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Ключевое слово tfbs [158 articles]

Recent papers classified by the tag tfbs.
  • Assessing computational tools for the discovery of transcription factor binding sites
    Nature Biotechnology, Vol. 23, No. 1. (06 January 2005), pp. 137-144.
    by Martin Tompa, Nan Li, Timothy L Bailey, George M Church, Bart D De Moor, Eleazar Eskin, Alexander V Favorov, Martin C Frith, Yutao Fu, James J Kent, Vsevolod J Makeev, Andrei A Mironov, William S Noble, Giulio Pavesi, Graziano Pesole, Mireille Régnier, Nicolas Simonis, Saurabh Sinha, Gert Thijs, Jacques v van Helden, Mathias Vandenbogaert, Zhiping Weng, Christopher Workman, Chun Ye, Zhou Zhu
    posted to algorithm analysis review tfbs by xiaobeizhao on 2006-10-09 06:03:55 as **** along with 26 people and 6 groups emptyhb bryankr icases ana barry aalibes aprasad jfr tuck chad_davis lyongu tabu dquest neveaire ranb johncumbers noano olympos GustavoLacerda nklee mdimon dandaman vietanh0 ep161302 nuin Stew structural_bioinformatics Biostatistics Computational-Genomics Bioinformatics Neuroscience TNT
  • Weeder Web: discovery of transcription factor binding sites in a set of sequences from co-regulated genes.
    Nucleic Acids Res, Vol. 32, No. Web Server issue. (1 July 2004)
    by G Pavesi, P Mereghetti, G Mauri, G Pesole
    posted to algorithm tfbs by xiaobeizhao on 2006-10-09 05:38:59 as read along with 3 people dquest dandaman bryankr
  • Gibbs Recursive Sampler: finding transcription factor binding sites
    Nucl. Acids Res., Vol. 31, No. 13. (1 July 2003), pp. 3580-3585.
    by William Thompson, Eric C Rouchka, Charles E Lawrence
    posted to algorithm gibbs-sampler tfbs by xiaobeizhao on 2006-10-09 05:49:57 as **** along with 5 people jmartin49 lyongu dquest daniel_quest johncumbers
  • Discovery of novel transcription factor binding sites by statistical overrepresentation.
    Nucleic Acids Res, Vol. 30, No. 24. (15 December 2002), pp. 5549-5560.
    by S Sinha, M Tompa
    posted to algorithm tfbs by xiaobeizhao on 2006-10-09 15:33:50 as ** along with 9 people kaarsinogen dquest smiddha GeeSharpMinor xi03 xili03 ep161302 wenhan pradiptaray
  • Cyclical DNA methylation of a transcriptionally active promoter
    Nature, Vol. 452, No. 7183. (6 March 2008), pp. 45-50.
    by Raphael Metivier, Rozenn Gallais, Christophe Tiffoche, Christine Le Peron, Renata Z Jurkowska, Richard P Carmouche, David Ibberson, Peter Barath, Florence Demay, George Reid, Vladimir Benes, Albert Jeltsch, Frank Gannon, Gilles Salbert
    posted to chromatin tfbs by vega on 2008-03-06 10:38:31 as ** along with 3 people djkt epigenetics clearbluespring
  • High-throughput mapping of the chromatin structure of human promoters
    Nat Biotech, Vol. 25, No. 2. (February 2007), pp. 244-248.
    by Fatih Ozsolak, Jun S Song, Shirley X Liu, David E Fisher
    posted to chromatin tfbs by vega on 2008-03-03 02:15:19 as ** along with 5 people and 2 groups jyuh aalibes jfr dchughes ccr G4ID Genetics-of-Gambling
  • DNA Immunoprecipitation (DIP) for the Determination of DNA-Binding Specificity
    Cold Spring Harbor Protocols, Vol. 2008, No. 4. (1 March 2008), pdb.prot4972.
    by Andrea J Gossett, Jason D Lieb
    posted to chromatin tfbs by vega on 2008-06-18 09:40:17 as ** along with 2 people jyuh dacrotty
  • A systematic model to predict transcriptional regulatory mechanisms based on overrepresentation of transcription factor binding profiles.
    Genome Res, Vol. 16, No. 3. (March 2006), pp. 405-413.
    by LW Chang, R Nagarajan, JA Magee, J Milbrandt, GD Stormo
    posted to modules motif tfbs by vega on 2006-05-15 10:17:05 as *** along with 3 people jfr johncumbers sconlan
  • Transient cyclical methylation of promoter DNA
    Nature, Vol. 452, No. 7183. (6 March 2008), pp. 112-115.
    by Sara Kangaspeska, Brenda Stride, Raphael Metivier, Maria Polycarpou-Schwarz, David Ibberson, Richard P Carmouche, Vladimir Benes, Frank Gannon, George Reid
    posted to chromatin tfbs by vega on 2008-03-06 10:38:18 as ** along with 4 people djkt maximilianh clearbluespring dunnp
  • Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing.
    Nat Methods (11 June 2007)
    by Gordon Robertson, Martin Hirst, Matthew Bainbridge, Misha Bilenky, Yongjun Zhao, Thomas Zeng, Ghia Euskirchen, Bridget Bernier, Richard Varhol, Allen Delaney, Nina Thiessen, Obi L L Griffith, Ann He, Marco Marra, Michael Snyder, Steven Jones
    posted to bioinformatics chip tfbs by vega on 2008-02-07 03:01:09 as read along with 6 people and 1 group jyuh kengg ghattem slevy03 dquest raiyar Plantandetc
  • DBD: a transcription factor prediction database.
    Nucleic Acids Res, Vol. 34, No. Database issue. (1 January 2006)
    by SK Kummerfeld, SA Teichmann
    posted to database prediction tfbs by troels_marstrand on 2006-01-05 12:54:02 as ** along with 5 people and 1 group gpalidwor nickluscombe nklee mariakmejia natstreet EBI-regulation
  • TRANSFAC(R) and its module TRANSCompel(R): transcriptional gene regulation in eukaryotes.
    Nucleic Acids Res, Vol. 34, No. Database issue. (1 January 2006)
    by V Matys, OV Kel-Margoulis, E Fricke, I Liebich, S Land, A Barre-Dirrie, I Reuter, D Chekmenev, M Krull, K Hornischer, N Voss, P Stegmaier, B Lewicki-Potapov, H Saxel, AE Kel, E Wingender
    posted to tfbs transfac by troels_marstrand on 2006-01-05 12:54:30 as ** along with 3 people reidy frohike jyuh
  • Toucan: deciphering the cis-regulatory logic of coregulated genes.
    Nucleic Acids Res, Vol. 31, No. 6. (15 March 2003), pp. 1753-1764.
    by S Aerts, G Thijs, B Coessens, M Staes, Y Moreau, B De Moor
    posted to platform tfbs tool by troels_marstrand on 2006-01-05 14:33:36 as read along with 5 people and 1 group kaspermunch nur77 nklee yevishere xili03 Bioinformatics
  • Identification of conserved regulatory elements by comparative genome analysis.
    J Biol, Vol. 2, No. 2. (2003)
    by B Lenhard, A Sandelin, L Mendoza, P Engström, N Jareborg, WW Wasserman
    posted to consite phylo tfbs by troels_marstrand on 2006-02-09 06:23:52 as **** along with 1 person and 1 group cisevol cis-regulatory-evolution
  • Prediction of cis-regulatory elements using binding site matrices--the successes, the failures and the reasons for both.
    Curr Opin Genet Dev, Vol. 15, No. 4. (August 2005), pp. 395-402.
    by T Vavouri, G Elgar
    posted to preditction review tfbs by troels_marstrand on 2006-01-05 21:05:16 as read along with 6 people and 2 groups kaspermunch dpollard adepace lusk Stew brant Bioinformatics EisenLab
  • HTPSELEX--a database of high-throughput SELEX libraries for transcription factor binding sites.
    Nucleic Acids Res, Vol. 34, No. Database issue. (1 January 2006)
    by V Jagannathan, E Roulet, M Delorenzi, P Bucher
    posted to database tfbs by troels_marstrand on 2006-01-05 12:51:18 as **
  • ConSite: web-based prediction of regulatory elements using cross-species comparison.
    Nucleic Acids Res, Vol. 32, No. Web Server issue. (1 July 2004)
    by A Sandelin, WW Wasserman, B Lenhard
    posted to conservation tfbs by troels_marstrand on 2006-02-10 08:18:31 as ****
  • Identification of transcription factor binding sites with variable-order Bayesian networks.
    Bioinformatics, Vol. 21, No. 11. (1 June 2005), pp. 2657-2666.
    by I Ben-Gal, A Shani, A Gohr, J Grau, S Arviv, A Shmilovici, S Posch, I Grosse
    posted to bayesian prediction tfbs by troels_marstrand on 2006-01-05 21:06:09 as read along with 1 person wnpx
  • A global map of p53 transcription-factor binding sites in the human genome.
    Cell, Vol. 124, No. 1. (13 January 2006), pp. 207-219.
    by CL Wei, Q Wu, VB Vega, KP Chiu, P Ng, T Zhang, A Shahab, HC Yong, Y Fu, Z Weng, J Liu, XD Zhao, JL Chew, YL Lee, VA Kuznetsov, WK Sung, LD Miller, B Lim, ET Liu, Q Yu, HH Ng, Y Ruan
    posted to p53 tfbs by tabu on 2006-03-28 01:33:15 as ** along with 11 people and 1 group drestion kaarsinogen jfr balajis vega kengg jackjackjjj jtomasch karfunkel maralena bozdagd Plantandetc
  • Predicted transcription factor binding sites as predictors of operons in Escherichia coli and Streptomyces coelicolor.
    BMC Genomics, Vol. 9 (12 February 2008), 79.
    by Emma Laing, Khushwant Sidhu, Simon J Hubbard
    posted to operons regulation tf tfbs by sdyxz on 2008-02-20 15:08:19 as * along with 1 person msuarezdiez
  • Eukaryotic transcription factor binding sites - modeling and integrative search methods
    Bioinformatics (21 April 2008), btn198.
    by Sridhar Hannenhalli
    posted to tfbs transc by sameetmehta on 2008-05-20 01:32:04 as ** along with 8 people oannes hplatero maximilianh heliopais bootsy Ema jyuh chad_davis
  • Close sequence comparisons are sufficient to identify human cis-regulatory elements.
    Genome Res (12 June 2006)
    by Shyam Prabhakar, Francis Poulin, Malak Shoukry, Veena Afzal, Edward M M Rubin, Olivier Couronne, Len A A Pennacchio
    posted to alignment annotation conserved constraint evolution footprinting human mammal mammals no-tag prediction rate selection tfbs transcription turnover by samal on 2006-08-22 05:18:32 as ** along with 8 people and 2 groups indigoviolet dpollard nickluscombe olympos emptyhb bpcusack mariakmejia kcrawlik EisenLab EBI-regulation
  • Integrating large-scale functional genomic data to dissect the complexity of yeast regulatory networks.
    Nature genetics (15 June 2008)
    by Jun Zhu, Bin Zhang, Erin N N Smith, Becky Drees, Rachel B B Brem, Leonid Kruglyak, Roger E E Bumgarner, Eric E E Schadt
    posted to network regulatory tfbs yeast by realzhang on 2008-06-20 10:04:06 as ** along with 10 people kengg maralena ptrobajo tmmurali jyuh roys marck caseybrown djkt srp33
  • Evolution of candidate transcriptional regulatory motifs since the human-chimpanzee divergence
    Genome Biology, Vol. 7 (29 June 2006), R52.
    by Ian J Donaldson, Berthold Göttgens
    posted to evolution primates tfbs by ranb on 2006-06-30 15:24:43 as ***** along with 4 people and 2 groups indigoviolet djkt cisevol idonaldson EisenLab cis-regulatory-evolution
  • Evolutionary analysis of the cis-regulatory region of the spicule matrix gene SM50 in strongylocentrotid sea urchins.
    Developmental biology, Vol. 315, No. 2. (15 March 2008), pp. 567-578.
    by J Walters, E Binkley, R Haygood, LA Romano
    posted to crm evolution motif purpuratus regulation sea sm50 tfbs urchin by pradiptaray on 2008-08-07 16:38:42 as ** along with 1 person emptyhb
  • Phylogenetic footprinting of transcription factor binding sites in proteobacterial genomes.
    Nucleic Acids Res, Vol. 29, No. 3. (1 February 2001), pp. 774-782.
    by L McCue, W Thompson, C Carmack, MP Ryan, JS Liu, V Derbyshire, CE Lawrence
    posted to bacteria footprinting motif phylogeny prokaryote regulation tfbs by pradiptaray on 2008-08-07 16:23:07 as ** along with 3 people and 1 group dquest adepace nklee EisenLab
  • Composite Module Analyst: a fitness-based tool for identification of transcription factor binding site combinations.
    Bioinformatics, Vol. 22, No. 10. (15 May 2006), pp. 1190-1197.
    by A Kel, T Konovalova, T Waleev, E Cheremushkin, O Kel-Margoulis, E Wingender
    posted to crm tfbs by oannes on 2006-06-01 03:18:40 as ***** along with 1 group Regulomics_UCHSC
  • Transcription in four dimensions: nuclear receptor-directed initiation of gene expression.
    EMBO Rep, Vol. 7, No. 2. (February 2006), pp. 161-167.
    by R Métivier, G Reid, F Gannon
    posted to dynamic tfbs by oannes on 2006-05-25 17:26:35 as ** along with 1 group Regulomics_UCHSC
  • Modeling gene expression control using Omes Law
    Mol Syst Biol, Vol. 2, No. 1. (11 April 2006), pp. msb4100055-E1-msb4100055-E3.
    by Harmen J Bussemaker
    posted to pair tfbs by oannes on 2006-05-09 21:11:26 as ** along with 2 people and 2 groups okarsligil nsamways Bioinformatics Regulomics_UCHSC
  • SUMO and ubiquitin in the nucleus: different functions, similar mechanisms?
    Genes Dev., Vol. 18, No. 17. (1 September 2004), pp. 2046-2059.
    by Grace Gill
    posted to sumo tfbs by oannes on 2006-05-25 17:12:41 as ** along with 2 people and 1 group imouthesmp cjeans Regulomics_UCHSC
  • Quantitative evaluation of protein-DNA interactions using an optimized knowledge-based potential.
    Nucleic Acids Res, Vol. 33, No. 2. (2005), pp. 546-558.
    by Z Liu, F Mao, JT Guo, B Yan, P Wang, Y Qu, Y Xu
    posted to structure tfbs by oannes on 2006-05-18 05:57:41 as ** along with 1 person and 1 group kaarsinogen Regulomics_UCHSC
  • Distance preferences in the arrangement of binding motifs and hierarchical levels in organization of transcription regulatory information.
    Nucleic Acids Res, Vol. 31, No. 20. (15 October 2003), pp. 6016-6026.
    by VJ Makeev, AP Lifanov, AG Nazina, DA Papatsenko
    posted to distance pair tfbs by oannes on 2006-04-27 20:16:27 as read along with 2 people and 2 groups dpollard lusk EisenLab Regulomics_UCHSC
  • Human Transcription Factors Contain a High Fraction of Intrinsically Disordered Regions Essential for Transcriptional Regulation.
    J Mol Biol (25 April 2006)
    by Yoshiaki Minezaki, Keiichi Homma, Akira R R Kinjo, Ken Nishikawa
    posted to structure tfbs by oannes on 2006-06-01 03:12:36 as **** along with 1 person and 1 group biomcgary Regulomics_UCHSC
  • Predicting transcription factor synergism.
    Nucleic Acids Res, Vol. 30, No. 19. (1 October 2002), pp. 4278-4284.
    by S Hannenhalli, S Levy
    posted to pair tfbs by oannes on 2006-04-27 20:13:23 as read along with 1 group Regulomics_UCHSC
  • The transcriptional regulatory code of eukaryotic cells - insights from genome-wide analysis of chromatin organization and transcription factor binding
    Current Opinion in Cell Biology, Vol. 18, No. 3. (June 2006), pp. 291-298.
    by Leah O Barrera, Bing Ren
    posted to chromatin tfbs by oannes on 2006-06-01 03:23:43 as ***** along with 4 people and 4 groups dchughes cmm lusk vietanh0 FAB-lab G4ID Regulomics_UCHSC Genetics-of-Gambling
  • Annotating significant pairs of transcription factor binding sites in regulatory DNA.
    In Silico Biol, Vol. 4, No. 4. (2004), pp. 479-487.
    by K Rateitschak, T Müller, M Vingron
    posted to pair tfbs by oannes on 2006-04-27 20:17:24 as ** along with 1 group Regulomics_UCHSC
  • Genome-wide computational prediction of transcriptional regulatory modules reveals new insights into human gene expression.
    Genome Res (10 April 2006)
    by Mathieu Blanchette, Alain R R Bataille, Xiaoyu Chen, Christian Poitras, Josée Laganière, Céline Lefèbvre, Geneviève Deblois, Vincent Giguère, Vincent Ferretti, Dominique Bergeron, Benoit Coulombe, François Robert
    posted to tfbs by oannes on 2006-04-27 20:24:12 as ***** along with 1 group Regulomics_UCHSC
  • Genome-wide prediction and characterization of interactions between transcription factors in Saccharomyces cerevisiae.
    Nucleic Acids Res, Vol. 34, No. 3. (2006), pp. 917-927.
    by X Yu, J Lin, T Masuda, N Esumi, DJ Zack, J Qian
    posted to distance pair tfbs by oannes on 2006-04-21 21:53:08 as ***** along with 3 people and 1 group balajis malcook lusk Regulomics_UCHSC
  • Protein-DNA binding specificity predictions with structural models.
    Nucleic Acids Res, Vol. 33, No. 18. (2005), pp. 5781-5798.
    by AV Morozov, JJ Havranek, D Baker, ED Siggia
    posted to tfbs by oannes on 2006-04-27 20:20:00 as ** along with 1 group Regulomics_UCHSC
  • Activation of TRAP/Mediator Subunit TRAP220/Med1 Is Regulated by Mitogen-Activated Protein Kinase-Dependent Phosphorylation
    Mol. Cell. Biol., Vol. 25, No. 24. (15 December 2005), pp. 10695-10710.
    by Pradeep K Pandey, TS Udayakumar, Xinjie Lin, Dipali Sharma, Paul S Shapiro, Joseph D Fondell
    posted to mediator pair tfbs by oannes on 2006-05-18 23:15:58 as ** along with 1 group Regulomics_UCHSC
  • Regulatory element detection using correlation with expression.
    Nat Genet, Vol. 27, No. 2. (February 2001), pp. 167-171.
    by HJ Bussemaker, H Li, ED Siggia
    posted to expression tfbs by nickluscombe on 2006-06-29 14:55:38 as ** along with 4 people and 2 groups dpollard heliopais tvdbulck isimpson EisenLab EBI-regulation
  • PhyloGibbs: A Gibbs Sampling Motif Finder That Incorporates Phylogeny.
    PLoS Comput Biol, Vol. 1, No. 7. (December 2005)
    by R Siddharthan, ED Siggia, E van Nimwegen
    posted to chip-chip tfbs by nickluscombe on 2006-06-30 10:46:57 as ** along with 12 people and 3 groups druvus ana postrational dquest AaronDarling noano adsmitty lusk lilou idonaldson yevishere isimpson structural_bioinformatics Bioinformatics EBI-regulation
  • Predicting gene expression from sequence.
    Cell, Vol. 117, No. 2. (16 April 2004), pp. 185-198.
    by MA Beer, S Tavazoie
    posted to bayesian expression predictions regulation tfbs by nickluscombe on 2006-06-30 12:16:01 as ** along with 9 people and 5 groups tharris ana xwbcn adepace noano koller jrest phoenixzxl klo C. elegans / WormBase structural_bioinformatics Bioinformatics EisenLab EBI-regulation
  • VOMBAT: prediction of transcription factor binding sites using variable order Bayesian trees.
    Nucleic acids research, Vol. 34, No. Web Server issue. (1 July 2006)
    by J Grau, I Ben-Gal, S Posch, I Grosse
    posted to vom vobn tfbs by mgledi on 2008-09-30 13:03:04 as read
  • Identification of transcription factor binding sites with variable-order Bayesian networks
    Bioinformatics, Vol. 21, No. 11. (1 June 2005), pp. 2657-2666.
    by I Ben-Gal, A Shani, A Gohr, J Grau, S Arviv, A Shmilovici, S Posch, I Grosse
    posted to vobn tfbs statistical models by mgledi on 2008-09-30 13:12:21 as read along with 2 people lyongu nuin
  • Recognition of cis-regulatory elements with vombat.
    Journal of bioinformatics and computational biology, Vol. 5, No. 2B. (April 2007), pp. 561-577.
    by S Posch, J Grau, A Gohr, I Ben-Gal, AE Kel, I Grosse
    posted to vombat vom vobn tfbs by mgledi on 2008-09-30 15:56:42 as ****
  • REDfly: a Regulatory Element Database for Drosophila
    Bioinformatics, Vol. 22, No. 3. (1 February 2006), pp. 381-383.
    by Steven M Gallo, Long Li, Zihua Hu, Marc S Halfon
    posted to tfbs by malcook on 2006-03-06 20:52:27 as **
  • Evolution and Selection in Yeast Promoters: Analyzing the Combined Effect of Diverse Transcription Factor Binding Sites
    PLoS Computational Biology, Vol. 4, No. 1. (1 January 2008), e7.
    by Daniela Raijman, Ron Shamir, Amos Tanay
    posted to evolution tfbs by lusk on 2008-01-21 22:07:56 as ***** along with 7 people and 1 group aalibes chad_davis sebastien_vigneau Garamonfok nklee maximilianh emptyhb BioinfoCIPF
  • Rank order metrics for quantifying the association of sequence features with gene regulation.
    Bioinformatics, Vol. 19, No. 2. (22 January 2003), pp. 212-218.
    by ND Clarke, JA Granek
    posted to over-representation promoter regulation tfbs by kaspermunch on 2006-02-06 10:49:29 as **** along with 2 people and 1 group nklee xili03 Bioinformatics
  • BSS-HMM 3 s: An improved HMM method for identifying transcription factor binding sites
    DNA Sequence - The Journal of Sequencing and Mapping, Vol. 16, No. 6. (December 2005), pp. 403-411.
    by Dong Xu, Hai J Liu, Yi F Wang
    posted to hmm promoter tfbs by kaspermunch on 2005-11-20 19:45:10 as ** along with 1 person and 1 group seitentaisei Bioinformatics
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