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	A hypothesis-based approach for identifying the binding specificity of regulatory proteins from chromatin immunoprecipitation data. [My Copy] Bioinformatics (Oxford, England), Vol. 22, No. 4. (15 February 2006), pp. 423-429. by Kenzie D. Macisaac, D. Benjamin Gordon, Lena Nekludova, et al.Duncan T. Odom, Joerg Schreiber, David K. Gifford, Richard A. Young, Ernest Fraenkel posted to transcription_factors by aalibes on 2009-10-30 13:17:51 as along with 3 people dquest johncumbers eukfn
	Experimental determination of the evolvability of a transcription factor. [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 106, No. 44. (3 November 2009), pp. 18650-18655. by Sebastian J. Maerkl, Stephen R. Quake posted to transcription_factors by aalibes on 2009-10-30 11:54:36 as along with 5 people maximilianh kintoki emptyhb sameersoi bpcusack
	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 transcription_factors by aalibes on 2009-09-02 10:06:17 as along with 11 people and 2 groups venancio fenghezi idonaldson daveGerrard megraw scjparker maximilianh djkt isimpson Stew druvus BergmanLab Bioinformatics - CRUK
	A Multiparameter Network Reveals Extensive Divergence between C. elegans bHLH Transcription Factors [My Copy] Vol. 138, No. 2. (23 July 2009), pp. 314-327. by Christian A. Grove, Federico De Masi, M. Inmaculada Barrasa, et al.Daniel E. Newburger, Mark J. Alkema, Martha L. Bulyk, Albertha J. M. Walhout posted to transcription_factors by aalibes on 2009-07-24 10:59:12 as
	Construction of a Protein Library of Arabidopsis Transcription Factors Using a Wheat Cell-Free Protein Production System and Its Application for DNA Binding Analysis. [My Copy] Bioscience, biotechnology, and biochemistry (7 July 2009) by Akira Nozawa, Yuko Matsubara, Yoshinori Tanaka, et al.Hirotaka Takahashi, Tatsuya Akagi, Motoaki Seki, Kazuo Shinozaki, Yaeta Endo, Tatsuya Sawasaki posted to transcription_factors by aalibes on 2009-07-13 10:49:55 as along with 1 person tprpip
	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 to transcription_factors by aalibes on 2009-05-18 10:04:47 as along with 22 people and 1 group nklee sconlan isimpson jbhiatt daforerog absterga mingzhi galka8_diploma fenghezi TRHvidsten ilyashl cambray rpatward tibbitts dpollard siebert JustinCrocker burak dipenps roys emptyhb tmmurali RockmanLab
	A library of yeast transcription factor motifs reveals a widespread function for Rsc3 in targeting nucleosome exclusion at promoters. [My Copy] Molecular cell, Vol. 32, No. 6. (26 December 2008), pp. 878-887. by G. Badis, E. T. Chan, H. van Bakel, et al.L. Pena-Castillo, D. Tillo, K. Tsui, C. D. Carlson, A. J. Gossett, M. J. Hasinoff, C. L. Warren, M. Gebbia, S. Talukder, A. Yang, S. Mnaimneh, D. Terterov, D. Coburn, A. Li Yeo, Z. X. Yeo, N. D. Clarke, J. D. Lieb, A. Z. Ansari, C. Nislow, T. R. Hughes posted to transcription_factors by aalibes on 2009-03-17 11:39:36 as along with 1 person idonaldson
	STAMP: a web tool for exploring DNA-binding motif similarities. [My Copy] Nucleic acids research, Vol. 35, No. Web Server issue. (3 July 2007) by Shaun Mahony, Panayiotis V. Benos posted to transcription_factors by aalibes on 2009-02-06 11:18:33 as along with 3 people and 1 group yuslinaz raylim dpollard EisenLab
	Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities [My Copy] Nature Biotechnology, Vol. 24, No. 11. (24 September 2006), pp. 1429-1435. by Michael F. Berger, Anthony A. Philippakis, Aaron M. Qureshi, Fangxue S. He, Preston W. Estep, Martha L. Bulyk posted to transcription_factors by aalibes on 2009-01-23 15:30:28 as along with 11 people and 1 group seb1 absterga cambray jfr dpollard stsaft maldi cthachuk olympos yevishere kristallreiner EisenLab
	High-resolution DNA-binding specificity analysis of yeast transcription factors. [My Copy] Genome research, Vol. 19, No. 4. (21 April 2009), pp. 556-566. by Cong Zhu, Kelsey J. Byers, Rachel Patton P. McCord, et al.Zhenwei Shi, Michael F. Berger, Daniel E. Newburger, Katrina Saulrieta, Zachary Smith, Mita V. Shah, Mathangi Radhakrishnan, Anthony A. Philippakis, Yanhui Hu, Federico De Masi, Marcin Pacek, Andreas Rolfs, Tal Murthy, Joshua Labaer, Martha L. Bulyk posted to transcription_factors by aalibes on 2009-01-23 10:43:13 as along with 9 people matted austin_mcdonald siebert dolchan rpatward xwbcn absterga djkt kristallreiner
	Structural Basis of Restoring Sequence-Specific DNA Binding and Transactivation to Mutant p53 by Suppressor Mutations☆ [My Copy] Journal of Molecular Biology, Vol. 385, No. 1. (09 January 2009), pp. 249-265. by O. Suad, H. Rozenberg, R. Brosh, et al.Y. Diskinposner, N. Kessler, L. Shimon, F. Frolow, A. Liran, V. Rotter, Z. Shakked posted to cancer transcription_factors by aalibes on 2009-01-20 15:54:25 as
	Investigation of transcription factor Ndt80 affinity differences for wild type and mutant DNA: A molecular dynamics study [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 73, No. 2. (2008), pp. 325-337. by Katarina Hart, Lennart Nilsson posted to protein_dna transcription_factors by aalibes on 2008-11-07 16:13:10 as
	Prediction of TF target sites based on atomistic models of protein-DNA complexes [My Copy] BMC Bioinformatics, Vol. 9 (16 October 2008), 436. by Vladimir E. Angarica, Abel G. Perez, Ana T. Vasconcelos, Julio Collado-Vides, Bruno Contreras-Moreira posted to protein_dna transcription_factors by aalibes on 2008-10-22 09:16:34 as along with 2 people emptyhb lptolik
	A bacterial one-hybrid system for determining the DNA-binding specificity of transcription factors [My Copy] Nature Biotechnology, Vol. 23, No. 8. (24 July 2005), pp. 988-994. by Xiangdong Meng, Michael H. Brodsky, Scot A. Wolfe posted to paper protein_dna transcription_factors by aalibes on 2008-10-17 11:11:02 as along with 3 people and 1 group austin_mcdonald jbhiatt ajarman Jarman Lab
	Predicting transcription factor specificity with all-atom models. [My Copy] Nucleic acids research (1 October 2008) by Sahand Jamal J. Rahi, Peter Virnau, Leonid A A. Mirny, Mehran Kardar posted to transcription_factors by aalibes on 2008-10-06 09:38:12 as along with 6 people Jporci chrn reyez maximilianh lptolik zwang
	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 to transcription_factors by aalibes on 2008-08-29 11:48:49 as along with 29 people and 8 groups viren4388 daveGerrard Dulce talponer wowalz siebert alokm tuck lyongu kaspermunch dpollard balicea kt dchughes nirfriedman cmm nickluscombe kengg gespim koller lusk nklee cisevol njcitulike xili03 brant mariakmejia kristallreiner snow_dragon Bioinformatics EisenLab FAB-lab G4ID EBI-regulation Plantandetc Genetics-of-Gambling BergmanLab
	A Feature-Based Approach to Modeling Protein–DNA Interactions [My Copy] PLoS Comput Biol, Vol. 4, No. 8. (2008), e1000154. by Eilon Sharon, Shai Lubliner, Eran Segal posted to protein_dna transcription_factors by aalibes on 2008-08-28 15:51:00 as along with 5 people ptrobajo dakelley Stew emptyhb zwang
	Computational prediction of transcription-factor binding site locations [My Copy] Genome Biology, Vol. 5, No. 1. (2003), 201. by Martha Bulyk posted to transcription_factors by aalibes on 2008-07-22 11:09:57 as along with 9 people and 1 group Baschl marti tkmaia kaarsinogen lusk Stew nklee yevishere xili03 EisenLab
	Specific DNA-binding by Apicomplexan AP2 transcription factors [My Copy] Proceedings of the National Academy of Sciences (9 June 2008), 0801993105. by Erandi K. De Silva, Andrew R. Gehrke, Kellen Olszewski, et al.Ilsa Leon, Jasdave S. Chahal, Martha L. Bulyk, Manuel Llinas posted to transcription_factors by aalibes on 2008-06-10 13:36:35 as along with 1 person maximilianh
	Structure-based prediction of transcription factor binding sites using a protein-DNA docking approach [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2008), NA. by Zhijie Liu, Jun-Tao Guo, Ting Li, Ying Xu posted to transcription_factors by aalibes on 2008-03-11 09:20:24 as along with 1 person neils
	Evolution and Selection in Yeast Promoters: Analyzing the Combined Effect of Diverse Transcription Factor Binding Sites [My Copy] PLoS Comput Biol, Vol. 4, No. 1. (11 January 2008), e7. by Daniela Raijman, Ron Shamir, Amos Tanay posted to transcription_factors by aalibes on 2008-01-14 10:40:24 as along with 8 people and 1 group marck xili03 sebastien_vigneau lusk Garamonfok nklee maximilianh emptyhb BioinfoCIPF
	A Nucleosome-Guided Map of Transcription Factor Binding Sites in Yeast [My Copy] PLoS Computational Biology, Vol. 3, No. 11. (1 November 2007), e215. by Leelavati Narlikar, Raluca Gordân, Alexander J. Hartemink posted to nucleosome transcription_factors by aalibes on 2007-11-12 10:56:12 as along with 5 people TRHvidsten zwang nklee maximilianh megraw
	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 to transcription_factors by aalibes on 2007-11-11 19:12:17 as along with 38 people and 6 groups mpizbioinfo megraw Dulce farhat wowalz mhofree jasontsai heliopais pengchy daforerog yylin cambray emptyhb bryankr icases ana barry aprasad jfr tuck chad_davis lyongu tabu dquest neveaire ranb johncumbers noano xiaobeizhao olympos GustavoLacerda nklee mdimon dandaman vietanh0 ep161302 nuin Stew structural_bioinformatics Biostatistics Computational-Genomics Bioinformatics Neuroscience TNT
	Position dependencies in transcription factor binding sites. [My Copy] Bioinformatics, Vol. 23, No. 8. (15 April 2007), pp. 933-941. by A. Tomovic, E. J. Oakeley posted to transcription_factors by aalibes on 2007-10-09 11:58:29 as along with 2 people nklee yevishere
	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 transcription_factors by aalibes on 2007-08-10 09:48:11 as along with 22 people and 2 groups pradiptaray gdb fenghezi dbensasson caseybrown bryankr chad_davis dpollard djkt mikaelhuss lusk cjeans sujaikumar zwang GustavoLacerda Jporci maximilianh cisevol njcitulike emptyhb nklee anka EisenLab cis-regulatory-evolution
	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 to transcription_factors by aalibes on 2007-07-13 11:42:33 as along with 2 people nklee xili03
	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 to protein_dna transcription_factors by aalibes on 2007-06-08 12:10:09 as along with 24 people and 5 groups oannes daforerog tonamswish ewilban1 aprasad jo_davies balicea andersbj JeremyZucker aswin kengg giovanni cjeans ghattem zwang epigenetics biomcgary george_g cabbagezs Jporci blobbybirdman caseybrown emptyhb dquest Bioinformatics microRNA Marcotte_Lab UH - Computational Biology Myxo group
	Human SRF-related proteins: DNA-binding properties and potential regulatory targets. [My Copy] Genes Dev, Vol. 5, No. 12A. (December 1991), pp. 2327-2341. by R. Pollock, R. Treisman posted to tf_exp transcription_factors by aalibes on 2007-05-18 12:09:58 as
	JASPAR: an open-access database for eukaryotic transcription factor binding profiles [My Copy] Nucl. Acids Res., Vol. 32, No. suppl_1. (1 January 2004), pp. D91-94. by Albin Sandelin, Wynand Alkema, Par Engstrom, Wyeth W. Wasserman, Boris Lenhard posted to tools transcription_factors by aalibes on 2007-05-17 15:17:52 as along with 5 people and 2 groups antonkratz indigoviolet jguinney nklee heliopais EisenLab Motif Discovery
	Decoding transcriptional regulatory interactions. [My Copy] Physica D, Vol. 224, No. 1-2. (December 2006), pp. 174-181. by L Angela A. Liu, Joel S S. Bader posted to transcription_factors by aalibes on 2007-05-17 15:11:07 as
	Connecting protein structure with predictions of regulatory sites [My Copy] Proceedings of the National Academy of Sciences, Vol. 104, No. 17. (24 April 2007), pp. 7068-7073. by Alexandre V. Morozov, Eric D. Siggia posted to protein_dna transcription_factors by aalibes on 2007-05-17 15:09:20 as along with 7 people and 2 groups vingron nklee maximilianh ana kaarsinogen johncumbers lusk structural_bioinformatics Bioinformatics
	Measuring similarities between transcription factor binding sites [My Copy] BMC Bioinformatics, Vol. 6, No. 1. (2005) by Szymon Kielbasa, Didier Gonze, Hanspeter Herzel posted to transcription_factors by aalibes on 2007-05-16 14:44:01 as along with 1 person nklee
	A statistical analysis of the TRANSFAC database [My Copy] Biosystems, Vol. 81, No. 2. (August 2005), pp. 137-154. by Gary B. Fogel, Dana G. Weekes, Gabor Varga, et al.Ernst R. Dow, Andrew M. Craven, Harry B. Harlow, Eric W. Su, Jude E. Onyia, Chen Su posted to transcription_factors by aalibes on 2007-05-15 16:27:53 as
	TRANSFAC: transcriptional regulation, from patterns to profiles. [My Copy] Nucleic Acids Res, Vol. 31, No. 1. (1 January 2003), pp. 374-378. by V. Matys, E. Fricke, R. Geffers, et al.E. Gössling, M. Haubrock, R. Hehl, K. Hornischer, D. Karas, A. E. Kel, O. V. Kel-Margoulis, D. U. Kloos, S. Land, B. Lewicki-Potapov, H. Michael, R. Münch, I. Reuter, S. Rotert, H. Saxel, M. Scheer, S. Thiele, E. Wingender posted to transcription_factors by aalibes on 2007-05-15 16:07:58 as along with 8 people and 1 group raylim aprasad setar chad_davis GustavoLacerda marti Auger kmdaily Dead 60's
	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 protein_dna transcription_factors by aalibes on 2007-05-11 15:57:47 as along with 7 people and 1 group pradiptaray nklee dpollard medic0747 GustavoLacerda mircea marti EisenLab

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protein_dna	44
nucleosome	37
transcription_factors	35
tools	27
zinc_fingers	27
networks	19
protein_structure	19
folding_rate	14
proteins_and_networks	12
marta	11
meganucleases	9
systems_biology	9
tf_exp	8
cancer	7
godzik	7
libeb	6
protein_engineering	6
protein_stability	6
thermostability	6
database	5
protein_folding	4
protein_models	4
protein_mutation	4
bioinformatics_general	3
contact_order	3
paper	3
proteins	3
sigma_factor	3
snp	3
synthetic_biology	3
bzip	2
dna	2
endonucleases	2
gene_expression	2
general_science	2
genomics	2
go	2
groel	2
ontologies	2
protein_interaction	2
software	2
atheism	1
bhlh	1
crap	1
data_mining	1
docking	1
expression_networks	1
gcn4	1
general	1
ignobel	1
microarrays	1
oligos	1
p53	1
protein_diffusion	1
protein_evolution	1
regulation_mutation	1
software_development	1
transcriptional_networks	1
translation_networks	1

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