Research  

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 (14 December 2010)

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Research  

Mimosa: Mixture model of co-expression to detect modulators of regulatory interaction

Matthew Hansen, Logan Everett, Larry Singh, Sridhar Hannenhalli Algorithms for Molecular Biology 2010, 5:4 (4 January 2010)

This article is part of a collection on Selected papers from WABI...

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Research article  

Uncovering transcriptional interactions via an adaptive fuzzy logic approach

Cheng-Long Chuang, Kenneth Hung, Chung-Ming Chen, Grace S Shieh BMC Bioinformatics 2009, 10:400 (6 December 2009)

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Research article  

Transcriptional programs: Modelling higher order structure in transcriptional control

John E Reid, Sascha Ott, Lorenz Wernisch BMC Bioinformatics 2009, 10:218 (16 July 2009)

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Research article  

Comparative analysis of module-based versus direct methods for reverse-engineering transcriptional regulatory networks

Tom Michoel, Riet De Smet, Anagha Joshi, Yves Van de Peer, Kathleen Marchal BMC Systems Biology 2009, 3:49 (7 May 2009)

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Method  

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 Biology 2009, 10:R27 (6 March 2009)

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Research  

Systems biology-defined NF-κB regulons, interacting signal pathways and networks are implicated in the malignant phenotype of head and neck cancer cell lines differing in p53 status

Bin Yan, Guang Chen, Kunal Saigal, Xinping Yang, Shane T Jensen, Carter Van Waes, Christian J Stoeckert, Zhong Chen Genome Biology 2008, 9:R53 (11 March 2008)

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Method  

High-resolution analysis of condition-specific regulatory modules in Saccharomyces cerevisiae

Hun-Goo Lee, Hyo-Soo Lee, Sang-Hoon Jeon, Tae-Hoon Chung, Young-Sung Lim, Won-Ki Huh Genome Biology 2008, 9:R2 (3 January 2008)

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Research article  

In situ analysis of cross-hybridisation on microarrays and the inference of expression correlation

Tineke Casneuf, Yves Van de Peer, Wolfgang Huber BMC Bioinformatics 2007, 8:461 (26 November 2007)

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Research article  

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 (3 August 2007)

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