ASSIGN: context-specific genomic profiling of multiple heterogeneous biological pathways

Unsupervised Bayesian linear unmixing of gene expression microarrays

(2013) Cécile Bazot et al.   BMC BIOINFORMATICS

Network quantification of EGFR signaling unveils potential for targeted combination therapy

(2013) B. Klinger et al.   Molecular Systems Biology

Data, information, knowledge and principle: back to metabolism in KEGG

(2013) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Multiplatform single-sample estimates of transcriptional activation

(2013) S. R. Piccolo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

FacPad: Bayesian sparse factor modeling for the inference of pathways responsive to drug treatment

(2012) Haisu Ma et al.   BIOINFORMATICS

A single-sample microarray normalization method to facilitate personalized-medicine workflows

(2012) Stephen R. Piccolo et al.   GENOMICS

Comprehensive molecular portraits of human breast tumours

(2012) Daniel C. Koboldt et al.   NATURE

Molecular signatures database (MSigDB) 3.0

(2011) A. Liberzon et al.   BIOINFORMATICS

Sparse Bayesian infinite factor models

(2011) A. Bhattacharya et al.   BIOMETRIKA

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

Feedback regulation of EGFR signalling: decision making by early and delayed loops

(2011) Roi Avraham et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Frozen robust multiarray analysis (fRMA)

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

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

MapSplice: Accurate mapping of RNA-seq reads for splice junction discovery

(2010) Kai Wang et al.   NUCLEIC ACIDS RESEARCH

Airway PI3K Pathway Activation Is an Early and Reversible Event in Lung Cancer Development

(2010) A. M. Gustafson et al.   Science Translational Medicine

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

In vivo Antitumor Activity of MEK and Phosphatidylinositol 3-Kinase Inhibitors in Basal-Like Breast Cancer Models

(2009) K. P. Hoeflich et al.   CLINICAL CANCER RESEARCH

PI3K pathway activation in breast cancer is associated with the basal-like phenotype and cancer-specific mortality

(2009) Elena López-Knowles et al.   INTERNATIONAL JOURNAL OF CANCER

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

(2009) David A. Barbie et al.   NATURE

A comparative study of different machine learning methods on microarray gene expression data

(2008) Mehdi Pirooznia et al.   BMC GENOMICS

Basal-Like Breast Cancer Defined by Five Biomarkers Has Superior Prognostic Value than Triple-Negative Phenotype

(2008) M. C.U. Cheang et al.   CLINICAL CANCER RESEARCH