In silico Pathway Activation Network Decomposition Analysis (iPANDA) as a method for biomarker development

Integrative modeling of multi-omics data to identify cancer drivers and infer patient-specific gene activity

(2016) Ana B. Pavel et al.   BMC Systems Biology

Applications of Deep Learning in Biomedicine

(2016) Polina Mamoshina et al.   MOLECULAR PHARMACEUTICS

Deep Learning Applications for Predicting Pharmacological Properties of Drugs and Drug Repurposing Using Transcriptomic Data

(2016) Alexander Aliper et al.   MOLECULAR PHARMACEUTICS

Cancer statistics, 2015

(2015) Rebecca L. Siegel et al.   CA-A CANCER JOURNAL FOR CLINICIANS

Combinatorial high-throughput experimental and bioinformatic approach identifies molecular pathways linked with the sensitivity to anticancer target drugs

(2015) Larisa Venkova et al.   Oncotarget

Multivariate inference of pathway activity in host immunity and response to therapeutics

(2014) Gautam Goel et al.   NUCLEIC ACIDS RESEARCH

COXPRESdb in 2015: coexpression database for animal species by DNA-microarray and RNAseq-based expression data with multiple quality assessment systems

(2014) Yasunobu Okamura et al.   NUCLEIC ACIDS RESEARCH

Molecular and Cellular Heterogeneity in Breast Cancer

(2013) Ashley G. Rivenbark et al.   AMERICAN JOURNAL OF PATHOLOGY

Strengths and limitations of microarray-based phenotype prediction: lessons learned from the IMPROVER Diagnostic Signature Challenge

(2013) Adi L. Tarca et al.   BIOINFORMATICS

GSVA: gene set variation analysis for microarray and RNA-Seq data

(2013) Sonja Hänzelmann et al.   BMC BIOINFORMATICS

TGF-β inhibition enhances chemotherapy action against triple-negative breast cancer

(2013) Neil E. Bhola et al.   JOURNAL OF CLINICAL INVESTIGATION

A Comparison of Gene Set Analysis Methods in Terms of Sensitivity, Prioritization and Specificity

(2013) Adi L. Tarca et al.   PLoS One

Down-weighting overlapping genes improves gene set analysis

(2012) Adi Tarca et al.   BMC BIOINFORMATICS

Centrality-based pathway enrichment: a systematic approach for finding significant pathways dominated by key genes

(2012) Zuguang Gu et al.   BMC Systems Biology

PPAR signaling pathway may be an important predictor of breast cancer response to neoadjuvant chemotherapy

(2012) Y. Z. Chen et al.   CANCER CHEMOTHERAPY AND PHARMACOLOGY

DART: Denoising Algorithm based on Relevance network Topology improves molecular pathway activity inference

(2011) Yan Jiao et al.   BMC BIOINFORMATICS

Triple-negative breast cancer: Present challenges and new perspectives

(2010) Franca Podo et al.   Molecular Oncology

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

(2010)   NATURE BIOTECHNOLOGY

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

(2009) David A. Barbie et al.   NATURE

ITFP: an integrated platform of mammalian transcription factors

(2008) G. Zheng et al.   BIOINFORMATICS

Merging two gene-expression studies via cross-platform normalization

(2008) Andrey A. Shabalin et al.   BIOINFORMATICS

A novel signaling pathway impact analysis

(2008) Adi Laurentiu Tarca et al.   BIOINFORMATICS

Empirical Bayes accomodation of batch-effects in microarray data using identical replicate reference samples: application to RNA expression profiling of blood from Duchenne muscular dystrophy patients

(2008) Wynn L Walker et al.   BMC GENOMICS

Pathway analysis of seven common diseases assessed by genome-wide association

(2008) Ali Torkamani et al.   GENOMICS

Domain-oriented reduction of rule-based network models

(2008) N.M. Borisov et al.   IET Systems Biology