Identifying combinatorial regulation of transcription factors and binding motifs
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* Corresponding author: Michael Q Zhang mzhang@cshl.edu
Genome Biology 2004, 5:R56 doi:10.1186/gb-2004-5-8-r56
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BioMed Central: 25 citations
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Proceedings
Tzong-Yi Lee, Wen-Chi Chang, Justin Hsu, Tzu-Hao Chang, Dray-Ming Shien BMC Genomics 2012, 13(Suppl 1):S3 (17 January 2012) |
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Method
Chao Cheng, Chong Shou, Kevin Y Yip, Mark B Gerstein Genome Biology 2011, 12:R111 (7 November 2011) A method that uses both chromatin features and motif identification to predict transcription factor binding sites
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Methodology article
Jeh-Ting Hsu, Chien-Hua Peng, Wen-Ping Hsieh, Chung-Yu Lan, Chuan Tang BMC Bioinformatics 2011, 12:281 (12 July 2011) |
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Research
Reconstruct gene regulatory network using slice pattern model Yadong Wang, Guohua Wang, Bo Yang, Haijun Tao, Jack Y Yang, Youping Deng, Yunlong Liu BMC Genomics 2009, 10(Suppl 1):S2 (7 July 2009) |
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Proceedings
Identification of temporal association rules from time-series microarray data sets Hojung Nam, KiYoung Lee, Doheon Lee BMC Bioinformatics 2009, 10(Suppl 3):S6 (19 March 2009) |
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Research article
Combinatorial control of gene expression by the three yeast repressors Mig1, Mig2 and Mig3 Jakub Westholm, Niklas Nordberg, Eva Murén, Adam Ameur, Jan Komorowski, Hans Ronne BMC Genomics 2008, 9:601 (16 December 2008) |
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Methodology article
Compo: composite motif discovery using discrete models Geir Sandve, Osman Abul, Finn Drabløs BMC Bioinformatics 2008, 9:527 (8 December 2008) |
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Methodology article
Systematic identification of yeast cell cycle transcription factors using multiple data sources Wei-Sheng Wu, Wen-Hsiung Li BMC Bioinformatics 2008, 9:522 (5 December 2008) |
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Database
Wen-Chi Chang, Tzong-Yi Lee, Hsien-Da Huang, His-Yuan Huang, Rong-Long Pan BMC Genomics 2008, 9:561 (26 November 2008) |
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Research article
Jakub Westholm, Feifei Xu, Hans Ronne, Jan Komorowski BMC Bioinformatics 2008, 9:484 (17 November 2008) |
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Research article
Identifying gene regulatory modules of heat shock response in yeast Wei-Sheng Wu, Wen-Hsiung Li BMC Genomics 2008, 9:439 (23 September 2008) |
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Method
Prediction of synergistic transcription factors by function conservation Zihua Hu, Boyu Hu, James F Collins Genome Biology 2007, 8:R257 (5 December 2007) A new strategy is proposed for identifying synergistic transcription factors by function conservation, leading to the identification of 51 homotypic transcription-factor combinations. |
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Research article
Claes R Andersson, Torgeir R Hvidsten, Anders Isaksson, Mats G Gustafsson, Jan Komorowski BMC Systems Biology 2007, 1:45 (16 October 2007) |
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Research
Valentina Boeva, Julien Clément, Mireille Régnier, Mikhail A Roytberg, Vsevolod J Makeev Algorithms for Molecular Biology 2007, 2:13 (10 October 2007) |
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Research
Dynamic cumulative activity of transcription factors as a mechanism of quantitative gene regulation Feng He, Jan Buer, An-Ping Zeng, Rudi Balling Genome Biology 2007, 8:R181 (4 September 2007) By combining information on the yeast transcription network and high-resolution time-series data with a series of factors, support is provided for the concept that dynamic cumulative regulation is a major principle of quantitative transcriptional control. |
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Research article
Wei-Sheng Wu, Wen-Hsiung Li, Bor-Sen Chen BMC Bioinformatics 2007, 8:188 (8 June 2007) |
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Software
MotifCombinator: a web-based tool to search for combinations of cis-regulatory motifs Mamoru Kato, Tatsuhiko Tsunoda BMC Bioinformatics 2007, 8:100 (22 March 2007) |
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Methodology article
Bioinformatics analysis of the early inflammatory response in a rat thermal injury model Eric Yang, Timothy Maguire, Martin L Yarmush, Francois Berthiaume, Ioannis P Androulakis BMC Bioinformatics 2007, 8:10 (10 January 2007) |
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Software
Unraveling transcriptional control and cis-regulatory codes using the software suite GeneACT Tom Cheung, Yin Kwan, Micah Hamady, Xuedong Liu Genome Biology 2006, 7:R97 (25 October 2006) GENEACT, a new software suite for the detection of evolutionarily conserved transcription factor binding sites or microRNAs from differentially expressed genes from DNA microarray data, is described. |
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Research article
Computational reconstruction of transcriptional regulatory modules of the yeast cell cycle Wei-Sheng Wu, Wen-Hsiung Li, Bor-Sen Chen BMC Bioinformatics 2006, 7:421 (29 September 2006) |
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Method
Guandong Wang, Weixiong Zhang Genome Biology 2006, 7:R49 (20 June 2006) WordSpy, a novel, steganalysis-based approach for genome-wide motif-finding is described and applied to yeast and |
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Method
Inferring transcriptional modules from ChIP-chip, motif and microarray data Karen Lemmens, Thomas Dhollander, Tijl De Bie, Pieter Monsieurs, Kristof Engelen, Bart Smets, Joris Winderickx, Bart De Moor, Kathleen Marchal Genome Biology 2006, 7:R37 (5 May 2006) ReMoDiscovery, a module discovery algorithm and software that uses ChIP-chip data, motif information and gene-expression profiles, is presented. |
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Review
A survey of motif discovery methods in an integrated framework Geir Sandve, Finn Drabløs Biology Direct 2006, 1:11 (6 April 2006) |
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Methodology article
Li-Hsieh Lin, Hsiao-Ching Lee, Wen-Hsiung Li, Bor-Sen Chen BMC Bioinformatics 2005, 6:258 (18 October 2005) |
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Research
Anne-Laure Boulesteix, Korbinian Strimmer Theoretical Biology and Medical Modelling 2005, 2:23 (24 June 2005) |