Dr. T. Ian Simpson's Top Recommendations

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	A survey of motif discovery methods in an integrated framework [My Copy] Biology Direct, Vol. 1, No. 1. (06 April 2006), 11. by Geir K. Sandve, Finn Drabløs posted by 14 people bsamal tomhebbron Scis0000002 maximilianh wowalz AbnerCYH aprasad dpollard samal EisenLab yevishere csdhwang idonaldson yoonk
	W-ChIPMotifs: a web application tool for de novo motif discovery from ChIP-based high-throughput data [My Copy] Bioinformatics In Bioinformatics, Vol. 25, No. 23. (1 December 2009), pp. 3191-3193. by Victor X. Jin, Jeff Apostolos, Naga S. Nagisetty, Peggy J. Farnham posted by 5 people bsamal idonaldson farhat nklee maximilianh
	Evolutionary Conserved Motif Finder (ECMFinder) for genome-wide identification of clustered YY1- and CTCF-binding sites [My Copy] Nucl. Acids Res. In Nucl. Acids Res., Vol. 37, No. 6. (1 April 2009), pp. 2003-2013. by Keunsoo Kang, Jae H. Chung, Joomyeong Kim posted by 5 people bsamal idonaldson nklee wowalz maximilianh
	Positional distribution of human transcription factor binding sites. [My Copy] Nucleic acids research (25 October 2008) by Mark Koudritsky, Eytan Domany posted by 13 people bsamal daforerog jfr jforman SIMR bioinformatics ghattem BenosLab barriot fpattyn nklee maximilianh idonaldson nuin
	Evolutionary computation for discovery of composite transcription factor binding sites [My Copy] Nucl. Acids Res. In Nucl. Acids Res., Vol. 36, No. 21. (1 December 2008), e142. by Gary B. Fogel, V. William Porto, Gabor Varga, et al.Ernst R. Dow, Andrew M. Craven, David M. Powers, Harry B. Harlow, Eric W. Su, Jude E. Onyia, Chen Su posted by 7 people bsamal nklee wowalz lptolik idonaldson davfre maximilianh
	Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data [My Copy] Nature Methods, Vol. 5, No. 9. (17 August 2008), pp. 829-834. by Anton Valouev, David S. Johnson, Andreas Sundquist, et al.Catherine Medina, Elizabeth Anton, Serafim Batzoglou, Richard M. Myers, Arend Sidow posted by 23 people torfinnnome bsamal jwfoley ewilban1 nklee bertelsen Mycology stajich smiddha clearbluespring WanderingAengus polivares ptrobajo mdperry idonaldson gdb megraw kengg alhufton guhjy kjglennie bryankr maximilianh
	A deterministic motif finding algorithm with application to the human genome [My Copy] Bioinformatics In Bioinformatics, Vol. 22, No. 9. (1 May 2006), pp. 1047-1054. by Lawrence S. Hon, Ajay N. Jain posted by 8 people bsamal wowalz shwu idonaldson dquest nklee Motif Discovery maximilianh
	CEAS: cis-regulatory element annotation system [My Copy] Bioinformatics, Vol. 25, No. 19. (1 October 2009), pp. 2605-2606. by Hyunjin Shin, Tao Liu, Arjun K. Manrai, X. Shirley Liu posted by 7 people bsamal maximilianh druvus ewilban1 guhjy idonaldson nuin
	Measuring spatial preferences at fine-scale resolution identifies known and novel cis-regulatory element candidates and functional motif-pair relationships [My Copy] Nucleic acids research In Nucl. Acids Res., Vol. 37, No. 13. (1 July 2009), e92. by Ken D. Yokoyama, Uwe Ohler, Gregory A. Wray posted by 3 people bsamal idonaldson maximilianh
	DISCOVER: a feature-based discriminative method for motif search in complex genomes [My Copy] Bioinformatics (Oxford, England) In Bioinformatics, Vol. 25, No. 12. (15 June 2009), pp. i321-329. by Wenjie Fu, Pradipta Ray, Eric P. Xing posted by 8 people bsamal guhjy dquest Bioinformatics - CRUK Stew idonaldson thegoose maximilianh
	Efficient exact motif discovery [My Copy] Bioinformatics (Oxford, England) In Bioinformatics, Vol. 25, No. 12. (15 June 2009), pp. i356-364. by Tobias Marschall, Sven Rahmann posted by 6 people bsamal wowalz dquest nuin idonaldson maximilianh
	MEME SUITE: tools for motif discovery and searching. [My Copy] Nucleic acids research, Vol. 37, No. Web Server issue. (1 July 2009), pp. W202-208. by Timothy L. Bailey, Mikael Boden, Fabian A. Buske, et al.Martin Frith, Charles E. Grant, Luca Clementi, Jingyuan Ren, Wilfred W. Li, William S. Noble posted by 8 people bsamal suizifish jlike maximilianh natstreet idonaldson nuin cassj
	New scoring schema for finding motifs in DNA Sequences [My Copy] BMC Bioinformatics, Vol. 10 (20 March 2009), 93. by Fatemeh, Bahram Goliaei posted by 8 people bsamal svenrahmann cassj idonaldson maximilianh cube_and_beyond ElenaGrassi nuin
	TFCat: the curated catalog of mouse and human transcription factors. [My Copy] Genome biology, Vol. 10, No. 3. (2009) by Debra L. Fulton, Saravanan Sundararajan, Gwenael Badis, et al.Timothy R. Hughes, Wyeth W. Wasserman, Jared C. Roach, Rob Sladek posted by 10 people bsamal maximilianh megraw natstreet idonaldson bmajoros dolchan BergmanLab cisevol druvus
	Finding evolutionarily conserved cis-regulatory modules with a universal set of motifs [My Copy] BMC Bioinformatics, Vol. 10, No. 1. (2009), 82. by Bartek Wilczynski, Norbert Dojer, Mateusz Patelak, Jerzy Tiuryn posted by 13 people bsamal daveGerrard ilyashl svenrahmann idonaldson maximilianh bmajoros nuin idoerg cis-regulatory-evolution BergmanLab cisevol dquest
	PASTAA: identifying transcription factors associated with sets of co-regulated genes [My Copy] Bioinformatics In Bioinformatics, Vol. 25, No. 4. (15 February 2009), pp. 435-442. by Helge G. Roider, Thomas Manke, Sean O'Keeffe, Martin Vingron, Stefan A. Haas posted by 13 people bsamal TRHvidsten maximilianh jimineep cassj idonaldson Bioinformatics dswan djkt dolchan nuin natstreet druvus
	MotifVoter: a novel ensemble method for fine-grained integration of generic motif finders [My Copy] Bioinformatics (Oxford, England) In Bioinformatics, Vol. 24, No. 20. (15 October 2008), pp. 2288-2295. by Edward Wijaya, Siu-Ming Yiu, Ngo T. Son, Rajaraman Kanagasabai, Wing-Kin Sung posted by 7 people bsamal wowalz druvus nuin chad_davis maximilianh idonaldson
	RSAT: regulatory sequence analysis tools [My Copy] Nucl. Acids Res. (21 May 2008), gkn304. by Morgane Thomas-Chollier, Olivier Sand, Jean-Valery Turatsinze, et al.Rekin's Janky, Matthieu Defrance, Eric Vervisch, Sylvain Brohee, Jacques van Helden posted by 8 people bsamal cassj idonaldson natstreet druvus maximilianh guhjy dullhunk
	TFBScluster web server for the identification of mammalian composite regulatory elements [My Copy] Nucleic Acids Res In Nucl. Acids Res., Vol. 34, No. suppl_2. (1 July 2006), pp. W524-528. by Ian J. Donaldson, Berthold Gottgens posted by 3 people bsamal maximilianh idonaldson
	Natural similarity measures between position frequency matrices with an application to clustering [My Copy] Bioinformatics In Bioinformatics, Vol. 24, No. 3. (1 February 2008), pp. 350-357. by Utz J. Pape, Sven Rahmann, Martin Vingron posted by 6 people bsamal nklee maximilianh mclarenv csdhwang kmdaily
	SPACER: identification of cis-regulatory elements with non-contiguous critical residues [My Copy] Bioinformatics In Bioinformatics, Vol. 23, No. 8. (15 April 2007), pp. 1029-1031. by Arijit Chakravarty, Jonathan M. Carlson, Radhika S. Khetani, Charles E. DeZiel, Robert H. Gross posted by 5 people bsamal nklee maximilianh wenhan csdhwang
	Analysis of computational approaches for motif discovery [My Copy] Algorithms for Molecular Biology, Vol. 1, No. 1. (19 May 2006), 8. by Nan Li, Martin Tompa posted by 15 people bsamal wowalz yevishere ana barry tuck chad_davis dquest lusk nklee structural_bioinformatics Bioinformatics maximilianh xi03 csdhwang
	Distinguishing direct versus indirect transcription factor-DNA interactions. [My Copy] Genome research, Vol. 19, No. 11. (3 November 2009), pp. 2090-2100. by Raluca Gordân, Alexander J. Hartemink, Martha L. Bulyk posted by 14 people roys sebastien_vigneau oannes nklee djkt vingron venancio owhitney tmmurali emptyhb idonaldson maximilianh jbhiatt frohike
	28-Way vertebrate alignment and conservation track in the UCSC Genome Browser [My Copy] Genome Res. (5 November 2007), gr.6761107. by Webb Miller, Kate Rosenbloom, Ross C. Hardison, et al.Minmei Hou, James Taylor, Brian Raney, Richard Burhans, David C. King, Robert Baertsch, Daniel Blankenberg, Kosakovsky, Anton Nekrutenko, Belinda Giardine, Robert S. Harris, Svitlana Tyekucheva, Mark Diekhans, Thomas H. Pringle, William J. Murphy, Arthur Lesk, George M. Weinstock, Kerstin Lindblad-Toh, Richard A. Gibbs, Eric S. Lander, Adam Siepel, David Haussler, James W. Kent posted by 12 people rschulz aprasad dchughes nklee maximilianh idonaldson fpattyn gjuggler clearbluespring joavah AaronDarling guhjy
	A Universal Framework for Regulatory Element Discovery across All Genomes and Data Types [My Copy] Molecular Cell, Vol. 28, No. 2. (26 October 2007), pp. 337-350. by Olivier Elemento, Noam Slonim, Saeed Tavazoie posted by 20 people cerca ilyashl TRHvidsten leelarcombe kieran101 ana brant cwbrown aswin cjeans zwang cabbagezs nklee EisenLab maximilianh idonaldson sb_journal_club kristen barwil Motif Discovery
	Discriminative motif discovery in DNA and protein sequences using the DEME algorithm. [My Copy] BMC bioinformatics, Vol. 8, No. 1. (2007) by E. Redhead, T. L. Bailey posted by 9 people wowalz tmarscha dpollard cjeans nklee niallhaslam EisenLab maximilianh idonaldson
	Informative priors based on transcription factor structural class improve de novo motif discovery [My Copy] Bioinformatics, Vol. 22, No. 14. (15 July 2006), pp. e384-392. by Leelavati Narlikar, Raluca Gordan, Uwe Ohler, Alexander J. Hartemink posted by 7 people frohike megraw maximilianh dquest nklee idonaldson yevishere
	Insights from genomic profiling of transcription factors [My Copy] Nature Reviews Genetics, Vol. 10, No. 9. (11 August 2009), pp. 605-616. by Peggy J. Farnham posted by 25 people vingron roys guhjy provero bsamal heliopais inesdesantiago fenghezi nklee samanthacooper fpattyn druvus frohike stubrown Journal picks qayub megraw TRHvidsten Chinnaiyan Lab mkiyer ericrpaquet ilyashl jbhiatt idonaldson danmaclean
	Computational methods for the detection of cis-regulatory modules [My Copy] Brief Bioinform In Brief Bioinform, Vol. 10, No. 5. (4 June 2009), pp. bbp025-524. by Peter V. Loo, Peter Marynen posted by 8 people bsamal reyez idonaldson kshameer nklee BergmanLab cisevol druvus
	Hierarchical hidden Markov model with application to joint analysis of ChIP-chip and ChIP-seq data [My Copy] Bioinformatics (Oxford, England) In Bioinformatics, Vol. 25, No. 14. (15 July 2009), pp. 1715-1721. by Hyungwon Choi, Alexey I. Nesvizhskii, Debashis Ghosh, Zhaohui S. Qin posted by 15 people bsamal jfr tonamswish rdiaz fpattyn Journal picks jcbarret guhjy hendrik85 inesdesantiago nklee polivares ewilban1 idonaldson humburg
	MotifMap: a human genome-wide map of candidate regulatory motif sites [My Copy] Bioinformatics, Vol. 25, No. 2. (15 January 2009), pp. 167-174. by Xiaohui Xie, Paul Rigor, Pierre Baldi posted by 13 people bsamal jakebiesinger kmdaily guhjy wowalz ilyashl jfr abizar heliopais nklee idonaldson nuin djkt
	A practical comparison of methods for detecting transcription factor binding sites in ChIP-seq experiments. [My Copy] BMC genomics, Vol. 10, No. 1. (18 December 2009), 618. by Teemu D. Laajala, Sunil Raghav, Soile Tuomela, Riitta Lahesmaa, Tero Aittokallio, Laura L. Elo posted by 2 people maximilianh idonaldson
	DISPARE: DIScriminative PAttern REfinement for Position Weight Matrices [My Copy] BMC Bioinformatics, Vol. 10, No. 1. (26 November 2009), 388. by Isabelle da Piedade, Man H. Tang, Olivier Elemento posted by 5 people idonaldson maximilianh oelemento barriot bedo
	Combinatorial binding predicts spatio-temporal cis-regulatory activity [My Copy] Nature In Nature, Vol. 462, No. 7269. (05 November 2009), pp. 65-70. by Robert P. Zinzen, Charles Girardot, Julien Gagneur, Martina Braun, Eileen E. M. Furlong posted by 15 people gderwin idonaldson maximilianh cajunsushi emptyhb toszko roys inesdesantiago fenghezi balabu iskathy djkt megraw TRHvidsten pedrobeltrao
	Profiling the Human Protein-DNA Interactome Reveals ERK2 as a Transcriptional Repressor of Interferon Signaling [My Copy] Cell, Vol. 139, No. 3. (30 October 2009), pp. 610-622. by Shaohui Hu, Zhi Xie, Akishi Onishi, et al.Xueping Yu, Lizhi Jiang, Jimmy Lin, Hee-sool Rho, Crystal Woodard, Hong Wang, Jun-Seop Jeong posted by 5 people psique tmmurali renatomilani idonaldson maximilianh
	Discovering multiple realistic TFBS motifs based on a generalized model [My Copy] BMC Bioinformatics, Vol. 10, No. 1. (7 October 2009), 321. by Tak M. Chan, Gang Li, Kwong S. Leung, Kin H. Lee posted by 5 people nuin heliopais idonaldson maximilianh ashishanand
	CpG-depleted promoters harbor tissue-specific transcription factor binding signals--implications for motif overrepresentation analyses [My Copy] Nucl. Acids Res., Vol. 37, No. 19. (1 October 2009), pp. 6305-6315. by Helge G. Roider, Boris Lenhard, Aditi Kanhere, Stefan A. Haas, Martin Vingron posted by 5 people bmajoros BergmanLab daveGerrard idonaldson maximilianh
	RegAnalyst: a web interface for the analysis of regulatory motifs, networks and pathways. [My Copy] Nucleic acids research, Vol. 37, No. Web Server issue. (1 July 2009), gkp388. by Deepak Sharma, Debasisa Mohanty, Avadhesha Surolia posted by 5 people maximilianh idonaldson guhjy renatomilani cassj
	Dynamic reprogramming of transcription factors to and from the subtelomere. [My Copy] Genome research, Vol. 19, No. 6. (16 June 2009), pp. 1014-1025. by H. C. Mak, L. Pillus, T. Ideker posted by 7 people megraw HawkinsJohnC epigenetics idonaldson JustinCrocker maximilianh BenosLab
	Genome-wide discovery of functional transcription factor binding sites by comparative genomics: The case of Stat3 [My Copy] Proceedings of the National Academy of Sciences (12 March 2009) by Francesco Vallania, Davide Schiavone, Sarah Dewilde, et al.Emanuela Pupo, Serge Garbay, Raffaele Calogero, Marco Pontoglio, Paolo Provero, Valeria Poli posted by 3 people maximilianh idonaldson merpublic
	Local DNA topography correlates with functional noncoding regions of the human genome. [My Copy] Science (New York, N.Y.), Vol. 324, No. 5925. (17 April 2009), pp. 389-392. by Stephen C. Parker, Loren Hansen, Hatice Ozel O. Abaan, Thomas D. Tullius, Elliott H. Margulies posted by 47 people provero rsaito BergmanLab daveGerrard operon sujaikumar antonkratz pradiptaray roys gjuggler benjaminsb gdb hagechouchin443 tomtullius scjparker psique orzenil emptyhb ilyashl coela VGreiff APRegier myzhang pkonings akundaje athma absterga rpatward timflutre Mycology stajich bpcusack jbhiatt djkt structural_bioinformatics dhlbh friendpine RockmanLab EisenLab cis-regulatory-evolution dpollard inesdesantiago JustinCrocker aprasad maximilianh idonaldson kshundyak
	ModuleDigger: an itemset mining framework for the detection of cis-regulatory modules. [My Copy] BMC bioinformatics, Vol. 10 Suppl 1 (2009) by H. Sun, T. De Bie, V. Storms, et al.Q. Fu, T. Dhollander, K. Lemmens, A. Verstuyf, B. De Moor, K. Marchal posted by 2 people maximilianh idonaldson
	A Bayesian Hidden Markov Model for Motif Discovery Through Joint Modeling of Genomic Sequence and ChIP-Chip Data [My Copy] Biometrics, Vol. 9999, No. 9999. (2009) by Jonathan A. L. Gelfond, Mayetri Gupta, Joseph G. Ibrahim posted by 3 people wowalz maximilianh idonaldson
	Extracting transcription factor binding sites from unaligned gene sequences with statistical models. [My Copy] BMC bioinformatics, Vol. 9 Suppl 12 (2008) by C. C. Lu, W. H. Yuan, T. M. Chen posted by 5 people Mycology stajich kristallreiner idonaldson maximilianh
	A predictive model for identifying mini-regulatory modules in the mouse genome. [My Copy] Bioinformatics (Oxford, England) (3 December 2008) by Mahesh Yaragatti, Ted Sandler, Lyle Ungar posted by 7 people TRHvidsten cassj djkt idonaldson druvus operon maximilianh
	Transcriptional enhancement by GATA1-occupied DNA segments is strongly associated with evolutionary constraint on the binding site motif. [My Copy] Genome research, Vol. 18, No. 12. (25 December 2008), pp. 1896-1905. by Yong Cheng, David C. King, Louis C. Dore, et al.Xinmin Zhang, Yuepin Zhou, Ying Zhang, Christine Dorman, Demesew Abebe, Swathi A. Kumar, Francesca Chiaromonte, Webb Miller, Roland D. Green, Mitchell J. Weiss, Ross C. Hardison posted by 3 people idonaldson emptyhb maximilianh
	Retroviral promoters in the human genome [My Copy] Bioinformatics, Vol. 24, No. 14. (15 July 2008), pp. 1563-1567. by Andrew B. Conley, Jittima Piriyapongsa, King I. Jordan posted by 5 people idonaldson BergmanLab maximilianh cisevol cis-regulatory-evolution
	The biological function of some human transcription factor binding motifs varies with position relative to the transcription start site. [My Copy] Nucleic acids research, Vol. 36, No. 8. (26 May 2008), pp. 2777-2786. by Kannan Tharakaraman, Olivier Bodenreider, David Landsman, John L. Spouge, Leonardo Mariño-Ramírez posted by 5 people daforerog maximilianh fpattyn idonaldson inesdesantiago
	Generic eukaryotic core promoter prediction using structural features of DNA [My Copy] Genome Research, Vol. 18, No. 2. (20 February 2008), pp. 310-323. by Thomas Abeel, Yvan Saeys, Eric Bonnet, Pierre RouzÃ©, Yves Van de Peer posted by 10 people provero timflutre chvlyl hagechouchin443 rsaito tonamswish cjeans cabbagezs maximilianh idonaldson
	Conserved eukaryotic transposable elements and the evolution of gene regulation. [My Copy] Cell Mol Life Sci (20 November 2007) by J Jurka posted by 8 people gpappas dchughes Stew maximilianh cisevol cis-regulatory-evolution idonaldson BergmanLab
	A code for transcription initiation in mammalian genomes. [My Copy] Genome research, Vol. 18, No. 1. (21 January 2008), pp. 1-12. by M. C. Frith, E. Valen, A. Krogh, Y. Hayashizaki, P. Carninci, A. Sandelin posted by 13 people megraw guhjy rpatward inesdesantiago myrtilus dchughes cabbagezs maximilianh idonaldson oelemento gjuggler ohara gracio
	Predicting combinatorial binding of transcription factors to regulatory elements in the human genome by association rule mining [My Copy] BMC Bioinformatics, Vol. 8, No. 1. (2007) by Xochitl Morgan, Shulin Ni, Daniel Miranker, Vishwanath Iyer posted by 5 people maximilianh barriot idonaldson dps sconlan
	Discovering motifs with transcription factor domain knowledge. [My Copy] Pac Symp Biocomput (2007), pp. 472-483. by H. C. Leung, F. Y. Chin, B. M. Chan posted by 2 people maximilianh idonaldson
	Gata2, Fli1, and Scl form a recursively wired gene-regulatory circuit during early hematopoietic development. [My Copy] Proc Natl Acad Sci U S A (25 October 2007) by John E E. Pimanda, Katrin Ottersbach, Kathy Knezevic, et al.Sarah Kinston, Wan Y I Y. Chan, Nicola K K. Wilson, Josette-Renée R. Landry, Andrew D D. Wood, Anja Kolb-Kokocinski, Anthony R R. Green, David Tannahill, Georges Lacaud, Valerie Kouskoff, Berthold Göttgens posted by 3 people jjray maximilianh idonaldson
	A Quick Guide to Teaching R Programming to Computational Biology Students [My Copy] PLoS Comput Biol, Vol. 5, No. 8. (28 August 2009), e1000482. by Stephen J. Eglen posted by 72 people mgaldino provero PabloMarin idonaldson bsamal nuin kaliczp maren sobolevnrm ltitodem zchen75 artaban421 natstreet jasonn tomhebbron psique Bioinformatics - CRUK Stew eshirdel guhjy polivares ajw fishtank diamantis fastjoe23 kshameer daveGerrard hrogers JoeBanks BergmanLab cisevol srijit hwright Ayest VGreiff welliegirl asadrahman rdiaz ptrobajo heliopais coffeerv Vincent_Rouilly marekrud tnhh barry ansobol Zephyrus walshtp bertelsen fgibson pkonings Borelli klauso dlizcano dswan skembel djkt jclau lwaldron phoenixzxl timhubbard eLearning in Leicester AJCann thegoose dullhunk brianb neils silberbauer daforerog Journal picks ppgardne druvus
	Statistical detection of cooperative transcription factors with similarity adjustment [My Copy] Bioinformatics (Oxford, England) In Bioinformatics, Vol. 25, No. 16. (15 August 2009), pp. 2103-2109. by Utz J. Pape, Holger Klein, Martin Vingron posted by 4 people bsamal idonaldson TRHvidsten djkt
	Identifying regulatory elements in eukaryotic genomes [My Copy] Brief Funct Genomic Proteomic In Brief Funct Genomic Proteomic, Vol. 8, No. 4. (1 July 2009), pp. 215-230. by Leelavati Narlikar, Ivan Ovcharenko posted by 6 people bsamal daveGerrard Journal picks ppgardne natstreet idonaldson
	WebGBrowse--a web server for GBrowse. [My Copy] Bioinformatics (Oxford, England), Vol. 25, No. 12. (15 June 2009), pp. 1550-1551. by Ram Podicheti, Rajesh Gollapudi, Qunfeng Dong posted by 10 people bsamal guhjy idonaldson Bioinformatics dswan nuin operon orzenil natstreet druvus
	ProbeMatch: rapid alignment of oligonucleotides to genome allowing both gaps and mismatches [My Copy] Bioinformatics, Vol. 25, No. 11. (1 June 2009), pp. 1424-1425. by You Jung Kim, Nikhil Teletia, Victor Ruotti, et al.Christopher A. Maher, Arul M. Chinnaiyan, Ron Stewart, James A. Thomson, Jignesh M. Patel posted by 17 people bsamal Julien_Fayolle Bioinformatics jfr mmartin n00c guhjy nuin idonaldson Journal picks AlexBateman bmajoros humburg Thaverkamp druvus svenrahmann djkt
	COTRASIF: conservation-aided transcription-factor-binding site finder [My Copy] Nucl. Acids Res. In Nucl. Acids Res., Vol. 37, No. 7. (1 April 2009), e49. by Bogdan Tokovenko, Rostyslav Golda, Oleksiy Protas, Maria Obolenskaya, Anna El'skaya posted by 6 people bsamal Ensembl Compara citations avilella druvus nuin idonaldson
	RNA-Seq: a revolutionary tool for transcriptomics [My Copy] Nature Reviews Genetics, Vol. 10, No. 1. (01 January 2009), pp. 57-63. by Zhong Wang, Mark Gerstein, Michael Snyder posted by 45 people bsamal zufar CUBES hongkeun_park ngehlenborg hzoltan sandfire maren jwfoley urgi RNA-protein cthachuk heliopais GustavoLacerda rdiaz TRHvidsten dswan roys woodson8 jonilaserson gdb n00c ThomasDOtto burak natstreet athma druvus tonamswish fishtank daed JohnBallam jmcq dandaman cassj xingxu idonaldson raiyar inesdesantiago vplagnol jbhiatt giovanni orzenil nuin guhjy GeeSharpMinor
	DiRE: identifying distant regulatory elements of co-expressed genes [My Copy] Nucl. Acids Res. In Nucl. Acids Res., Vol. 36, No. suppl_2. (1 July 2008), pp. W133-139. by Valer Gotea, Ivan Ovcharenko posted by 6 people bsamal tonamswish wowalz heliopais Borelli idonaldson
	Jane: suggesting journals, finding experts [My Copy] Bioinformatics, Vol. 24, No. 5. (1 March 2008), pp. 727-728. by Martijn J. Schuemie, Jan A. Kors posted by 11 people bsamal freesci druvus guhjy chad_davis dullhunk farhat idonaldson renatomilani Barend merj
	Mining biological networks for unknown pathways [My Copy] Bioinformatics In Bioinformatics, Vol. 23, No. 20. (15 October 2007), pp. 2775-2783. by Ali Cakmak, Gultekin Ozsoyoglu posted by 10 people bsamal cswinburne guhjy tmmurali bluto shigepong cabbagezs idonaldson acakmak mdstobbe
	A computational genomics approach to identify cis-regulatory modules from chromatin immunoprecipitation microarray dataâA case study using E2F1 [My Copy] Genome Res In Genome Research, Vol. 16, No. 12. (19 December 2006), pp. 1585-1595. by Victor X. Jin, Alina Rabinovich, Sharon L. Squazzo, Roland Green, Peggy J. Farnham posted by 4 people bsamal aprasad jfr idonaldson
	Martini: using literature keywords to compare gene sets [My Copy] Nucl. Acids Res., Vol. 38, No. 1. (1 January 2010), pp. 26-38. by Theodoros G. Soldatos, Sean I. O'Donoghue, Venkata P. Satagopam, et al.Lars J. Jensen, Nigel P. Brown, Adriano Barbosa-Silva, Reinhard Schneider posted by 2 people idonaldson bsamal
	Modeling tissue-specific structural patterns in human and mouse promoters [My Copy] Nucl. Acids Res. In Nucl. Acids Res., Vol. 38, No. 1. (1 January 2010), pp. 17-25. by Alexis Vandenbon, Kenta Nakai posted by 2 people idonaldson bsamal
	CORE_TF: a user-friendly interface to identify evolutionary conserved transcription factor binding sites in sets of co-regulated genes. [My Copy] BMC bioinformatics, Vol. 9, No. 1. (2008), 495. by Matthew S. Hestand, Michiel van Galen, Michel P. Villerius, Gert-Jan J. van Ommen, Johan T. den Dunnen, Peter A. 't Hoen posted by 12 people bsamal farhat Ensembl Compara citations avilella heliopais lptolik nklee nuin GustavoLacerda natstreet maximilianh druvus
	Motif Tool Manager: a web-based framework for motif discovery [My Copy] Bioinformatics (Oxford, England) In Bioinformatics, Vol. 24, No. 24. (15 December 2008), pp. 2930-2931. by Vinhthuy Phan, Nicholas A. Furlotte posted by 7 people bsamal wowalz nklee maximilianh nuin natstreet druvus
	Locating mammalian transcription factor binding sites: A survey of computational and experimental techniques [My Copy] Genome Research In Genome Research, Vol. 16, No. 12. (19 December 2006), pp. 1455-1464. by Laura Elnitski, Victor X. Jin, Peggy J. Farnham, Steven J. M. Jones posted by 15 people bsamal matted gdb wowalz Bioinformatics - CRUK Stew heliopais dquest bryankr giovanni lusk SeungjoonOh cabbagezs GeschwindLab maximilianh
	CoMoDis: composite motif discovery in mammalian genomes. [My Copy] Nucleic Acids Res, Vol. 35, No. 1. (2007) by I. J. Donaldson, B. Göttgens posted by 3 people Bioinformatics idonaldson csdhwang
	Computational discovery of cis-regulatory modules in Drosophila without prior knowledge of motifs [My Copy] Genome Biology, Vol. 9, No. 1. (28 January 2008), R22. by Andra Ivan, Marc Halfon, Saurabh Sinha posted by 5 people roys maximilianh cisevol cis-regulatory-evolution csdhwang
	Effective transcription factor binding site prediction using a combination of optimization, a genetic algorithm and discriminant analysis to capture distant interactions [My Copy] BMC Bioinformatics, Vol. 8, No. 1. (2007) by Victor Levitsky, Elena Ignatieva, Elena Ananko, et al.Igor Turnaev, Tatyana Merkulova, Nikolay Kolchanov, T. Hodgman posted by 6 people druvus nklee maximilianh yevishere csdhwang xili03
	Global analysis of in vivo Foxa2-binding sites in mouse adult liver using massively parallel sequencing [My Copy] Nucl. Acids Res., Vol. 36, No. 14. (1 August 2008), pp. 4549-4564. by Elizabeth D. Wederell, Mikhail Bilenky, Rebecca Cullum, et al.Nina Thiessen, Melis Dagpinar, Allen Delaney, Richard Varhol, Yongjun Zhao, Thomas Zeng, Bridget Bernier, Matthew Ingham, Martin Hirst, Gordon Robertson, Marco A. Marra, Steven Jones, Pamela A. Hoodless posted by 1 person idonaldson
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	Comparative genome analysis across a kingdom of eukaryotic organisms: Specialization and diversification in the Fungi [My Copy] Genome Res. (5 November 2007), gr.6531807. by Michael J. Cornell, Intikhab Alam, Darren M. Soanes, et al.Han M. Wong, Cornelia Hedeler, Norman W. Paton, Magnus Rattray, Simon J. Hubbard, Nicholas J. Talbot, Stephen G. Oliver posted by 8 people stajich grahamc GustavoLacerda nklee idonaldson Mycology seitentaisei alanrw
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	An improved map of conserved regulatory sites for Saccharomyces cerevisiae [My Copy] BMC Bioinformatics, Vol. 7, No. 1. (7 March 2006), 113. by Kenzie Macisaac, Ting Wang, D. Benjamin Gordon, David Gifford, Gary Stormo, Ernest Fraenkel posted by 10 people roys idonaldson tuck eckart_bindewald cconboy raiyar lusk nklee barwil kristallreiner
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	The balance of reproducibility, sensitivity, and specificity of lists of differentially expressed genes in microarray studies. [My Copy] BMC bioinformatics, Vol. 9 Suppl 9, No. Suppl 9. (2008), S10. by Leming Shi, Wendell D. Jones, Roderick V. Jensen, et al.Stephen C. Harris, Roger G. Perkins, Federico M. Goodsaid, Lei Guo, Lisa J. Croner, Cecilie Boysen, Hong Fang, Feng Qian, Shashi Amur, Wenjun Bao, Catalin C. Barbacioru, Vincent Bertholet, Xiaoxi Megan M. Cao, Tzu-Ming M. Chu, Patrick J. Collins, Xiao-Hui H. Fan, Felix W. Frueh, James C. Fuscoe, Xu Guo, Jing Han, Damir Herman, Huixiao Hong, Ernest S. Kawasaki, Quan-Zhen Z. Li, Yuling Luo, Yunqing Ma, Nan Mei, Ron L. Peterson, Raj K. Puri, Richard Shippy, Zhenqiang Su, Yongming Andrew A. Sun, Hongmei Sun, Brett Thorn, Yaron Turpaz, Charles Wang, Sue Jane J. Wang, Janet A. Warrington, James C. Willey, Jie Wu, Qian Xie, Liang Zhang, Lu Zhang, Sheng Zhong, Russell D. Wolfinger, Weida Tong posted by 23 people bertelsen frohike bsamal maximilianh GustavoG mayercd Zephyrus daforerog oliviawi zufar bandrewfox lwaldron mdharsee shikin rdiaz jfr ugengma Bioinformatics dswan guhjy GeeSharpMinor ptrobajo Jonesy
	STREAM: Static Thermodynamic REgulAtory Model of transcription [My Copy] Bioinformatics (Oxford, England) In Bioinformatics, Vol. 24, No. 21. (1 November 2008), pp. 2544-2545. by Denis C. Bauer, Timothy L. Bailey posted by 3 people bsamal lptolik maximilianh
	MOPAT: a graph-based method to predict recurrent cis-regulatory modules from known motifs [My Copy] Nucl. Acids Res. In Nucl. Acids Res., Vol. 36, No. 13. (1 August 2008), pp. 4488-4497. by Jianfei Hu, Haiyan Hu, Xiaoman Li posted by 4 people bsamal fenghezi wowalz maximilianh
	Predicting functional transcription factor binding through alignment-free and affinity-based analysis of orthologous promoter sequences [My Copy] Bioinformatics In Bioinformatics, Vol. 24, No. 13. (1 July 2008), pp. i165-171. by Lucas D. Ward, Harmen J. Bussemaker posted by 8 people bsamal mox druvus kittipat emptyhb hplatero xili03 maximilianh
	TREMOR a tool for retrieving transcriptional modules by incorporating motif covariance [My Copy] Nucl. Acids Res. In Nucl. Acids Res., Vol. 35, No. 21. (18 December 2007), pp. 7360-7371. by Larry N. Singh, Li-San Wang, Sridhar Hannenhalli posted by 3 people bsamal tmmurali maximilianh
	CoMoDis: composite motif discovery in mammalian genomes [My Copy] Nucleic Acids Research In Nucl. Acids Res., Vol. 35, No. 1. (12 January 2007), pp. e1-e1. by Ian J. Donaldson, Berthold Gottgens posted by 4 people bsamal maximilianh wowalz dquest
	Practical Strategies for Discovering Regulatory DNA Sequence Motifs [My Copy] PLoS Comput Biol, Vol. 2, No. 4. (28 April 2006), e36. by Kenzie D. MacIsaac, Ernest Fraenkel posted by 21 people bsamal Jporci leemond31 Dulce maximilianh heliopais daforerog natstreet druvus giovenko nuin bryankr ana chad_davis balicea hggr GustavoLacerda structural_bioinformatics Bioinformatics svdate kristallreiner
	A systematic model to predict transcriptional regulatory mechanisms based on overrepresentation of transcription factor binding profiles [My Copy] Genome Res In Genome Research, Vol. 16, No. 3. (March 2006), pp. 405-413. by Li-Wei Chang, Rakesh Nagarajan, Jeffrey A. Magee, Jeffrey Milbrandt, Gary D. Stormo posted by 7 people bsamal maximilianh heliopais jfr vega johncumbers sconlan
	Fast and practical algorithms for planted (l, d) motif search. [My Copy] IEEE/ACM transactions on computational biology and bioinformatics / IEEE, ACM, Vol. 4, No. 4. (c 2007), pp. 544-552. by J. Davila, S. Balla, S. Rajasekaran posted by 3 people wowalz maximilianh csdhwang