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	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
	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
	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
	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
	ConTra: a promoter alignment analysis tool for identification of transcription factor binding sites across species [My Copy] Nucl. Acids Res. In Nucl. Acids Res., Vol. 36, No. suppl_2. (1 July 2008), pp. W128-132. 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 5 people bsamal idonaldson maximilianh maralena guhjy
	A hybrid model for robust detection of transcription factor binding sites [My Copy] Bioinformatics In Bioinformatics, Vol. 24, No. 4. (15 February 2008), pp. 484-491. 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 4 people bsamal guhjy maximilianh idonaldson
	JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update [My Copy] Nucl. Acids Res. In 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 8 people bsamal natstreet druvus guhjy dullhunk idonaldson sci91078 jfr
	Relationship between gene co-expression and sharing of transcription factor binding sites in Drosophila melanogaster [My Copy] Bioinformatics In 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 9 people and 1 group bsamal Garamonfok TRHvidsten djkt rdiaz natstreet nuin sebastien_vigneau maximilianh Jarman Lab
	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
	Developmental roles of 21 Drosophila transcription factors are determined by quantitative differences in binding to an overlapping set of thousands of genomic regions [My Copy] Genome Biology, Vol. 10, No. 7. (23 July 2009), R80. by Stewart MacArthur, Xiao Y. Li, Jingyi Li, et al.James Brown, Hou C. Chu, Lucy Zeng, Brandi Grondona, Aaron Hechmer, Lisa Simirenko, Soile Keranen, David Knowles, Mark Stapleton, Peter Bickel, Mark Biggin, Michael Eisen posted to drosophila tfbs transcription-factor by isimpson on 2009-07-24 13:51:12 as along with 12 people and 2 groups bsamal venancio aalibes fenghezi idonaldson daveGerrard megraw scjparker maximilianh djkt Stew druvus BergmanLab Bioinformatics - CRUK
	Statistical methods in integrative analysis for gene regulatory modules. [My Copy] Statistical applications in genetics and molecular biology, Vol. 7 (2008) by L. Zeng, J. Wu, J. Xie posted to wtg09 hidden-markov-models hmm regulatory tfbs transcription-factor transcription-regulation by isimpson on 2009-06-19 14:20:29 as along with 3 people natstreet druvus ptrobajo
	Computation-Based Discovery of Cis-Regulatory Modules by Hidden Markov Model. [My Copy] J Comput Biol (11 March 2008) by Jing Wu, Jun Xie posted to cis-regulatory-element hidden-markov-models hmms tfbs transcription-factor by isimpson on 2009-06-19 13:27:13 as along with 5 people and 1 group daveGerrard maximilianh cisevol csdhwang pradiptaray BergmanLab
	Unlocking the secrets of the genome [My Copy] Nature, Vol. 459, No. 7249. (17 June 2009), pp. 927-930. by Susan E. Celniker, Laura A. L. Dillon, Mark B. Gerstein, et al.Kristin C. Gunsalus, Steven Henikoff, Gary H. Karpen, Manolis Kellis, Eric C. Lai, Jason D. Lieb, David M. MacAlpine, Gos Micklem, Fabio Piano, Michael Snyder, Lincoln Stein, Kevin P. White, Robert H. Waterston posted to must-read tfbs transcription-factor transcription-regulation by isimpson on 2009-06-18 14:48:07 as along with 4 people and 2 groups daveGerrard polivares roys TRHvidsten BergmanLab Jarman Lab
	Pscan: finding over-represented transcription factor binding site motifs in sequences from co-regulated or co-expressed genes [My Copy] Nucl. Acids Res. In Nucl. Acids Res., Vol. 37, No. suppl_2. (1 July 2009), pp. W247-252. by Federico Zambelli, Graziano Pesole, Giulio Pavesi posted to motif-discovery motifs prediction software tfbs transcription-factor by isimpson on 2009-06-04 12:11:40 as along with 6 people bsamal druvus natstreet idonaldson nklee nuin
	ReXSpecies--a tool for the analysis of the evolution of gene regulation across species. [My Copy] BMC evolutionary biology, Vol. 8 (14 April 2008), 111. by Stephan Struckmann, Marcos J. Araúzo-Bravo, Hans R. Schöler, Rolland A. Reinbold, Georg Fuellen posted to evolution regulation tfbs by isimpson on 2009-06-01 17:13:21 as along with 3 people and 1 group sim82 maximilianh cisevol cis-regulatory-evolution
	Eukaryotic transcription factor binding sites--modeling and integrative search methods [My Copy] Bioinformatics (Oxford, England) In Bioinformatics, Vol. 24, No. 11. (1 June 2008), pp. 1325-1331. by Sridhar Hannenhalli posted to must-read review tfbs transcription-factor transcription-regulation by isimpson on 2009-05-13 09:45:15 as along with 15 people bsamal fenghezi wowalz cassj druvus nklee oannes hplatero maximilianh heliopais bootsy Ema sameetmehta guhjy chad_davis
	Analysis of combinatorial cis-regulation in synthetic and genomic promoters [My Copy] Nature, Vol. 457, No. 7226. (23 November 2008), pp. 215-218. by Jason Gertz, Eric D. Siggia, Barak A. Cohen posted to combinatorial promoter regulation tfbs by isimpson on 2008-11-27 14:38:31 as along with 17 people and 4 groups Vincent_Rouilly pcarbo emptyhb TRHvidsten rpatward jbhiatt lusk maximilianh roys dpollard druvus sebastien_vigneau pengchy sandersl djkt siebert xianjun TranscriptionalRegulationWithThermodynamicModels RockmanLab cis-regulatory-evolution microbiology_nijmegen
	Predicting expression patterns from regulatory sequence in Drosophila segmentation [My Copy] Nature, Vol. 451, No. 7178. (02 January 2008), pp. 535-540. by Eran Segal, Tali Raveh-Sadka, Mark Schroeder, Ulrich Unnerstall, Ulrike Gaul posted to must-read prediction tfbs transcription-regulation by isimpson on 2008-09-16 15:24:31 as along with 19 people and 2 groups TRHvidsten daveGerrard koller dlmace ptrobajo dakelley tmmurali eckart_bindewald djkt bootsy biomcgary idonaldson roys emptyhb pkharchenko meiklej jrest tresch siebert BergmanLab TranscriptionalRegulationWithThermodynamicModels
	GIMSAN: A Gibbs motif finder with significance analysis [My Copy] Bioinformatics (14 August 2008), btn408. by Patrick Ng, Uri Keich posted to algorithm must-read prediction tfbs by isimpson on 2008-08-15 11:02:24 as
	Identification of functional clusters of transcription factor binding motifs in genome sequences: the MSCAN algorithm. [My Copy] Bioinformatics, Vol. 19 Suppl 1 (2003) by O. Johansson, W. Alkema, W. W. Wasserman, J. Lagergren posted to prediction tfbs by isimpson on 2008-08-14 10:19:35 as along with 2 people and 1 group indigoviolet xili03 EisenLab
	Applied bioinformatics for the identification of regulatory elements. [My Copy] Nat Rev Genet, Vol. 5, No. 4. (April 2004), pp. 276-287. by W. W. Wasserman, A. Sandelin posted to prediction tfbs by isimpson on 2008-08-14 10:18:46 as along with 19 people and 8 groups bsamal wowalz yas icases ana chad_davis moborg gpalidwor dchughes nickluscombe johncumbers giovanni xiaobeizhao bertelsen Stew nklee jdiezperezj ArtemPankin mariakmejia structural_bioinformatics Bioinformatics EisenLab G4ID EBI-regulation GeschwindLab TNT Genetics-of-Gambling
	Conservation of sequence and function of the pag-3 genes from C. elegans and C. briggsae. [My Copy] Gene, Vol. 243, No. 1-2. (8 February 2000), pp. 67-74. by E. Aamodt, L. Shen, M. Marra, J. Schein, B. Rose, J. B. McDermott posted to senseless site-source tfbs by isimpson on 2008-08-13 14:30:02 as along with 2 people and 1 group thegoose2 tharris C. elegans / WormBase
	Senseless physically interacts with proneural proteins and functions as a transcriptional co-activator. [My Copy] Development (Cambridge, England), Vol. 133, No. 10. (May 2006), pp. 1979-1989. by M. Acar, H. Jafar-Nejad, N. Giagtzoglou, et al.S. Yallampalli, G. David, Y. He, C. Delidakis, H. J. Bellen posted to senseless site-source tfbs by isimpson on 2008-08-13 14:28:49 as
	Gfi-1 encodes a nuclear zinc finger protein that binds DNA and functions as a transcriptional repressor. [My Copy] Molecular and cellular biology, Vol. 16, No. 8. (August 1996), pp. 4024-4034. by P. A. Zweidler-Mckay, H. L. Grimes, M. M. Flubacher, P. N. Tsichlis posted to site-source tfbs by isimpson on 2008-08-13 14:09:22 as
	Target Explorer: An automated tool for the identification of new target genes for a specified set of transcription factors. [My Copy] Nucleic acids research, Vol. 31, No. 13. (1 July 2003), pp. 3589-3592. by A. Sosinsky, C. P. Bonin, R. S. Mann, B. Honig posted to prediction software tfbs transcription-regulation by isimpson on 2008-08-13 13:12:54 as along with 2 people wenhan oelemento

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