Identifying gene function and module connections by the integration of multispecies expression compendia

Mapping the Genetic Landscape of Human Cells

(2018) Max A. Horlbeck et al.   CELL

An unexpected link between fatty acid synthase and cholesterol synthesis in proinflammatory macrophage activation

(2018) Richard G. Carroll et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Quantifying and Localizing the Mitochondrial Proteome Across Five Tissues in A Mouse Population

(2018) Evan Graehl Williams et al.   MOLECULAR & CELLULAR PROTEOMICS

Mutations in the SWI/SNF complex induce a targetable dependence on oxidative phosphorylation in lung cancer

(2018) Yonathan Lissanu Deribe et al.   NATURE MEDICINE

An Integrated Systems Genetics and Omics Toolkit to Probe Gene Function

(2018) Hao Li et al.   Cell Systems

Large-scale investigation of the reasons why potentially important genes are ignored

(2018) Thomas Stoeger et al.   PLOS BIOLOGY

Human Disease Ontology 2018 update: classification, content and workflow expansion

(2018) Lynn M Schriml et al.   NUCLEIC ACIDS RESEARCH

COXPRESdb v7: a gene coexpression database for 11 animal species supported by 23 coexpression platforms for technical evaluation and evolutionary inference

(2018) Takeshi Obayashi et al.   NUCLEIC ACIDS RESEARCH

WDFY4 is required for cross-presentation in response to viral and tumor antigens

(2018) Derek J. Theisen et al.   SCIENCE

The most popular genes in the human genome

(2017)   NATURE

Architecture of the human interactome defines protein communities and disease networks

(2017) Edward L. Huttlin et al.   NATURE

Deubiquitylating enzymes and drug discovery: emerging opportunities

(2017) Jeanine A. Harrigan et al.   NATURE REVIEWS DRUG DISCOVERY

Cytosolic Proteostasis Networks of the Mitochondrial Stress Response

(2017) Davide D’Amico et al.   TRENDS IN BIOCHEMICAL SCIENCES

CLIC, a tool for expanding biological pathways based on co-expression across thousands of datasets

(2017) Yang Li et al.   PLoS Computational Biology

Two Conserved Histone Demethylases Regulate Mitochondrial Stress-Induced Longevity

(2016) Carsten Merkwirth et al.   CELL

Mitochondrial Stress Induces Chromatin Reorganization to Promote Longevity and UPR mt

(2016) Ye Tian et al.   CELL

A Genome-wide CRISPR Death Screen Identifies Genes Essential for Oxidative Phosphorylation

(2016) Jason D. Arroyo et al.   Cell Metabolism

Mitochondrial Protein Interaction Mapping Identifies Regulators of Respiratory Chain Function

(2016) Brendan J. Floyd et al.   MOLECULAR CELL

High-throughput discovery of novel developmental phenotypes

(2016) Mary E. Dickinson et al.   NATURE

Accessory subunits are integral for assembly and function of human mitochondrial complex I

(2016) David A. Stroud et al.   NATURE

DisGeNET: a comprehensive platform integrating information on human disease-associated genes and variants

(2016) Janet Piñero et al.   NUCLEIC ACIDS RESEARCH

Mutations in the GABA Transporter SLC6A1 Cause Epilepsy with Myoclonic-Atonic Seizures

(2015) Gemma L. Carvill et al.   AMERICAN JOURNAL OF HUMAN GENETICS

The Convergence of Systems and Reductionist Approaches in Complex Trait Analysis

(2015) Evan G. Williams et al.   CELL

A Human Interactome in Three Quantitative Dimensions Organized by Stoichiometries and Abundances

(2015) Marco Y. Hein et al.   CELL

Understanding multicellular function and disease with human tissue-specific networks

(2015) Casey S Greene et al.   NATURE GENETICS

Targeted exploration and analysis of large cross-platform human transcriptomic compendia

(2015) Qian Zhu et al.   NATURE METHODS

WeGET: predicting new genes for molecular systems by weighted co-expression

(2015) Radek Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

MitoCarta2.0: an updated inventory of mammalian mitochondrial proteins

(2015) Sarah E. Calvo et al.   NUCLEIC ACIDS RESEARCH

Tissue-based map of the human proteome

(2015) M. Uhlen et al.   SCIENCE

ARID1A Is Essential for Endometrial Function during Early Pregnancy

(2015) Tae Hoon Kim et al.   PLoS Genetics

Multilayered Genetic and Omics Dissection of Mitochondrial Activity in a Mouse Reference Population

(2014) Yibo Wu et al.   CELL

Expansion of Biological Pathways Based on Evolutionary Inference

(2014) Yang Li et al.   CELL

A Proteome-Scale Map of the Human Interactome Network

(2014) Thomas Rolland et al.   CELL

Mistargeting of Peroxisomal EHHADH and Inherited Renal Fanconi's Syndrome

(2014) Enriko D. Klootwijk et al.   NEW ENGLAND JOURNAL OF MEDICINE

GeneFriends: a human RNA-seq-based gene and transcript co-expression database

(2014) Sipko van Dam et al.   NUCLEIC ACIDS RESEARCH

ArrayExpress update—simplifying data submissions

(2014) Nikolay Kolesnikov et al.   NUCLEIC ACIDS RESEARCH

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

(2014) Damian Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

Functionally Enigmatic Genes: A Case Study of the Brain Ignorome

(2014) Ashutosh K. Pandey et al.   PLoS One

Ubiquitin–proteasome system involvement in Huntington’s disease

(2014) Zaira Ortega et al.   Frontiers in Molecular Neuroscience

Epigenetic Silencing Mediates Mitochondria Stress-Induced Longevity

(2013) Elizabeth A. Schroeder et al.   Cell Metabolism

A large-scale evaluation of computational protein function prediction

(2013) Predrag Radivojac et al.   NATURE METHODS

Identification of small RNA pathway genes using patterns of phylogenetic conservation and divergence

(2012) Yuval Tabach et al.   NATURE

Using probabilistic estimation of expression residuals (PEER) to obtain increased power and interpretability of gene expression analyses

(2012) Oliver Stegle et al.   Nature Protocols

Camera: a competitive gene set test accounting for inter-gene correlation

(2012) Di Wu et al.   NUCLEIC ACIDS RESEARCH

NCBI GEO: archive for functional genomics data sets—update

(2012) Tanya Barrett et al.   NUCLEIC ACIDS RESEARCH

Ten Years of Pathway Analysis: Current Approaches and Outstanding Challenges

(2012) Purvesh Khatri et al.   PLoS Computational Biology

Mutations in Iron-Sulfur Cluster Scaffold Genes NFU1 and BOLA3 Cause a Fatal Deficiency of Multiple Respiratory Chain and 2-Oxoacid Dehydrogenase Enzymes

(2011) Jessie M. Cameron et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Too many roads not taken

(2011) Aled M. Edwards et al.   NATURE

I-TASSER: a unified platform for automated protein structure and function prediction

(2010) Ambrish Roy et al.   Nature Protocols

Network medicine: a network-based approach to human disease

(2010) Albert-László Barabási et al.   NATURE REVIEWS GENETICS

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

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

The Genetic Landscape of a Cell

(2010) M. Costanzo et al.   SCIENCE

Identification of Cholesterol-Regulating Genes by Targeted RNAi Screening

(2009) Fabian Bartz et al.   Cell Metabolism

A global pathway crosstalk network

(2008) Yong Li et al.   BIOINFORMATICS

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

Mapping the Genetic Architecture of Gene Expression in Human Liver

(2008) Eric E Schadt et al.   PLOS BIOLOGY