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	Assessment of composite motif discovery methods. [My Copy] BMC bioinformatics, Vol. 9, No. 1. (2008) by K. Klepper, G. K. Sandve, O. Abul, J. Johansen, F. Drablos posted by 10 people wowalz chad_davis nklee maximilianh idonaldson xili03 Motif Discovery csdhwang isimpson yoonk
	TFBS Identification Based on Genetic Algorithm with Combined Representations and Adaptive Post-processing. [My Copy] Bioinformatics (6 December 2007) by Tak-Ming M. Chan, Kwong-Sak S. Leung, Kin-Hong H. Lee posted by 7 people wowalz nklee maximilianh idonaldson xili03 csdhwang isimpson
	Regulatory motif discovery using a population clustering evolutionary algorithm. [My Copy] IEEE/ACM Trans Comput Biol Bioinform, Vol. 4, No. 3. (p 2007), pp. 403-414. by M. A. Lones, A. M. Tyrrell posted by 7 people Dulce wowalz nklee idonaldson xili03 csdhwang isimpson
	CSMET: comparative genomic motif detection via multi-resolution phylogenetic shadowing. [My Copy] PLoS computational biology, Vol. 4, No. 6. (6 June 2008), e1000090. by P. Ray, S. Shringarpure, M. Kolar, E. P. Xing posted by 9 people dquest emptyhb madreach xili03 djkt cisevol cis-regulatory-evolution Stew Ema
	Statistical significance of cis-regulatory modules [My Copy] BMC Bioinformatics, Vol. 8, No. 1. (2007) by Dustin Schones, Andrew Smith, Michael Zhang posted by 12 people druvus indigoviolet dpollard dquest sebastien_vigneau shigepong SeungjoonOh GustavoLacerda nklee EisenLab xili03 sconlan
	In silico representation and discovery of transcription factor binding sites [My Copy] Brief Bioinform, Vol. 5, No. 3. (1 January 2004), pp. 217-236. by Giulio Pavesi, Giancarlo Mauri, Graziano Pesole posted by 4 people wowalz dquest xili03 gdb
	An algorithm for finding signals of unknown length in DNA sequences [My Copy] Bioinformatics, Vol. 17, No. suppl_1. (1 June 2001), pp. S207-214. by Giulio Pavesi, Giancarlo Mauri, Graziano Pesole posted by 7 people wowalz dquest xiaobeizhao smiddha nklee xili03 ep161302
	A higher-order background model improves the detection of promoter regulatory elements by Gibbs sampling [My Copy] Bioinformatics, Vol. 17, No. 12. (1 December 2001), pp. 1113-1122. by Gert Thijs, Magali Lescot, Kathleen Marchal, et al.Stephane Rombauts, Bart De Moor, Pierre Rouze, Yves Moreau posted by 8 people lusk raylim Mehlhorn lyongu dquest natstreet nklee xili03
	Orthologous Transcription Factors in Bacteria Have Different Functions and Regulate Different Genes [My Copy] PLoS Comput Biol, Vol. 3, No. 9. (7 September 2007), e175. by Morgan N. Price, Paramvir S. Dehal, Adam P. Arkin posted by 15 people Jporci druvus treangen carlk operon dpollard dquest djkt zwang cabbagezs EisenLab heliopais blobbybirdman cis-regulatory-evolution Myxo group
	Genome-Wide Mapping of in Vivo Protein-DNA Interactions [My Copy] Science, Vol. 316, No. 5830. (8 June 2007), pp. 1497-1502. by David S. Johnson, Ali Mortazavi, Richard M. Myers, Barbara Wold posted by 30 people oannes daforerog tonamswish ewilban1 aprasad jo_davies aalibes balicea andersbj JeremyZucker aswin kengg giovanni cjeans ghattem zwang epigenetics biomcgary george_g cabbagezs Jporci Bioinformatics microRNA Marcotte_Lab blobbybirdman UH - Computational Biology caseybrown emptyhb Myxo group dquest
	Computational discovery of cis-regulatory modules in Drosophila without prior knowledge of motifs. [My Copy] Genome biology, Vol. 9, No. 1. (28 January 2008) by Andra Ivan, Marc S. Halfon, Saurabh Sinha posted by 4 people maximilianh cisevol cis-regulatory-evolution csdhwang
	Natural Similarity Measures between Position Frequency Matrices with an Application to Clustering [My Copy] Bioinformatics (2 January 2008), btm610. by Utz J. Pape, Sven Rahmann, Martin Vingron posted by 5 people nklee maximilianh mclarenv csdhwang kmdaily
	SPACER: identification of cis-regulatory elements with non-contiguous critical residues [My Copy] 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 4 people nklee maximilianh wenhan csdhwang
	Computational technique for improvement of the position-weight matrices for the DNA/protein binding sites. [My Copy] Nucleic Acids Res, Vol. 33, No. 7. (2005), pp. 2290-2301. by N. I. Gershenzon, G. D. Stormo, I. P. Ioshikhes posted by 2 people Kiarostami csdhwang
	Advances in the Discovery of cis-Regulatory Elements [My Copy] Current Bioinformatics, Vol. 1, No. 3. (August 2006), pp. 321-336. by Pan, Youlian posted by 5 people wowalz druvus natstreet nklee csdhwang
	High-throughput chromatin information enables accurate tissue-specific prediction of transcription factor binding sites. [My Copy] Nucleic acids research, Vol. 37, No. 1. (1 January 2009), pp. 14-25. by Tom Whitington, Andrew C. Perkins, Timothy L. Bailey posted by 8 people vingron akundaje inesdesantiago polivares lptolik WanderingAengus xili03 maximilianh
	A Semi-Supervised Method for Predicting Transcription Factor–Gene Interactions in Escherichia coli [My Copy] PLoS Comput Biol, Vol. 4, No. 3. (28 March 2008), e1000044. by Jason Ernst, Qasim K. Beg, Krin A. Kay, Gábor Balázsi, Zoltán N. Oltvai, Ziv Bar-Joseph posted by 4 people roys nklee xili03 eskay
	H2r: Identification of evolutionary important residues by means of an entropy based analysis of multiple sequence alignments [My Copy] BMC Bioinformatics, Vol. 9, No. 1. (2008) by Rainer Merkl, Matthias Zwick posted by 4 people mgomes qluo RebeccaHamer xili03
	Comparative analysis of regulatory patterns in bacterial genomes [My Copy] Brief Bioinform, Vol. 1, No. 4. (1 January 2000), pp. 357-371. by Mikhail S. Gelfand, Pavel S. Novichkov, Elena S. Novichkov, Andrey A. Mironov posted by 2 people nklee xili03
	An analysis of the positional distribution of DNA motifs in promoter regions and its biological relevance [My Copy] BMC Bioinformatics, Vol. 9 (07 February 2008), 89. by Ana C. Casimiro, Susana Vinga, Ana T. Freitas, Arlindo L. Oliveira posted by 4 people wowalz idonaldson xili03 isimpson
	Evaluation of phylogenetic footprint discovery for predicting bacterial cis-regulatory elements and revealing their evolution [My Copy] BMC Bioinformatics, Vol. 9 (23 January 2008), 37. by Rekin's Janky, Jacques van Helden posted by 4 people druvus cisevol cis-regulatory-evolution xili03
	Evolution and Selection in Yeast Promoters: Analyzing the Combined Effect of Diverse Transcription Factor Binding Sites [My Copy] PLoS Computational Biology, Vol. 4, No. 1. (1 January 2008), e7. by Daniela Raijman, Ron Shamir, Amos Tanay posted by 10 people marck xili03 aalibes sebastien_vigneau lusk Garamonfok nklee BioinfoCIPF maximilianh emptyhb
	Efficient and accurate P-value computation for Position Weight Matrices [My Copy] Algorithms for Molecular Biology, Vol. 2, No. 1. (2007) by Helene Touzet, Jean S. Varre posted by 3 people nklee barriot xili03
	Discovery, validation, and genetic dissection of transcription factor binding sites by comparative and functional genomics [My Copy] Genome Res., Vol. 15, No. 8. (1 August 2005), pp. 1145-1152. by Jason Gertz, Linda Riles, Peter Turnbaugh, Su-Wen Ho, Barak A. Cohen posted by 2 people nklee xili03
	Generalization through similarity: motif discourse in the discovery and elaboration of zinc finger proteins [My Copy] Journal of Biomedical Discovery and Collaboration, Vol. 2 (03 October 2007), 5. by Celeste M. Condit, Bruce L. Railsback posted by 2 people nklee xili03
	Integrated analysis of yeast regulatory sequences for biologically linked clusters of genes. [My Copy] Funct Integr Genomics, Vol. 3, No. 3. (July 2003), pp. 125-134. by A. Sandelin, A. Höglund, B. Lenhard, W. W. Wasserman posted by 3 people aalibes nklee xili03
	Detection of generic spaced motifs using submotif pattern mining. [My Copy] Bioinformatics (Oxford, England), Vol. 23, No. 12. (15 June 2007), pp. 1476-1485. by E. Wijaya, K. Rajaraman, S. M. Yiu, W. K. Sung posted by 5 people fenghezi wowalz grahamc cjeans xili03
	Large-Scale cis-Element Detection by Analysis of Correlated Expression and Sequence Conservation between Arabidopsis and Brassica oleracea [My Copy] Plant Physiol., Vol. 142, No. 4. (1 December 2006), pp. 1589-1602. by Georg Haberer, Michael T. Mader, Peter Kosarev, Manuel Spannagl, Li Yang, Klaus F. X. Mayer posted by 7 people operon dpollard xwbcn kengg nklee EisenLab xili03
	Background rareness-based iterative multiple sequence alignment algorithm for regulatory element detection. [My Copy] Bioinformatics, Vol. 19, No. 15. (12 October 2003), pp. 1952-1963. by C. Narasimhan, P. LoCascio, E. Uberbacher posted by 3 people xiaobeizhao nklee xili03
	Rank order metrics for quantifying the association of sequence features with gene regulation. [My Copy] Bioinformatics, Vol. 19, No. 2. (22 January 2003), pp. 212-218. by N. D. Clarke, J. A. Granek posted by 4 people kaspermunch nklee Bioinformatics xili03
	Transcriptional regulatory code of a eukaryotic genome [My Copy] Nature, Vol. 431, No. 7004. (02 September 2004), pp. 99-104. by Christopher T. Harbison, D. Benjamin Gordon, Tong I. Lee, et al.Nicola J. Rinaldi, Kenzie D. Macisaac, Timothy W. Danford, Nancy M. Hannett, Jean-Bosco Tagne, David B. Reynolds, Jane Yoo, Ezra G. Jennings, Julia Zeitlinger, Dmitry K. Pokholok, Manolis Kellis, P. Alex Rolfe, Ken T. Takusagawa, Eric S. Lander, David K. Gifford, Ernest Fraenkel, Richard A. Young posted by 38 people viren4388 daveGerrard Dulce talponer wowalz siebert alokm tuck lyongu kaspermunch dpollard balicea kt dchughes nirfriedman cmm nickluscombe kengg gespim koller lusk nklee Bioinformatics EisenLab FAB-lab G4ID EBI-regulation Plantandetc Genetics-of-Gambling cisevol BergmanLab njcitulike xili03 brant mariakmejia kristallreiner snow_dragon aalibes
	The design of transcription-factor binding sites is affected by combinatorial regulation. [My Copy] Genome Biol, Vol. 6, No. 12. (2005) by Y. Bilu, N. Barkai posted by 9 people chrn dpollard tabu samal adepace lewbin nklee EisenLab xili03
	MTAP: The Motif Tool Assessment Platform [My Copy] BMC Bioinformatics, Vol. 9, No. Suppl 9. (2008) by Daniel Quest, Kathryn Dempsey, Mohammad Shafiullah, Dhundy Bastola, Hesham Ali posted by 6 people wowalz nklee cassj YuvalTabach Stew dquest
	Genome-wide analysis of Fis binding in Escherichia coli indicates a causative role for A-/AT-tracts. [My Copy] Genome research, Vol. 18, No. 6. (June 2008), pp. 900-910. by B. K. Cho, E. M. Knight, C. L. Barrett, B. Ø. Palsson posted by 1 person dquest
	SeqAn an efficient, generic C++ library for sequence analysis. [My Copy] BMC bioinformatics, Vol. 9, No. 1. (2008) by Andreas Döring, David Weese, Tobias Rausch, Knut Reinert posted by 17 people aheilbut MarcelSchulz n00c druvus mmartin dquest daforerog groepl guhjy chad_davis laughcry ryanraaum nklee barriot mailund magusina reyez
	Bayesian hierarchical model for transcriptional module discovery by jointly modeling gene expression and ChIP-chip data [My Copy] BMC Bioinformatics, Vol. 8 (03 August 2007), 283. by Xiangdong Liu, Walter J. Jessen, Siva Sivaganesan, Bruce J. Aronow, Mario Medvedovic posted by 5 people bais dquest nklee naegele ic4
	PhyloScan: Identification of transcription factor binding sites using cross-species evidence [My Copy] Algorithms for Molecular Biology, Vol. 2 (23 January 2007), 1. by Steven C. Carmack, Lee A. Mccue, Lee A. Newberg, Charles E. Lawrence posted by 5 people dpollard dquest lusk nklee EisenLab
	Large-Scale Discovery of Promoter Motifs in Drosophila melanogaster [My Copy] PLoS Comput Biol, Vol. 3, No. 1. (19 January 2007), e7. by Thomas A. Down, Casey M. Bergman, Jing Su, Tim J. P. Hubbard posted by 13 people daveGerrard ychromosome timhubbard lusk wowalz indigoviolet dpollard dquest SeungjoonOh nklee EisenLab emptyhb isimpson
	Locating mammalian transcription factor binding sites: A survey of computational and experimental techniques [My Copy] 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 14 people matted gdb wowalz Bioinformatics - CRUK Stew heliopais dquest bryankr giovanni lusk SeungjoonOh cabbagezs GeschwindLab maximilianh
	A multistep bioinformatic approach detects putative regulatory elements in gene promoters. [My Copy] BMC Bioinformatics, Vol. 6 (2005) by S. Bortoluzzi, A. Coppe, A. Bisognin, C. Pizzi, G. A. Danieli posted by 3 people wowalz nklee dquest
	Finding functional sequence elements by multiple local alignment [My Copy] Nucl. Acids Res., Vol. 32, No. 1. (2 January 2004), pp. 189-200. by Martin C. Frith, Ulla Hansen, John L. Spouge, Zhiping Weng posted by 8 people wyatt111 idonaldson wowalz treangen dquest kengg nklee Plantandetc
	Weeder Web: discovery of transcription factor binding sites in a set of sequences from co-regulated genes [My Copy] Nucl. Acids Res., Vol. 32, No. suppl_2. (1 July 2004), pp. W199-203. by Giulio Pavesi, Paolo Mereghetti, Giancarlo Mauri, Graziano Pesole posted by 9 people farhat Dulce wowalz coldmeadow djkt dquest xiaobeizhao dandaman bryankr
	TRANSFAC: a database on transcription factors and their DNA binding sites [My Copy] Nucl. Acids Res., Vol. 24, No. 1. (1 January 1996), pp. 238-241. by E. Wingender, P. Dietze, H. Karas, R. Knuppel posted by 6 people tonamswish Mehlhorn ea indigoviolet dquest EisenLab
	Phylogenetic footprinting of transcription factor binding sites in proteobacterial genomes. [My Copy] Nucleic Acids Res, Vol. 29, No. 3. (1 February 2001), pp. 774-782. by L. McCue, W. Thompson, C. Carmack, et al.M. P. Ryan, J. S. Liu, V. Derbyshire, C. E. Lawrence posted by 6 people azazello dquest adepace nklee EisenLab pradiptaray
	An introduction to ROC analysis [My Copy] Pattern Recogn. Lett. In ROC Analysis in Pattern Recognition, Vol. 27, No. 8. (June 2006), pp. 861-874. by Tom Fawcett posted by 42 people singhsh TLVincent module qluo q_w_e_r_t_y makrehchi Borelli mthomure sbarthelme jjrodriguez cen4ik jmetzen MosesCheckley ldietz vavi dquest sdvillal xiaoyan2006 dwf camu schlauchi vmoa drivard nklee imrchen kmdaily gsiwo Bioinformatics Crypto VT_DLRL Randomness LIVIA tgyork idonaldson BergmanLab napvasconcelos cdeane haiyeong AbnerCYH isimpson guhjy nherveg
	Discriminative motifs. [My Copy] Journal of computational biology : a journal of computational molecular cell biology, Vol. 10, No. 3-4. (2003), pp. 599-615. by Saurabh Sinha posted by 4 people operon wowalz nklee dquest
	Algorithms for phylogenetic footprinting. [My Copy] J Comput Biol, Vol. 9, No. 2. (2002), pp. 211-223. by M. Blanchette, B. Schwikowski, M. Tompa posted by 3 people nklee chad_davis dquest
	A deterministic motif finding algorithm with application to the human genome [My Copy] Bioinformatics, Vol. 22, No. 9. (1 May 2006), pp. 1047-1054. by Lawrence S. Hon, Ajay N. Jain posted by 7 people wowalz shwu idonaldson dquest nklee Motif Discovery maximilianh
	Profile hidden Markov models [My Copy] Bioinformatics, Vol. 14, No. 9. (1 October 1998), pp. 755-763. by S. R. Eddy posted by 15 people ldiambra farhat BioNica druvus albert_swart miguel chad_davis eweaver dgront rabio cjeans suizan nklee yoanjacquemin ca3295
	Eukaryotic Regulatory Element Conservation Analysis and Identification Using Comparative Genomics [My Copy] Genome Res., Vol. 14, No. 3. (1 March 2004), pp. 451-458. by Yueyi Liu, Shirley X. Liu, Liping Wei, Russ B. Altman, Serafim Batzoglou posted by 6 people cis-regulatory-evolution cisevol lyongu gpalidwor dquest nklee
	LAGAN and Multi-LAGAN: efficient tools for large-scale multiple alignment of genomic DNA. [My Copy] Genome Res, Vol. 13, No. 4. (April 2003), pp. 721-731. by M. Brudno, C. B. Do, G. M. Cooper, et al.M. F. Kim, E. Davydov, E. D. Green, A. Sidow, S. Batzoglou, posted by 16 people treangen operon balajis dpollard xwbcn dquest adepace hdopazo lusk Garamonfok adijr natstreet nklee EisenLab Neeperando kcrawlik
	Prediction of complete gene structures in human genomic DNA. [My Copy] Journal of molecular biology, Vol. 268, No. 1. (25 April 1997), pp. 78-94. by C. Burge, S. Karlin posted by 15 people rshe jmartin49 Ayest pcahan1 indigoviolet kaspermunch dullhunk dquest wenhan GustavoLacerda nicholso Bioinformatics EisenLab nklee bandrewfox
	Factors influencing the identification of transcription factor binding sites by cross-species comparison. [My Copy] Genome Res, Vol. 12, No. 10. (October 2002), pp. 1523-1532. by L. A. McCue, W. Thompson, C. S. Carmack, C. E. Lawrence posted by 3 people kaarsinogen dquest nklee
	BEST: Binding-site Estimation Suite of Tools [My Copy] Bioinformatics, Vol. 21, No. 12. (15 June 2005), pp. 2909-2911. by Dongsheng Che, Shane Jensen, Liming Cai, Jun S. Liu posted by 2 people nklee dquest
	Assessing computational tools for the discovery of transcription factor binding sites [My Copy] Nat Biotech, Vol. 23, No. 1. (06 January 2005), pp. 137-144. by Martin Tompa, Nan Li, Timothy L. Bailey, et al.George M. Church, Bart De Moor, Eleazar Eskin, Alexander V. Favorov, Martin C. Frith, Yutao Fu, W. James Kent, Vsevolod J. Makeev, Andrei A. Mironov, William S. Noble, Giulio Pavesi, Graziano Pesole, Mireille Regnier, Nicolas Simonis, Saurabh Sinha, Gert Thijs, Jacques van Helden, Mathias Vandenbogaert, Zhiping Weng, Christopher Workman, Chun Ye, Zhou Zhu posted by 45 people mpizbioinfo megraw Dulce farhat wowalz mhofree jasontsai heliopais pengchy daforerog yylin cambray emptyhb bryankr icases ana barry aalibes aprasad jfr tuck chad_davis lyongu tabu dquest neveaire ranb johncumbers noano xiaobeizhao olympos GustavoLacerda nklee mdimon structural_bioinformatics Biostatistics Computational-Genomics Bioinformatics Neuroscience TNT dandaman vietanh0 ep161302 nuin Stew
	Transcriptional Regulatory Networks in Saccharomyces cerevisiae [My Copy] Science, Vol. 298, No. 5594. (25 October 2002), pp. 799-804. by Tong I. Lee, Nicola J. Rinaldi, Francois Robert, et al.Duncan T. Odom, Ziv Bar-Joseph, Georg K. Gerber, Nancy M. Hannett, Christopher T. Harbison, Craig M. Thompson, Itamar Simon, Julia Zeitlinger, Ezra G. Jennings, Heather L. Murray, D. Benjamin Gordon, Bing Ren, John J. Wyrick, Jean-Bosco Tagne, Thomas L. Volkert, Ernest Fraenkel, David K. Gifford, Richard A. Young posted by 35 people viren4388 mjoach kmdaily kinop junehlee lillo80 camster snuppepuppan icases forluvoft ggrot alokm opheliav samal sameetmehta cconboy koller jguinney franklin timflutre jpoyatos lusk nklee karfunkel mimulus_99 dbk-lab TNT roys njcitulike brant kristallreiner Borelli Takayuki dquest siebert
	Chipper: discovering transcription-factor targets from chromatin immunoprecipitation microarrays using variance stabilization [My Copy] Genome Biology, Vol. 6, No. 11. (2005), R96. by Francis Gibbons, Markus Proft, Kevin Struhl, Frederick Roth posted by 5 people nklee humburg oelemento blobbybirdman Myxo group
	A Systems Approach to Measuring the Binding Energy Landscapes of Transcription Factors [My Copy] Science, Vol. 315, No. 5809. (12 January 2007), pp. 233-237. by Sebastian J. Maerkl, Stephen R. Quake posted by 12 people absterga jjray dpollard emilyhare adepace aswin skoch3 EisenLab Koch_Lab blobbybirdman emptyhb brant
	Non-additivity in protein-DNA binding. [My Copy] Bioinformatics, Vol. 21, No. 10. (15 May 2005), pp. 2254-2263. by R. A. O'Flanagan, G. Paillard, R. Lavery, A. M. Sengupta posted by 4 people reidy blobbybirdman UH - Computational Biology nklee
	Discovery of Regulatory Elements by a Computational Method for Phylogenetic Footprinting [My Copy] Genome Res., Vol. 12, No. 5. (1 May 2002), pp. 739-748. by Mathieu Blanchette, Martin Tompa posted by 10 people wowalz coldmeadow chad_davis balajis lyongu dpollard dquest EisenLab cis-regulatory-evolution csdhwang
	SIGffRid: a tool to search for sigma factor binding sites in bacterial genomes using comparative approach and biologically driven statistics [My Copy] BMC Bioinformatics, Vol. 9 (31 January 2008), 73. by Fabrice Touzain, Sophie Schbath, Isabelle Debled-Rennesson, Bertrand Aigle, Gregory Kucherov, Pierre Leblond posted by 2 people dquest xili03
	Discovery of sequence motifs related to coexpression of genes using evolutionary computation. [My Copy] Nucleic Acids Res, Vol. 32, No. 13. (2004), pp. 3826-3835. by G. B. Fogel, D. G. Weekes, G. Varga, et al.E. R. Dow, H. B. Harlow, J. E. Onyia, C. Su posted by 6 people wowalz svenrahmann lptolik gpalidwor dquest xili03
	Modeling within-motif dependence for transcription factor binding site predictions. [My Copy] Bioinformatics, Vol. 20, No. 6. (12 April 2004), pp. 909-916. by Q. Zhou, J. S. Liu posted by 2 people dquest xili03
	Finding motifs using random projections. [My Copy] Journal of computational biology : a journal of computational molecular cell biology, Vol. 9, No. 2. (2002), pp. 225-242. by J. Buhler, M. Tompa posted by 4 people wowalz cmoewes dquest xili03
	Combinatorial approaches to finding subtle signals in DNA sequences. [My Copy] Proc Int Conf Intell Syst Mol Biol, Vol. 8 (2000), pp. 269-278. by P. A. Pevzner, S. H. Sze posted by 5 people wowalz dquest lesliehong xili03 ep161302
	A biophysical approach to transcription factor binding site discovery. [My Copy] Genome Res, Vol. 13, No. 11. (November 2003), pp. 2381-2390. by M. Djordjevic, A. M. Sengupta, B. I. Shraiman posted by 3 people dquest discreteonyxorb xili03
	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 by 11 people isimpson rsaito Mehlhorn treangen dquest AaronDarling johncumbers jguinney xili03 seitentaisei wenhan
	PhyME: a probabilistic algorithm for finding motifs in sets of orthologous sequences. [My Copy] BMC Bioinformatics, Vol. 5 (28 October 2004) by S. Sinha, M. Blanchette, M. Tompa posted by 6 people mgledi eckart_bindewald dquest adsmitty lusk xili03
	DNA binding sites: representation and discovery. [My Copy] Bioinformatics (Oxford, England), Vol. 16, No. 1. (January 2000), pp. 16-23. by G. D. Stormo posted by 11 people yylin Bioinformatics - CRUK Stew emptyhb isimpson kaarsinogen mbj dquest lusk ezralanglois xili03
	Discovery of novel transcription factor binding sites by statistical overrepresentation. [My Copy] Nucleic Acids Res, Vol. 30, No. 24. (15 December 2002), pp. 5549-5560. by S. Sinha, M. Tompa posted by 12 people wowalz GustavoLacerda kaarsinogen dquest xiaobeizhao smiddha GeeSharpMinor xi03 xili03 ep161302 wenhan pradiptaray
	W-ChIPMotifs: a web application tool for de novo motif discovery from ChIP-based high-throughput data [My Copy] 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 4 people idonaldson farhat nklee maximilianh
	Exhaustive Search for Over-represented DNA Sequence Motifs with CisFinder [My Copy] DNA Res, Vol. 16, No. 5. (1 October 2009), pp. 261-273. by Alexei A. Sharov, Minoru S. H. Ko posted by 6 people nklee CTCF sebastien_vigneau operon BergmanLab polivares
	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 20 people heliopais inesdesantiago fenghezi nklee samanthacooper fpattyn druvus frohike stubrown Journal picks qayub megraw TRHvidsten Chinnaiyan Lab mkiyer ericrpaquet ilyashl jbhiatt idonaldson danmaclean
	Distinguishing direct versus indirect transcription factorâDNA interactions [My Copy] Genome Research, Vol. 19, No. 11. (3 November 2009), pp. 2090-2100. by Raluca GordÃ¢n, Alexander J. Hartemink, Martha L. Bulyk posted by 12 people oannes nklee djkt vingron venancio owhitney tmmurali emptyhb idonaldson maximilianh jbhiatt frohike
	Towards accurate human promoter recognition: a review of currently used sequence features and classification methods [My Copy] Brief Bioinform, Vol. 10, No. 5. (1 September 2009), pp. 498-508. by Jia Zeng, Shanfeng Zhu, Hong Yan posted by 2 people reyez nklee
	Computational methods for the detection of cis-regulatory modules [My Copy] Brief Bioinform, Vol. 10, No. 5. (1 September 2009), pp. 509-524. by Peter Van Loo, Peter Marynen posted by 7 people reyez idonaldson kshameer nklee BergmanLab cisevol druvus
	Pscan: finding over-represented transcription factor binding site motifs in sequences from co-regulated or co-expressed genes [My Copy] Nucl. Acids Res., Vol. 37, No. suppl_2. (1 July 2009), pp. W247-252. by Federico Zambelli, Graziano Pesole, Giulio Pavesi posted by 6 people druvus natstreet idonaldson nklee nuin isimpson
	Hierarchical hidden Markov model with application to joint analysis of ChIP-chip and ChIP-seq data. [My Copy] Bioinformatics (Oxford, England), Vol. 25, No. 14. (15 July 2009), pp. 1715-1721. by Hyungwon Choi, Alexey I. Nesvizhskii, Debashis Ghosh, Zhaohui S. Qin posted by 14 people jfr tonamswish rdiaz fpattyn Journal picks jcbarret guhjy hendrik85 inesdesantiago nklee polivares ewilban1 idonaldson humburg
	Estimating the posterior probability that genome-wide association findings are true or false [My Copy] Bioinformatics, Vol. 25, No. 14. (15 July 2009), pp. 1807-1813. by Jozsef Bukszar, Joseph L. McClay, Edwin J. C. G. van den Oord posted by 4 people zufar nklee djkt guhjy
	Diversity and Complexity in DNA Recognition by Transcription Factors [My Copy] Science, Vol. 324, No. 5935. (26 June 2009), pp. 1720-1723. by Gwenael Badis, Michael F. Berger, Anthony A. Philippakis, et al.Shaheynoor Talukder, Andrew R. Gehrke, Savina A. Jaeger, Esther T. Chan, Genita Metzler, Anastasia Vedenko, Xiaoyu Chen, Hanna Kuznetsov, Chi-Fong Wang, David Coburn, Daniel E. Newburger, Quaid Morris, Timothy R. Hughes, Martha L. Bulyk posted by 24 people nklee sconlan isimpson jbhiatt daforerog absterga mingzhi galka8_diploma fenghezi TRHvidsten ilyashl cambray rpatward tibbitts RockmanLab dpollard siebert JustinCrocker burak aalibes dipenps roys emptyhb tmmurali
	Affinity Density: a novel genomic approach to the identification of transcription factor regulatory targets. [My Copy] Bioinformatics (Oxford, England), Vol. 25, No. 13. (1 July 2009), pp. 1617-1624. by Dennis J. Hazelett, Daniel L. Lakeland, Joseph B. Weiss posted by 7 people guhjy nklee TRHvidsten nuin cis-regulatory-evolution BergmanLab cisevol
	Genome-wide promoter analysis of the SOX4 transcriptional network in prostate cancer cells. [My Copy] Cancer research, Vol. 69, No. 2. (15 January 2009), pp. 709-717. by Christopher D. Scharer, Colleen D. McCabe, Mohamed Ali-Seyed, Michael F. Berger, Martha L. Bulyk, Carlos S. Moreno posted by 3 people Bioinformatics - CRUK Stew nklee
	GADEM: a genetic algorithm guided formation of spaced dyads coupled with an EM algorithm for motif discovery. [My Copy] Journal of computational biology : a journal of computational molecular cell biology, Vol. 16, No. 2. (February 2009), pp. 317-329. by L. Li posted by 2 people wowalz nklee
	Evolutionary Conserved Motif Finder (ECMFinder) for genome-wide identification of clustered YY1- and CTCF-binding sites [My Copy] Nucl. Acids Res. (10 February 2009), gkp077. by Keunsoo Kang, Jae H. Chung, Joomyeong Kim posted by 4 people idonaldson nklee wowalz maximilianh
	Compound poisson approximation of the number of occurrences of a position frequency matrix (PFM) on both strands. [My Copy] Journal of computational biology : a journal of computational molecular cell biology, Vol. 15, No. 6. (g 2008), pp. 547-564. by U. J. Pape, S. Rahmann, F. Sun, M. Vingron posted by 2 people wowalz nklee
	Genome wide identification of regulatory motifs in Bacillus subtilis. [My Copy] BMC bioinformatics, Vol. 4 (16 May 2003) by M. M. Mwangi, E. D. Siggia posted by 1 person nklee
	An approach to identify over-represented cis-elements in related sequences [My Copy] Nucl. Acids Res., Vol. 31, No. 7. (1 April 2003), pp. 1995-2005. by Jiashun Zheng, Jiajin Wu, Zhirong Sun posted by 1 person nklee
	Comparison of methods for estimating the nucleotide substitution matrix [My Copy] BMC Bioinformatics, Vol. 9, No. 1. (2008) by Maribeth Oscamou, Daniel Mcdonald, Von B. Yap, Gavin Huttley, Manuel Lladser, Rob Knight posted by 5 people sconlan nklee nuin treangen druvus
	c-REDUCE: Incorporating sequence conservation to detect motifs that correlate with expression [My Copy] BMC Bioinformatics, Vol. 9, No. 1. (2008) by Katerina Kechris, Hao Li posted by 7 people tmarscha heliopais GustavoLacerda maximilianh druvus Md_2007 neils
	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 11 people 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), Vol. 24, No. 24. (15 December 2008), pp. 2930-2931. by Vinhthuy Phan, Nicholas A. Furlotte posted by 6 people wowalz nklee maximilianh nuin natstreet druvus
	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 12 people jakebiesinger kmdaily guhjy wowalz ilyashl jfr abizar heliopais nklee idonaldson nuin djkt
	Genome-scale study of the importance of binding site context for transcription factor binding and gene regulation [My Copy] BMC Bioinformatics, Vol. 9 (17 November 2008), 484. by Jakub, Jan Komorowski posted by 2 people imina lptolik
	Low conservation and species-specific evolution of alternative splicing in humans and mice: comparative genomics analysis using well-annotated full-length cDNAs [My Copy] Nucl. Acids Res., Vol. 36, No. 20. (1 November 2008), pp. 6386-6395. by Jun-Ichi Takeda, Yutaka Suzuki, Ryuichi Sakate, et al.Yoshiharu Sato, Masahide Seki, Takuma Irie, Nono Takeuchi, Takuya Ueda, Mitsuteru Nakao, Sumio Sugano, Takashi Gojobori, Tadashi Imanishi posted by 1 person Cortel
	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 by 6 people nklee Jarman Lab isimpson dolchan druvus guhjy
	Estimation of the Transition/Transversion Rate Bias and Species Sampling [My Copy] Journal of Molecular Evolution, Vol. 48, No. 3. (24 March 1999), pp. 274-283. by Ziheng Yang, Anne D. Yoder posted by 1 person nklee
	Whole-genome comparison of Leu3 binding in vitro and in vivo reveals the importance of nucleosome occupancy in target site selection. [My Copy] Genome research, Vol. 16, No. 12. (December 2006), pp. 1517-1528. by X. Liu, C. K. Lee, J. A. Granek, N. D. Clarke, J. D. Lieb
	Using RSAT oligo-analysis and dyad-analysis tools to discover regulatory signals in nucleic sequences [My Copy] Nature Protocols, Vol. 3, No. 10. (18 September 2008), pp. 1589-1603. by Matthieu Defrance, Rekin's Janky, Olivier Sand, Jacques van Helden posted by 4 people druvus BergmanLab polivares natstreet
	DOOR: a database for prokaryotic operons [My Copy] Nucl. Acids Res. (6 November 2008), gkn757. by Fenglou Mao, Phuongan Dam, Jacky Chou, Victor Olman, Ying Xu posted by 2 people coela barriot
	Phylogenetic footprinting analysis in the upstream regulatory regions of the Drosophila enhancer of split genes. [My Copy] Genetics, Vol. 177, No. 3. (November 2007), pp. 1377-1394. by M. L. Maeder, B. J. Polansky, B. E. Robson, D. A. Eastman