isimpson's library 257 articles Export

	Using RSAT to scan genome sequences for transcription factor binding sites and cis-regulatory modules. [My Copy] Nature protocols, Vol. 3, No. 10. (18 September 2008), pp. 1578-1588. by Jean-Valery V. Turatsinze, Morgane Thomas-Chollier, Matthieu Defrance, Jacques van Helden posted to tools tfbs prediction cis-regulatory-element by isimpson on 2009-11-16 15:33:35 as along with 7 people and 1 group kshameer heliopais druvus fhsantanna polivares idonaldson natstreet BergmanLab
	Analyzing multiple data sets by interconnecting RSAT programs via SOAP Web services: an example with ChIP-chip data. [My Copy] Nature protocols, Vol. 3, No. 10. (18 September 2008), pp. 1604-1615. by Olivier Sand, Morgane Thomas-Chollier, Eric Vervisch, Jacques van Helden posted to web-services tfbs soap prediction cis-regulatory-element by isimpson on 2009-11-16 15:32:06 as along with 2 people and 1 group druvus polivares BergmanLab
	BioMart Central Portal--unified access to biological data. [My Copy] Nucleic acids research, Vol. 37, No. Web Server issue. (1 July 2009), pp. W23-27. by Syed Haider, Benoit Ballester, Damian Smedley, Junjun Zhang, Peter Rice, Arek Kasprzyk posted to web-services soap restful perl biomart api by isimpson on 2009-11-16 15:31:01 as along with 18 people and 1 group Yanno cisevol brianb sjcockell n00c stharward VGreiff nuin joergkurtwegner natstreet druvus dullhunk H-Arrietaumn Zephyrus guhjy daforerog neils renatomilani BergmanLab
	Taverna: a tool for the composition and enactment of bioinformatics workflows. [My Copy] Bioinformatics (Oxford, England), Vol. 20, No. 17. (22 November 2004), pp. 3045-3054. by Tom Oinn, Matthew Addis, Justin Ferris, et al.Darren Marvin, Martin Senger, Mark Greenwood, Tim Carver, Kevin Glover, Matthew R. Pocock, Anil Wipat, Peter Li posted to taverna by isimpson on 2009-11-16 15:05:54 as along with 23 people and 1 group kshameer mtaschuk djohnson egonw pekrau gquigley thegoose2 tjtaylor shikin oeli4321 zufar niallhaslam druvus irenas guhjy moborg wnpx dullhunk fisherp marpin nicklynch tharris alanrw dbk-lab
	Using R in Taverna: RShell v1.2 [My Copy] BMC Research Notes, Vol. 2, No. 1. (16 July 2009), 138. by Ingo Wassink, Han Rauwerda, Pieter Neerincx, et al.Paul E. Vet, Timo Breit, Jack Leunissen, Anton Nijholt posted to taverna r plugin by isimpson on 2009-11-16 14:37:52 as along with 7 people Yanno guhjy Thaverkamp daforerog natstreet druvus dullhunk
	Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. [My Copy] Science (New York, N.Y.), Vol. 286, No. 5439. (15 October 1999), pp. 531-537. by T. R. Golub, D. K. Slonim, P. Tamayo, et al.C. Huard, M. Gaasenbeek, J. P. Mesirov, H. Coller, M. L. Loh, J. R. Downing, M. A. Caligiuri, C. D. Bloomfield, E. S. Lander posted to microarray class-discovery by isimpson on 2009-11-11 14:40:31 as along with 20 people and 2 groups srp33 ipark-kaist kentz esyoun stharward gstiglic ctaraujo ihpark winterschlaefer hhhhssss balajis sdvillal archroad giovanni santhosh ugengma jo_davies akastrin zchen raiyar Network Analysis of Genes Regulated in Renal Diseases GeschwindLab
	An introduction to scripting in Ruby for biologists. [My Copy] BMC bioinformatics, Vol. 10, No. 1. (2009), 221. by Jan Aerts, Andy Law posted to ruby programming bioinformatics by isimpson on 2009-11-05 09:45:21 as along with 25 people and 3 groups kshameer n00c Zephyrus nuin sobolevnrm jago lwaldron apaydin natstreet Stew silberbauer mfenner phoenixzxl renatomilani abhishek_tiwari rschulz sjcockell dullhunk druvus neils daforerog fgibson leemond31 brianb dswan Bioinformatics - CRUK Journal picks Bioinformatics
	Motif-Blind, Genome-Wide Discovery of cis-Regulatory Modules in Drosophila and Mouse [My Copy] Vol. 17, No. 4. (20 October 2009), pp. 568-579. by Miriam R. Kantorovitz, Majid Kazemian, Sarah Kinston, et al.Diego Miranda-Saavedra, Qiyun Zhu, Gene E. Robinson, Berthold Göttgens, Marc S. Halfon, Saurabh Sinha posted to tools tfbs prediction motifs motif-discovery algorithm by isimpson on 2009-10-27 14:16:21 as along with 1 person and 1 group daveGerrard BergmanLab
	Muscle stem cells and model systems for their investigation. [My Copy] Developmental dynamics : an official publication of the American Association of Anatomists, Vol. 236, No. 12. (December 2007), pp. 3332-3342. by Nicolas Figeac, Malgorzata Daczewska, Christophe Marcelle, Krzysztof Jagla posted to stem-cell review muscle development by isimpson on 2009-10-21 11:01:22 as
	Genome-wide transcription factor localization and function in stem cells [My Copy] StemBook (2008) by Lim posted to transcription_factor stem_cells gene_regulation differentiation by isimpson on 2009-10-14 22:50:00 as along with 1 person kshameer
	K-ary clustering with optimal leaf ordering for gene expression data [My Copy] Bioinformatics, Vol. 19, No. 9. (12 June 2003), pp. 1070-1078. by Ziv Bar-Joseph, Erik D. Demaine, David K. Gifford, Nathan Srebro, Angele M. Hamel, Tommi S. Jaakkola posted to microarray heirarchical ensemble-clustering clustering algorithm by isimpson on 2009-10-13 16:36:06 as along with 2 people tmmurali capitall
	Insect oenocytes: a model system for studying cell-fate specification by Hox genes. [My Copy] Journal of anatomy, Vol. 199, No. Pt 1-2. (g 2001), pp. 25-33. by A. P. Gould, P. R. Elstob, V. Brodu posted to oenocytes gene_regulation fate-specification by isimpson on 2009-10-08 13:36:43 as
	Antennal Circadian Clocks Coordinate Sun Compass Orientation in Migratory Monarch Butterflies [My Copy] Science, Vol. 325, No. 5948. (25 September 2009), pp. 1700-1704. by Christine Merlin, Robert J. Gegear, Steven M. Reppert posted to pns antennae by isimpson on 2009-10-02 23:20:56 as
	Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment. [My Copy] Science (New York, N.Y.), Vol. 262, No. 5131. (8 October 1993), pp. 208-214. by C. E. Lawrence, S. F. Altschul, M. S. Boguski, J. S. Liu, A. F. Neuwald, J. C. Wootton posted to wtg09 by isimpson on 2009-09-18 14:32:14 as along with 10 people rsaito Mehlhorn treangen dquest AaronDarling johncumbers jguinney xili03 seitentaisei wenhan
	BioProspector: discovering conserved DNA motifs in upstream regulatory regions of co-expressed genes. [My Copy] Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing (2001), pp. 127-138. by X. Liu, D. L. Brutlag, J. S. Liu posted to wtg09 by isimpson on 2009-09-18 14:31:05 as along with 4 people farhat wowalz heliopais dquest
	Endless forms: the evolution of gene regulation and morphological diversity. [My Copy] Cell, Vol. 101, No. 6. (9 June 2000), pp. 577-580. by S. B. Carroll posted to wtg09 gene_regulation evolution evodevo by isimpson on 2009-09-18 14:30:15 as
	Identifying Cis-Regulatory Sequences by Word Profile Similarity [My Copy] PLoS ONE, Vol. 4, No. 9. (4 September 2009), e6901. by Garmay Leung, Michael B. Eisen posted to tfbs software prediction must-read cis-regulatory-element by isimpson on 2009-09-17 14:51:07 as along with 1 person and 1 group daveGerrard BergmanLab
	Deep homology and the origins of evolutionary novelty. [My Copy] Nature, Vol. 457, No. 7231. (12 February 2009), pp. 818-823. by Neil Shubin, Cliff Tabin, Sean Carroll posted to transcription-regulation review grn evolution evodevo by isimpson on 2009-09-17 13:34:09 as along with 5 people and 1 group nhp provero tomhebbron ramiro2k jjray Jarman Lab
	Uncovering a Macrophage Transcriptional Program by Integrating Evidence from Motif Scanning and Expression Dynamics [My Copy] PLoS Comput Biol, Vol. 4, No. 3. (21 March 2008), e1000021. by Stephen A. Ramsey, Sandy L. Klemm, Daniel E. Zak, et al.Kathleen A. Kennedy, Vesteinn Thorsson, Bin Li, Mark Gilchrist, Elizabeth S. Gold, Carrie D. Johnson, Vladimir Litvak, Garnet Navarro, Jared C. Roach, Carrie M. Rosenberger, Alistair G. Rust, Natalya Yudkovsky, Alan Aderem, Ilya Shmulevich posted to tfbs must-read motifs motif-discovery bayesian by isimpson on 2009-08-26 16:53:14 as along with 3 people and 1 group nicholasflann talponer ptrobajo Jarman Lab
	A data integration framework for prediction of transcription factor targets. [My Copy] Annals of the New York Academy of Sciences, Vol. 1158 (March 2009), pp. 205-214. by Matti Nykter, Harri Lähdesmäki, Alistair Rust, Vesteinn Thorsson, Ilya Shmulevich posted to wtg09 tfbs must-read motifs motif-discovery bayesian by isimpson on 2009-08-26 16:53:14 as along with 1 group Jarman Lab
	Probabilistic Inference of Transcription Factor Binding from Multiple Data Sources [My Copy] PLoS ONE, Vol. 3, No. 3. (26 March 2008), e1820. by Harri Lähdesmäki, Alistair G. Rust, Ilya Shmulevich posted to wtg09 tfbs software must-read motifs motif-discovery bayesian by isimpson on 2009-08-26 16:49:30 as along with 4 people and 1 group nklee dolchan druvus guhjy Jarman Lab
	Genomic characterization of a repetitive motif strongly associated with developmental genes in Drosophila. [My Copy] BMC genomics, Vol. 4, No. 1. (16 December 2003) by Javier Costas, Cristina P. Vieira, Fernando Casares, Jorge Vieira posted to transcription-regulation motifs drosophila development by isimpson on 2009-08-21 09:44:03 as along with 1 person operon
	De novo identification of repeat families in large genomes. [My Copy] Bioinformatics (Oxford, England), Vol. 21 Suppl 1, No. suppl_1. (1 June 2005), pp. i351-358. by Alkes L. Price, Neil C. Jones, Pavel A. Pevzner posted to software repeats by isimpson on 2009-08-14 16:03:43 as along with 8 people sujaikumar natstreet treangen druvus aprasad hoangmit timflutre urgi
	Flynet: a genomic resource for Drosophila melanogaster transcriptional regulatory networks. [My Copy] Bioinformatics (Oxford, England), Vol. 25, No. 22. (15 November 2009), pp. 3001-3004. by Feng Tian, Parantu K. Shah, Xiangjun Liu, et al.Nicolas Negre, Jia Chen, Oleksiy Karpenko, Kevin P. White, Robert L. Grossman posted to wtg09 transcription-regulation transcription-factor software must-read grn by isimpson on 2009-08-14 11:54:03 as along with 2 people guhjy druvus
	Inferring Pathway Activity toward Precise Disease Classification [My Copy] PLoS Comput Biol, Vol. 4, No. 11. (7 November 2008), e1000217. by Eunjung Lee, Han-Yu Chuang, Jong-Won Kim, Trey Ideker, Doheon Lee posted to pathways network inference by isimpson on 2009-08-13 22:30:29 as along with 13 people rschulz yaredo frohike ipark-kaist jfr aviad_work ajbattle zufar carlk renatomilani dragonrez tmmurali ptrobajo
	Coupling and coordination in gene expression processes: a systems biology view. [My Copy] Nat Rev Genet (11 December 2007) by Suzanne Komili, Pamela A A. Silver posted to review high-dimensionality expression by isimpson on 2009-08-13 22:29:14 as along with 9 people jfr guhjy tmmurali margaritis bootsy cabbagezs Ema renatomilani klo
	Mammalian RNA polymerase II core promoters: insights from genome-wide studies. [My Copy] Nature reviews. Genetics, Vol. 8, No. 6. (08 June 2007), pp. 424-436. by Albin Sandelin, Piero Carninci, Boris Lenhard, Jasmina Ponjavic, Yoshihide Hayashizaki, David A. Hume posted to review promoter genomics by isimpson on 2009-08-13 22:27:32 as along with 16 people and 3 groups inesdesantiago megraw guhjy tonamswish maximilianh siebert rpatward Lauren_Jones agustinarce dchughes xiaobeizhao zwang cabbagezs cisevol GeeSharpMinor idonaldson G4ID Genetics-of-Gambling cis-regulatory-evolution
	The Oct4 and Nanog transcription network regulates pluripotency in mouse embryonic stem cells. [My Copy] Nature genetics, Vol. 38, No. 4. (05 April 2006), pp. 431-440. by Yuin-Han H. Loh, Qiang Wu, Joon-Lin L. Chew, et al.Vinsensius B. Vega, Weiwei Zhang, Xi Chen, Guillaume Bourque, Joshy George, Bernard Leong, Jun Liu, Kee-Yew Y. Wong, Ken W. Sung, Charlie W. Lee, Xiao-Dong D. Zhao, Kuo-Ping P. Chiu, Leonard Lipovich, Vladimir A. Kuznetsov, Paul Robson, Lawrence W. Stanton, Chia-Lin L. Wei, Yijun Ruan, Bing Lim, Huck-Hui H. Ng posted to stem-cell grn by isimpson on 2009-08-13 22:26:45 as along with 11 people inesdesantiago tonamswish guhjy cmmorel gpalidwor brixtonmc vega eukfn mikaelhuss idonaldson tdmckee
	ConTra: a promoter alignment analysis tool for identification of transcription factor binding sites across species [My Copy] Nucl. Acids Res. (3 May 2008), gkn195. by Bart Hooghe, Paco Hulpiau, Frans van Roy, Pieter De Bleser posted to transcription-factor tfbs software phylogenetics must-read motif-discovery by isimpson on 2009-08-13 22:25:40 as along with 4 people idonaldson maximilianh maralena guhjy
	A Hybrid Model for Robust Detection of Transcription Factor Binding Sites. [My Copy] Bioinformatics (9 January 2008) by Sumedha Gunewardena, Zhaolei Zhang posted to transcription-factor tfbs must-read motif-discovery by isimpson on 2009-08-13 22:24:01 as along with 3 people guhjy maximilianh idonaldson
	How to infer gene networks from expression profiles [My Copy] Molecular Systems Biology, Vol. 3 (13 February 2007) by Mukesh Bansal, Vincenzo Belcastro, Alberto Ambesi-Impiombato, Diego di Bernardo posted to review network must-read inference grn algorithm by isimpson on 2009-08-13 22:21:35 as along with 37 people and 3 groups beete tonamswish zufar nicholasflann icq242500260 guhjy Zephyrus antonkratz phoenixzxl bertelsen daforerog poirel agonzale roys Neeperando APRegier rdiaz klo Borelli ggallone ptrobajo druvus cswinburne jfr eckart_bindewald wnpx nickluscombe kengg mikaelhuss jrbanga BIBLIOma RockHI lp2 natstreet heliopais mariakmejia tmmurali Jarman Lab EBI-regulation Plantandetc
	Regulatory networks define phenotypic classes of human stem cell lines [My Copy] Nature (24 August 2008) by Franz-Josef Müller, Louise C. Laurent, Dennis Kostka, et al.Igor Ulitsky, Roy Williams, Christina Lu, In-Hyun Park, Mahendra S. Rao, Ron Shamir, Philip H. Schwartz, Nils O. Schmidt, Jeanne F. Loring posted to stem-cell specification network grn differentiation by isimpson on 2009-08-13 22:19:37 as along with 10 people and 1 group guhjy jfr zwang ajaymalik ptrobajo heliopais wsjames roys tmmurali caseybrown Oxford Virology
	Protein networks in disease. [My Copy] Genome research, Vol. 18, No. 4. (1 April 2008), pp. 644-652. by Trey Ideker, Roded Sharan posted to review network by isimpson on 2009-08-13 22:18:04 as along with 27 people shikin carlk chica saket zufar kaarsinogen giovenko guhjy balicea tmmurali Borelli jwdietrich frohike bootsy nedwards roys mclarenv phoenixzxl brianb schuylrp jfr paolomarcatili gracio thomaskelder ptrobajo raiyar zwang
	Identification of tissue-specific cis-regulatory modules based on interactions between transcription factors [My Copy] BMC Bioinformatics, Vol. 8, No. 1. (09 November 2007), 437. by Xueping Yu, Jimmy Lin, Donald Zack, Jiang Qian posted to transcription-factor tfbd must-read interaction crm cis-regulatory-element by isimpson on 2009-08-13 22:16:45 as along with 10 people roys guhjy chad_davis mikaelhuss nklee maximilianh idonaldson njcitulike bootsy snow_dragon
	Identification of the proliferation/differentiation switch in the cellular network of multicellular organisms. [My Copy] PLoS Comput Biol, Vol. 2, No. 11. (24 November 2006) by K. Xia, H. Xue, D. Dong, et al.S. Zhu, J. Wang, Q. Zhang, L. Hou, H. Chen, R. Tao, Z. Huang, Z. Fu, Y. G. Chen, J. D. Han posted to proliferation network must-read differentiation by isimpson on 2009-08-13 22:12:12 as along with 2 people and 1 group tmmurali jfr Bioinformatics
	JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update [My Copy] Nucl. Acids Res., Vol. 36, No. suppl_1. (11 January 2008), pp. D102-106. by Jan C. Bryne, Eivind Valen, Man-Hung E. Tang, et al.Troels Marstrand, Ole Winther, Isabelle da Piedade, Anders Krogh, Boris Lenhard, Albin Sandelin posted to transcription-factor tfbs database by isimpson on 2009-08-13 22:05:21 as along with 7 people natstreet druvus guhjy dullhunk idonaldson sci91078 jfr
	The properties of high-dimensional data spaces: implications for exploring gene and protein expression data [My Copy] Nat Rev Cancer, Vol. 8, No. 1. (01 January 2008), pp. 37-49. by Robert Clarke, Habtom W. Ressom, Antai Wang, et al.Jianhua Xuan, Minetta C. Liu, Edmund A. Gehan, Yue Wang posted to review high-dimensionality expression by isimpson on 2009-08-13 22:04:35 as along with 17 people and 1 group Zephyrus aviad_work ipark-kaist Scis0000002 baizhang bertelsen ptrobajo jfr guhjy tmmurali dwf frohike cjeans nedwards shikin blackm0k brianb Bioinformatics
	An integrated software system for analyzing ChIP-chip and ChIP-seq data. [My Copy] Nature biotechnology, Vol. 26, No. 11. (02 November 2008), pp. 1293-1300. by Hongkai Ji, Hui Jiang, Wenxiu Ma, David S. Johnson, Richard M. Myers, Wing H. Wong posted to software chip-seq by isimpson on 2009-08-13 22:02:25 as along with 24 people and 3 groups hzoltan fpattyn stubrown huali tonamswish ewilban1 sebastien_vigneau jfr kmdaily cassj bryankr malcook rschulz mcm behindtherabbit psique renatomilani polivares guhjy inesdesantiago pengchy kengg bais idonaldson Neuroblastoma SIMR bioinformatics BenosLab
	Identification of functional modules using network topology and high-throughput data. [My Copy] BMC systems biology, Vol. 1, No. 1. (2007), 8. by Igor Ulitsky, Ron Shamir posted to network must-read integration by isimpson on 2009-08-13 21:58:36 as along with 18 people greg akshayk ptrobajo yaredo qluo aheilbut zufar roys frohike tmmurali dragonrez jfr wnpx Ao_Li2007 lyndon bertelsen ellakat carlk
	Protein interactions and disease: computational approaches to uncover the etiology of diseases [My Copy] Brief Bioinform, Vol. 8, No. 5. (1 September 2007), pp. 333-346. by Maricel G. Kann posted to protein-interaction must-read integration by isimpson on 2009-08-13 21:56:18 as along with 8 people carlk saket winterschlaefer guhjy tmmurali jfr AbnerCYH barriot
	A statistical framework for genomic data fusion. [My Copy] Bioinformatics, Vol. 20, No. 16. (1 November 2004), pp. 2626-2635. by G. R. Lanckriet, T. D. De Bie, N. Cristianini, M. I. Jordan, W. S. Noble posted to statistics integration genomics by isimpson on 2009-08-13 21:53:56 as along with 8 people dragonrez tmmurali jfr mbeautru nedwards carlk ptrobajo mdstobbe
	Geometric interpretation of gene coexpression network analysis. [My Copy] PLoS computational biology, Vol. 4, No. 8. (15 August 2008), e1000117. by Steve Horvath, Jun Dong posted to network microarray expression by isimpson on 2009-08-13 21:52:50 as along with 22 people jeremymiller zufar dolchan sficklin rdiaz guhjy cswinburne jfr ptrobajo pengchy nolodie druvus aramesh2 kengg roys Ema tmmurali Borelli Totobox AbnerCYH davidchavalarias caseybrown
	Evolution, biogenesis, expression, and target predictions of a substantially expanded set of Drosophila microRNAs. [My Copy] Genome research, Vol. 17, No. 12. (7 December 2007), pp. 1850-1864. by J. Graham Ruby, Alexander Stark, Wendy K. Johnston, Manolis Kellis, David P. Bartel, Eric C. Lai posted to drosophila microrna by isimpson on 2009-08-06 16:59:15 as along with 9 people and 3 groups valeriehilgers pengchy hrogers stajich lp2 cabbagezs heliopais urgi Alexander_Kanitz Jarman Lab microRNA Mycology
	Detecting microRNA binding and siRNA off-target effects from expression data. [My Copy] Nature methods, Vol. 5, No. 12. (2 December 2008), pp. 1023-1025. by Stijn van Dongen, Cei Abreu-Goodger, Anton J. Enright posted to wtg09 microrna by isimpson on 2009-08-03 13:25:55 as along with 7 people and 2 groups heliopais gdb jfr valeriehilgers russel12 megraw samgj Jarman Lab microRNA
	Relationship between gene co-expression and sharing of transcription factor binding sites in Drosophila melanogaster [My Copy] Bioinformatics, Vol. 25, No. 19. (1 October 2009), pp. 2473-2477. by Antonio Marco, Charlotte Konikoff, Timothy L. Karr, Sudhir Kumar posted to microarray tfbs transcription-factor by isimpson on 2009-07-28 16:42:31 as along with 8 people and 1 group Garamonfok TRHvidsten djkt rdiaz natstreet nuin sebastien_vigneau maximilianh Jarman Lab
	Automatic clustering of orthologs and in-paralogs from pairwise species comparisons. [My Copy] Journal of molecular biology, Vol. 314, No. 5. (14 December 2001), pp. 1041-1052. by M. Remm, C. E. Storm, E. L. Sonnhammer posted to bp by isimpson on 2009-07-28 11:02:42 as along with 15 people and 3 groups biomcgary thegoose2 operon cgaugain tharris tmmurali indigoviolet Sharpshoot jhc gurkanbebek bluto incovoma ninch cerca wiedehopf C. elegans / WormBase EisenLab BioinfoCIPF
	Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. [My Copy] Nature, Vol. 447, No. 7146. (14 June 2007), pp. 799-816. by ENCODE Project Consortium, Ewan Birney, John A. Stamatoyannopoulos, et al.Anindya Dutta, Roderic Guigó, Thomas R. Gingeras, Elliott H. Margulies, Zhiping Weng, Michael Snyder, Emmanouil T. Dermitzakis, Robert E. Thurman, Michael S. Kuehn, Christopher M. Taylor, Shane Neph, Christoph M. Koch, Saurabh Asthana, Ankit Malhotra, Ivan Adzhubei, Jason A. Greenbaum, Robert M. Andrews, Paul Flicek, Patrick J. Boyle, Hua Cao, Nigel P. Carter, Gayle K. Clelland, Sean Davis, Nathan Day, Pawandeep Dhami, Shane C. Dillon, Michael O. Dorschner, Heike Fiegler, Paul G. Giresi, Jeff Goldy, Michael Hawrylycz, Andrew Haydock, Richard Humbert, Keith D. James, Brett E. Johnson, Ericka M. Johnson, Tristan T. Frum, Elizabeth R. Rosenzweig, Neerja Karnani, Kirsten Lee, Gregory C. Lefebvre, Patrick A. Navas, Fidencio Neri, Stephen C. Parker, Peter J. Sabo, Richard Sandstrom, Anthony Shafer, David Vetrie, Molly Weaver, Sarah Wilcox, Man Yu, Francis S. Collins, Job Dekker, Jason D. Lieb, Thomas D. Tullius, Gregory E. Crawford, Shamil Sunyaev, William S. Noble, Ian Dunham, France Denoeud, Alexandre Reymond, Philipp Kapranov, Joel Rozowsky, Deyou Zheng, Robert Castelo, Adam Frankish, Jennifer Harrow, Srinka Ghosh, Albin Sandelin, Ivo L. Hofacker, Robert Baertsch, Damian Keefe, Sujit Dike, Jill Cheng, Heather A. Hirsch, Edward A. Sekinger, Julien Lagarde, Josep F. Abril, Atif Shahab, Christoph Flamm, Claudia Fried, Jörg Hackermüller, Jana Hertel, Manja Lindemeyer, Kristin Missal, Andrea Tanzer, Stefan Washietl, Jan Korbel, Olof Emanuelsson, Jakob S. Pedersen, Nancy Holroyd, Ruth Taylor, David Swarbreck, Nicholas Matthews, Mark C. Dickson, Daryl J. Thomas, Matthew T. Weirauch, James Gilbert, Jorg Drenkow, Ian Bell, XiaoDong Zhao, K. G. Srinivasan, Wing-Kin K. Sung, Hong Sain S. Ooi, Kuo Ping P. Chiu, Sylvain Foissac, Tyler Alioto, Michael Brent, Lior Pachter, Michael L. Tress, Alfonso Valencia, Siew Woh W. Choo, Chiou Yu Y. Choo, Catherine Ucla, Caroline Manzano, Carine Wyss, Evelyn Cheung, Taane G. Clark, James B. Brown, Madhavan Ganesh, Sandeep Patel, Hari Tammana, Jacqueline Chrast, Charlotte N. Henrichsen, Chikatoshi Kai, Jun Kawai, Ugrappa Nagalakshmi, Jiaqian Wu, Zheng Lian, Jin Lian, Peter Newburger, Xueqing Zhang, Peter Bickel, John S. Mattick, Piero Carninci, Yoshihide Hayashizaki, Sherman Weissman, Tim Hubbard, Richard M. Myers, Jane Rogers, Peter F. Stadler, Todd M. Lowe, Chia-Lin L. Wei, Yijun Ruan, Kevin Struhl, Mark Gerstein, Stylianos E. Antonarakis, Yutao Fu, Eric D. Green, Ulaş Karaöz, Adam Siepel, James Taylor, Laura A. Liefer, Kris A. Wetterstrand, Peter J. Good, Elise A. Feingold, Mark S. Guyer, Gregory M. Cooper, George Asimenos, Colin N. Dewey, Minmei Hou, Sergey Nikolaev, Juan I. Montoya-Burgos, Ari Löytynoja, Simon Whelan, Fabio Pardi, Tim Massingham, Haiyan Huang, Nancy R. Zhang, Ian Holmes, James C. Mullikin, Abel Ureta-Vidal, Benedict Paten, Michael Seringhaus, Deanna Church, Kate Rosenbloom, W. James Kent, Eric A. Stone, NISC Comparative Sequencing Program, Baylor College of Medicine Human Genome Sequencing Center, Washington University Genome Sequencing Center, Broad Institute, Children's Hospital Oakland Research Institute, Serafim Batzoglou, Nick Goldman, Ross C. Hardison, David Haussler, Webb Miller, Arend Sidow, Nathan D. Trinklein, Zhengdong D. Zhang, Leah Barrera, Rhona Stuart, David C. King, Adam Ameur, Stefan Enroth, Mark C. Bieda, Jonghwan Kim, Akshay A. Bhinge, Nan Jiang, Jun Liu, Fei Yao, Vinsensius B. Vega, Charlie W. Lee, Patrick Ng, Atif Shahab, Annie Yang, Zarmik Moqtaderi, Zhou Zhu, Xiaoqin Xu, Sharon Squazzo, Matthew J. Oberley, David Inman, Michael A. Singer, Todd A. Richmond, Kyle J. Munn, Alvaro Rada-Iglesias, Ola Wallerman, Jan Komorowski, Joanna C. Fowler, Phillippe Couttet, Alexander W. Bruce, Oliver M. Dovey, Peter D. Ellis, Cordelia F. Langford, David A. Nix, Ghia Euskirchen, Stephen Hartman, Alexander E. Urban, Peter Kraus, Sara Van Calcar, Nate Heintzman, Tae Hoon H. Kim, Kun Wang, Chunxu Qu, Gary Hon, Rosa Luna, Christopher K. Glass, M. Geoff Rosenfeld, Shelley Force F. Aldred, Sara J. Cooper, Anason Halees, Jane M. Lin, Hennady P. Shulha, Xiaoling Zhang, Mousheng Xu, Jaafar N. Haidar, Yong Yu, Yijun Ruan, Vishwanath R. Iyer, Roland D. Green, Claes Wadelius, Peggy J. Farnham, Bing Ren, Rachel A. Harte, Angie S. Hinrichs, Heather Trumbower, Hiram Clawson, Jennifer Hillman-Jackson, Ann S. Zweig, Kayla Smith, Archana Thakkapallayil, Galt Barber, Robert M. Kuhn, Donna Karolchik, Lluis Armengol, Christine P. Bird, Paul I. de Bakker, Andrew D. Kern, Nuria Lopez-Bigas, Joel D. Martin, Barbara E. Stranger, Abigail Woodroffe, Eugene Davydov, Antigone Dimas, Eduardo Eyras, Ingileif B. Hallgrímsdóttir, Julian Huppert, Michael C. Zody, Gonçalo R. Abecasis, Xavier Estivill, Gerard G. Bouffard, Xiaobin Guan, Nancy F. Hansen, Jacquelyn R. Idol, Valerie V. Maduro, Baishali Maskeri, Jennifer C. McDowell, Morgan Park, Pamela J. Thomas, Alice C. Young, Robert W. Blakesley, Donna M. Muzny, Erica Sodergren, David A. Wheeler, Kim C. Worley, Huaiyang Jiang, George M. Weinstock, Richard A. Gibbs, Tina Graves, Robert Fulton, Elaine R. Mardis, Richard K. Wilson, Michele Clamp, James Cuff, Sante Gnerre, David B. Jaffe, Jean L. Chang, Kerstin Lindblad-Toh, Eric S. Lander, Maxim Koriabine, Mikhail Nefedov, Kazutoyo Osoegawa, Yuko Yoshinaga, Baoli Zhu, Pieter J. de Jong posted to bp by isimpson on 2009-07-28 11:02:42 as along with 25 people and 2 groups bartjacobse daveGerrard daforerog sharpton jessopher timhubbard scjparker polivares coela ilyashl aprasad myrtilus daed waszak guhjy jfr chad_davis kengg olympos blobbybirdman shikin fpattyn yevishere elfar eskay Bioinformatics UH - Computational Biology
	GOtcha: a new method for prediction of protein function assessed by the annotation of seven genomes. [My Copy] BMC Bioinformatics, Vol. 5 (18 November 2004) by D. M. Martin, M. Berriman, G. J. Barton posted to bp by isimpson on 2009-07-28 11:02:42 as along with 5 people fbristow eckart_bindewald Sharpshoot sgoetz bootsy
	Integration of external signaling pathways with the core transcriptional network in embryonic stem cells. [My Copy] Cell, Vol. 133, No. 6. (13 June 2008), pp. 1106-1117. by X. Chen, H. Xu, P. Yuan, et al.F. Fang, M. Huss, V. B. Vega, E. Wong, Y. L. Orlov, W. Zhang, J. Jiang, Y. H. Loh, H. C. Yeo, Z. X. Yeo, V. Narang, K. R. Govindarajan, B. Leong, A. Shahab, Y. Ruan, G. Bourque, W. K. Sung, N. D. Clarke, C. L. Wei, H. H. Ng posted to bp by isimpson on 2009-07-28 11:02:42 as along with 12 people and 2 groups shikin sebastien_vigneau cassj rschulz FJ fhalbrit djkt jjray inesdesantiago caseybrown kengg gdb Epigenetics CTCF
	ChIP-seq accurately predicts tissue-specific activity of enhancers [My Copy] Nature, Vol. 457, No. 7231. (12 February 2009), pp. 854-858. by Axel Visel, Matthew J. Blow, Zirong Li, et al.Tao Zhang, Jennifer A. Akiyama, Amy Holt, Ingrid Plajzer-Frick, Malak Shoukry, Crystal Wright, Feng Chen, Veena Afzal, Bing Ren, Edward M. Rubin, Len A. Pennacchio posted to chip-seq tfbs transcription transcription-factor transcription-regulation by isimpson on 2009-07-27 12:21:40 as along with 23 people and 2 groups hzoltan tonamswish ewilban1 samanthacooper ashkelon13 gdb dnewburger jochenG bertelsen oelemento rpatward cajunsushi WanderingAengus absterga provero cassj anphony dpollard caseybrown biomcgary xingxu idonaldson djkt RockmanLab cis-regulatory-evolution

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must-read	47
tfbs	28
transcription-regulation	23
review	22
transcription-factor	19
motif-discovery	18
motifs	15
ensemble-clustering	13
eccb08	12
network	12
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wtg09	10
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drosophila	9
clustering	8
database	8
evolution	7
microarray	7
proneural	7
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grn	5
pns	5
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bayesian	4
bp	4
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regulation	4
regulatory	4
site-source	4
bioinformatics	3
ciliogenesis	3
evodevo	3
gene_regulation	3
integration	3
orthologues	3
paralogues	3
r	3
stem-cell	3
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chip-seq	2
cilia	2
cilium	2
development	2
genomics	2
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microrna	2
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perl	2
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senseless	2
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taverna	2
web-services	2
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antennae	1
api	1
bhlh	1
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bootstrap	1
chordotonal	1
class-discovery	1
clest	1
combinatorial	1
comparative-genomics	1
crm	1
differential-expression	1
false_discovery_rate	1
fate-specification	1
fdr	1
genetic	1
heirarchical	1
helix-loop-helix	1
hmm	1
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interaction	1
johnstons-organ	1
literature-mining	1
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oenocytes	1
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