Development of a Drug-Response Modeling Framework to Identify Cell Line Derived Translational Biomarkers That Can Predict Treatment Outcome to Erlotinib or Sorafenib

A community effort to assess and improve drug sensitivity prediction algorithms

(2014) James C Costello et al.   NATURE BIOTECHNOLOGY

Comprehensive Biomarker Analysis and Final Efficacy Results of Sorafenib in the BATTLE Trial

(2013) G. R. Blumenschein et al.   CLINICAL CANCER RESEARCH

GENESHIFT: A Nonparametric Approach for Integrating Microarray Gene Expression Data Based on the Inner Product as a Distance Measure between the Distributions of Genes

(2013) Cosmin Lazar et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Batch effect removal methods for microarray gene expression data integration: a survey

(2012) C. Lazar et al.   BRIEFINGS IN BIOINFORMATICS

CellMiner: A Web-Based Suite of Genomic and Pharmacologic Tools to Explore Transcript and Drug Patterns in the NCI-60 Cell Line Set

(2012) W. C. Reinhold et al.   CANCER RESEARCH

Systematic identification of genomic markers of drug sensitivity in cancer cells

(2012) Mathew J. Garnett et al.   NATURE

The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity

(2012) Jordi Barretina et al.   NATURE

Thawing Frozen Robust Multi-array Analysis (fRMA)

(2011) Matthew N McCall et al.   BMC BIOINFORMATICS

Sparse PLS discriminant analysis: biologically relevant feature selection and graphical displays for multiclass problems

(2011) Kim-Anh Lê Cao et al.   BMC BIOINFORMATICS

Overcoming Molecular Mechanisms of Resistance to First-Generation Epidermal Growth Factor Receptor Tyrosine Kinase Inhibitors

(2011) Jair Bar et al.   Clinical Lung Cancer

The BATTLE Trial: Personalizing Therapy for Lung Cancer

(2011) Edward S. Kim et al.   Cancer Discovery

Frozen robust multiarray analysis (fRMA)

(2010) M. N. McCall et al.   BIOSTATISTICS

How Informatics Can Potentiate Precompetitive Open-Source Collaboration to Jump-Start Drug Discovery and Development

(2010) E D Perakslis et al.   CLINICAL PHARMACOLOGY & THERAPEUTICS

Sparse partial least squares regression for simultaneous dimension reduction and variable selection

(2010) Hyonho Chun et al.   JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES B-STATISTICAL METHODOLOGY

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

(2010)   NATURE BIOTECHNOLOGY

Understanding resistance to EGFR inhibitors—impact on future treatment strategies

(2010) Deric L. Wheeler et al.   Nature Reviews Clinical Oncology

A comparison of batch effect removal methods for enhancement of prediction performance using MAQC-II microarray gene expression data

(2010) J Luo et al.   PHARMACOGENOMICS JOURNAL

“Topological Significance” Analysis of Gene Expression and Proteomic Profiles from Prostate Cancer Cells Reveals Key Mechanisms of Androgen Response

(2010) Adaikkalam Vellaichamy et al.   PLoS One

Sparse canonical methods for biological data integration: application to a cross-platform study

(2009) Kim-Anh Lê Cao et al.   BMC BIOINFORMATICS

Identifying disease-specific genes based on their topological significance in protein networks

(2009) Zoltán Dezső et al.   BMC Systems Biology

Expression Quantitative Trait Loci Mapping With Multivariate Sparse Partial Least Squares Regression

(2009) H. Chun et al.   GENETICS

Extensions of Sparse Canonical Correlation Analysis with Applications to Genomic Data

(2009) Daniela M Witten et al.   Statistical Applications in Genetics and Molecular Biology

High-risk myeloma: a gene expression based risk-stratification model for newly diagnosed multiple myeloma treated with high-dose therapy is predictive of outcome in relapsed disease treated with single-agent bortezomib or high-dose dexamethasone

(2008) F. Zhan et al.   BLOOD

Prediction of Survival in Multiple Myeloma Based on Gene Expression Profiles Reveals Cell Cycle and Chromosomal Instability Signatures in High-Risk Patients and Hyperdiploid Signatures in Low-Risk Patients: A Study of the Intergroupe Francophone du Myélome

(2008) Olivier Decaux et al.   JOURNAL OF CLINICAL ONCOLOGY