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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 Biol. 2006; 7(5): R37. Published online 2006 May 5. doi: 10.1186/gb-2006-7-5-r37
PMCID:
PMC1779513
Abstract Full Text PDF–626K Supplementary Material
 Is Cited by the Following 24 Articles in this Archive:
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
Inference of hierarchical regulatory network of estrogen-dependent breast cancer through ChIP-based data
Fei Gu, Hang-Kai Hsu, Pei-Yin Hsu, Jiejun Wu, Yilin Ma, Jeffrey Parvin, Tim H-M Huang, Victor X Jin
BMC Syst Biol. 2010; 4: 170. Published online 2010 December 17. doi: 10.1186/1752-0509-4-170
PMCID:
PMC3012048
Abstract Full Text PDF–1.3M Supplementary Material
TF-centered downstream gene set enrichment analysis: Inference of causal regulators by integrating TF-DNA interactions and protein post-translational modifications information
Qi Liu, Yejun Tan, Tao Huang, Guohui Ding, Zhidong Tu, Lei Liu, Yixue Li, Hongyue Dai, Lu Xie
BMC Bioinformatics. 2010; 11(Suppl 11): S5. Published online 2010 December 14. doi: 10.1186/1471-2105-11-S11-S5
PMCID:
PMC3024863
Abstract Full Text PDF–710K Supplementary Material
Learning transcriptional networks from the integration of ChIP–chip and expression data in a non-parametric model
Ahrim Youn, David J. Reiss, Werner Stuetzle
Bioinformatics. 2010 August 1; 26(15): 1879–1886. Published online 2010 June 4. doi: 10.1093/bioinformatics/btq289
PMCID:
PMC2913654
Abstract Full Text PDF–424K Supplementary Material
Revealing global regulatory perturbations across human cancers
Hani Goodarzi, Olivier Elemento, Saeed Tavazoie
Mol Cell. Author manuscript; available in PMC 2010 December 11.
Published in final edited form as: Mol Cell. 2009 December 11; 36(5): 900–911. doi: 10.1016/j.molcel.2009.11.016
PMCID:
PMC2900319
Abstract Full Text PDF–3.3M Supplementary Material
Impact of DNA-binding position variants on yeast gene expression
Krishna B. S. Swamy, Chung-Yi Cho, Sufeng Chiang, Zing Tsung-Yeh Tsai, Huai-Kuang Tsai
Nucleic Acids Res. 2009 November; 37(21): 6991–7001. Published online 2009 November. doi: 10.1093/nar/gkp743
PMCID:
PMC2790881
Abstract Full Text PDF–463K Supplementary Material
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
Integrating functional genomics data using maximum likelihood based simultaneous component analysis
Robert A van den Berg, Iven Van Mechelen, Tom F Wilderjans, Katrijn Van Deun, Henk AL Kiers, Age K Smilde
BMC Bioinformatics. 2009; 10: 340. Published online 2009 October 16. doi: 10.1186/1471-2105-10-340
PMCID:
PMC2771021
Abstract Full Text PDF–407K
A structured overview of simultaneous component based data integration
Katrijn Van Deun, Age K Smilde, Mariët J van der Werf, Henk AL Kiers, Iven Van Mechelen
BMC Bioinformatics. 2009; 10: 246. Published online 2009 August 11. doi: 10.1186/1471-2105-10-246
PMCID:
PMC2752463
Abstract Full Text PDF–576K Supplementary Material
An integrative ChIP-chip and gene expression profiling to model SMAD regulatory modules
Huaxia Qin, Michael WY Chan, Sandya Liyanarachchi, Curtis Balch, Dustin Potter, Irene J Souriraj, Alfred SL Cheng, Francisco J Agosto-Perez, Elena V Nikonova, Pearlly S Yan, Huey-Jen Lin, Kenneth P Nephew, Joel H Saltz, Louise C Showe, Tim HM Huang, Ramana V Davuluri
BMC Syst Biol. 2009; 3: 73. Published online 2009 July 17. doi: 10.1186/1752-0509-3-73
PMCID:
PMC2724489
Abstract Full Text PDF–892K Supplementary Material
Transcriptional programs: Modelling higher order structure in transcriptional control
John E Reid, Sascha Ott, Lorenz Wernisch
BMC Bioinformatics. 2009; 10: 218. Published online 2009 July 16. doi: 10.1186/1471-2105-10-218
PMCID:
PMC2725141
Abstract Full Text PDF–504K Supplementary Material
DISTILLER: a data integration framework to reveal condition dependency of complex regulons in Escherichia coli
Karen Lemmens, Tijl De Bie, Thomas Dhollander, Sigrid C De Keersmaecker, Inge M Thijs, Geert Schoofs, Ami De Weerdt, Bart De Moor, Jos Vanderleyden, Julio Collado-Vides, Kristof Engelen, Kathleen Marchal
Genome Biol. 2009; 10(3): R27. Published online 2009 March 6. doi: 10.1186/gb-2009-10-3-r27
PMCID:
PMC2690998
Abstract Full Text PDF–639K Supplementary Material
Gene set-based module discovery in the breast cancer transcriptome
Atsushi Niida, Andrew D Smith, Seiya Imoto, Hiroyuki Aburatani, Michael Q Zhang, Tetsu Akiyama
BMC Bioinformatics. 2009; 10: 71. Published online 2009 February 26. doi: 10.1186/1471-2105-10-71
PMCID:
PMC2674431
Abstract Full Text PDF–818K 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
Meta Analysis of Gene Expression Data within and Across Species
Ana C Fierro, Filip Vandenbussche, Kristof Engelen, Yves Van de Peer, Kathleen Marchal
Curr Genomics. 2008 December; 9(8): 525–534. doi: 10.2174/138920208786847935
PMCID:
PMC2694560
Abstract Full Text PDF–234K
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
Unraveling transcriptional regulatory programs by integrative analysis of microarray and transcription factor binding data
Huai Li, Ming Zhan
Bioinformatics. 2008 September 1; 24(17): 1874–1880. Published online 2008 June 27. doi: 10.1093/bioinformatics/btn332
PMCID:
PMC2519161
Abstract Full Text PDF–545K Supplementary Material
Inferring transcriptional compensation interactions in yeast via stepwise structure equation modeling
Grace S Shieh, Chung-Ming Chen, Ching-Yun Yu, Juiling Huang, Woei-Fuh Wang, Yi-Chen Lo
BMC Bioinformatics. 2008; 9: 134. Published online 2008 March 3. doi: 10.1186/1471-2105-9-134
PMCID:
PMC2323972
Abstract Full Text PDF–328K Supplementary Material
Prioritization of gene regulatory interactions from large-scale modules in yeast
Ho-Joon Lee, Thomas Manke, Ricardo Bringas, Martin Vingron
BMC Bioinformatics. 2008; 9: 32. Published online 2008 January 22. doi: 10.1186/1471-2105-9-32
PMCID:
PMC2244593
Abstract Full Text PDF–1.7M Supplementary Material
Transcription factor target prediction using multiple short expression time series from Arabidopsis thaliana
Henning Redestig, Daniel Weicht, Joachim Selbig, Matthew A Hannah
BMC Bioinformatics. 2007; 8: 454. Published online 2007 November 18. doi: 10.1186/1471-2105-8-454
PMCID:
PMC2198923
Abstract Full Text PDF–725K Supplementary Material
Bayesian hierarchical model for transcriptional module discovery by jointly modeling gene expression and ChIP-chip data
Xiangdong Liu, Walter J Jessen, Siva Sivaganesan, Bruce J Aronow, Mario Medvedovic
BMC Bioinformatics. 2007; 8: 283. Published online 2007 August 3. doi: 10.1186/1471-2105-8-283
PMCID:
PMC1994961
Abstract Full Text PDF–1.4M Supplementary Material
Validating module network learning algorithms using simulated data
Tom Michoel, Steven Maere, Eric Bonnet, Anagha Joshi, Yvan Saeys, Tim Van den Bulcke, Koenraad Van Leemput, Piet van Remortel, Martin Kuiper, Kathleen Marchal, Yves Van de Peer
BMC Bioinformatics. 2007; 8(Suppl 2): S5. Published online 2007 May 3. doi: 10.1186/1471-2105-8-S2-S5
PMCID:
PMC1892074
Abstract Full Text PDF–631K Supplementary Material
Recent Computational Approaches to Understand Gene Regulation: Mining Gene Regulation In Silico
I Abnizova, T Subhankulova, WR Gilks
Curr Genomics. 2007 April; 8(2): 79–91.
PMCID:
PMC2435357
Abstract Full Text PDF–231K
Clustering of genes into regulons using integrated modeling-COGRIM
Guang Chen, Shane T Jensen, Christian J Stoeckert, Jr
Genome Biol. 2007; 8(1): R4. Published online 2007 January 4. doi: 10.1186/gb-2007-8-1-r4
PMCID:
PMC1839128
Abstract Full Text PDF–680K Supplementary Material
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