idonaldson's tfbs [54 articles] Export

Recent papers added to idonaldson's library classified by the tag tfbs. You can also see everyone's tfbs.

	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 2 people roys daforerog
	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
	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
	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 12 people and 2 groups bsamal venancio aalibes fenghezi daveGerrard megraw scjparker maximilianh djkt isimpson Stew druvus BergmanLab Bioinformatics - CRUK
	Statistical detection of cooperative transcription factors with similarity adjustment [My Copy] Bioinformatics (Oxford, England) In Bioinformatics, 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 3 people bsamal 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
	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 regulation scanning tfbs tool by idonaldson on 2009-07-22 11:00:11 as along with 6 people bsamal druvus natstreet nklee nuin isimpson
	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
	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 motif nucleosome tfbs yeast by idonaldson on 2009-06-08 09:09:31 as along with 1 person aalibes
	An improved map of conserved regulatory sites for Saccharomyces cerevisiae [My Copy] BMC Bioinformatics, Vol. 7, No. 1. (7 March 2006), 113. by Kenzie Macisaac, Ting Wang, D. Benjamin Gordon, David Gifford, Gary Stormo, Ernest Fraenkel posted to conserved motif tfbs yeast by idonaldson on 2009-04-30 14:43:51 as along with 9 people roys tuck eckart_bindewald cconboy raiyar lusk nklee barwil kristallreiner
	New scoring schema for finding motifs in DNA Sequences [My Copy] BMC Bioinformatics, Vol. 10 (20 March 2009), 93. by Fatemeh, Bahram Goliaei posted to motif scoring tfbs by idonaldson on 2009-03-30 08:58:01 as along with 6 people and 1 group bsamal svenrahmann cassj maximilianh ElenaGrassi nuin cube_and_beyond
	Genome-wide discovery of functional transcription factor binding sites by comparative genomics: The case of Stat3 [My Copy] Proceedings of the National Academy of Sciences (12 March 2009) by Francesco Vallania, Davide Schiavone, Sarah Dewilde, et al.Emanuela Pupo, Serge Garbay, Raffaele Calogero, Marco Pontoglio, Paolo Provero, Valeria Poli posted to conserved discovery genome tfbs by idonaldson on 2009-03-16 10:30:59 as along with 2 people maximilianh merpublic
	COTRASIF: conservation-aided transcription-factor-binding site finder [My Copy] Nucl. Acids Res. In Nucl. Acids Res., Vol. 37, No. 7. (1 April 2009), e49. by Bogdan Tokovenko, Rostyslav Golda, Oleksiy Protas, Maria Obolenskaya, Anna El'skaya posted to tfbs tool by idonaldson on 2009-03-09 09:30:51 as along with 4 people and 1 group bsamal avilella druvus nuin Ensembl Compara citations
	Evolutionary Conserved Motif Finder (ECMFinder) for genome-wide identification of clustered YY1- and CTCF-binding sites. [My Copy] Nucleic acids research (10 February 2009) by Keunsoo Kang, Jae Hoon H. Chung, Joomyeong Kim posted to ecm tfbs tool by idonaldson on 2009-02-16 09:29:03 as along with 2 people clearbluespring sebastien_vigneau
	Extracting transcription factor binding sites from unaligned gene sequences with statistical models. [My Copy] BMC bioinformatics, Vol. 9 Suppl 12 (2008) by C. C. Lu, W. H. Yuan, T. M. Chen posted to chip-chip tfbs tool by idonaldson on 2009-01-15 09:56:34 as along with 3 people and 1 group stajich kristallreiner maximilianh Mycology
	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 to conserved motif tfbs tool by idonaldson on 2008-11-24 14:18:37 as along with 12 people bsamal jakebiesinger kmdaily guhjy wowalz ilyashl jfr abizar heliopais nklee nuin djkt
	High-throughput chromatin information enables accurate tissue-specific prediction of transcription factor binding sites. [My Copy] Nucleic acids research (6 November 2008) by Tom Whitington, Andrew C C. Perkins, Timothy L L. Bailey posted to chromatin tfbs tissue-specific by idonaldson on 2008-11-13 13:16:42 as along with 1 person polivares
	Positional distribution of human transcription factor binding sites. [My Copy] Nucleic acids research (25 October 2008) by Mark Koudritsky, Eytan Domany posted to distribution tfbs tss by idonaldson on 2008-11-03 09:11:41 as along with 10 people and 2 groups bsamal daforerog jfr jforman ghattem barriot fpattyn nklee maximilianh nuin SIMR bioinformatics BenosLab
	E2F in vivo binding specificity: Comparison of consensus versus nonconsensus binding sites [My Copy] Genome Research, Vol. 18, No. 11. (3 November 2008), pp. 1763-1777. by Alina Rabinovich, Victor X. Jin, Roman Rabinovich, Xiaoqin Xu, Peggy J. Farnham posted to binding chip-chip specificity tfbs by idonaldson on 2008-10-13 09:21:25 as along with 1 person fenghezi
	Transcription factor and microRNA motif discovery: The Amadeus platform and a compendium of metazoan target sets [My Copy] Genome Research In Genome Research, Vol. 18, No. 7. (14 July 2008), pp. 1180-1189. by Chaim Linhart, Yonit Halperin, Ron Shamir posted to motif-discovery tfbs tool by idonaldson on 2008-04-22 09:26:03 as along with 15 people and 2 groups heliopais bsamal roys dolchan akshayk wowalz natstreet valeriehilgers jfr ealloza maralena fpattyn isimpson tmmurali maximilianh microRNA BergmanLab
	An efficient method for statistical significance calculation of transcription factor binding sites. [My Copy] Bioinformation, Vol. 2, No. 5. (2007), pp. 169-174. by Z. Qian, L. Lu, L. Qi, Y. Li posted to statistics tfbs by idonaldson on 2008-03-03 09:44:21 as along with 4 people and 1 group bsamal nklee maximilianh isimpson Motif Discovery
	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 to distribution motif promoter tfbs by idonaldson on 2008-02-15 09:30:51 as along with 4 people bsamal wowalz xili03 isimpson
	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 crm tfbs tissue-specific by idonaldson on 2008-02-15 09:28:41 as along with 10 people roys isimpson guhjy chad_davis mikaelhuss nklee maximilianh njcitulike bootsy snow_dragon
	Model-based deconvolution of genome-wide DNA binding. [My Copy] Bioinformatics (1 December 2007) by David J J. Reiss, Marc T T. Facciotti, Nitin S S. Baliga posted to chip-chip deconvolution tfbs by idonaldson on 2008-01-31 11:10:21 as along with 5 people djkt yevishere guhjy vega isimpson
	TFBS identification based on genetic algorithm with combined representations and adaptive post-processing [My Copy] Bioinformatics In Bioinformatics, Vol. 24, No. 3. (1 February 2008), pp. 341-349. by Tak-Ming Chan, Kwong-Sak Leung, Kin-Hong Lee posted to motif-discovery tfbs tool by idonaldson on 2008-01-31 11:07:05 as along with 7 people bsamal wowalz nklee maximilianh xili03 csdhwang isimpson
	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 motif-discovery tfbs tool by idonaldson on 2008-01-14 09:30:49 as along with 4 people bsamal isimpson guhjy maximilianh
	Predicting and understanding transcription factor interactions based on sequence level determinants of combinatorial control [My Copy] Bioinformatics, Vol. 24, No. 1. (1 January 2008), pp. 26-33. by A. D. J. van Dijk, Ter, R. G. Immink, G. C. Angenent, R. C. H. J. van Ham posted to combinatorial interaction tfbs by idonaldson on 2007-12-20 12:33:25 as along with 3 people heliopais maximilianh isimpson
	A profile-based deterministic sequential Monte Carlo algorithm for motif discovery. [My Copy] Bioinformatics (Oxford, England), Vol. 24, No. 1. (1 January 2008), pp. 46-55. by K. C. Liang, X. Wang, D. Anastassiou posted to cis-regulation tfbs tool by idonaldson on 2007-11-27 14:46:52 as along with 7 people and 1 group bsamal wowalz grahamc cjeans nklee maximilianh isimpson Motif Discovery
	OSCAR: One-class SVM for accurate recognition of cis-elements [My Copy] Bioinformatics In Bioinformatics, Vol. 23, No. 21. (1 November 2007), pp. 2823-2828. by Bo Jiang, Michael Q. Zhang, Xuegong Zhang posted to cis-regulation tfbs tool by idonaldson on 2007-11-27 14:42:52 as along with 8 people bsamal suizifish cassj tmmurali chad_davis cabbagezs maximilianh isimpson
	Predicting combinatorial binding of transcription factors to regulatory elements in the human genome by association rule mining [My Copy] BMC Bioinformatics, Vol. 8, No. 1. (2007) by Xochitl Morgan, Shulin Ni, Daniel Miranker, Vishwanath Iyer posted to combinatorial tfbs by idonaldson on 2007-11-27 14:09:15 as along with 4 people maximilianh barriot dps sconlan
	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 matrix tfbs tool by idonaldson on 2007-11-19 11:15:24 as along with 8 people bsamal isimpson natstreet druvus guhjy dullhunk sci91078 jfr
	Ab initio prediction of transcription factor binding sites. [My Copy] Pac Symp Biocomput (2007), pp. 484-495. by L. A. Liu, J. S. Bader posted to prediction tfbs by idonaldson on 2007-11-12 09:14:45 as along with 1 person aalibes
	Discovering motifs with transcription factor domain knowledge. [My Copy] Pac Symp Biocomput (2007), pp. 472-483. by H. C. Leung, F. Y. Chin, B. M. Chan posted to motif-discovery tfbs tool by idonaldson on 2007-11-12 08:50:57 as along with 1 person maximilianh
	A computational genomics approach to identify cis-regulatory modules from chromatin immunoprecipitation microarray dataâA case study using E2F1 [My Copy] Genome Res In Genome Research, Vol. 16, No. 12. (19 December 2006), pp. 1585-1595. by Victor X. Jin, Alina Rabinovich, Sharon L. Squazzo, Roland Green, Peggy J. Farnham posted to chip-chip crm tfbs tool by idonaldson on 2007-11-08 08:50:56 as along with 3 people bsamal aprasad jfr
	A Universal Framework for Regulatory Element Discovery across All Genomes and Data Types [My Copy] Molecular Cell, Vol. 28, No. 2. (26 October 2007), pp. 337-350. by Olivier Elemento, Noam Slonim, Saeed Tavazoie posted to conserved crm expression tfbs by idonaldson on 2007-11-06 09:23:09 as along with 17 people and 2 groups cerca ilyashl TRHvidsten leelarcombe kieran101 ana brant cwbrown aswin cjeans zwang cabbagezs nklee maximilianh sb_journal_club kristen barwil EisenLab Motif Discovery
	HeliCis: a DNA motif discovery tool for colocalized motif pairs with periodic spacing. [My Copy] BMC bioinformatics, Vol. 8 (28 October 2007), 418. by Erik Larsson, Per Lindahl, Petter Mostad posted to motif-discovery spacing tfbs tool by idonaldson on 2007-11-06 09:18:26 as along with 3 people operon maximilianh isimpson
	Fine-Tuning Enhancer Models to Predict Transcriptional Targets across Multiple Genomes. [My Copy] PLoS ONE, Vol. 2, No. 11. (2007) by S. Aerts, J. van Helden, O. Sand, B. A. Hassan posted to conserved crm tfbs by idonaldson on 2007-11-06 09:17:37 as along with 5 people and 1 group operon brant maximilianh barwil isimpson cis-regulatory-evolution
	dPattern: transcription factor binding site (TFBS) discovery in human genome using a discriminative pattern analysis [My Copy] Bioinformatics In Bioinformatics, Vol. 23, No. 19. (1 October 2007), pp. 2619-2621. by Seung-Hee Bae, Haixu Tang, Jing Wu, Jun Xie, Sun Kim posted to motif-discovery tfbs tool by idonaldson on 2007-10-29 11:42:16 as along with 4 people bsamal maximilianh isimpson nuin
	Informative priors based on transcription factor structural class improve de novo motif discovery [My Copy] Bioinformatics, Vol. 22, No. 14. (15 July 2006), pp. e384-392. by Leelavati Narlikar, Raluca Gordan, Uwe Ohler, Alexander J. Hartemink posted to motif-discovery structural tfbs by idonaldson on 2007-10-29 10:42:19 as along with 6 people frohike megraw maximilianh dquest nklee yevishere
	PhyloGibbs: a Gibbs sampling motif finder that incorporates phylogeny. [My Copy] PLoS computational biology, Vol. 1, No. 7. (December 2005) by Rahul Siddharthan, Eric D. Siggia, Erik van Nimwegen posted to conserved motif-discovery tfbs tool by idonaldson on 2007-10-29 10:39:49 as along with 17 people and 3 groups farhat wowalz aprasad cajunsushi treangen druvus ana postrational dquest AaronDarling nickluscombe noano adsmitty lusk lilou yevishere isimpson structural_bioinformatics Bioinformatics EBI-regulation
	Gata2, Fli1, and Scl form a recursively wired gene-regulatory circuit during early hematopoietic development. [My Copy] Proc Natl Acad Sci U S A (25 October 2007) by John E E. Pimanda, Katrin Ottersbach, Kathy Knezevic, et al.Sarah Kinston, Wan Y I Y. Chan, Nicola K K. Wilson, Josette-Renée R. Landry, Andrew D D. Wood, Anja Kolb-Kokocinski, Anthony R R. Green, David Tannahill, Georges Lacaud, Valerie Kouskoff, Berthold Göttgens posted to cis-regulation crm gottgens haematopoiesis networks tfbs by idonaldson on 2007-10-29 10:30:29 as along with 2 people jjray maximilianh
	IEM: An Algorithm for Iterative Enhancement of Motifs Using Comparative Genomics Data. [My Copy] Comput Syst Bioinformatics Conf, Vol. 6 (2007), pp. 227-235. by E. Zeng, K. Mathee, G. Narasimhan posted to cis-regulation conserved tfbs tool by idonaldson on 2007-10-29 10:04:48 as along with 4 people wowalz maximilianh annacarina07 isimpson
	How does DNA sequence motif discovery work? [My Copy] Nature Biotechnology, Vol. 24, No. 8., pp. 959-961. by Patrik D'Haeseleer posted to cis-regulation motif-discovery primer tfbs by idonaldson on 2007-10-26 14:26:18 as along with 9 people and 1 group Dulce wowalz cambray bryankr okarsligil Evangelia antonkratz xi03 isimpson Bioinformatics
	The Oct4 and Nanog transcription network regulates pluripotency in mouse embryonic stem cells. [My Copy] Nature genetics, Vol. 38, No. 4. (05 April 2006), pp. 431-440. by Yuin-Han H. Loh, Qiang Wu, Joon-Lin L. Chew, et al.Vinsensius B. Vega, Weiwei Zhang, Xi Chen, Guillaume Bourque, Joshy George, Bernard Leong, Jun Liu, Kee-Yew Y. Wong, Ken W. Sung, Charlie W. Lee, Xiao-Dong D. Zhao, Kuo-Ping P. Chiu, Leonard Lipovich, Vladimir A. Kuznetsov, Paul Robson, Lawrence W. Stanton, Chia-Lin L. Wei, Yijun Ruan, Bing Lim, Huck-Hui H. Ng posted to tfbs cis-regulation mouse networks stem-cells by idonaldson on 2007-10-24 10:11:38 as along with 11 people isimpson inesdesantiago tonamswish guhjy cmmorel gpalidwor brixtonmc vega eukfn mikaelhuss tdmckee
	Identifying tissue-selective transcription factor binding sites in vertebrate promoters. [My Copy] Proc Natl Acad Sci U S A, Vol. 102, No. 5. (1 February 2005), pp. 1560-1565. by A. D. Smith, P. Sumazin, M. Q. Zhang posted to cis-regulation promoter tfbs tool by idonaldson on 2007-10-24 09:14:11 as along with 2 people raylim heliopais
	MATLIGN: a motif clustering, comparison and matching tool [My Copy] BMC Bioinformatics, Vol. 8 (08 June 2007), 189. by Matti Kankainen, Ari Loytynoja posted to matrix tfbs tool by idonaldson on 2007-10-22 09:36:12 as along with 3 people and 1 group smbe2008 isimpson xili03 BergmanLab
	MyoD uses overlapping but distinct elements to bind E-box and tetraplex structures of regulatory sequences of muscle-specific genes. [My Copy] Nucleic Acids Res (16 October 2007) by Jeny Shklover, Shulamit Etzioni, Pnina Weisman-Shomer, Anat Yafe, Eyal Bengal, Michael Fry posted to cis-regulation ebox muscle myod tfbs by idonaldson on 2007-10-22 09:23:27 as along with 1 person and 1 group jmrivort G-quadruplex
	Analysis of multiple genomic sequence alignments: a web resource, online tools, and lessons learned from analysis of mammalian SCL loci. [My Copy] Genome Res, Vol. 14, No. 2. (February 2004), pp. 313-318. by M. A. Chapman, I. J. Donaldson, J. Gilbert, et al.D. Grafham, J. Rogers, A. R. Green, B. Göttgens posted to alignment cis-regulation me tfbs tool by idonaldson on 2007-10-19 12:58:15 as
	Genome-wide analysis of repressor element 1 silencing transcription factor/neuron-restrictive silencing factor (REST/NRSF) target genes. [My Copy] Proc Natl Acad Sci U S A, Vol. 101, No. 28. (13 July 2004), pp. 10458-10463. by A. W. Bruce, I. J. Donaldson, I. C. Wood, et al.S. A. Yerbury, M. I. Sadowski, M. Chapman, B. Göttgens, N. J. Buckley posted to cis-regulation me tfbs tool by idonaldson on 2007-10-19 12:54:15 as along with 1 person klo
	TFBScluster web server for the identification of mammalian composite regulatory elements [My Copy] Nucleic Acids Res In Nucl. Acids Res., Vol. 34, No. suppl_2. (1 July 2006), pp. W524-528. by Ian J. Donaldson, Berthold Gottgens posted to cis-regulation crm me tfbs tool by idonaldson on 2007-10-19 12:51:59 as along with 2 people bsamal maximilianh

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