavesdropping on Ecosystems
I really like the sound of the healthy coral reefs^_^
推荐：
1. The Robustness and Evolvability of Transcription Factor Binding Sites
Yeast and mice
More connected TF Binding Sites also bind more TF
小知识：
1. FDA Considers Trials of ‘Three-Parent Embryos’
mitochondrial DNA replacement
2. DNA Sequencers Still Waiting for The Nanopore Revolution
3. Eavesdropping on Ecosystems
I really like the sound of the healthy coral reefs^_^
m*g
186 楼
Nature 14.02.27
推荐：
1. Genetics of single-cell protein abundance variation in large yeast
populations
稍微了解一下：
1. Sequential evolution of bacterial morphology by co-option of a
developmental regulator
小知识：
1. Molecule makes blind mice see light
2. Monkey brains wired to share
prisoner's dilemma
3. Crowd-sourcing: Strength in numbers
4. Skin pigmentation provides evidence of convergent melanism in extinct
marine
reptiles
5. A discrete genetic locus confers xyloglucan metabolism in select human
gut Bacteroidetes
推荐：
1. Genetics of single-cell protein abundance variation in large yeast
populations
稍微了解一下：
1. Sequential evolution of bacterial morphology by co-option of a
developmental regulator
小知识：
1. Molecule makes blind mice see light
2. Monkey brains wired to share
prisoner's dilemma
3. Crowd-sourcing: Strength in numbers
4. Skin pigmentation provides evidence of convergent melanism in extinct
marine
reptiles
5. A discrete genetic locus confers xyloglucan metabolism in select human
gut Bacteroidetes
m*g
187 楼
今天考完期末，应该会很快更新到最新一期，哈哈。
PNAS 14.02.25
稍微了解一下：
1. The double-stranded transcriptome of Escherichia coli
2. The predictability of molecular evolution during functional innovation
小知识：
1. Control of a Salmonella virulence operon by proline-charged tRNAPro
2. Pheromone evolution and sexual behavior in Drosophila are shaped by male
sensory
exploitation of other males
PNAS 14.02.25
稍微了解一下：
1. The double-stranded transcriptome of Escherichia coli
2. The predictability of molecular evolution during functional innovation
小知识：
1. Control of a Salmonella virulence operon by proline-charged tRNAPro
2. Pheromone evolution and sexual behavior in Drosophila are shaped by male
sensory
exploitation of other males
m*g
188 楼
Science 14.02.28
推荐：
1. Lost in Transition: Start-Up of Glycolysis Yields Subpopulations of
Nongrowing Cells
稍微了解一下：
1. Silencing in Fragile X Syndrome Promoter-Bound Trinucleotide Repeat mRNA
Drives Epigenetic
2. Resurrecting Surviving Neandertal Lineages from Modern Human Genomes
Look at proportions and methodology
小知识：
1. Out of Beringia?
shrub tundra refugium
2. Phonetic Feature Encoding in Human Superior Temporal Gyrus
推荐：
1. Lost in Transition: Start-Up of Glycolysis Yields Subpopulations of
Nongrowing Cells
稍微了解一下：
1. Silencing in Fragile X Syndrome Promoter-Bound Trinucleotide Repeat mRNA
Drives Epigenetic
2. Resurrecting Surviving Neandertal Lineages from Modern Human Genomes
Look at proportions and methodology
小知识：
1. Out of Beringia?
shrub tundra refugium
2. Phonetic Feature Encoding in Human Superior Temporal Gyrus
m*g
189 楼
PNAS 14.03.04
稍微了解一下：
1. Gene expression differences underlying genotype-bygenotype specificity in
a host–parasite system
2. Global analysis of cell cycle gene expression of the legume symbiont
Sinorhizobium meliloti
稍微了解一下：
1. Gene expression differences underlying genotype-bygenotype specificity in
a host–parasite system
2. Global analysis of cell cycle gene expression of the legume symbiont
Sinorhizobium meliloti
m*g
190 楼
Science 14.03.07
推荐：
1. The Secret Garden—Epigenetic Alleles Underlie Complex Traits
inherited across generations in plant genomes
QTL mapping for traits
future: environmentally induced transgenerationally stable epialleles
Actual paper: Mapping the Epigenetic Basis of Complex Traits
稍微了解一下：
1. A Genomic Road Map for Complex Human Disease
小知识：
1. Combating Evolution to Fight Disease
2. Review - Developments in X-ray Crystallographic Structure Determination
of Biological Macromolecules
3. A Single Gene Affects Both Ecological Divergence and Mate Choice in
Drosophila
推荐：
1. The Secret Garden—Epigenetic Alleles Underlie Complex Traits
inherited across generations in plant genomes
QTL mapping for traits
future: environmentally induced transgenerationally stable epialleles
Actual paper: Mapping the Epigenetic Basis of Complex Traits
稍微了解一下：
1. A Genomic Road Map for Complex Human Disease
小知识：
1. Combating Evolution to Fight Disease
2. Review - Developments in X-ray Crystallographic Structure Determination
of Biological Macromolecules
3. A Single Gene Affects Both Ecological Divergence and Mate Choice in
Drosophila
m*g
191 楼
Nature 14.03.06
稍微了解一下：
1. A predictive fitness model for influenza
2. DNA interrogation by the CRISPR RNA-guided endonuclease Cas9
a short trinucleotide protospacer adjacent motif (PAM)
3. Cell-autonomous correction of ring chromosomes in human induced
pluripotent stem cells
lost the abnormal chromosome and duplicated the wild-type homologue
through the compensatory uniparental disomy
小知识：
1. Genes make bacteria magnetic
2. Worms bond to reach new heights
towers with up to 1,000 individuals, reaching as high as 1 centimetre, which
can attach to a host -> Wow!
稍微了解一下：
1. A predictive fitness model for influenza
2. DNA interrogation by the CRISPR RNA-guided endonuclease Cas9
a short trinucleotide protospacer adjacent motif (PAM)
3. Cell-autonomous correction of ring chromosomes in human induced
pluripotent stem cells
lost the abnormal chromosome and duplicated the wild-type homologue
through the compensatory uniparental disomy
小知识：
1. Genes make bacteria magnetic
2. Worms bond to reach new heights
towers with up to 1,000 individuals, reaching as high as 1 centimetre, which
can attach to a host -> Wow!
m*g
192 楼
Nature 14.03.13
推荐：
1. Evolutionary biology: Sex, lies and butterflies
doublesex is a mimicry supergene
稍微了解一下：
1. Evolutionary biology: Speciation undone
large finch has become extinct through interbreeding with another
small and medium tree finches on Floreana may also be fusing into one
species
2. DNA-guided DNA interference by a prokaryotic Argonaute
a barrier for the uptake and propagation of foreign DNA
TtAgo is loaded with 5′-phosphorylated DNA guides, 13–25 nucleotides in
length
小知识：
1. How the fish got its fins
Adipose fin evolved separately in different fish lineages
2. Dynamic sensory cues shape song structure in Drosophila
pattern variability in Drosophila courtship song
explained by taking into account the dynamic sensory experience of the male
3. A transcriptional switch underlies commitment to sexual development in
malaria parasites
推荐：
1. Evolutionary biology: Sex, lies and butterflies
doublesex is a mimicry supergene
稍微了解一下：
1. Evolutionary biology: Speciation undone
large finch has become extinct through interbreeding with another
small and medium tree finches on Floreana may also be fusing into one
species
2. DNA-guided DNA interference by a prokaryotic Argonaute
a barrier for the uptake and propagation of foreign DNA
TtAgo is loaded with 5′-phosphorylated DNA guides, 13–25 nucleotides in
length
小知识：
1. How the fish got its fins
Adipose fin evolved separately in different fish lineages
2. Dynamic sensory cues shape song structure in Drosophila
pattern variability in Drosophila courtship song
explained by taking into account the dynamic sensory experience of the male
3. A transcriptional switch underlies commitment to sexual development in
malaria parasites
m*g
193 楼
PNAS 14.03.11
推荐：
1. Human coding RNA editing is generally nonadaptive
稍微了解一下：
1. High-throughput sequencing reveals inbreeding depression in a natural
population
2. Evolutionary history and metabolic insights of ancient mammalian uricases
allowed ancient frugivorous apes to rapidly convert fructose into fat
小知识：
1. Homology-directed repair of DNA nicks via pathways distinct from
canonical double-strand break repair
HDR at nicks, but not DSBs, is associated with transcription
8-fold more efficient at a nick on the transcribed strand than at a nick on
the nontranscribed strand
推荐：
1. Human coding RNA editing is generally nonadaptive
稍微了解一下：
1. High-throughput sequencing reveals inbreeding depression in a natural
population
2. Evolutionary history and metabolic insights of ancient mammalian uricases
allowed ancient frugivorous apes to rapidly convert fructose into fat
小知识：
1. Homology-directed repair of DNA nicks via pathways distinct from
canonical double-strand break repair
HDR at nicks, but not DSBs, is associated with transcription
8-fold more efficient at a nick on the transcribed strand than at a nick on
the nontranscribed strand
m*g
194 楼
Science 14.03.14
推荐：
1. Internal mRNA Methylation Finally Finds Functions
Related with splicing
enriched cloe to stop codons
commonly seem in mRNA
小知识：
1. Cas9 Solved
Structures of Cas9 Endonucleases Reveal RNA-Mediated Conformational
Activation
2. The Parable of Google Flu: Traps in Big Data Analysis
推荐：
1. Internal mRNA Methylation Finally Finds Functions
Related with splicing
enriched cloe to stop codons
commonly seem in mRNA
小知识：
1. Cas9 Solved
Structures of Cas9 Endonucleases Reveal RNA-Mediated Conformational
Activation
2. The Parable of Google Flu: Traps in Big Data Analysis
m*g
195 楼
Nature 14.03.20
稍微了解一下：
1. The genomic landscape of Neanderthal ancestry in present-day humans
2. Two independent transcription initiation codes overlap on vertebrate core
promoters
小知识：
1. How proteins find their DNA target
trials and errors
2. Hominin explorers were poor planners
3. Melanosome evolution indicates a key physiological shift within feathered
dinosaurs
稍微了解一下：
1. The genomic landscape of Neanderthal ancestry in present-day humans
2. Two independent transcription initiation codes overlap on vertebrate core
promoters
小知识：
1. How proteins find their DNA target
trials and errors
2. Hominin explorers were poor planners
3. Melanosome evolution indicates a key physiological shift within feathered
dinosaurs
m*g
196 楼
PNAS 14.03.18
稍微了解一下：
1. Individual letters of the RNA polymerase II CTD code govern distinct gene
expression programs in fission yeast
小知识：
1. Oxygen requirements of the earliest animals
Modern demosponges can endure low oxygen conditions
2. Long-range interaction and correlation between MYC enhancer and oncogenic
long noncoding RNACARLo-5
a case study of a lncRNA
稍微了解一下：
1. Individual letters of the RNA polymerase II CTD code govern distinct gene
expression programs in fission yeast
小知识：
1. Oxygen requirements of the earliest animals
Modern demosponges can endure low oxygen conditions
2. Long-range interaction and correlation between MYC enhancer and oncogenic
long noncoding RNACARLo-5
a case study of a lncRNA
m*g
197 楼
Science 14.03.21
推荐：
1. Highly Multiplexed Subcellular RNA Sequencing in Situ
稍微了解一下：
1. Epistasis and Allele Specificity in the Emergence of a Stable
Polymorphism in Escherichia coli
小知识：
1. From Parasitism to Mutualism: Unexpected Interactions Between a Cuckoo
and Its Host
Lower predation-induced falure due to repellent secretion by cuckoo chicks
2. Humans Can Discriminate More than 1 Trillion Olfactory Stimuli
推荐：
1. Highly Multiplexed Subcellular RNA Sequencing in Situ
稍微了解一下：
1. Epistasis and Allele Specificity in the Emergence of a Stable
Polymorphism in Escherichia coli
小知识：
1. From Parasitism to Mutualism: Unexpected Interactions Between a Cuckoo
and Its Host
Lower predation-induced falure due to repellent secretion by cuckoo chicks
2. Humans Can Discriminate More than 1 Trillion Olfactory Stimuli
e*o
198 楼
来看看小朋友 哈哈
【在 m******g 的大作中提到】
: Science 14.03.21
: 推荐：
: 1. Highly Multiplexed Subcellular RNA Sequencing in Situ
: 稍微了解一下：
: 1. Epistasis and Allele Specificity in the Emergence of a Stable
: Polymorphism in Escherichia coli
: 小知识：
: 1. From Parasitism to Mutualism: Unexpected Interactions Between a Cuckoo
: and Its Host
: Lower predation-induced falure due to repellent secretion by cuckoo chicks
【在 m******g 的大作中提到】
: Science 14.03.21
: 推荐：
: 1. Highly Multiplexed Subcellular RNA Sequencing in Situ
: 稍微了解一下：
: 1. Epistasis and Allele Specificity in the Emergence of a Stable
: Polymorphism in Escherichia coli
: 小知识：
: 1. From Parasitism to Mutualism: Unexpected Interactions Between a Cuckoo
: and Its Host
: Lower predation-induced falure due to repellent secretion by cuckoo chicks
m*g
199 楼
Science 14.03.28
推荐：
1. Building the Ultimate Yeast Genome
Total Synthesis of a Functional Designer Eukaryotic Chromosome
the power of students' army, haha
稍微了解一下：
1. Oldest Homo sapiens Genome Pinpoints Neandertal Input
小知识：
1. Tweaking a Switch
a single-molecule chase assay
equilibrium binding of the repressor to its operator
2. Synthetic Biologists Design 'Living Materials' That Build Themselves
3. Quantifying Global International Migration Flows
推荐：
1. Building the Ultimate Yeast Genome
Total Synthesis of a Functional Designer Eukaryotic Chromosome
the power of students' army, haha
稍微了解一下：
1. Oldest Homo sapiens Genome Pinpoints Neandertal Input
小知识：
1. Tweaking a Switch
a single-molecule chase assay
equilibrium binding of the repressor to its operator
2. Synthetic Biologists Design 'Living Materials' That Build Themselves
3. Quantifying Global International Migration Flows
S*h
200 楼
一起读要加上讨论挺不错。推荐个网站给你（plancky dot com),可以在上面为每个杂
志创建一个group，然后为每个论文创建个主题，大家进行讨论。
【在 m******g 的大作中提到】
: 本来在开始读PhD的时候，就打算要广泛阅读主流学术杂志，比如Nature, Science,
: PNAS, Plos genetics等等，但是自己总是拖拖拉拉，偶尔有心血来潮就一口气读很久
: ，没兴趣／时间的话就个把月都不翻一下。
: 就好比动漫监督需要看其他畅销动漫（暴露兴趣了，太不学术了），我们也应该多多看
: 看生物的杂志，以增强自己对整个领域的理解，并且了解一些文献的逻辑、方法和写法
: 。所以我打算开这个贴说说每周最喜欢的几篇文章什么的，每周一更（日期不定），以
: 监督自己，防止自己不读文献。如果没有做到，请大家不要用砖头砸，把好吃的狠狠地
: 砸过来就好了，然后再狠狠地鄙视我就好。
: 我是学遗传进化方向的，做实验和编程都做一点（但是为什么现在还这么菜呢，果然是
: 因为我太懒惰了），总之看看文献没有坏处，也欢迎相似方向的大家一起来贴贴推荐的
志创建一个group，然后为每个论文创建个主题，大家进行讨论。
【在 m******g 的大作中提到】
: 本来在开始读PhD的时候，就打算要广泛阅读主流学术杂志，比如Nature, Science,
: PNAS, Plos genetics等等，但是自己总是拖拖拉拉，偶尔有心血来潮就一口气读很久
: ，没兴趣／时间的话就个把月都不翻一下。
: 就好比动漫监督需要看其他畅销动漫（暴露兴趣了，太不学术了），我们也应该多多看
: 看生物的杂志，以增强自己对整个领域的理解，并且了解一些文献的逻辑、方法和写法
: 。所以我打算开这个贴说说每周最喜欢的几篇文章什么的，每周一更（日期不定），以
: 监督自己，防止自己不读文献。如果没有做到，请大家不要用砖头砸，把好吃的狠狠地
: 砸过来就好了，然后再狠狠地鄙视我就好。
: 我是学遗传进化方向的，做实验和编程都做一点（但是为什么现在还这么菜呢，果然是
: 因为我太懒惰了），总之看看文献没有坏处，也欢迎相似方向的大家一起来贴贴推荐的
H*g
201 楼
碰见Hopi了，果然是个大美女啊 :)
m*g
202 楼
谢谢！我看了一下，网站还是design得挺不错的。不过我就是大致看看~ 有什么有趣的
paper会找人一起讨论什么的。
【在 S**********h 的大作中提到】
: 一起读要加上讨论挺不错。推荐个网站给你（plancky dot com),可以在上面为每个杂
: 志创建一个group，然后为每个论文创建个主题，大家进行讨论。
paper会找人一起讨论什么的。
【在 S**********h 的大作中提到】
: 一起读要加上讨论挺不错。推荐个网站给你（plancky dot com),可以在上面为每个杂
: 志创建一个group，然后为每个论文创建个主题，大家进行讨论。
m*g
203 楼
Hopi Hoekstra吗? 之前在SMBE听过她的讲座，讲的特别有条理和趣味性。（而且同意
你的观点，真的好漂亮哇）
【在 H*********g 的大作中提到】
: 碰见Hopi了，果然是个大美女啊 :)
你的观点，真的好漂亮哇）
【在 H*********g 的大作中提到】
: 碰见Hopi了，果然是个大美女啊 :)
m*g
204 楼
Nature 14.03.27
推荐：
1. A promoter-level mammalian expression atlas
single-molecule cDNA sequencing
mapped transcription start sites (TSSs) and their usage
稍微了解一下：
1. An atlas of active enhancers across human cell types and tissues
小知识：
1. How squid control their shine
Separate for pigmentary colors and dynamic iridescence
2. A primitive placoderm sheds light on the origin of the jawed vertebrate
face
推荐：
1. A promoter-level mammalian expression atlas
single-molecule cDNA sequencing
mapped transcription start sites (TSSs) and their usage
稍微了解一下：
1. An atlas of active enhancers across human cell types and tissues
小知识：
1. How squid control their shine
Separate for pigmentary colors and dynamic iridescence
2. A primitive placoderm sheds light on the origin of the jawed vertebrate
face
m*g
205 楼
PNAS 14.04.01
推荐：
1. Genetic odyssey to generate marked clones in Drosophila mosaics
Review paper on several common systems
小知识：
1. Extinct New Zealand megafauna were not in decline before human
colonization
No loss of heterozygosity and shifts in allele frequency over time
Before human-facilitated megafauna extinction
推荐：
1. Genetic odyssey to generate marked clones in Drosophila mosaics
Review paper on several common systems
小知识：
1. Extinct New Zealand megafauna were not in decline before human
colonization
No loss of heterozygosity and shifts in allele frequency over time
Before human-facilitated megafauna extinction
m*g
206 楼
Science 14.04.04
推荐：
1. Designer Chromosome
Total Synthesis of a Functional Designer Eukaryotic Chromosome
稍微了解一下：
1. Many individual stories for scientists
2. Designer Embryo
Construction of a Vertebrate Embryo from Two Opposing Morphogen Gradients
Nodal and BMP in Zebrafish
小知识：
1. Engineering Larger DNA Structures
Polyhedra Self-Assembled from DNA Tripods and Characterized with 3D DNA-
PAINT
推荐：
1. Designer Chromosome
Total Synthesis of a Functional Designer Eukaryotic Chromosome
稍微了解一下：
1. Many individual stories for scientists
2. Designer Embryo
Construction of a Vertebrate Embryo from Two Opposing Morphogen Gradients
Nodal and BMP in Zebrafish
小知识：
1. Engineering Larger DNA Structures
Polyhedra Self-Assembled from DNA Tripods and Characterized with 3D DNA-
PAINT
m*g
207 楼
最近好颓废，老是弄些没用的。Be focused!
Science 14.04.11
稍微了解一下：
1. Yeasty HIPHOP
Mapping the Cellular Response to Small Molecules Using Chemogenomic Fitness
Signatures
2. Tangling Evolutionary Trees
Acquisition of Germ Plasm Accelerates Vertebrate Evolution
epigenesis vs performation
小知识：
1. Taking Flight
Flies Evade Looming Targets by Executing Rapid Visually Directed Banked
Turns
2. Can Cloning Revive Spain's Extinct Mountain Goat?
3. Patterning Cues from the Altruistic Sibling
Science 14.04.11
稍微了解一下：
1. Yeasty HIPHOP
Mapping the Cellular Response to Small Molecules Using Chemogenomic Fitness
Signatures
2. Tangling Evolutionary Trees
Acquisition of Germ Plasm Accelerates Vertebrate Evolution
epigenesis vs performation
小知识：
1. Taking Flight
Flies Evade Looming Targets by Executing Rapid Visually Directed Banked
Turns
2. Can Cloning Revive Spain's Extinct Mountain Goat?
3. Patterning Cues from the Altruistic Sibling
m*g
208 楼
PNAS 14.04.08
推荐：
1. Origin, inheritance, and gene regulatory consequences of genome dominance
in polyploids
subgenome dominance: # gene loss and gene expression level
transposon load vs subgenome dominance
推荐：
1. Origin, inheritance, and gene regulatory consequences of genome dominance
in polyploids
subgenome dominance: # gene loss and gene expression level
transposon load vs subgenome dominance
w*r
209 楼
你把生物版当成你的笔记本了
请认真一些，看看f1000参考一下吧
请认真一些，看看f1000参考一下吧
m*g
210 楼
f1000是挺好的，谢谢建议。但我基本只是过一遍，遇到喜欢的文献就打印出来慢慢划
划。
不能把生物版当作笔记本吗？QAQ。只占一个post的位置哦。而且时候浏览起来也方便
，看一眼标题就知道是什么了。
【在 w***r 的大作中提到】
: 你把生物版当成你的笔记本了
: 请认真一些，看看f1000参考一下吧
划。
不能把生物版当作笔记本吗？QAQ。只占一个post的位置哦。而且时候浏览起来也方便
，看一眼标题就知道是什么了。
【在 w***r 的大作中提到】
: 你把生物版当成你的笔记本了
: 请认真一些，看看f1000参考一下吧
t*z
211 楼
支持楼主！楼主的认真而单纯的读书笔记让版上的浮躁气氛褪色。
【在 m******g 的大作中提到】
: f1000是挺好的，谢谢建议。但我基本只是过一遍，遇到喜欢的文献就打印出来慢慢划
: 划。
: 不能把生物版当作笔记本吗？QAQ。只占一个post的位置哦。而且时候浏览起来也方便
: ，看一眼标题就知道是什么了。
【在 m******g 的大作中提到】
: f1000是挺好的，谢谢建议。但我基本只是过一遍，遇到喜欢的文献就打印出来慢慢划
: 划。
: 不能把生物版当作笔记本吗？QAQ。只占一个post的位置哦。而且时候浏览起来也方便
: ，看一眼标题就知道是什么了。
w*r
212 楼
我是城管，还是做火柴的？
m*g
213 楼
上周去了SMBE，感觉一年比一年好呢（因为能听懂的部分越来越多了）。
希望明年可以（略去若干字）。
Science 14.04.11
稍微了解一下：
1. Yeasty HIPHOP
Mapping the Cellular Response to Small Molecules Using Chemogenomic Fitness
Signatures
2. Tangling Evolutionary Trees
Acquisition of Germ Plasm Accelerates Vertebrate Evolution
epigenesis vs performation
小知识：
1. Taking Flight
Flies Evade Looming Targets by Executing Rapid Visually Directed Banked
Turns
2. Can Cloning Revive Spain's Extinct Mountain Goat?
3. Patterning Cues from the Altruistic Sibling
希望明年可以（略去若干字）。
Science 14.04.11
稍微了解一下：
1. Yeasty HIPHOP
Mapping the Cellular Response to Small Molecules Using Chemogenomic Fitness
Signatures
2. Tangling Evolutionary Trees
Acquisition of Germ Plasm Accelerates Vertebrate Evolution
epigenesis vs performation
小知识：
1. Taking Flight
Flies Evade Looming Targets by Executing Rapid Visually Directed Banked
Turns
2. Can Cloning Revive Spain's Extinct Mountain Goat?
3. Patterning Cues from the Altruistic Sibling
m*g
214 楼
Nature 14.04.17
稍微了解一下：
1. miRNAs trigger widespread epigenetically activated siRNAs from
transposons in Arabidopsis
easiRNA resemble secondary siRNA
latent mechanism that targets tranposon transcripts
小知识：
1. Sperm RNA carries marks of trauma
Stress alters miRNA expression level in mice
which leads to depressive behavior in later generations
stress on mother, F2 generation of F1 males shows disorder
so does F3
2. Dissecting appetite
The hunger circuits has been mapped in mouse
3. Mouse already being charted gene by gene
knockout mutant for each gene
4. Evolutionary biology: Dating chimpanzees
Chimps are philopatric
different cultural groups
Y chromosome mutations for dating
5. Diet rapidly and reproducibly alters the human gut microbiome
6. Domains of genome-wide gene expression dysregulation in Down’s syndrome
study a pair of monozygotic twins discordant for trisomy21
7. Caenorhabditis eleganspathways that surveil and defend mitochondria
genome-wide RNAi
after inhibition of mt function by drug or genetic disruption
8. The ensemble nature of allostery
a rich spectrum of regulatory strategies
9. Rapid and tunable post-translational coupling of genetic circuits
稍微了解一下：
1. miRNAs trigger widespread epigenetically activated siRNAs from
transposons in Arabidopsis
easiRNA resemble secondary siRNA
latent mechanism that targets tranposon transcripts
小知识：
1. Sperm RNA carries marks of trauma
Stress alters miRNA expression level in mice
which leads to depressive behavior in later generations
stress on mother, F2 generation of F1 males shows disorder
so does F3
2. Dissecting appetite
The hunger circuits has been mapped in mouse
3. Mouse already being charted gene by gene
knockout mutant for each gene
4. Evolutionary biology: Dating chimpanzees
Chimps are philopatric
different cultural groups
Y chromosome mutations for dating
5. Diet rapidly and reproducibly alters the human gut microbiome
6. Domains of genome-wide gene expression dysregulation in Down’s syndrome
study a pair of monozygotic twins discordant for trisomy21
7. Caenorhabditis eleganspathways that surveil and defend mitochondria
genome-wide RNAi
after inhibition of mt function by drug or genetic disruption
8. The ensemble nature of allostery
a rich spectrum of regulatory strategies
9. Rapid and tunable post-translational coupling of genetic circuits
m*g
215 楼
PNAS 14.04.15
小知识：
1. Methanogenic burst in the end-Permian carbon cycle
小知识：
1. Methanogenic burst in the end-Permian carbon cycle
m*g
216 楼
Science 14.04.18
推荐：
1. Ancient DNA Holds Clues to Gene Activity in Extinct Humans
Reconstructing the DNA Methylation Maps of the Neandertal and the Denisovan
harnessing the natural degradation processes
of methylated and unmethylated cytosines
unmethylated cytosines decay with time to uracils
methylated cytosines decay to thymines
小知识：
1. Sleep Tight, Fly
sleep pattern characteristic of youthful flies is critical to brain
development
2. Changing Assemblages
Assemblage Time Series Reveal Biodiversity Change but Not Systematic Loss
do not find evidence of systematic biodiversity loss
homogenization of species assemblages by invasive species
[expected result and conclusion?]
3. 'Humanized' Mouse Detects Deadly Drug Side Effects
推荐：
1. Ancient DNA Holds Clues to Gene Activity in Extinct Humans
Reconstructing the DNA Methylation Maps of the Neandertal and the Denisovan
harnessing the natural degradation processes
of methylated and unmethylated cytosines
unmethylated cytosines decay with time to uracils
methylated cytosines decay to thymines
小知识：
1. Sleep Tight, Fly
sleep pattern characteristic of youthful flies is critical to brain
development
2. Changing Assemblages
Assemblage Time Series Reveal Biodiversity Change but Not Systematic Loss
do not find evidence of systematic biodiversity loss
homogenization of species assemblages by invasive species
[expected result and conclusion?]
3. 'Humanized' Mouse Detects Deadly Drug Side Effects
t*z
217 楼
楼主你有没有来北卡参加Evolution2014？如果在的话能否站内透露下行踪，我想从楼
主本尊身上汲取勇气和力量。
Denisovan
【在 m******g 的大作中提到】
: Science 14.04.18
: 推荐：
: 1. Ancient DNA Holds Clues to Gene Activity in Extinct Humans
: Reconstructing the DNA Methylation Maps of the Neandertal and the Denisovan
: harnessing the natural degradation processes
: of methylated and unmethylated cytosines
: unmethylated cytosines decay with time to uracils
: methylated cytosines decay to thymines
: 小知识：
: 1. Sleep Tight, Fly
主本尊身上汲取勇气和力量。
Denisovan
【在 m******g 的大作中提到】
: Science 14.04.18
: 推荐：
: 1. Ancient DNA Holds Clues to Gene Activity in Extinct Humans
: Reconstructing the DNA Methylation Maps of the Neandertal and the Denisovan
: harnessing the natural degradation processes
: of methylated and unmethylated cytosines
: unmethylated cytosines decay with time to uracils
: methylated cytosines decay to thymines
: 小知识：
: 1. Sleep Tight, Fly
m*g
218 楼
Nature 14.04.24
推荐：
1. Guidelines for investigating causality of sequence variants in human
disease
some status quo and general guidelines
稍微了解一下：
Paper1. Mammalian Y chromosomes retain widely expressed dosage-sensitive
regulators
Paper2. Origins and functional evolution of Y chromosomes across mammals
sequencing by cloning into BAC
multi-species comparison
fast survey using genes expressed in males also only appear in male genomic
DNA
Y chromosome currently stable
evolutionary history and enriched genes identified
小知识：
1. Biocide boosts bacterial binding
biocide triclosan in nosal secretions has S. aureus more frequently
triclosan were used in toothpastes, soaps etc
推荐：
1. Guidelines for investigating causality of sequence variants in human
disease
some status quo and general guidelines
稍微了解一下：
Paper1. Mammalian Y chromosomes retain widely expressed dosage-sensitive
regulators
Paper2. Origins and functional evolution of Y chromosomes across mammals
sequencing by cloning into BAC
multi-species comparison
fast survey using genes expressed in males also only appear in male genomic
DNA
Y chromosome currently stable
evolutionary history and enriched genes identified
小知识：
1. Biocide boosts bacterial binding
biocide triclosan in nosal secretions has S. aureus more frequently
triclosan were used in toothpastes, soaps etc
m*g
219 楼
PNAS 14.04.22
推荐：
1. DNA methylation and evolution of duplicate genes
DNA methylation clearly distinguishes young and old duplicates
DNA methylation of duplicate genes are associated with functional
differences in expression
[wish to see some experimental evolution result in the future]
稍微了解一下：
1. Massive programmed translational jumping in mitochondria
Report 81 translational bypassing elements (byps) in mitochondria of the
yeast Magnusiomyces capitatus
Byp-like sequences lack bypassing activity
小知识：
1. Long-term morphological stasis maintained by a plant–pollinator
mutualism
2. Social disadvantage, genetic sensitivity, and children’s telomere length
推荐：
1. DNA methylation and evolution of duplicate genes
DNA methylation clearly distinguishes young and old duplicates
DNA methylation of duplicate genes are associated with functional
differences in expression
[wish to see some experimental evolution result in the future]
稍微了解一下：
1. Massive programmed translational jumping in mitochondria
Report 81 translational bypassing elements (byps) in mitochondria of the
yeast Magnusiomyces capitatus
Byp-like sequences lack bypassing activity
小知识：
1. Long-term morphological stasis maintained by a plant–pollinator
mutualism
2. Social disadvantage, genetic sensitivity, and children’s telomere length
m*g
220 楼
我挺弱的啦，只是好奇心比较旺盛。每年都去SMBE，不知道你去不去。也许明年可以见
到呢。保持联系！
【在 t*****z 的大作中提到】
: 楼主你有没有来北卡参加Evolution2014？如果在的话能否站内透露下行踪，我想从楼
: 主本尊身上汲取勇气和力量。
:
: Denisovan
到呢。保持联系！
【在 t*****z 的大作中提到】
: 楼主你有没有来北卡参加Evolution2014？如果在的话能否站内透露下行踪，我想从楼
: 主本尊身上汲取勇气和力量。
:
: Denisovan
t*z
221 楼
谢谢你的回复！我去年去了SMBE，今年改去Evolution了。如果我还继续做进化，多半
明年会在SMBE见到吧。感谢你经常的热情分享。
【在 m******g 的大作中提到】
: 我挺弱的啦，只是好奇心比较旺盛。每年都去SMBE，不知道你去不去。也许明年可以见
: 到呢。保持联系！
明年会在SMBE见到吧。感谢你经常的热情分享。
【在 m******g 的大作中提到】
: 我挺弱的啦，只是好奇心比较旺盛。每年都去SMBE，不知道你去不去。也许明年可以见
: 到呢。保持联系！
m*g
222 楼
Science 14.04.25
稍微了解一下：
1. Single-Cell Genomics Reveals Hundreds of Coexisting Subpopulations in
Wild Prochlorococcus
hundreds of subpopulations coexist with distinct “genomic backbones”
2. High-Resolution Genomic Analysis of Human Mitochondrial RNA Sequence
Variation
小知识：
1. Mapping Neural Activation onto Behavior in an Entire Animal
in Drosophila melanogaster
Optogenetics, in particular light-activated ion channels
allow precisely timed, noninvasive activation and deactivation of individual
neurons
systematically stimulated the identified neurons and recorded behavioral
output
2. A Chloroplast Retrograde Signal Regulates Nuclear Alternative Splicing
稍微了解一下：
1. Single-Cell Genomics Reveals Hundreds of Coexisting Subpopulations in
Wild Prochlorococcus
hundreds of subpopulations coexist with distinct “genomic backbones”
2. High-Resolution Genomic Analysis of Human Mitochondrial RNA Sequence
Variation
小知识：
1. Mapping Neural Activation onto Behavior in an Entire Animal
in Drosophila melanogaster
Optogenetics, in particular light-activated ion channels
allow precisely timed, noninvasive activation and deactivation of individual
neurons
systematically stimulated the identified neurons and recorded behavioral
output
2. A Chloroplast Retrograde Signal Regulates Nuclear Alternative Splicing
m*g
223 楼
PNAS 14.04.29
稍微了解一下：
1. Beyond the single gene: How epistasis and gene-by-Environment effects
influence crop domestication
Shattering and flowering time
Have large phenotypic effects and are relatively insensitive to genetic
background and environmental effects
Unlikely to be due to these two factors
2. Enhanced evolution by stochastically variable modification of epigenetic
marks in the early embryo
小知识：
1. Partner choice and fidelity stabilize coevolution in a Cretaceous-age
defensive symbiosis
稍微了解一下：
1. Beyond the single gene: How epistasis and gene-by-Environment effects
influence crop domestication
Shattering and flowering time
Have large phenotypic effects and are relatively insensitive to genetic
background and environmental effects
Unlikely to be due to these two factors
2. Enhanced evolution by stochastically variable modification of epigenetic
marks in the early embryo
小知识：
1. Partner choice and fidelity stabilize coevolution in a Cretaceous-age
defensive symbiosis
m*g
224 楼
Nature 14.05.01
小知识：
1. False positives
A correlation between error rate and success undermines promise of stem-cell
trials
A linear relationship between the number of discrepancies and the claimed
effect size
2. Synthetic biology revives antibiotics
小知识：
1. False positives
A correlation between error rate and success undermines promise of stem-cell
trials
A linear relationship between the number of discrepancies and the claimed
effect size
2. Synthetic biology revives antibiotics
m*g
225 楼
Science 14.05.02
推荐：
1. Reconstructing the DNA Methylation Maps of the Neandertal and the
Denisovan
小知识：
1. Male Scent May Compromise Biomedical Studies
The mice that didn't show pain had been handled by male students
Rodents exposed to male odors were actually feeling less pain
2. Therapeutic Cloning Reaches Milestone
Two teams have independently derived human embryonic stem cells
By cloning adult skin cells
3. Genomic Signatures of Specialized Metabolism in Plants
How algae and land plants have been able to evolve secondary metabolism
biochemistry
4. Deception by Flexible Alarm Mimicry in an African Bird
5. Polarization of the Effects of Autoimmune and Neurodegenerative Risk
Alleles in Leukocytes
eQTL mapping
推荐：
1. Reconstructing the DNA Methylation Maps of the Neandertal and the
Denisovan
小知识：
1. Male Scent May Compromise Biomedical Studies
The mice that didn't show pain had been handled by male students
Rodents exposed to male odors were actually feeling less pain
2. Therapeutic Cloning Reaches Milestone
Two teams have independently derived human embryonic stem cells
By cloning adult skin cells
3. Genomic Signatures of Specialized Metabolism in Plants
How algae and land plants have been able to evolve secondary metabolism
biochemistry
4. Deception by Flexible Alarm Mimicry in an African Bird
5. Polarization of the Effects of Autoimmune and Neurodegenerative Risk
Alleles in Leukocytes
eQTL mapping
m*g
226 楼
Nature 14.05.08
推荐：
1. Synthetic biology: Construction of a yeast chromosome
2. A semi-synthetic organism with an expanded genetic alphabet
小知识：
1. Hunger marks offspring's genome
In Utero Undernutrition in Male Mice Programs Liver Lipid Metabolism in the
Second-Generation Offspring Involving Altered Lxra DNA Methylation
推荐：
1. Synthetic biology: Construction of a yeast chromosome
2. A semi-synthetic organism with an expanded genetic alphabet
小知识：
1. Hunger marks offspring's genome
In Utero Undernutrition in Male Mice Programs Liver Lipid Metabolism in the
Second-Generation Offspring Involving Altered Lxra DNA Methylation
m*g
227 楼
Science 14.05.09
稍微了解一下：
1. Large-Scale Psychological Differences Within China Explained by Rice
Versus Wheat Agriculture
Control: tested people from neighboring counties along the rice-wheat border
and found differences that were just as large
小知识：
1. Hippocampal Neurogenesis Regulates Forgetting During Adulthood and
Infancy
2. Rock Soup
Phosphorylated sugar intermediates were probably present in Earth's earliest
oceans
Observed 29 interconversion reactions, including the formation of ribose 5-
phosphate
稍微了解一下：
1. Large-Scale Psychological Differences Within China Explained by Rice
Versus Wheat Agriculture
Control: tested people from neighboring counties along the rice-wheat border
and found differences that were just as large
小知识：
1. Hippocampal Neurogenesis Regulates Forgetting During Adulthood and
Infancy
2. Rock Soup
Phosphorylated sugar intermediates were probably present in Earth's earliest
oceans
Observed 29 interconversion reactions, including the formation of ribose 5-
phosphate
m*g
228 楼
PNAS 14.05.06
稍微了解一下：
1. Hypermutable DNA chronicles the evolution of human colon cancer
A simple PCR-based assay
Interrogating somatic variation in hypermutable polyguanine (poly-G) repeats
2. Exploration of sequence space as the basis of viral RNA genome
segmentation
小知识：
1. Patterns of coding variation in the complete exomes of three Neandertals
2. Horizontal transfer of an adaptive chimeric photoreceptor from bryophytes
to ferns
稍微了解一下：
1. Hypermutable DNA chronicles the evolution of human colon cancer
A simple PCR-based assay
Interrogating somatic variation in hypermutable polyguanine (poly-G) repeats
2. Exploration of sequence space as the basis of viral RNA genome
segmentation
小知识：
1. Patterns of coding variation in the complete exomes of three Neandertals
2. Horizontal transfer of an adaptive chimeric photoreceptor from bryophytes
to ferns
m*g
229 楼
PNAS 14.05.13
推荐：
1. Microfluidic single-cell whole-transcriptome sequencing
稍微了解一下：
1. Evolutionary history of redox metal-binding domains across the tree of
life
推荐：
1. Microfluidic single-cell whole-transcriptome sequencing
稍微了解一下：
1. Evolutionary history of redox metal-binding domains across the tree of
life
m*g
230 楼
悲剧，最近注意力有点涣散。估计是实验不够顺利，内心郁闷，要尽快解决，fighting！
Nature 14.05.15
推荐：
1. Dynamics and associations of microbial community types across the human
body
稍微了解一下：
1. Reconstructing lineage hierarchies of the distal lung epithelium using
single-cell RNA-seq
小知识：
1. Galanin neurons in the medial preoptic area govern parental behaviour
2. Anthropogenic electromagnetic noise disrupts magnetic compass orientation
in a migratory bird
Nature 14.05.15
推荐：
1. Dynamics and associations of microbial community types across the human
body
稍微了解一下：
1. Reconstructing lineage hierarchies of the distal lung epithelium using
single-cell RNA-seq
小知识：
1. Galanin neurons in the medial preoptic area govern parental behaviour
2. Anthropogenic electromagnetic noise disrupts magnetic compass orientation
in a migratory bird
m*g
231 楼
Science 14.05.16
推荐：
1. The Hunt for Missing Genes
稍微了解一下：
1. Cas9 Targeting and the CRISPR Revolution
2. Border Control - A Membrane-Linked Interactome of Arabidopsis
3. Stick Insect Genomes Reveal Natural Selection's Role in Parallel
speciation
推荐：
1. The Hunt for Missing Genes
稍微了解一下：
1. Cas9 Targeting and the CRISPR Revolution
2. Border Control - A Membrane-Linked Interactome of Arabidopsis
3. Stick Insect Genomes Reveal Natural Selection's Role in Parallel
speciation
m*g
232 楼
Nature 14.05.22
推荐：
1. High-throughput screening of a CRISPR/Cas9 library for functional
genomics in human cells
稍微了解一下：
1. The role of senescent cells in ageing
小知识：
1. Epigenetics: Keeping one's sex
Genome-defence small RNAs exapted for epigenetic mating-type inheritance
推荐：
1. High-throughput screening of a CRISPR/Cas9 library for functional
genomics in human cells
稍微了解一下：
1. The role of senescent cells in ageing
小知识：
1. Epigenetics: Keeping one's sex
Genome-defence small RNAs exapted for epigenetic mating-type inheritance
m*g
233 楼
PNAS 14.05.20
小知识：
1. Noninvasive in vivo monitoring of tissue-specific global gene expression
in humans
cell-free RNA in the blood
tissue specific genes
小知识：
1. Noninvasive in vivo monitoring of tissue-specific global gene expression
in humans
cell-free RNA in the blood
tissue specific genes
m*g
234 楼
某项目的实验部分终于做完了~~~
在一边等测序结果一边写程序中。期待！
Science 14.05.23
推荐：
1. Stop codon reassignments in the wild
稍微了解一下：
1. FoxP influences the speed and accuracy of a perceptual decision in
drosophila
在一边等测序结果一边写程序中。期待！
Science 14.05.23
推荐：
1. Stop codon reassignments in the wild
稍微了解一下：
1. FoxP influences the speed and accuracy of a perceptual decision in
drosophila
m*g
235 楼
PNAS 14.05.27
推荐：
1. Repair of DNA double-strand breaks by templated nucleotide sequence
insertions derived from distant regions of the genome
2. Genome-wide high-resolution mapping of chromosome fragile sites in
Saccharomyces cerevisiae
reduced level of DNA pol alpha
galactose-inducible GAL1 promoter to control level
map LOH after crossing two strains
稍微了解一下：
1. Interactions between chromosomal and nonchromosomal elements reveal
missing heritability
小知识：
1. Selection and constraint underlie irreversibility of tooth loss in
cypriniform fishes
Dollo's Law
2. Genetic degeneration of old and young Y chromosomes in the flowering
plant Rumex hastatulus
推荐：
1. Repair of DNA double-strand breaks by templated nucleotide sequence
insertions derived from distant regions of the genome
2. Genome-wide high-resolution mapping of chromosome fragile sites in
Saccharomyces cerevisiae
reduced level of DNA pol alpha
galactose-inducible GAL1 promoter to control level
map LOH after crossing two strains
稍微了解一下：
1. Interactions between chromosomal and nonchromosomal elements reveal
missing heritability
小知识：
1. Selection and constraint underlie irreversibility of tooth loss in
cypriniform fishes
Dollo's Law
2. Genetic degeneration of old and young Y chromosomes in the flowering
plant Rumex hastatulus
m*g
236 楼
Nature 14.05.29
稍微了解一下：
1. A draft map of the human proteome
2. Mass-spectrometry-based draft of the human proteome
小知识：
1. Wild mice run for fun on wheels
2. Three known unknowns
About understanding cancer
3. Chicken project gets off the ground
4. Bacterial phylogeny structures soil resistomes across habitats
5. A single female-specific piRNA is the primary determiner of sex in the
silkworm
稍微了解一下：
1. A draft map of the human proteome
2. Mass-spectrometry-based draft of the human proteome
小知识：
1. Wild mice run for fun on wheels
2. Three known unknowns
About understanding cancer
3. Chicken project gets off the ground
4. Bacterial phylogeny structures soil resistomes across habitats
5. A single female-specific piRNA is the primary determiner of sex in the
silkworm
m*g
237 楼
Science 14.05.30
推荐：
1. A pause sequence enriched at translation start sites drives transcription
dynamics in vivo
稍微了解一下：
1. Clues from the resilient
understanding how individuals remain resilient to diseases given high risk
of disease
2. A bacterial seek-and-destroy system for foreign DNA
Argonaute-like proteins
小知识：
1. The biodiversity of species and their rates of extinction, distribution,
and protection
推荐：
1. A pause sequence enriched at translation start sites drives transcription
dynamics in vivo
稍微了解一下：
1. Clues from the resilient
understanding how individuals remain resilient to diseases given high risk
of disease
2. A bacterial seek-and-destroy system for foreign DNA
Argonaute-like proteins
小知识：
1. The biodiversity of species and their rates of extinction, distribution,
and protection
m*g
238 楼
Nature 14.06.05
小知识：
1. Increasing CO2 threatens human nutrition
lower concentrations of zinc and iron
C3 plants
小知识：
1. Increasing CO2 threatens human nutrition
lower concentrations of zinc and iron
C3 plants
m*g
239 楼
PNAS 14.06.03
推荐：
1. Inferring fitness landscapes by regression produces biased estimates of
epistasis
2. Precise estimates of mutation rate and spectrum in yeast
Any way to reduce/distinguish from sequencing error? Didn't get that
important part.
稍微了解一下：
1. Linkage disequilibrium and signatures of positive selection around LINE-1
retrotransposons in the human genome
2. The counterintuitive role of sexual selection in species maintenance and
speciation
推荐：
1. Inferring fitness landscapes by regression produces biased estimates of
epistasis
2. Precise estimates of mutation rate and spectrum in yeast
Any way to reduce/distinguish from sequencing error? Didn't get that
important part.
稍微了解一下：
1. Linkage disequilibrium and signatures of positive selection around LINE-1
retrotransposons in the human genome
2. The counterintuitive role of sexual selection in species maintenance and
speciation
m*g
240 楼
Science 14.06.06
推荐：
Lengthy RNAs earn respect as cellular players
推荐：
Lengthy RNAs earn respect as cellular players
m*g
241 楼
Nature 14.06.12
小知识：
1. Gene therapy: Repair and replace
Targeted genome editing in human repopulating haematopoietic stem cells
小知识：
1. Gene therapy: Repair and replace
Targeted genome editing in human repopulating haematopoietic stem cells
m*g
242 楼
PNAS 14.06.10
稍微了解一下：
1. Hedgehog signaling mediates adaptive variation in a dynamic functional
system in the cichlid feeding apparatus
2. Identification of genes preventing transgenerational transmission of
stress-induced epigenetic states
in Arabidopsis
稍微了解一下：
1. Hedgehog signaling mediates adaptive variation in a dynamic functional
system in the cichlid feeding apparatus
2. Identification of genes preventing transgenerational transmission of
stress-induced epigenetic states
in Arabidopsis
m*g
243 楼
Science 14.06.13
稍微了解一下：
1. Molecular basis of transcription pausing
Interactions between RNA polymerase and the “core recognition element”
counteract pausing
2. Strong male bias drives germline mutation in chimpanzees
小知识：
1. Dinosaur metabolism neither hot nor cold, but just right
Evidence for mesothermy in dinosaurs
稍微了解一下：
1. Molecular basis of transcription pausing
Interactions between RNA polymerase and the “core recognition element”
counteract pausing
2. Strong male bias drives germline mutation in chimpanzees
小知识：
1. Dinosaur metabolism neither hot nor cold, but just right
Evidence for mesothermy in dinosaurs
m*g
244 楼
Nature 14.06.19
推荐：
1. Single-cell RNA-seq reveals dynamic paracrine control of cellular
variation
小知识：
1. How ants link up to build bridges
2. Stick together to fight disease
Tracked more than 4,000 populations of the weed Plantago lanceolata over 12
years
Resistance genes are more readily exchanged among populations?
3. Genome editing of stem cells
推荐：
1. Single-cell RNA-seq reveals dynamic paracrine control of cellular
variation
小知识：
1. How ants link up to build bridges
2. Stick together to fight disease
Tracked more than 4,000 populations of the weed Plantago lanceolata over 12
years
Resistance genes are more readily exchanged among populations?
3. Genome editing of stem cells
m*g
245 楼
Science 14.06.20
稍微了解一下：
1. Single-cell RNA-seq highlights intratumoral heterogeneity in primary
glioblastoma
小知识：
1. Screening for noise in gene expression identifies drug synergies
2. Life-span extension by a metacaspase in the yeast Saccharomyces
cerevisiae
3. The genomic landscape underlying phenotypic integrity in the face of gene
flow in crows
稍微了解一下：
1. Single-cell RNA-seq highlights intratumoral heterogeneity in primary
glioblastoma
小知识：
1. Screening for noise in gene expression identifies drug synergies
2. Life-span extension by a metacaspase in the yeast Saccharomyces
cerevisiae
3. The genomic landscape underlying phenotypic integrity in the face of gene
flow in crows
m*g
246 楼
Nature 14.06.26
小知识：
1. Magnetic compass guides butterflies
2. To and from the Horn of Africa
Humans were moving back to the Horn of Africa as early as 23,000 years ago
before the advent of agriculture
3. Tanning might be addictive
4. Human oocytes reprogram adult somatic nuclei of a type 1 diabetic to
diploid pluripotent stem cells
5. Decoding the regulatory landscape of medulloblastoma using DNA
methylation sequencing
6. Structural biology: Wobble puts RNA on target
The selective tRNA aminoacylation mechanism based on a single G•U pair
小知识：
1. Magnetic compass guides butterflies
2. To and from the Horn of Africa
Humans were moving back to the Horn of Africa as early as 23,000 years ago
before the advent of agriculture
3. Tanning might be addictive
4. Human oocytes reprogram adult somatic nuclei of a type 1 diabetic to
diploid pluripotent stem cells
5. Decoding the regulatory landscape of medulloblastoma using DNA
methylation sequencing
6. Structural biology: Wobble puts RNA on target
The selective tRNA aminoacylation mechanism based on a single G•U pair
m*g
247 楼
Science 14.06.27
推荐：
1. Global epistasis makes adaptation predictable despite sequence-level
stochasticity
2. Predicting microbial growth
小知识：
1. Flower discrimination by pollinators in a dynamic chemical environment
2. Genomic basis for the convergent evolution of electric organs
推荐：
1. Global epistasis makes adaptation predictable despite sequence-level
stochasticity
2. Predicting microbial growth
小知识：
1. Flower discrimination by pollinators in a dynamic chemical environment
2. Genomic basis for the convergent evolution of electric organs
m*g
248 楼
Nature 14.06.26
小知识：
1. Magnetic compass guides butterflies
2. To and from the Horn of Africa
Humans were moving back to the Horn of Africa as early as 23,000 years ago
before the advent of agriculture
3. Tanning might be addictive
4. Human oocytes reprogram adult somatic nuclei of a type 1 diabetic to
diploid pluripotent stem cells
5. Decoding the regulatory landscape of medulloblastoma using DNA
methylation sequencing
6. Structural biology: Wobble puts RNA on target
The selective tRNA aminoacylation mechanism based on a single G•U pair
小知识：
1. Magnetic compass guides butterflies
2. To and from the Horn of Africa
Humans were moving back to the Horn of Africa as early as 23,000 years ago
before the advent of agriculture
3. Tanning might be addictive
4. Human oocytes reprogram adult somatic nuclei of a type 1 diabetic to
diploid pluripotent stem cells
5. Decoding the regulatory landscape of medulloblastoma using DNA
methylation sequencing
6. Structural biology: Wobble puts RNA on target
The selective tRNA aminoacylation mechanism based on a single G•U pair
m*g
249 楼
PNAS 14.07.01
稍微了解一下：
1. HBx induces hypomethylation of distal intragenic CpG islands required for
active expression of developmental regulators
稍微了解一下：
1. HBx induces hypomethylation of distal intragenic CpG islands required for
active expression of developmental regulators
m*g
250 楼
Science 14.07.04
推荐：
1. The birth of cooperation
Niche engineering demonstrates a latent capacity for fungal-algal mutualism
Comment: This is an interesting experiment that could have been done many
years ago. The commentary is a little bit negative, and don't believe the
result of the paper reveals the general pattern of co-evolution. I think the
result is somewhat expected. There are multiple previous papers for
cooperation using engineered systems.
小知识：
1. A Teaching Strategy with a Focus on Argumentation to Improve
Undergraduate Students' Ability to Read Research Articles
2. Evolution of early Homo: An integrated biological perspective
推荐：
1. The birth of cooperation
Niche engineering demonstrates a latent capacity for fungal-algal mutualism
Comment: This is an interesting experiment that could have been done many
years ago. The commentary is a little bit negative, and don't believe the
result of the paper reveals the general pattern of co-evolution. I think the
result is somewhat expected. There are multiple previous papers for
cooperation using engineered systems.
小知识：
1. A Teaching Strategy with a Focus on Argumentation to Improve
Undergraduate Students' Ability to Read Research Articles
2. Evolution of early Homo: An integrated biological perspective
m*g
251 楼
Nature 14.07.03
稍微了解一下：
1. Analysis of orthologous groups reveals archease and DDX1 as tRNA splicing
factors
小知识：
1. Evolutionary developmental biology: Use it or lose it
Multiple avenues to digit loss
Patterning and post-patterning modes of evolutionary digit loss in mammals
2. New specimen of Archaeopteryx provides insights into the evolution of
pennaceous feathers
Most likely display -> exaptation, later recruited for aerodynamic functions
稍微了解一下：
1. Analysis of orthologous groups reveals archease and DDX1 as tRNA splicing
factors
小知识：
1. Evolutionary developmental biology: Use it or lose it
Multiple avenues to digit loss
Patterning and post-patterning modes of evolutionary digit loss in mammals
2. New specimen of Archaeopteryx provides insights into the evolution of
pennaceous feathers
Most likely display -> exaptation, later recruited for aerodynamic functions
m*g
252 楼
Nature 14.07.10
稍微了解一下：
1. Horizontal genome transfer as an asexual path to the formation of new
species
Upon grafting, entire nuclear genomes can be transferred between plant cells
Natural grafting as a potential asexual mechanism of speciation
小知识：
1. Abnormalities in human pluripotent cells due to reprogramming mechanisms
DNA methylation and transcriptome profiles of NT ES cells,
but not iPS, corresponded closely to those of IVF ES cells
IVF ES - in vitro fertilized embryos
NT - nuclear transfer
2. Cooperating with the future
Solving the intergenerational ‘tragedy of the commons’ through voting
稍微了解一下：
1. Horizontal genome transfer as an asexual path to the formation of new
species
Upon grafting, entire nuclear genomes can be transferred between plant cells
Natural grafting as a potential asexual mechanism of speciation
小知识：
1. Abnormalities in human pluripotent cells due to reprogramming mechanisms
DNA methylation and transcriptome profiles of NT ES cells,
but not iPS, corresponded closely to those of IVF ES cells
IVF ES - in vitro fertilized embryos
NT - nuclear transfer
2. Cooperating with the future
Solving the intergenerational ‘tragedy of the commons’ through voting
m*g
253 楼
PNAS 14.07.08
稍微了解一下：
1. Defining a personal, allele-specific, and single-molecule long-read
transcriptome
Combine PacBio with Illumina for three family member
稍微了解一下：
1. Defining a personal, allele-specific, and single-molecule long-read
transcriptome
Combine PacBio with Illumina for three family member
m*g
254 楼
Science 14.07.11
稍微了解一下：
Several HIV related papers
小知识：
1. Multispecies diel transcriptional oscillations in open ocean
heterotrophic bacterial assemblages
稍微了解一下：
Several HIV related papers
小知识：
1. Multispecies diel transcriptional oscillations in open ocean
heterotrophic bacterial assemblages
m*g
255 楼
Nature 14.07.17
稍微了解一下：
1. Genetics of ecological divergence during speciation
Genetic architecture of niche differentiation in a sympatric species pair of
threespine stickleback fish
小知识：
1. Chimp intelligence partly inherited
half of the difference in performance between individual apes was genetic
2. The structural basis of transfer RNA mimicry and conformational
plasticity by a viral RNA
稍微了解一下：
1. Genetics of ecological divergence during speciation
Genetic architecture of niche differentiation in a sympatric species pair of
threespine stickleback fish
小知识：
1. Chimp intelligence partly inherited
half of the difference in performance between individual apes was genetic
2. The structural basis of transfer RNA mimicry and conformational
plasticity by a viral RNA
m*g
256 楼
PNAS 14.07.15
稍微了解一下：
1. Evolutionary origin of insect–Wolbachia nutritional mutualism
小知识：
1. Evolution of the ribosome at atomic resolution
稍微了解一下：
1. Evolutionary origin of insect–Wolbachia nutritional mutualism
小知识：
1. Evolution of the ribosome at atomic resolution
m*g
257 楼
最近打算新开一个项目，正在集中阅读那方面文献，哈哈。
所以感觉很少看这些general的paper.
Science 14.07.18
推荐：
1. (recommended Elife paper) Genome rearrangements and pervasive meiotic
drive cause hybrid infertility in fission yeast
稍微了解一下：
1. Human tRNA synthetase catalytic nulls with diverse functions
2. Putting the genetic breaks on breeding
小知识：
1. How the worm changes its tastes
Synaptic PI3K is crucial for the behavioral switch caused by learning
2. Organogenesis in a dish: Modeling development and disease using organoid
technologies
所以感觉很少看这些general的paper.
Science 14.07.18
推荐：
1. (recommended Elife paper) Genome rearrangements and pervasive meiotic
drive cause hybrid infertility in fission yeast
稍微了解一下：
1. Human tRNA synthetase catalytic nulls with diverse functions
2. Putting the genetic breaks on breeding
小知识：
1. How the worm changes its tastes
Synaptic PI3K is crucial for the behavioral switch caused by learning
2. Organogenesis in a dish: Modeling development and disease using organoid
technologies
m*g
258 楼
PNAS 14.07.22
推荐：
1. Extensive pathogenicity of mitochondrial heteroplasmy in healthy human
individuals
稍微了解一下：
1. Drastic population fluctuations explain the rapid extinction of the
passenger pigeon
推荐：
1. Extensive pathogenicity of mitochondrial heteroplasmy in healthy human
individuals
稍微了解一下：
1. Drastic population fluctuations explain the rapid extinction of the
passenger pigeon
m*g
259 楼
Science 14.07.20
稍微了解一下：
1. Ribosome rescue and neurodegeneration
小知识：
1. The common marmoset genome provides insight into primate biology and
evolution
稍微了解一下：
1. Ribosome rescue and neurodegeneration
小知识：
1. The common marmoset genome provides insight into primate biology and
evolution
m*g
260 楼
Nature 14.07.24
小知识：
1. Selective transcriptional regulation by Myc in cellular growth control
and lymphomagenesis
2. A cheesy tool for the laboratory
3. Biological insights from 108 schizophrenia-associated genetic loci
小知识：
1. Selective transcriptional regulation by Myc in cellular growth control
and lymphomagenesis
2. A cheesy tool for the laboratory
3. Biological insights from 108 schizophrenia-associated genetic loci
m*g
261 楼
好诡异，我明明重新开了一个八月的文献帖子，结果发布之后发现不见了。
PNAS 14.08.05
小知识：
1. Fast running restricts evolutionary change of the vertebral column in
mammals
2. Complete genome of a nonphotosynthetic cyanobacterium in a diatom reveals
recent adaptations to an intracellular lifestyle
PNAS 14.08.05
小知识：
1. Fast running restricts evolutionary change of the vertebral column in
mammals
2. Complete genome of a nonphotosynthetic cyanobacterium in a diatom reveals
recent adaptations to an intracellular lifestyle
m*g
262 楼
Nature 14.08.07
推荐：
1. Genome-scale functional characterization of Drosophiladevelopmental
enhancers in vivo
小知识：
1. A year with your microbes
2. Tooth structure re-engineered
Replaying evolutionary transitions from the dental fossil record
推荐：
1. Genome-scale functional characterization of Drosophiladevelopmental
enhancers in vivo
小知识：
1. A year with your microbes
2. Tooth structure re-engineered
Replaying evolutionary transitions from the dental fossil record
f*g
263 楼
ding, but this is not my field.
m*g
264 楼
最近有人QQ问我这个帖子是不是不更了，其实只是换了个地方继续挖坑，标题是“[八
月新番]遗传进化方向的文献推荐”，不过好像没有什么人看或者回帖，不过本人是比
较喜欢自娱自乐型~所以继续看文献去啦。
月新番]遗传进化方向的文献推荐”，不过好像没有什么人看或者回帖，不过本人是比
较喜欢自娱自乐型~所以继续看文献去啦。
相关阅读
请问有没有人从生物公司买QPCR 引物实在想不明白，朱毅干嘛去惹方舟子斑竹们，该删的贴就删啊。Best Places to Work Postdocs 2013 对正在找博后的也许有参考说说生物里的应用研究How to choose the right doctoral advisor对于一些发了疯的， 大家都不要理他，当他一驼东西在哪儿就行pierce的extra thick filter paper物理博士做生物薄厚无法离境回国？找工作还是要看老板啊求找工作建议求证：鲨鱼和鹅不得癌症？公正的说，生物系还是有优点的！ (转载)江苏卫视【一站到底】清华的刘也行是施一公实验室的由拔火罐刮痧所想到的请推荐peptide systhesis的公司包子求paperRe: 公正的说，生物系还是有优点的！ (转载)感觉被二老板（中国人）背后捅刀子了。求推荐LIMS系统 (转载)