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idonaldson tfbs [35 articles]

Recent papers added to idonaldson library classified by the tag tfbs. You can also see everyone's tfbs.
  • Transcription factor and microRNA motif discovery: The Amadeus platform and a compendium of metazoan target sets.
    Genome research (14 April 2008)
    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 6 people and 1 group tmmurali isimpson fpattyn maximilianh ealloza maralena BergmanLab
  • An efficient method for statistical significance calculation of transcription factor binding sites.
    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 3 people and 1 group isimpson nklee maximilianh Motif Discovery
  • An analysis of the positional distribution of DNA motifs in promoter regions and its biological relevance
    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 3 people isimpson chad_davis xili03
  • Identification of tissue-specific cis-regulatory modules based on interactions between transcription factors
    BMC Bioinformatics, Vol. 8 (09 November 2007), 437.
    by Xueping Yu, Jimmy Lin, Donald J Zack, Jiang Qian
    posted to crm tfbs tissue-specific by idonaldson on 2008-02-15 09:28:41 as *** along with 7 people bootsy jyuh chad_davis mikaelhuss nklee maximilianh njcitulike
  • Model-based deconvolution of genome-wide DNA binding.
    Bioinformatics (1 December 2007)
    by David J J Reiss, Marc T T Facciotti, Nitin S S Baliga
    posted to chip-on-chip deconvolution tfbs by idonaldson on 2008-01-31 11:10:21 as *** along with 5 people isimpson vega jyuh djkt yevishere
  • TFBS Identification Based on Genetic Algorithm with Combined Representations and Adaptive Post-processing.
    Bioinformatics (6 December 2007)
    by Tak-Ming M Chan, Kwong-Sak S Leung, Kin-Hong H Lee
    posted to motif-discovery tfbs tool by idonaldson on 2008-01-31 11:07:05 as *** along with 5 people isimpson nklee maximilianh xili03 csdhwang
  • A Hybrid Model for Robust Detection of Transcription Factor Binding Sites.
    Bioinformatics (9 January 2008)
    by Sumedha Gunewardena, Zhaolei Zhang
    posted to motif-discovery tfbs tool by idonaldson on 2008-01-14 09:30:49 as *** along with 2 people jyuh maximilianh
  • Predicting and understanding transcription factor interactions based on sequence level determinants of combinatorial control
    Bioinformatics, Vol. 24, No. 1. (1 January 2008), pp. 26-33.
    by ADJ van Dijk, Ter, RG Immink, GC Angenent, RCHJ van Ham
    posted to combinatorial interaction tfbs by idonaldson on 2007-12-20 12:33:25 as ** along with 2 people isimpson maximilianh
  • A Profile-Based Deterministic Sequential Monte Carlo Algorithm for Motif Discovery.
    Bioinformatics (17 November 2007)
    by Kuo-Ching C Liang, Xiaodong Wang, Dimitris Anastassiou
    posted to cis-regulation tfbs tool by idonaldson on 2007-11-27 14:46:52 as ** along with 5 people and 1 group isimpson grahamc cjeans nklee maximilianh Motif Discovery
  • OSCAR: One-class SVM for Accurate Recognition of Cis-elements
    Bioinformatics (5 October 2007), btm473.
    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 6 people and 1 group isimpson cassj tmmurali chad_davis cabbagezs maximilianh csb_journal_club_public
  • Predicting combinatorial binding of transcription factors to regulatory elements in the human genome by association rule mining
    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 5 people sconlan ihpark maximilianh barriot dps
  • JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update.
    Nucleic Acids Res (15 November 2007)
    by Jan Christian C Bryne, Eivind Valen, Man-Hung Eric H Tang, 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 read along with 4 people jfr jyuh dullhunk sci91078
  • Ab initio prediction of transcription factor binding sites.
    Pac Symp Biocomput (2007), pp. 484-495.
    by LA Liu, JS 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.
    Pac Symp Biocomput (2007), pp. 472-483.
    by HC Leung, FY Chin, BM 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 data--A case study using E2F1.
    Genome Res (19 October 2006)
    by Victor X X Jin, Alina Rabinovich, Sharon L L Squazzo, Roland Green, Peggy J J Farnham
    posted to chip-on-chip crm tfbs tool by idonaldson on 2007-11-08 08:50:56 as ***** along with 2 people aprasad jfr
  • A Universal Framework for Regulatory Element Discovery across All Genomes and Data Types.
    Mol Cell, Vol. 28, No. 2. (26 October 2007), pp. 337-350.
    by O Elemento, N Slonim, S Tavazoie
    posted to conserved crm expression tfbs by idonaldson on 2007-11-06 09:23:09 as read along with 12 people and 2 groups 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
    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 read along with 2 people isimpson maximilianh
  • Fine-Tuning Enhancer Models to Predict Transcriptional Targets across Multiple Genomes.
    PLoS ONE, Vol. 2, No. 11. (2007)
    by S Aerts, J van Helden, O Sand, BA Hassan
    posted to conserved crm tfbs by idonaldson on 2007-11-06 09:17:37 as ** along with 4 people and 1 group isimpson brant maximilianh barwil cis-regulatory-evolution
  • dPattern: transcription factor binding site (TFBS) discovery in human genome using a discriminative pattern analysis
    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 3 people isimpson nuin maximilianh
  • Informative priors based on transcription factor structural class improve de novo motif discovery
    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 3 people dquest nklee yevishere
  • 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 conserved motif-discovery tfbs tool by idonaldson on 2007-10-29 10:39:49 as read along with 11 people and 3 groups isimpson ana postrational dquest AaronDarling nickluscombe noano adsmitty lusk lilou yevishere structural_bioinformatics Bioinformatics EBI-regulation
  • Gata2, Fli1, and Scl form a recursively wired gene-regulatory circuit during early hematopoietic development.
    Proc Natl Acad Sci U S A (25 October 2007)
    by John E E Pimanda, Katrin Ottersbach, Kathy Knezevic, 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.
    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 3 people isimpson maximilianh annacarina07
  • How does DNA sequence motif discovery work?
    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 4 people and 1 group isimpson okarsligil antonkratz xi03 Bioinformatics
  • The Oct4 and Nanog transcription network regulates pluripotency in mouse embryonic stem cells
    Nature Genetics, Vol. 38, No. 4. (05 March 2006), pp. 431-440.
    by Yuin-Han Loh, Qiang Wu, Joon-Lin Chew, Vinsensius B Vega, Weiwei Zhang, Xi Chen, Guillaume Bourque, Joshy George, Bernard Leong, Jun Liu, Kee-Yew Wong, Ken W Sung, Charlie WH Lee, Xiao-Dong Zhao, Kuo-Ping Chiu, Leonard Lipovich, Vladimir A Kuznetsov, Paul Robson, Lawrence W Stanton, Chia-Lin Wei, Yijun Ruan, Bing Lim, Huck-Hui Ng
    posted to tfbs cis-regulation mouse networks stem-cells by idonaldson on 2007-10-24 10:11:38 as *** along with 9 people MllePapillon jyuh cmmorel gpalidwor brixtonmc vega eukfn mikaelhuss tdmckee
  • Identifying tissue-selective transcription factor binding sites in vertebrate promoters.
    Proc Natl Acad Sci U S A, Vol. 102, No. 5. (1 February 2005), pp. 1560-1565.
    by AD Smith, P Sumazin, MQ Zhang
    posted to cis-regulation promoter tfbs tool by idonaldson on 2007-10-24 09:14:11 as read along with 1 person heliopais
  • MATLIGN: a motif clustering, comparison and matching tool
    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 read along with 2 people and 1 group isimpson smbe2008 BergmanLab
  • MyoD uses overlapping but distinct elements to bind E-box and tetraplex structures of regulatory sequences of muscle-specific genes.
    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.
    Genome Res, Vol. 14, No. 2. (February 2004), pp. 313-318.
    by MA Chapman, IJ Donaldson, J Gilbert, D Grafham, J Rogers, AR Green, B Göttgens
    posted to alignment cis-regulation me tfbs tool by idonaldson on 2007-10-19 12:58:15 as read
  • Genome-wide analysis of repressor element 1 silencing transcription factor/neuron-restrictive silencing factor (REST/NRSF) target genes.
    Proc Natl Acad Sci U S A, Vol. 101, No. 28. (13 July 2004), pp. 10458-10463.
    by AW Bruce, IJ Donaldson, IC Wood, SA Yerbury, MI Sadowski, M Chapman, B Göttgens, NJ Buckley
    posted to cis-regulation me tfbs tool by idonaldson on 2007-10-19 12:54:15 as read
  • TFBScluster web server for the identification of mammalian composite regulatory elements.
    Nucleic Acids Res, Vol. 34, No. Web Server issue. (1 July 2006)
    by IJ Donaldson, B Göttgens
    posted to cis-regulation crm me tfbs tool by idonaldson on 2007-10-19 12:51:59 as read
  • TFBScluster: a resource for the characterization of transcriptional regulatory networks.
    Bioinformatics, Vol. 21, No. 13. (1 July 2005), pp. 3058-3059.
    by IJ Donaldson, M Chapman, B Göttgens
    posted to cis-regulation crm me tfbs tool by idonaldson on 2007-10-19 12:48:27 as read along with 1 person dquest
  • Genome-wide identification of cis-regulatory sequences controlling blood and endothelial development.
    Hum Mol Genet, Vol. 14, No. 5. (1 March 2005), pp. 595-601.
    by IJ Donaldson, M Chapman, S Kinston, JR Landry, K Knezevic, S Piltz, N Buckley, AR Green, B Göttgens
    posted to cis-regulation me tfbs transgenic by idonaldson on 2007-10-19 12:45:13 as read
  • CoMoDis: composite motif discovery in mammalian genomes.
    Nucleic Acids Res, Vol. 35, No. 1. (2007)
    by IJ Donaldson, B Göttgens
    posted to cis-regulation me motif-discovery tfbs tool by idonaldson on 2007-10-18 16:41:50 as read along with 1 person and 1 group csdhwang Bioinformatics
  • 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 chimp cis-regulation evolution human me tfbs by idonaldson on 2007-10-18 15:58:36 as read along with 4 people and 2 groups indigoviolet ranb djkt cisevol EisenLab cis-regulatory-evolution
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