SIGNATURE: A workbench for gene expression signature analysis

A gene expression signature of RAS pathway dependence predicts response to PI3K and RAS pathway inhibitors and expands the population of RAS pathway activated tumors

(2010) Andrey Loboda et al.   BMC Medical Genomics

The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models

(2010)   NATURE BIOTECHNOLOGY

Tackling the widespread and critical impact of batch effects in high-throughput data

(2010) Jeffrey T. Leek et al.   NATURE REVIEWS GENETICS

A pathway-based classification of human breast cancer

(2010) M. L. Gatza et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Gene Expression Signature Associated with “K-Ras Addiction” Reveals Regulators of EMT and Tumor Cell Survival

(2009) Anurag Singh et al.   CANCER CELL

Latent Bone Metastasis in Breast Cancer Tied to Src-Dependent Survival Signals

(2009) Xiang H.-F. Zhang et al.   CANCER CELL

A Genomic Strategy to Elucidate Modules of Oncogenic Pathway Signaling Networks

(2009) Jeffrey T. Chang et al.   MOLECULAR CELL

Systematic RNA interference reveals that oncogenic KRAS-driven cancers require TBK1

(2009) David A. Barbie et al.   NATURE

Cross-Study Projections of Genomic Biomarkers: An Evaluation in Cancer Genomics

(2009) Joseph E. Lucas et al.   PLoS One

Oncogenic Pathway Combinations Predict Clinical Prognosis in Gastric Cancer

(2009) Chia Huey Ooi et al.   PLoS Genetics

JCoast – A biologist-centric software tool for data mining and comparison of prokaryotic (meta)genomes

(2008) Michael Richter et al.   BMC BIOINFORMATICS

Performance comparison of two microarray platforms to assess differential gene expression in human monocyte and macrophage cells

(2008) Seraya Maouche et al.   BMC GENOMICS

MEGA: A biologist-centric software for evolutionary analysis of DNA and protein sequences

(2008) S. Kumar et al.   BRIEFINGS IN BIOINFORMATICS

Module Map of Stem Cell Genes Guides Creation of Epithelial Cancer Stem Cells

(2008) David J. Wong et al.   Cell Stem Cell

High-throughput functional annotation and data mining with the Blast2GO suite

(2008) S. Gotz et al.   NUCLEIC ACIDS RESEARCH

Singular value decomposition-based regression identifies activation of endogenous signaling pathways in vivo

(2008) Zhandong Liu et al.   GENOME BIOLOGY