In the light of evolution I: Adaptation and complex design http://www.pnas.org/content/104/suppl.1.toc In the light of evolution II: Biodiversity and extinction http://www.pnas.org/content/105/suppl.1.toc In the light of evolution III: Two centuries of Darwin http://www.pnas.org/content/106/suppl.1.toc In the light of evolution IV: The human condition http://www.pnas.org/content/107/suppl.2.toc In the Light of Evolution V: Cooperation and Conflict Sackler not available yet [...]
Archive for the ‘Data Collection’ Category
In the light of evolution series @ PNAS
Posted: June 22, 2011 in Data Collection, Reading, Science ReviewTags: evolution
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Notes about Genome Biology conference 2011 @ CSHL
Posted: May 11, 2011 in Data Collection, Note, Science ReviewThis is my notes about Genome Biology conference 2011 @ Cold spring harbor, NY. WARNING: all “we”, “our”, “us” below only refer to the origin authors. Please do NOT cite any part of this page for any proposes. Some of the conclusions may not appear as exact form as it ultimate publication. TFBS/enhancer: To integrate [...]
[旧文重发] 敦格萨普阿波昌巴 – 西藏行记 (21) – 附录 B 有关资料 2005/9.
Posted: October 22, 2010 in Ancient Post, Data Collection, Entertainment, Hobbies, Travel[旧文重发] 敦格萨普阿波昌巴 – 西藏行记 (21) – 附录 B 有关资料 2005/9. — 原文配图”()”中的文字是图解, 我懒得再编辑插入图片, 图片在(这里, click here for pictures), 这个题目实在是很傻X,不过历史就是如此,保持原样好了. — i/2010/10/22 附录 B 有关资料 表1.日喀则车站的车辆信息（9月18号数据）：如无注明，发车时间都是上午八点。 终点站 大巴 中巴 注备 亚东 60￥ 80￥ 定日 65￥ 80￥ 定结 65￥ 80￥ 聂达木 古都 萨嘎 125￥ 150￥ 下午有车 拉孜 [...]
"We created genome-wide chromatin-state maps for three mouse cell types: ES cells, neural progenitor cells (NPCs)8 and embryonic fibroblasts (MEFs). For each cell type, we prepared and sequenced ChIP DNA samples for some or all of the following features: pan- H3, trimethylated histone H3 lysine 4 (H3K4me3), H3K9me3, H3K27me3, H3K36me3, H4K20me3 and RNA polymerase II [...]
The Genetic Landscape of a Cell M. Costanzo et al. A genome-wide interaction map of yeast identifies genetic interactions, networks, and function. http://www.sciencemag.org/cgi/content/abstract/327/5964/425
CORUM: the comprehensive resource of mammalian protein complexes.
Posted: August 18, 2009 in Data CollectionCORUM: the comprehensive resource of mammalian protein complexes. Ruepp A, Brauner B, Dunger-Kaltenbach I, Frishman G, Montrone C, Stransky M, Waegele B, Schmidt T, Doudieu ON, Stümpflen V, Mewes HW. Institute for Bioinformatics (MIPS), German Research Center for Environmental Health, Ingolstaedter Landstrasse 1, D-85764 Neuherberg, Germany. andreas.ruepp@gsf.de Protein complexes are key molecular entities that integrate [...]
http://www.ncbi.nlm.nih.gov/projects/geo/info/ENCODE.html
http://www.nature.com/msb/journal/v5/n1/fig_tab/msb200917_T1.html FROM: TABLE 1 of Tissue specificity and the human protein interaction network Alice Bossi & Ben Lehner, msb, 2009 doi:10.1038/msb.2009.17 Table 1: Human protein interaction datasets used to construct or support the integrated human interaction network BIND Literature curation Bader et al (2001) BIOGRID Literature curation Stark et al (2006) Bioverse Data integration McDermott [...]
Nature Methods 6, 283 – 289 (2009) Published online: 22 March 2009 | doi:10.1038/nmeth.1313 http://www.nature.com/nmeth/journal/v6/n4/abs/nmeth.1313.html Global mapping of protein-DNA interactions in vivo by digital genomic footprinting Jay R Hesselberth1,6, Xiaoyu Chen2,6, Zhihong Zhang1,3,5, Peter J Sabo1, Richard Sandstrom1, Alex P Reynolds1, Robert E Thurman1, Shane Neph1, Michael S Kuehn1, William S Noble1,2, Stanley Fields1,3 & [...]
human and mouseData files for the 2002 GeneAtlas Data Set have been deposited at GEO under series numbers GSE96 (Human U95A) and GSE97 (Mouse U74A). The 2004 Rat GeneAtlas has also been deposited (GSE952). mouse onlyUpdated 10/21/2008:All data files for the Mouse GeneAtlas V3 data set (MOE430V2 chip set) are now available for download from [...]
Resources abstract Nature Methods 6, 47 – 54 (2008) Published online: 14 December 2008 | doi:10.1038/nmeth.1279 Empirically controlled mapping of the Caenorhabditis elegans protein-protein interactome network Nicolas Simonis1,2,11, Jean-François Rual1,2,10,11, Anne-Ruxandra Carvunis1,2,3,11, Murat Tasan4,11, Irma Lemmens5,11, Tomoko Hirozane-Kishikawa1,2, Tong Hao1,2, Julie M Sahalie1,2, Kavitha Venkatesan1,2,10, Fana Gebreab1,2, Sebiha Cevik1,2,10, Niels Klitgord1,2,10, Changyu Fan1,2, Pascal Braun1,2, [...]
Data collection: Transcription regulatory networks of protein-coding genes in C.elegans, fly and mammals.
Posted: December 12, 2008 in Data CollectionTranscription regulatory networks of protein-coding genes have been mapped and studied in yeast (Harbison et al. 2004), C. elegans (Deplancke et al. 2006a; Vermeirssen et al. 2007a), Drosophila melanogaster (Sandmann et al. 2007), and mammals (Boyer et al. 2005). C.elegans A Gene-Centered C. elegans Protein-DNA Interaction Network Bart Deplancke1, Arnab Mukhopadhyay1, 6, Wanyuan Ao2, [...]
Sanchez C, Lachaize C, Janody F, Bellon B, Roder L, Euzenat J, Rechenmann F, Jacq B: Grasping at molecular interactions and genetic networks in Drosophila melanogaster using FlyNets, an Internet database. Nucleic Acids Res 1999, 27:89-94. PubMed Abstract | Publisher Full Text | PubMed Central Full Text Return to text Ito T, Chiba T, Ozawa [...]
Itay tirosh, et al. A genetic signature of interspecies variations in gene expression. Nature genetics, V 38, 830. Using S.cerevisiae array, the authors build a data set for 4 other yeasts(S.paradoxus CBS 432 and NRRL Y-17217, s.mikatae, s.kudriavzevii) under several conditons.
the orhtologous between 14 fungis (yeast) and cis-regulatory elements
Posted: February 1, 2007 in Data CollectionAudrey P.Gasch, et.al. Conservation and evolution of cis-regulatory systems in Ascomycete Fungi. PLoS Biol 2(12):e398.
Frank C.P.Holstege, et al, dissecting the Regulatory circuity of a eukaryotic genome. Cell. v 95, 717-728, 1998
single gene deletion: Timothy r. Hughes, et. al, Functional discovery via a compendium of expression profiles. Cell, V 102, 109-126. 2000. expression data when essential gene was deleted. Sanie Mnaimneh, Exploration of essential gene functions via titratable promoter alleles. Cell, v 118, 31-44, 2004
Epigenetics data collection, nucleosome positions, modification and DNA modification.
Posted: January 23, 2007 in Data Collection[Genome-wide Measurements of nucleosome positions]A genomic code for nucleosome positioning http://www.nature.com/nature/journal/v442/n7104/pdf/nature04979.pdf three genome-wide measurements of nucleosome positions at low 29,30 or higher31 resolution. 29. Lee, C. K., Shibata, Y., Rao, B., Strahl, B. D. & Lieb, J. D. Evidence for nucleosome depletion at active regulatory regions genome-wide. Nature Genet. 36, 900–-905 (2004). 30. Bernstein, [...]
Genome Biol. 2006 Dec 21;7(12):R125 Evolutionary conservation of domain-domain interactions. Itzhaki Z, Akiva E, Altuvia Y, Margalit H. ABSTRACT: BACKGROUND: Recently, there has been much interest in relating domain-domain interactions (DDIs) to protein-protein interactions (PPIs) and vice versa, in an attempt to understand the molecular basis of PPIs. RESULTS: Here we map structurally-derived DDIs onto the [...]
