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Identifying combinatorial regulation of transcription factors and binding motifs
Mamoru Kato, Naoya Hata, Nilanjana Banerjee, Bruce Futcher, Michael Q Zhang
Genome Biol. 2004; 5(8): R56. Published online 2004 July 28. doi: 10.1186/gb-2004-5-8-r56
PMCID:
PMC507881
Abstract Full Text PDF–345K
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 Is Cited by the Following 47 Articles in this Archive:
A novel method to identify cooperative functional modules: study of module coordination in the Saccharomyces cerevisiae cell cycle
Jeh-Ting Hsu, Chien-Hua Peng, Wen-Ping Hsieh, Chung-Yu Lan, Chuan Yi Tang
BMC Bioinformatics. 2011; 12: 281. Published online 2011 July 12. doi: 10.1186/1471-2105-12-281
PMCID:
PMC3143111
Abstract Full Text PDF–5.2M Supplementary Material
Simplified Method to Predict Mutual Interactions of Human Transcription Factors Based on Their Primary Structure
Sebastian Schmeier, Boris Jankovic, Vladimir B. Bajic
PLoS One. 2011; 6(7): e21887. Published online 2011 July 5. doi: 10.1371/journal.pone.0021887
PMCID:
PMC3130058
Abstract Full Text PDF–116K Supplementary Material
The Reconstruction of Condition-Specific Transcriptional Modules Provides New Insights in the Evolution of Yeast AP-1 Proteins
Christel Goudot, Catherine Etchebest, Frédéric Devaux, Gaëlle Lelandais
PLoS One. 2011; 6(6): e20924. Published online 2011 June 9. doi: 10.1371/journal.pone.0020924
PMCID:
PMC3111461
Abstract Full Text PDF–764K Supplementary Material
Combinatorial regulation of transcription factors and microRNAs
Naifang Su, Yufu Wang, Minping Qian, Minghua Deng
BMC Syst Biol. 2010; 4: 150. Published online 2010 November 8. doi: 10.1186/1752-0509-4-150
PMCID:
PMC3225826
Abstract Full Text PDF–1.1M Supplementary Material
The transcriptional network activated by Cln3 cyclin at the G1-to-S transition of the yeast cell cycle
Francisco Ferrezuelo, Neus Colomina, Bruce Futcher, Martí Aldea
Genome Biol. 2010; 11(6): R67. Published online 2010 June 23. doi: 10.1186/gb-2010-11-6-r67
PMCID:
PMC2911115
Abstract Full Text PDF–2.1M Supplementary Material
Predicting protein-protein interactions in unbalanced data using the primary structure of proteins
Chi-Yuan Yu, Lih-Ching Chou, Darby Tien-Hao Chang
BMC Bioinformatics. 2010; 11: 167. Published online 2010 April 2. doi: 10.1186/1471-2105-11-167
PMCID:
PMC2868006
Abstract Full Text PDF–4.3M
Inferring Transcriptional Interactions by the Optimal Integration of ChIP-chip and Knock-out Data
Haoyu Cheng, Lihua Jiang, Maoying Wu, Qi Liu
Bioinform Biol Insights. 2009; 3: 129–140. Published online 2009 October 21.
PMCID:
PMC2808186
Abstract Full Text PDF–7.0M
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. Published online 2009 July 7. doi: 10.1186/1471-2164-10-S1-S2
PMCID:
PMC2709263
Abstract Full Text PDF–982K Supplementary Material
Identification of Yeast Transcriptional Regulation Networks Using Multivariate Random Forests
Yuanyuan Xiao, Mark R. Segal
PLoS Comput Biol. 2009 June; 5(6): e1000414. Published online 2009 June 19. doi: 10.1371/journal.pcbi.1000414
PMCID:
PMC2691601
Abstract Full Text PDF–1.1M Supplementary Material
In silico analysis of promoter regions from cold-induced genes in rice (Oryza sativa L.) and Arabidopsis thaliana reveals the importance of combinatorial control
Angelica Lindlöf, Marcus Bräutigam, Aakash Chawade, Olof Olsson, Björn Olsson
Bioinformatics. 2009 June 1; 25(11): 1345–1348. Published online 2009 March 25. doi: 10.1093/bioinformatics/btp172
PMCID:
PMC2682518
Abstract Full Text PDF–140K Supplementary Material
Identification of temporal association rules from time-series microarray data sets
Hojung Nam, KiYoung Lee, Doheon Lee
BMC Bioinformatics. 2009; 10(Suppl 3): S6. Published online 2009 March 19. doi: 10.1186/1471-2105-10-S3-S6
PMCID:
PMC2665054
Abstract Full Text PDF–885K
Combinatorial control of gene expression by the three yeast repressors Mig1, Mig2 and Mig3
Jakub Orzechowski Westholm, Niklas Nordberg, Eva Murén, Adam Ameur, Jan Komorowski, Hans Ronne
BMC Genomics. 2008; 9: 601. Published online 2008 December 16. doi: 10.1186/1471-2164-9-601
PMCID:
PMC2631581
Abstract Full Text PDF–395K Supplementary Material
Compo: composite motif discovery using discrete models
Geir Kjetil Sandve, Osman Abul, Finn Drabløs
BMC Bioinformatics. 2008; 9: 527. Published online 2008 December 8. doi: 10.1186/1471-2105-9-527
PMCID:
PMC2614996
Abstract Full Text PDF–359K Supplementary Material
Systematic identification of yeast cell cycle transcription factors using multiple data sources
Wei-Sheng Wu, Wen-Hsiung Li
BMC Bioinformatics. 2008; 9: 522. Published online 2008 December 5. doi: 10.1186/1471-2105-9-522
PMCID:
PMC2613934
Abstract Full Text PDF–509K Supplementary Material
PlantPAN: Plant promoter analysis navigator, for identifying combinatorial cis-regulatory elements with distance constraint in plant gene groups
Wen-Chi Chang, Tzong-Yi Lee, Hsien-Da Huang, His-Yuan Huang, Rong-Long Pan
BMC Genomics. 2008; 9: 561. Published online 2008 November 26. doi: 10.1186/1471-2164-9-561
PMCID:
PMC2633311
Abstract Full Text PDF–879K Supplementary Material
Genome-scale study of the importance of binding site context for transcription factor binding and gene regulation
Jakub Orzechowski Westholm, Feifei Xu, Hans Ronne, Jan Komorowski
BMC Bioinformatics. 2008; 9: 484. Published online 2008 November 17. doi: 10.1186/1471-2105-9-484
PMCID:
PMC2629780
Abstract Full Text PDF–375K Supplementary Material
Signatures of combinatorial regulation in intrinsic biological noise
Aryeh Warmflash, Aaron R. Dinner
Proc Natl Acad Sci U S A. 2008 November 11; 105(45): 17262–17267. Published online 2008 November 3. doi: 10.1073/pnas.0809314105
PMCID:
PMC2582248
Abstract Full Text PDF–774K Supplementary Material
Ab initio identification of functionally interacting pairs of cis-regulatory elements
Brad A. Friedman, Michael B. Stadler, Noam Shomron, Ye Ding, Christopher B. Burge
Genome Res. 2008 October; 18(10): 1643–1651. doi: 10.1101/gr.080085.108
PMCID:
PMC2556269
Abstract Full Text PDF–633K
GBNet: Deciphering regulatory rules in the co-regulated genes using a Gibbs sampler enhanced Bayesian network approach
Li Shen, Jie Liu, Wei Wang
BMC Bioinformatics. 2008; 9: 395. Published online 2008 September 24. doi: 10.1186/1471-2105-9-395
PMCID:
PMC2571992
Abstract Full Text PDF–636K Supplementary Material
Identifying gene regulatory modules of heat shock response in yeast
Wei-Sheng Wu, Wen-Hsiung Li
BMC Genomics. 2008; 9: 439. Published online 2008 September 23. doi: 10.1186/1471-2164-9-439
PMCID:
PMC2575218
Abstract Full Text PDF–593K Supplementary Material
Embedding mRNA Stability in Correlation Analysis of Time-Series Gene Expression Data
Lorenzo Farina, Alberto De Santis, Samanta Salvucci, Giorgio Morelli, Ida Ruberti
PLoS Comput Biol. 2008 August; 4(8): e1000141. Published online 2008 August 1. doi: 10.1371/journal.pcbi.1000141
PMCID:
PMC2453326
Abstract Full Text PDF–725K Supplementary Material
Positive feedback of G1 cyclins ensures coherent cell cycle entry
Jan M. Skotheim, Stefano Di Talia, Eric D. Siggia, Frederick R. Cross
Nature. Author manuscript; available in PMC 2009 January 17.
Published in final edited form as: Nature. 2008 July 17; 454(7202): 291–296. doi: 10.1038/nature07118
PMCID:
PMC2606905
Abstract Full Text PDF–4.3M
Topological comparison of methods for predicting transcriptional cooperativity in yeast
Daniel Aguilar, Baldo Oliva
BMC Genomics. 2008; 9: 137. Published online 2008 March 25. doi: 10.1186/1471-2164-9-137
PMCID:
PMC2315657
Abstract Full Text PDF–377K Supplementary Material
Prediction of synergistic transcription factors by function conservation
Zihua Hu, Boyu Hu, James F Collins
Genome Biol. 2007; 8(12): R257. Published online 2007 December 5. doi: 10.1186/gb-2007-8-12-r257
PMCID:
PMC2246259
Abstract Full Text PDF–667K Supplementary Material
Revealing cell cycle control by combining model-based detection of periodic expression with novel cis-regulatory descriptors
Claes R Andersson, Torgeir R Hvidsten, Anders Isaksson, Mats G Gustafsson, Jan Komorowski
BMC Syst Biol. 2007; 1: 45. Published online 2007 October 16. doi: 10.1186/1752-0509-1-45
PMCID:
PMC2200664
Abstract Full Text PDF–12M Supplementary Material
Nonlinear Dynamic Trans/Cis Regulatory Circuit for Gene Transcription via Microarray Data
Yu-Hsiang Chang, Yu-Chao Wang, Bor-Sen Chen
Gene Regul Syst Bio. 2007; 1: 151–166. Published online 2007 October 12.
PMCID:
PMC2759131
Abstract Full Text PDF–1.2M Supplementary Material
Exact p-value calculation for heterotypic clusters of regulatory motifs and its application in computational annotation of cis-regulatory modules
Valentina Boeva, Julien Clément, Mireille Régnier, Mikhail A Roytberg, Vsevolod J Makeev
Algorithms Mol Biol. 2007; 2: 13. Published online 2007 October 10. doi: 10.1186/1748-7188-2-13
PMCID:
PMC2174486
Abstract Full Text PDF–540K Supplementary Material
Dynamic cumulative activity of transcription factors as a mechanism of quantitative gene regulation
Feng He, Jan Buer, An-Ping Zeng, Rudi Balling
Genome Biol. 2007; 8(9): R181. Published online 2007 September 4. doi: 10.1186/gb-2007-8-9-r181
PMCID:
PMC2375019
Abstract Full Text PDF–1.3M Supplementary Material
Identifying regulatory targets of cell cycle transcription factors using gene expression and ChIP-chip data
Wei-Sheng Wu, Wen-Hsiung Li, Bor-Sen Chen
BMC Bioinformatics. 2007; 8: 188. Published online 2007 June 8. doi: 10.1186/1471-2105-8-188
PMCID:
PMC1906835
Abstract Full Text PDF–436K Supplementary Material
Binding Site Graphs: A New Graph Theoretical Framework for Prediction of Transcription Factor Binding Sites
Timothy E Reddy, Charles DeLisi, Boris E Shakhnovich
PLoS Comput Biol. 2007 May; 3(5): e90. Prepublished online 2007 April 10. Published online 2007 May 11. doi: 10.1371/journal.pcbi.0030090
PMCID:
PMC1866359
Abstract Full Text PDF–538K Supplementary Material
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