MCbiclust: a novel algorithm to discover large-scale functionally related gene sets from massive transcriptomics data collections

Mitonuclear communication in homeostasis and stress

(2016) Pedro M. Quirós et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

g:Profiler—a web server for functional interpretation of gene lists (2016 update)

(2016) Jüri Reimand et al.   NUCLEIC ACIDS RESEARCH

Systems proteomics of liver mitochondria function

(2016) E. G. Williams et al.   SCIENCE

Transcription factor networks regulating hepatic fatty acid metabolism

(2015) Panagiota Karagianni et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR AND CELL BIOLOGY OF LIPIDS

Integrating biological knowledge based on functional annotations for biclustering of gene expression data

(2015) Juan A. Nepomuceno et al.   COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE

Biclustering on expression data: A review

(2015) Beatriz Pontes et al.   JOURNAL OF BIOMEDICAL INFORMATICS

A cytosolic network suppressing mitochondria-mediated proteostatic stress and cell death

(2015) Xiaowen Wang et al.   NATURE

Transcriptional control of autophagy–lysosome function drives pancreatic cancer metabolism

(2015) Rushika M. Perera et al.   NATURE

Pyruvate carboxylation enables growth of SDH-deficient cells by supporting aspartate biosynthesis

(2015) Simone Cardaci et al.   NATURE CELL BIOLOGY

Pathway and network analysis of cancer genomes

(2015)   NATURE METHODS

Expression Atlas update—an integrated database of gene and protein expression in humans, animals and plants

(2015) Robert Petryszak et al.   NUCLEIC ACIDS RESEARCH

Metabolic Control of Redox and Redox Control of Metabolism in Plants

(2014) Peter Geigenberger et al.   ANTIOXIDANTS & REDOX SIGNALING

Antibiotic-Induced Replication Stress Triggers Bacterial Competence by Increasing Gene Dosage near the Origin

(2014) Jelle Slager et al.   CELL

STRING v10: protein–protein interaction networks, integrated over the tree of life

(2014) Damian Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

The Nrf2 regulatory network provides an interface between redox and intermediary metabolism

(2014) John D. Hayes et al.   TRENDS IN BIOCHEMICAL SCIENCES

A new measure for gene expression biclustering based on non-parametric correlation

(2013) Jose L. Flores et al.   COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE

Heterogeneity of tumor-induced gene expression changes in the human metabolic network

(2013) Jie Hu et al.   NATURE BIOTECHNOLOGY

The MIntAct project—IntAct as a common curation platform for 11 molecular interaction databases

(2013) Sandra Orchard et al.   NUCLEIC ACIDS RESEARCH

Characterizing the interplay between multiple levels of organization within bacterial sigma factor regulatory networks

(2013) Yu Qiu et al.   Nature Communications

EnrichNet: network-based gene set enrichment analysis

(2012) Enrico Glaab et al.   BIOINFORMATICS

Epithelial to Mesenchymal Transition Is Activated in Metastatic Pheochromocytomas and Paragangliomas Caused bySDHBGene Mutations

(2012) Céline Loriot et al.   JOURNAL OF CLINICAL ENDOCRINOLOGY & METABOLISM

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

(2012) Jordi Barretina et al.   NATURE

EcoCyc: fusing model organism databases with systems biology

(2012) Ingrid M. Keseler et al.   NUCLEIC ACIDS RESEARCH

Hallmarks of Cancer: The Next Generation

(2011) Douglas Hanahan et al.   CELL

ResponseNet: revealing signaling and regulatory networks linking genetic and transcriptomic screening data

(2011) A. Lan et al.   NUCLEIC ACIDS RESEARCH

RegulonDB version 7.0: transcriptional regulation of Escherichia coli K-12 integrated within genetic sensory response units (Gensor Units)

(2010) S. Gama-Castro et al.   NUCLEIC ACIDS RESEARCH

The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function

(2010) David Warde-Farley et al.   NUCLEIC ACIDS RESEARCH

Automated Network Analysis Identifies Core Pathways in Glioblastoma

(2010) Ethan Cerami et al.   PLoS One

Predicting Metabolic Fluxes Using Gene Expression Differences As Constraints

(2009) Rogier J P van Berlo et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

A Mitochondrial Protein Compendium Elucidates Complex I Disease Biology

(2008) David J. Pagliarini et al.   CELL