Tag tfbs [at least 200 articles] Export

Recent papers classified by the tag tfbs.

	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-Hung Eric H. Tang, Olivier Elemento posted to tfbs pwm motif by bedo on 2009-11-27 02:54:36 as along with 3 people maximilianh oelemento barriot
	Evolutionary changes in cis and trans gene regulation. [My Copy] Nature, Vol. 430, No. 6995. (1 July 2004), pp. 85-88. by Patricia J. Wittkopp, Belinda K. Haerum, Andrew G. Clark posted to tfbs prj_affinity expression_evolution by mox on 2009-11-26 14:29:52 as along with 12 people and 2 groups ajbattle athma balabu lyongu dpollard balicea tabu adepace emmahe emarker mimulus_99 cisevol EisenLab cis-regulatory-evolution
	Evolution of transcriptional control in mammals. [My Copy] Current opinion in genetics & development (11 November 2009) by Michael D. Wilson, Duncan T. Odom posted to tfbs prj_affinity expression_evolution by mox on 2009-11-26 14:28:44 as
	Discovery of Regulatory Elements is Improved by a Discriminatory Approach [My Copy] PLoS Comput Biol, Vol. 5, No. 11. (13 November 2009), e1000562. by Eivind Valen, Albin Sandelin, Ole Winther, Anders Krogh posted to tfbs motif by davfre on 2009-11-26 08:10:08 as along with 4 people ptrobajo maximilianh TRHvidsten bertelsen
	Shuffling of cis-regulatory elements is a pervasive feature of the vertebrate lineage [My Copy] Genome Biology, Vol. 7, No. 7. (19 July 2006), R56. by Remo Sanges, Eva Kalmar, Pamela Claudiani, Maria D'Amato, Ferenc Muller, Elia Stupka posted to tfbs shuffling by mox on 2009-11-23 11:24:41 as along with 3 people and 1 group xianjun JustinCrocker indigoviolet EisenLab
	ModuleMiner - improved computational detection of cis-regulatory modules: are there different modes of gene regulation in embryonic development and adult tissues? [My Copy] Genome Biology, Vol. 9, No. 4. (2008), R66. by Peter Van Loo, Stein Aerts, Bernard Thienpont, Bart De Moor, Yves Moreau, Peter Marynen posted to tfbs by mox on 2009-11-23 11:20:40 as along with 6 people heliopais brant djkt natstreet maximilianh phoenixzxl
	How much expression divergence after yeast gene duplication could be explained by regulatory motif evolution? [My Copy] Trends in genetics : TIG, Vol. 20, No. 9. (September 2004), pp. 403-407. by Zhongqi Zhang, Jianying Gu, Xun Gu posted to transcription_factor_binding_sites tfbs evolution by roys on 2009-11-22 01:49:12 as along with 3 people azazello xwbcn echinotrix
	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 to tfbs chipchip bulyk by oannes on 2009-11-18 05:20:31 as along with 11 people nklee djkt vingron venancio owhitney tmmurali emptyhb idonaldson maximilianh jbhiatt frohike
	Inferring transcriptional modules from ChIP-chip, motif and microarray data. [My Copy] Genome biology, Vol. 7, No. 5. (2006) by Karen Lemmens, Thomas Dhollander, Tijl De Bie, et al.Pieter Monsieurs, Kristof Engelen, Bart Smets, Joris Winderickx, Bart De Moor, Kathleen Marchal posted to tfbs modules module_nw by roys on 2009-11-17 06:58:37 as along with 4 people bozdagd alokm jfr kristallreiner
	Identifying combinatorial regulation of transcription factors and binding motifs. [My Copy] Genome biology, Vol. 5, No. 8. (2004) by Mamoru Kato, Naoya Hata, Nilanjana Banerjee, Bruce Futcher, Michael Q. Zhang posted to tfbs motif_identification combinatorial_control by roys on 2009-11-17 06:53:27 as along with 4 people fenghezi troels_marstrand wnpx jacky957
	Frequent gain and loss of functional transcription factor binding sites. [My Copy] PLoS computational biology, Vol. 3, No. 5. (1 May 2007), e99. by Scott W. Doniger, Justin C. Fay posted to tfbs evolution comparative_genomics by roys on 2009-11-17 05:45:30 as along with 12 people and 2 groups fenghezi lusk JustinCrocker pradiptaray brant dpollard sebastien_vigneau zwang maximilianh cisevol xili03 emptyhb EisenLab cis-regulatory-evolution
	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
	JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles [My Copy] Nucl. Acids Res. (11 November 2009), gkp950. by Elodie Portales-Casamar, Supat Thongjuea, Andrew T. Kwon, et al.David Arenillas, Xiaobei Zhao, Eivind Valen, Dimas Yusuf, Boris Lenhard, Wyeth W. Wasserman, Albin Sandelin posted to tfbs database by idonaldson on 2009-11-16 09:45:40 as along with 1 person daforerog
	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 tissue_specificity tfbs motif_discovery combinatorial_control by roys on 2009-11-14 23:27:18 as along with 10 people isimpson guhjy chad_davis mikaelhuss nklee maximilianh idonaldson njcitulike bootsy snow_dragon
	Probabilistic clustering of sequences: Inferring new bacterial regulons by comparative genomics [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 99, No. 11. (28 May 2002), pp. 7323-7328. by Erik van Nimwegen, Mihaela Zavolan, Nikolaus Rajewsky, Eric D. Siggia posted to tfprograms tfbs motif_clustering by roys on 2009-11-12 23:35:53 as along with 1 person Dulce
	Global analysis of the insulator binding protein CTCF in chromatin barrier regions reveals demarcation of active and repressive domains [My Copy] Genome Research, Vol. 19, No. 1. (January 2009), pp. 24-32. by Suresh Cuddapah, Raja Jothi, Dustin E. Schones, Tae-Young Roh, Kairong Cui, Keji Zhao posted to tfbs tf histone data_set ctcf chip-seq bioinformatics 2009 by suizifish on 2009-11-05 03:23:54 as along with 13 people and 1 group aprickett gdb fenghezi clearbluespring rschulz xingxu sebastien_vigneau cassj caseybrown polivares inesdesantiago oelemento maximilianh CTCF
	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 to tfbs promoter cpg by idonaldson on 2009-10-30 09:45:28 as along with 3 people and 1 group bmajoros daveGerrard maximilianh BergmanLab
	MEME SUITE: tools for motif discovery and searching [My Copy] Nucl. Acids Res., Vol. 37, No. suppl_2. (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 to tfbs motif bioinformatics 2009 by suizifish on 2009-10-28 05:55:27 as along with 6 people jlike maximilianh natstreet idonaldson nuin cassj
	Associating transcription factor-binding site motifs with target GO terms and target genes [My Copy] Nucl. Acids Res. (10 June 2008), gkn374. by Mikael Boden, Timothy L. Bailey posted to tfbs tf motif bioinformatics 2008 by suizifish on 2009-10-28 05:49:05 as along with 5 people aramesh2 mikaelboden maximilianh guhjy dgroth
	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
	Different gene regulation strategies revealed by analysis of binding motifs [My Copy] Trends in Genetics, Vol. 25, No. 10. (06 October 2009), pp. 434-440. by Zeba Wunderlich, Leonid A. Mirny posted to transcritpional tfbs regulation by francemirko on 2009-10-26 10:24:55 as along with 2 people and 1 group djkt behindtherabbit iSEEM
	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 to tfbs in_silico drosophila cis-regulatory_element by daveGerrard on 2009-10-23 11:50:04 as along with 11 people and 1 group ychromosome timhubbard lusk wowalz indigoviolet dpollard dquest SeungjoonOh nklee emptyhb isimpson EisenLab
	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 to topography tfbs structure motif evolution enhancer by pradiptaray on 2009-09-30 21:55:16 as along with 38 people and 6 groups daveGerrard operon sujaikumar antonkratz roys gjuggler benjaminsb gdb hagechouchin443 tomtullius scjparker psique orzenil emptyhb ilyashl coela VGreiff APRegier myzhang pkonings akundaje athma absterga rpatward timflutre stajich bpcusack jbhiatt djkt dhlbh friendpine dpollard inesdesantiago JustinCrocker aprasad maximilianh idonaldson kshundyak BergmanLab Mycology structural_bioinformatics RockmanLab EisenLab cis-regulatory-evolution
	Divergence of Transcription Factor Binding Sites Across Related Yeast Species [My Copy] Science, Vol. 317, No. 5839. (10 August 2007), pp. 815-819. by Anthony R. Borneman, Tara A. Gianoulis, Zhengdong D. Zhang, et al.Haiyuan Yu, Joel Rozowsky, Michael R. Seringhaus, Lu Y. Wang, Mark Gerstein, Michael Snyder posted to yeast tfbs motif evolution duplication divergence by pradiptaray on 2009-09-30 21:53:18 as along with 22 people and 2 groups gdb fenghezi dbensasson caseybrown bryankr aalibes chad_davis dpollard djkt mikaelhuss lusk cjeans sujaikumar zwang GustavoLacerda Jporci maximilianh cisevol njcitulike emptyhb nklee anka EisenLab cis-regulatory-evolution
	Functional Architecture and Evolution of Transcriptional Elements That Drive Gene Coexpression [My Copy] Science, Vol. 317, No. 5844. (14 September 2007), pp. 1557-1560. by Christopher D. Brown, David S. Johnson, Arend Sidow posted to tfbs motif evolution crm architecture by pradiptaray on 2009-09-30 21:52:13 as along with 10 people and 2 groups dpollard djkt joepickrell zwang Garamonfok Stew mimulus_99 maximilianh cisevol emptyhb EisenLab cis-regulatory-evolution
	M are better than one: an ensemble-based motif finder and its application to regulatory element prediction [My Copy] Bioinformatics, Vol. 25, No. 7. (1 April 2009), pp. 868-874. by Chen Yanover, Mona Singh, Elena Zaslavsky posted to tfbs motif ensemble by pradiptaray on 2009-09-30 21:33:50 as along with 5 people TRHvidsten djkt druvus mhamada maximilianh
	MotifCut: regulatory motifs finding with maximum density subgraphs [My Copy] Bioinformatics, Vol. 22, No. 14. (15 July 2006), pp. e150-157. by Eugene Fratkin, Brian T. Naughton, Douglas L. Brutlag, Serafim Batzoglou posted to tfbs motif clustering by pradiptaray on 2009-09-30 21:31:20 as along with 3 people and 1 group wowalz indigoviolet yevishere EisenLab
	Binding Site Graphs: A New Graph Theoretical Framework for Prediction of Transcription Factor Binding Sites [My Copy] PLoS Comput Biol, Vol. 3, No. 5. (11 May 2007), e90. by Timothy E. Reddy, Charles DeLisi, Boris E. Shakhnovich posted to tfbs motif genomics clustering by pradiptaray on 2009-09-30 21:22:10 as along with 7 people and 1 group nklee aalibes dpollard medic0747 GustavoLacerda mircea marti EisenLab
	Discovery of regulatory elements in vertebrates through comparative genomics [My Copy] Nature Biotechnology, Vol. 23, No. 10. (06 October 2005), pp. 1249-1256. by Amol Prakash, Martin Tompa posted to tfbs review regulatory_elements comparative_genomics by idonaldson on 2009-09-23 09:02:20 as along with 3 people and 3 groups aprasad indigoviolet dchughes EisenLab G4ID Genetics-of-Gambling
	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 to tfbs integration encode chromatin by akundaje on 2009-09-22 22:18:17 as along with 7 people vingron inesdesantiago polivares lptolik WanderingAengus xili03 maximilianh
	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
	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 tfbs drosophila chip-chip by idonaldson on 2009-09-01 11:18:15 as along with 11 people and 2 groups venancio aalibes fenghezi daveGerrard megraw scjparker maximilianh djkt isimpson Stew druvus BergmanLab Bioinformatics - CRUK
	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 to the group Jarman Lab on 2009-08-26 16:53:14 as along with 3 people nicholasflann talponer ptrobajo
	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 tfbs must-read motifs motif-discovery bayesian by isimpson to the group Jarman Lab on 2009-08-26 16:53:14 as
	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 tfbs software must-read motifs motif-discovery bayesian by isimpson to the group Jarman Lab on 2009-08-26 16:49:30 as along with 4 people nklee dolchan druvus guhjy
	Integrating large-scale functional genomic data to dissect the complexity of yeast regulatory networks. [My Copy] Nature genetics, Vol. 40, No. 7. (15 July 2008), pp. 854-861. by Jun Zhu, Bin Zhang, Erin N. Smith, et al.Becky Drees, Rachel B. Brem, Leonid Kruglyak, Roger E. Bumgarner, Eric E. Schadt posted to tfbs regulatory ppi network expression causal by arider1 on 2009-08-24 18:56:36 as along with 19 people and 1 group JoeBanks megraw TRHvidsten siebert ggallone jo_davies suteedee burak realzhang kengg maralena ptrobajo tmmurali guhjy roys marck caseybrown djkt srp33 Jarman Lab
	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
	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
	Statistical detection of cooperative transcription factors with similarity adjustment. [My Copy] Bioinformatics (Oxford, England), Vol. 25, No. 16. (15 August 2009), pp. 2103-2109. by Utz J. Pape, Holger Klein, Martin Vingron posted to tfbs cooperative binding by idonaldson on 2009-08-13 13:33:45 as along with 2 people TRHvidsten djkt
	Extracting transcription factor targets from ChIP-Seq data [My Copy] Nucl. Acids Res., Vol. 37, No. 17. (1 September 2009), e113. by Geetu Tuteja, Peter White, Jonathan Schug, Klaus H. Kaestner posted to tool tfbs chip-seq by idonaldson on 2009-08-11 13:47:54 as along with 14 people and 4 groups hzoltan Vincent_Rouilly mfgreen ewilban1 guhjy mkiyer rschulz fenghezi clearbluespring thegoose robeirne inesdesantiago malcook polivares Chinnaiyan Lab SIMR bioinformatics BergmanLab Journal picks
	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 to the group Jarman Lab on 2009-07-28 16:42:31 as along with 8 people Garamonfok TRHvidsten djkt rdiaz natstreet nuin sebastien_vigneau maximilianh
	Genomic Promoter Analysis Predicts Functional Transcription Factor Binding [My Copy] Advances in Bioinformatics, Vol. 2008 (2008), pp. 1-10. by J. Sunil Rao, Suresh Karanam, Colleen D. Mccabe, Carlos S. Moreno posted to confac finding motif tfbs by cassj on 2009-07-27 15:07:26 as
	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
	Whole-genome discovery of transcription factor binding sites by network-level conservation. [My Copy] Genome research, Vol. 14, No. 1. (1 January 2004), pp. 99-108. by M. Pritsker, Y. C. Liu, M. A. Beer, S. Tavazoie posted to genomic networks tfbs by alhufton on 2009-07-27 10:44:00 as along with 5 people Dulce aprasad kaarsinogen koller xili03
	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 to regulation scanning tfbs tool by idonaldson on 2009-07-22 11:00:11 as along with 5 people druvus natstreet nklee nuin isimpson
	Expression profile and transcription factor binding site exploration of imprinted genes in human and mouse. [My Copy] BMC genomics, Vol. 10 (31 March 2009), 144. by C. Steinhoff, M. Paulsen, S. Kielbasa, J. Walter, M. Vingron posted to 2009 imprinting tfbs by suizifish on 2009-07-16 08:35:40 as along with 1 person reyez
	Identification of candidate regulatory SNPs by combination of transcription-factor-binding site prediction, SNP genotyping and haploChIP. [My Copy] Nucleic acids research, Vol. 37, No. 12. (1 July 2009), e85. by A. Ameur, A. Rada-Iglesias, J. Komorowski, C. Wadelius posted to regulation snp tfbs by idonaldson on 2009-07-14 09:53:08 as along with 1 person and 1 group guhjy Journal picks
	The Smads. [My Copy] Genome Biol, Vol. 2, No. 8. (2001) by L. Attisano, S. Tuen Lee-Hoeflich posted to tfbs by HawkinsJohnC on 2009-07-08 12:39:56 as along with 1 person sennoma

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regulation	54
motif	48
prediction	35
cis-regulation	34
transcription	31
promoter	29
evolution	28
tool	28
transcription-factor	26
chromatin	25
expression	25
motif-discovery	25
enhancer	23
bioinformatics	21
factor	21
binding	20
genome	17
crm	16
drosophila	15
yeast	15
motifs	14
must-read	13
review	13
microarray	12
mouse	12
pair	12
transcription_factor	12
chip-chip	11
chip-seq	11
conservation	11
nucleosome	11
regulatory	11
bayesian	10
network	10
conserved	9
nucleosome-positioning	9
sites	9
human	8
regulatory-elements	8
software	8
structure	8
ctcf	7
database	7
me	7
transcription-regulation	7
algorithm	6
alignment	6
comparative_genomics	6
discovery	6
matrix	6
over-representation	6
cne	5
footprinting	5
insulator	5
integration	5
mirna	5
tissue-specific	5
transcript	5
zebrafish	5
analysis	4
chip_seq	4
chipseq	4
chromatin-structure	4
cis-regulatory-element	4
cmyc	4
development	4
distance	4
dna	4
duplication	4
epigenetics	4
gene	4
hmm	4
mammals	4
nanog	4
nmyc	4
oct4	4
p300	4
pwm	4
sequence	4
site	4
smad1	4
sox2	4
stat3	4
t-cells	4
tf	4
transcription_regulation	4
zfx	4
binding-sites	3
clustering	3
enhanceosome	3
esc	3
essrb	3
eve	3
in_silico	3
model	3
myeloid-cells	3
networks	3
pho	3
phylogen	3
weight	3

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