Babelomics 5.0: functional interpretation for new generations of genomic data

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

Understanding disease mechanisms with models of signaling pathway activities

(2014) Patricia Sebastian-Leon et al.   BMC Systems Biology

voom: precision weights unlock linear model analysis tools for RNA-seq read counts

(2014) Charity W Law et al.   GENOME BIOLOGY

OncodriveCLUST: exploiting the positional clustering of somatic mutations to identify cancer genes

(2013) David Tamborero et al.   BIOINFORMATICS

Genomics and transcriptomics in drug discovery

(2013) Joaquin Dopazo   DRUG DISCOVERY TODAY

Genome Maps, a new generation genome browser

(2013) Ignacio Medina et al.   NUCLEIC ACIDS RESEARCH

Inferring the functional effect of gene expression changes in signaling pathways

(2013) Patricia Sebastián-León et al.   NUCLEIC ACIDS RESEARCH

Systems Pharmacology to Predict Drug Toxicity: Integration Across Levels of Biological Organization

(2012) Jane P.F. Bai et al.   Annual Review of Pharmacology and Toxicology

CellBase, a comprehensive collection of RESTful web services for retrieving relevant biological information from heterogeneous sources

(2012) M. Bleda et al.   NUCLEIC ACIDS RESEARCH

Inferring the regulatory network behind a gene expression experiment

(2012) M. Bleda et al.   NUCLEIC ACIDS RESEARCH

Discovering the hidden sub-network component in a ranked list of genes or proteins derived from genomic experiments

(2012) Luz García-Alonso et al.   NUCLEIC ACIDS RESEARCH

Functional impact bias reveals cancer drivers

(2012) Abel Gonzalez-Perez et al.   NUCLEIC ACIDS RESEARCH

Ten Years of Pathway Analysis: Current Approaches and Outstanding Challenges

(2012) Purvesh Khatri et al.   PLoS Computational Biology

Differential expression in RNA-seq: A matter of depth

(2011) S. Tarazona et al.   GENOME RESEARCH

Predicting the functional impact of protein mutations: application to cancer genomics

(2011) Boris Reva et al.   NUCLEIC ACIDS RESEARCH

International network of cancer genome projects

(2010) Thomas J. Hudson (Chairperson) et al.   NATURE

Babelomics: an integrative platform for the analysis of transcriptomics, proteomics and genomic data with advanced functional profiling

(2010) Ignacio Medina et al.   NUCLEIC ACIDS RESEARCH

A scaling normalization method for differential expression analysis of RNA-seq data

(2010) Mark D Robinson et al.   GENOME BIOLOGY

Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm

(2009) Prateek Kumar et al.   Nature Protocols

Gene set-based analysis of polymorphisms: finding pathways or biological processes associated to traits in genome-wide association studies

(2009) Ignacio Medina et al.   NUCLEIC ACIDS RESEARCH

SNOW, a web-based tool for the statistical analysis of protein–protein interaction networks

(2009) Pablo Minguez et al.   NUCLEIC ACIDS RESEARCH

Methods for Detecting Associations with Rare Variants for Common Diseases: Application to Analysis of Sequence Data

(2008) Bingshan Li et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Formulating and testing hypotheses in functional genomics

(2008) Joaquin Dopazo   ARTIFICIAL INTELLIGENCE IN MEDICINE

Comprehensive genomic characterization defines human glioblastoma genes and core pathways

(2008) Roger McLendon et al.   NATURE

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

Babelomics: advanced functional profiling of transcriptomics, proteomics and genomics experiments

(2008) F. Al-Shahrour et al.   NUCLEIC ACIDS RESEARCH

GEPAS, a web-based tool for microarray data analysis and interpretation

(2008) J. Tarraga et al.   NUCLEIC ACIDS RESEARCH