Genome Biology

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Validation and refinement of gene-regulatory pathways on a network of physical interactions

Chen-Hsiang Yeang, H Craig Mak, Scott McCuine, Christopher Workman, Tommi Jaakkola and Trey Ideker*

Genome Biology 2005, 6:R62 doi:10.1186/gb-2005-6-7-r62

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Research   Open Access

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)

Methodology article   Open Access Highly Accessed

Inferring the role of transcription factors in regulatory networks

Philippe Veber, Carito Guziolowski, Michel Le Borgne, Ovidiu Radulescu, Anne Siegel BMC Bioinformatics 2008, 9:228 (6 May 2008)

Research article   Open Access Highly Accessed

Characterization of the proneural gene regulatory network during mouse telencephalon development

Julia M Gohlke, Olivier Armant, Frederick M Parham, Marjolein V Smith, Celine Zimmer, Diogo S Castro, Laurent Nguyen, Joel S Parker, Gerard Gradwohl, Christopher J Portier, François Guillemot BMC Biology 2008, 6:15 (31 March 2008)

Novel cofactors of Mash1 and Ngn2, proneural genes involved in mammalian brain development, have been identified by a combination of experimental and bioinformatic approaches, establishing a new understanding of the gene regulatory networks behind neurogenesis.

Review   Open Access Highly Accessed

Inferring cellular networks – a review

Florian Markowetz, Rainer Spang BMC Bioinformatics 2007, 8(Suppl 6):S5 (27 September 2007)

Methodology article   Open Access

A Three Stage Integrative Pathway Search (TIPS©) framework to identify toxicity relevant genes and pathways

Zheng Li, Shireesh Srivastava, Sheenu Mittal, Xuerui Yang, Lufang Sheng, Christina Chan BMC Bioinformatics 2007, 8:202 (14 June 2007)