DREM 2.0: Improved reconstruction of dynamic regulatory networks from time-series expression data

Inference of hierarchical regulatory network of estrogen-dependent breast cancer through ChIP-based data

(2011) Fei Gu et al.   BMC Systems Biology

Integrating multiple evidence sources to predict transcription factor binding in the human genome

(2010) J. Ernst et al.   GENOME RESEARCH

The mutation spectrum revealed by paired genome sequences from a lung cancer patient

(2010) William Lee et al.   NATURE

Evolutionary divergence in the fungal response to fluconazole revealed by soft clustering

(2010) Dwight Kuo et al.   GENOME BIOLOGY

A dynamic network of transcription in LPS-treated human subjects

(2009) Junhee Seok et al.   BMC Systems Biology

Dynamic and complex transcription factor binding during an inducible response in yeast

(2009) L. Ni et al.   GENES & DEVELOPMENT

Systems-level dynamic analyses of fate change in murine embryonic stem cells

(2009) Rong Lu et al.   NATURE

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

A Semi-Supervised Method for Predicting Transcription Factor–Gene Interactions in Escherichia coli

(2008) Jason Ernst et al.   PLoS Computational Biology