l**********1
发帖数: 5204 | 1 Bingo
alternatively LZ can try "CisGenome Browser"
Refernece:
Jiang H, Wang F, Dyer NP, Wong WH.
CisGenome Browser: a flexible tool for genomic data visualization.(2010)
Bioinformatics. 26:1781-1782.
PubMed link:
//www.ncbi.nlm.nih.gov/pubmed/20513664
and CGBroswer was from “JETTA”
//gluegrant1.stanford.edu/~junhee/JETTA/
and both of them now are using "Glue Grant Human Transcriptome Arrays”
that Project leader is:
Stanford Professor: Wing Hung Wong whom was Elected to the National Academy... 阅读全帖 |
|
l**********1
发帖数: 5204 | 2 continue again
陈 雪梅 (Xuemei Chen )
//www.hhmi.org/news/chenx_bg.html
//facultydirectory.ucr.edu/cgi-bin/pub/public_individual.pl?faculty=2491
//cepceb.ucr.edu/people/chen.html
//www.plantbiology.ucr.edu/faculty/chen.html
Chen X. (2012)
Small RNAs in development - insights from plants.
Curr Opin Genet Dev. May 9. [Epub ahead of print]
//www.ncbi.nlm.nih.gov/pubmed/22578318
//www.ncbi.nlm.nih.gov/pubmed?term=Chen%20Xuemei%20%20Riverside
Ps:
original hint was from
得到肯定答复后，朱健康教授随即与海外学者杨贞标、丁守伟、陈雪梅等... 阅读全帖 |
|
l**********1
发帖数: 5204 | 3 沈 her one new review:
Hwang I. et al. (2012)
Cytokinin signaling networks
Annu Rev Plant Biology. 63:353-380
PubMed link:
//www.ncbi.nlm.nih.gov/pubmed/22554243
full text you can free download from bottom icon of below link:
//ccib.mgh.harvard.edu/sheen/pi_bio |
|
l**********1
发帖数: 5204 | 4 continue again
陈 雪梅 (Xuemei Chen )
//www.hhmi.org/news/chenx_bg.html
//facultydirectory.ucr.edu/cgi-bin/pub/public_individual.pl?faculty=2491
//cepceb.ucr.edu/people/chen.html
//www.plantbiology.ucr.edu/faculty/chen.html
Chen X. (2012)
Small RNAs in development - insights from plants.
Curr Opin Genet Dev. May 9. [Epub ahead of print]
//www.ncbi.nlm.nih.gov/pubmed/22578318
//www.ncbi.nlm.nih.gov/pubmed?term=Chen%20Xuemei%20%20Riverside
Ps:
original hint was from
得到肯定答复后，朱健康教授随即与海外学者杨贞标、丁守伟、陈雪梅等... 阅读全帖 |
|
l**********1
发帖数: 5204 | 5 沈 her one new review:
Hwang I. et al. (2012)
Cytokinin signaling networks
Annu Rev Plant Biology. 63:353-380
PubMed link:
//www.ncbi.nlm.nih.gov/pubmed/22554243
full text you can free download from bottom icon of below link:
//ccib.mgh.harvard.edu/sheen/pi_bio |
|
l**********1
发帖数: 5204 | 6 One 2011 end their Science paper:
Science. 2011 334 :1408-12.
The competitive advantage of a dual-transporter system.
Levy S, Kafri M, Carmi M, Barkai N.
Department of Molecular Genetics, Weizmann Institute of Science, Rehovot
76100, Israel.
PubMed link:
//www.ncbi.nlm.nih.gov/pubmed/22158820
full text pdf link:
//barkai-serv.weizmann.ac.il/GroupPage/SagiMosheDual.pdf
more CNS papers from there please go to:
//barkai-serv.weizmann.ac.il/GroupPage/publications.htm |
|
|
s********n
发帖数: 2939 | 8 我只用过Papers和EndNote，遇到最大的问题是用这两个软件找到的文献和网上直接找
的差别很大，比如说用papers和EndNote找PubMed Library里的文献得到1300，但是网
上Pubmed直接找有2000，这是怎么回事？ |
|
s******r
发帖数: 2876 | 9 ReadCube用着感觉怎么样？
试了一下，发现一个好处是直接pubmed搜索，然后可以直接下载PDF，比Mendeley方便
不过他那个list很简单，不能创建子目录，这一点很费解，这个功能还是很方便的，
Mendeley就有这个功能，可惜不能直接搜索pubmed。
哪个软件能够集合这些功能？ |
|
l**********1
发帖数: 5204 | 10 Sure
plus
文章阅读：C++面试题目分享(2)
[同主题阅读] [版面： 待字闺中] [作者：skydoor] , 2010年04月28日
http://www.mitbbs.com/article/JobHunting/31590025_0.html
more just intraGoogle mitbbs with
//www.google.com/search?ie=UTF-8%2F&oe=UTF-
8%2F&q=Collins+&btnG=Hae&as_sitesearch=utu.fi#hl=en&sclient=psy-ab&q=C%2B%2B面试题目分享
+++site%3Awww.mitbbs.com&oq=C%2B%2B面试题目分享
+++site:www.mitbbs.com&aq=f&aqi=&aql=&gs_l=serp.12...145482.154746.12.155958.30.30.0.0.0.0.111
.1844.29j1.30.0...0.0.hx9H4asD8B4&pbx=1&bav=on.2,or.r_gc.r_... 阅读全帖 |
|
l**********1
发帖数: 5204 | 11 Alleviating interactions.
Please go to AMPK(Sip2) Nature paper:
Functional dissection of lysine deacetylases reveals that HDAC1 and p300
regulate AMPK (2012)
link:
//www.ncbi.nlm.nih.gov/pubmed/22318606
its pp251
called both as
[synthetic lethal (negative/aggravating) and rescue (positive/alleviating)
interactions]
more reference:
Acetylation of yeast AMPK controls intrinsic aging independently of caloric
Cell 146: 969-
//www.ncbi.nlm.nih.gov/pubmed/21906795 |
|
l**********1
发帖数: 5204 | 12 1)
from it is more exciting:
please focus on
Allometry and stoichiometry of unicellular, colonial and multicellular phytoplankton
by Population Genetics even Stochastic model methods
please go to below paper:
PubMed link:
//www.ncbi.nlm.nih.gov/pubmed/19121029
full text link:
//www.mmab.ca/lib/exe/fetch.php?media=pubs:beardall-2008-new-phytologist-
tansley.pdf
more please go to
allometric relationship between organism metabolism and body mass
recent paper:
Heritability is not Evolvability
Abstra... 阅读全帖 |
|
|
l**********1
发帖数: 5204 | 14 楼主少见啦
八年前的paper:
蜥蜴3D 运动记录的PNAS paper
Hsieh and Lauder (2004)
Running on water: Three-dimensional force generation by basilisk lizards.
PNAS 101: 16784-8.
//www.ncbi.nlm.nih.gov/pubmed/15550546
九年前的Nature paper:
水蛭 3D 运动 在水面 不会沉下去的Nature paper
Hu et al. (2003)
The hydrodynamics of water strider locomotion.
Nature 424: 663-6.
http://www.ncbi.nlm.nih.gov/pubmed/12904790
more about marine water strider 如何走过太平洋 大西洋的 papers please go
to:
CHENG, LANNA 新加坡华裔
Research Biologist of UCSD
//sio.ucsd.ed... 阅读全帖 |
|
l**********1
发帖数: 5204 | 15 楼主
试下这个
//www-personal.umich.edu/~jianghui/seqmap/
from 2012 one paper
Identification of a binding motif specific to HNF4 by comparative analysis
of multiple nuclear receptors
PubMed link:
//www.ncbi.nlm.nih.gov/pubmed/22383578
and
//bioinformatics.oxfordjournals.org/content/24/20/2395.short
Articles citing this article
Identification of a binding motif specific to HNF4 by comparative analysis
of multiple nuclear receptors
Nucleic Acids Res (2012) 0(2012): gks190v1-gks190
AbstractFull Text (HTML... 阅读全帖 |
|
l**********1
发帖数: 5204 | 16 上周偶然撞到一篇review
说的就是这个
pls go to
Yadav H. at al. (2012)
TGF-β/Smad3 Signaling Regulates Brown Adipocyte Induction in White Adipose
Tissue.
Front Endocrinol (Lausanne). 3:35.
PubMed link:
//www.ncbi.nlm.nih.gov/pubmed/22654861
发信人: Dua (Dua), 信区: Biology
标 题: Re: 有个很有意思的发现，大家看看该怎么继续下去--METABOLISM
发信站: BBS 未名空间站 (Sun Jun 17 11:35:04 2012, 美东)
kindey附近还有啊？从来木有见到啊，下次仔细看看。。。
。
肩胛骨那里是不是一直连到腋窝那里去的？腋窝下面还有一点？ |
|
l**********1
发帖数: 5204 | 17 12.4 hr interval should be taken between IN VIVO De Novo blood sampling of
same tissue of
--Mouse/+-Mouse/++Mouse her/his mRNAs and proteins
if that mRNAs and produced proteins are Circadian controlled
please check one paper:
Connor K. and Gracey A.(2011)
Circadian cycles are the dominant transcriptional rhythm in the intertidal
mussel Mytilus californianus.
PNAS 108:16110-16115.
Abstract
Residents in the marine intertidal, the zone where terrestrial and marine
habitats converge, inhabit an env... 阅读全帖 |
|
l**********1
发帖数: 5204 | 18 So what?
Is he (your PI) took left or right pathway? from below attached figure
from below b) nature sister?
a)
Huang S. (2009)
Non-genetic heterogeneity of cells in development: more than just noise.
Development.136: 3853-3862.
//www.ncbi.nlm.nih.gov/pubmed/19906852
b)
Strohman RC (1997)
The coming Kuhnian revolution in biology.
Nat Biotechnol. 15: 194-200.
//www.ncbi.nlm.nih.gov/pubmed/9062910
//bialystocker.net/files/kuhn.pdf |
|
l**********1
发帖数: 5204 | 19 云彩最近在忙要事? 不常来这里吧
matrix 10年前 市井巷口 听说有个 脑世纪 啥的
美 欧(主要是瑞士) 日 用MRI/fMRI 分析人脑的 stuff 项目
以下是Summary report:
A Decade after The Decade of the Brain
February 26, 2010
In 1990, Congress designated the 1990s the “Decade of the Brain.”
President George H. W. Bush proclaimed, “A new era of discovery is dawning
in brain research.” During the ensuing decade, scientists greatly advanced
our understanding of the brain.
The editors of Cerebrum asked the directors of seven brain-related
institutes at the Nat... 阅读全帖 |
|
l**********1
发帖数: 5204 | 20 Johns Hopkins too 连tenure都过不了
不是看已有领域的挖掘 还要看新领域的digged out data and results.
please refer:
for example:
Lee Martin, Ph.D.
Professor of Pathology, Neuroscience
//pathology.jhu.edu/department/divisions/neuropathology/faculty-staff.cfm
his group recent paper:
线粒体上的控制 NO 的通道控制着细胞老化和自然死亡的过程
"The mitochondrial permeability transition pore regulates nitric oxide-
mediated apoptosis of neurons induced by target deprivation.” (2011)
J Neurosci. 31: 359-370.
PubMed link:
//www.ncbi.nlm.nih.gov/pubmed/2... 阅读全帖 |
|
l**********1
发帖数: 5204 | 21 stable knockdown shRNA better performance from less off-target per cent age
details please refer
Klinghoffer RA at al. (2010)
Reduced seed region-based off-target activity with lentivirus-mediated RNAi.
RNA. 16: 879-84.
PubMed link:
//www.ncbi.nlm.nih.gov/pubmed/20348445 |
|
l**********1
发帖数: 5204 | 22 Mark!
LZ can try ultra-low attachment 96-well plate
plus two papers:
Zhang J et al. (2009)
Functional cardiomyocytes derived from human induced pluripotent stem cells.
Circ Res. 104: e30-41.
link:
//www.ncbi.nlm.nih.gov/pubmed/19213953
and
Sheridan SD et al.
Analysis of embryoid bodies derived from human induced pluripotent stem
cells as a means to assess pluripotency.
Stem Cells Int. 2012:738910.
link:
//www.ncbi.nlm.nih.gov/pubmed/22550517 |
|
l**********1
发帖数: 5204 | 23 If olfactory epithelium (OE) ES cell,
pls refer one paper:
Wang YZ. et al. (2011)
Canonical Wnt signaling promotes the proliferation and neurogenesis of
peripheral olfactory stem cells during postnatal development and adult
regeneration.
J Cell Sci. 124: 1553-63
Pubmed link:
//www.ncbi.nlm.nih.gov/pubmed/21486944
citation:
Tuj1+ (anti-neuron-specific class III beta-tubulin) neurons
were also located toward the periphery of the flattened sphere (Fig.
5E), and their neurites or axons passed among... 阅读全帖 |
|
l**********1
发帖数: 5204 | 24 Here you go.
Casals G. et al. (2009)
Hypoxia induces B-type natriuretic peptide release in cell lines derived
from human cardiomyocytes.
Am J Physiol Heart Circ Physiol. 297:H550-5.
link:
//www.ncbi.nlm.nih.gov/pubmed/19542490
citation:
Cell culture.
AC16 cells were generated from primary human
ventricular cardiomyocytes, as previously described (7). This immortalized,
stable cell line can be repeatedly frozen, thawed, and propagated.
Cells were seeded (1 106 cells/well) in gelatin-coated six-... 阅读全帖 |
|
l**********1
发帖数: 5204 | 25 召唤sunnyday
有个问题 哈
membrane ruffle actin 异常的时侯 SWI/SNF 和Rest/Nrsf 浓度
是 increase? or decrease?
虽有
References:
1)
Lepagnol-Bestel AM at al. (2009)
DYRK1A interacts with the REST/NRSF-SWI/SNF chromatin remodelling complex to
deregulate gene clusters involved in the neuronal phenotypic traits of Down
syndrome.
Hum Mol Genet. 18: 1405-14.
//www.ncbi.nlm.nih.gov/pubmed/19218269
citation:
>
we show here that the doses of Rest/Nrsf and Elmo2 in the mouse brains are
inversely proportional. Differential... 阅读全帖 |
|
l**********1
发帖数: 5204 | 26 Sure plus one paper from CA(gri)U
Yang R et al.(2010)
Analyzing circadian expression data by harmonic regression based on
autoregressive spectral estimation.
Bioinformatics. 26:i168-74.
PubMed link:
//www.ncbi.nlm.nih.gov/pubmed/20529902
and
its Fig. 6.
Area-proportional Venn diagram addresses the predictive power
of three algorithms for identifying Arabidopsis circadian-regulated genes.
The microarray data were originally analyzed by COSOPT in the study of
Edwards et al. (2006), and scored 350... 阅读全帖 |
|
l**********1
发帖数: 5204 | 27 Mulet X et al.
Antagonistic interactions of Pseudomonas aeruginosa antibiotic resistance
mechanisms in planktonic but not biofilm growth.
Antimicrob Agents Chemother. 55: 4560-8.
Abstract
Pseudomonas aeruginosa has an extraordinary capacity to evade the activity
of antibiotics through a complex interplay of intrinsic and mutation-driven
resistance pathways, which are, unfortunately, often additive or synergistic
, leading to multidrug (or even pandrug) resistance. However, we show that
one of th... 阅读全帖 |
|
l**********1
发帖数: 5204 | 28 ps:
LZ those two alle excluded HGT (horizontal gene transfer )acquired its/both
's possibility already?
unless even from 它物种 acquired HST gene that 物种 pathway/network can
control this 物种 ability 哦
Reference:
Chen HD et al. (2011)
Ancestral genes can control the ability of horizontally acquired loci to
confer new traits.
PLoS Genet. 7: e1002184.
//www.ncbi.nlm.nih.gov/pubmed/22363555
or
Kholodenko BN. (2006)
Cell-signalling dynamics in time and space.
Nat Rev Mol Cell Biol. 7: 165-76.
//www.nc... 阅读全帖 |
|
l**********1
发帖数: 5204 | 29 就是虫子
还有这个呢: cryptic development
pls refer:
Duveau F et al. (2012)
Role of pleiotropy in the evolution of a cryptic developmental variation in
Caenorhabditis elegans.
PLoS Biol. 10: e1001230.
link:
//www.ncbi.nlm.nih.gov/pubmed/22235190
and
Chandler CH (2010)
Cryptic intraspecific variation in sex determination in Caenorhabditis
elegans revealed by mutations.
Heredity 105: 473-82.
link:
//www.ncbi.nlm.nih.gov/pubmed/20502478
NB: LZ 没有透露任何 模式生物 或非模式生物其名称 也没有透露那两alleles 是否
有关性分化 或 进化 所以如果这两线虫的文章 ... 阅读全帖 |
|
l**********1
发帖数: 5204 | 30 If Human
try Netpath
//www.netpath.org/
if mouse or rat
try David
//idconverter.bioinfo.cnio.es/
Protein Level
SwissProt
Taken from Ensembl Embl
Taken from Ensembl PDB id
Taken from Ensembl IPI
Taken from Ensembl
OMIM*
Taken from Ensembl
GO
Taken from Ensembl KEGG Pathways
Taken from KEGG Reactome Pathway
Taken from Reactome Reactome Reaction
Taken from Reactome
PubMed id
Taken from NCBI
or
//david.abcc.ncifcrf.gov/conversion.jsp
if crop ... 阅读全帖 |
|
D*a
发帖数: 6830 | 31 汗。。。叫得太那啥了吧。。。
这篇在pubmed自己的数据库是free，你可以从pubmed过去，我email给你也行。
我们老鼠是不用做了，买cre再跟cre交配也要交一年啊。。。
loxp
300bp |
|
l**********1
发帖数: 5204 | 32 Cell 2012 may 同一期
三姐/妹 印度裔英国人 Serena Nik-Zainal
Supervisor: Mike Stratton
Exploring the cancer genomes of tumours derived from germline BRCA1 and
BRCA2 mutations carriers
//www.cimr.cam.ac.uk/study/clinicians/current_fellows.html
Nik-Zainal S et al. (2012)
The life history of 21 breast cancers.
Cell. 149:994-1007.
//www.ncbi.nlm.nih.gov/pubmed/22608083
Nik-Zainal S et al. (2012)
Mutational processes molding the genomes of 21 breast cancers.
Cell.149: 979-93.
//www.ncbi.nlm.nih.gov/pubmed/22... 阅读全帖 |
|
l**********1
发帖数: 5204 | 33 Re; Cosimo2014 (柯希莫)
两重串联Mass 乃至傅立叶变换 三重串联Mass 和传统Mass的分析蛋白质的区别是
后者只有分子量的定性 和相对稳定同位素标示后的比如 SILAC Mass的定量
而前者 可以测 wild pH (NH4)2 SO4 溶液 pH 6.9 中的蛋白 二级结构 数据 乃至
dimer trimer etc. 三级结构数据
please go to below link:
//www.findnano.fi/fi/NanoCrmEquipment:UserView/id/1431
only some titles are Finnish
for example:
Tärkeimmät spesifikaatiot:
(NB: Key Specifications by //translate.google.fr/?hl=fr/
from Finnish to English bla bla bla...)
then almost rest is english:
Multistage MS (MS3 gua... 阅读全帖 |
|
|
|
|
|
s**********t
发帖数: 680 | 38 Crit Rev Eukaryot Gene Expr. 2000;10(2):179-212.
Title: Chromosome territories, interchromatin domain compartment, and
nuclear matrix: an integrated view of the functional nuclear architecture.
Cremer T, Kreth G, Koester H, Fink RH, Heintzmann R, Cremer M, Solovei I,
Zink D, Cremer C.
Journal link:http://www.begellhouse.com/journals/6dbf508d3b17c437,0e3100b11d4c829b,09458a4d2245ffe0.html
Pubmed link: http://www.ncbi.nlm.nih.gov/pubmed/11186332
Please send it to: b************[email protected]
Thank ... 阅读全帖 |
|
l**********1
发帖数: 5204 | 39 Sure.
LZ pls refer one 2012article from Harvad
Optical Coherence Microscopy (OCM) for in vivo imaging of neuronal cell
bodies and cortical myelination up to depths of ~1.3 mm in the rat neocortex
by
Srinivasan VJ et al. (2012)
Optical coherence microscopy for deep tissue imaging of the cerebral cortex
with intrinsic contrast.
Opt Express. 20: 2220-39.
its PubMed link:
http://www.ncbi.nlm.nih.gov/pubmed/22330462
>
----------------------------
人家问得是最大厚度啊。估计是要做 confocal 吧。
我也有这个问题。做小鼠的骨髓切片，我们这里死活也做... 阅读全帖 |
|
l**********1
发帖数: 5204 | 40 LZ can try long hairpin RNAi
Reference:
Tomimoto K et al. (2012)
Construction of a long hairpin RNA expression library using Cre recombinase.
J Biotechnol. 160: 129-39.
PubMed link:
http://www.ncbi.nlm.nih.gov/pubmed/22484114
发信人: Wanshington (Joudon), 信区: Biology
标 题: Re: 讨论：信号通路上的蛋白酶功能研究策略哪种好？
发信站: BBS 未名空间站 (Fri Sep 28 03:33:37 2012, 美东)
RNAi不是有脱靶的问题吗？ 以前没有做过，所以对这个问题是否严重没有很好的把握
。这个蛋白的磷酸化位点不能突变成模拟磷酸化的蛋白，所以这条道路不通。 |
|
|
|
|
l**********1
发帖数: 5204 | 44 not 大侠 but 小虾米
>在不确定binding site的情况下,怎么区别antagonist 和 negative allosteric
modulator?
sometimes even antagonistic actions are biased.
pls refer pituitary gonadotropin follicle stimulating hormone (FSH) and its
receptor actions by ADX61623 compound as A negative allosteric modulator
References:
Dias JA et al. (2011)
A negative allosteric modulator demonstrates biased antagonism of the
follicle stimulating hormone receptor.
Mol Cell Endocrinol. 333: 143-50.
PubMed link:
http://www.ncbi.nlm.nih.go... 阅读全帖 |
|
l**********1
发帖数: 5204 | 45 pls try Monte Carlo Markov Chain Stochastic simulation
因为目前的技术无法在deterministic 纳米反应酶动力学 确定 PAM or NAM or even
both.
One reference:
Trzaskowski B et al. (2012)
Action of molecular switches in GPCRs--theoretical and experimental studies.
Curr Med Chem. 19: 1090-109.
PubMed link:
http://www.ncbi.nlm.nih.gov/pubmed/22300046
Ps:
具体啥叫 Markov Chain model
pls 考古本版 下
发信人: kdfox11 (狂奔的蜗牛), 信区: Biology
标 题: Re: 感慨一下数学/物理 和 生物 合作之难
发信站: BBS 未名空间站 (Mon Sep 3 14:21:33 2012, 美东)
如果你想用马尔可夫过程来表示因果关系，也很简单，就是... 阅读全帖 |
|
l**********1
发帖数: 5204 | 46 PAM or NAM 需要用针对上游和下游的targets 不同的agonist or antagonist
进一步测试的
具体麻烦 参考一综述
Coddou C et al. (2011)
Activation and regulation of purinergic P2X receptor channels.
Pharmacol Rev. 63: 641-83.
PubMed link:
http://www.ncbi.nlm.nih.gov/pubmed/21737531
its contents likes
>The term cooperativity is frequently
used to describe the magnitude of an allosteric
effect, which could be either positive or negative, leading
to up- or down-regulation of receptor function.
and
>A common aspect of P2XRs is their
regu... 阅读全帖 |
|
l**********1
发帖数: 5204 | 47 看错啦 matrix
作为将功补过
LZ
pls refer
Castellone MD et al. (2005)
title:
Prostaglandin E2 Promotes Colon Cancer Cell Growth Through a
Gs-Axin-b-Catenin Signaling Axis
Science. 310: 1504-10.
its Fig. 2B
PubMed link:
http://www.ncbi.nlm.nih.gov/pubmed/16293724 |
|
a*****x
发帖数: 901 | 48 statistics来说，科研水平和pubmed水平还是密切相关的，但是你不是一直认为自己是
outlier吗？你可以成为pubmed的outlier，为什么不能成为王院士眼中的outlier。。。 |
|
|
l**********1
发帖数: 5204 | 50 LZ is doing Mitochondrial Ca(2+) apoptosis works now?
If Yes,
pls refer below figure which just cited from
Giorgi C et al. (2012)
Mitochondrial Ca(2+) and apoptosis.
Cell Calcium. 52: 36-43.
web link:
http://www.ncbi.nlm.nih.gov/pubmed/22480931
more references:
Patergnani S et al. (2011)
Calcium signaling around Mitochondria Associated Membranes (MAMs).
Cell Commun Signal. 9:19.
link:
http://www.ncbi.nlm.nih.gov/pubmed/21939514 |
|
