Protein Networks as Logic Functions in Development and Cancer

Boosting Signal-to-Noise in Complex Biology: Prior Knowledge Is Power

(2011) Trey Ideker et al.   CELL

MODEVO: exploring modularity and evolution of protein interaction networks

(2010) M. Wozniak et al.   BIOINFORMATICS

An Atlas of Combinatorial Transcriptional Regulation in Mouse and Man

(2010) Timothy Ravasi et al.   CELL

A human B-cell interactome identifies MYB and FOXM1 as master regulators of proliferation in germinal centers

(2010) Celine Lefebvre et al.   Molecular Systems Biology

Chromatin remodelling during development

(2010) Lena Ho et al.   NATURE

Heat-shock transcription factor HSF1 has a critical role in human epidermal growth factor receptor-2-induced cellular transformation and tumorigenesis

(2010) L Meng et al.   ONCOGENE

DEGAS: De Novo Discovery of Dysregulated Pathways in Human Diseases

(2010) Igor Ulitsky et al.   PLoS One

An Integrative -omics Approach to Identify Functional Sub-Networks in Human Colorectal Cancer

(2010) Rod K. Nibbe et al.   PLoS Computational Biology

Hoxc8 represses BMP-induced expression of Smad6

(2009) Myengmo Kang et al.   MOLECULES AND CELLS

The transcriptional network for mesenchymal transformation of brain tumours

(2009) Maria Stella Carro et al.   NATURE

Dynamic modularity in protein interaction networks predicts breast cancer outcome

(2009) Ian W Taylor et al.   NATURE BIOTECHNOLOGY

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

Detecting gene–gene interactions that underlie human diseases

(2009) Heather J Cordell   NATURE REVIEWS GENETICS

An embryonic stem cell chromatin remodeling complex, esBAF, is essential for embryonic stem cell self-renewal and pluripotency

(2009) L. Ho et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The mammalian phenotype ontology: enabling robust annotation and comparative analysis

(2009) Cynthia L. Smith et al.   Wiley Interdisciplinary Reviews-Systems Biology and Medicine

Regulatory networks define phenotypic classes of human stem cell lines

(2008) Franz-Josef Müller et al.   NATURE

What are decision trees?

(2008) Carl Kingsford et al.   NATURE BIOTECHNOLOGY

The Mouse Genome Database genotypes::phenotypes

(2008) J. A. Blake et al.   NUCLEIC ACIDS RESEARCH

Inferring Pathway Activity toward Precise Disease Classification

(2008) Eunjung Lee et al.   PLoS Computational Biology