High-resolution network biology: connecting sequence with function

From Structure to Systems: High-Resolution, Quantitative Genetic Analysis of RNA Polymerase II

(2013) Hannes Braberg et al.   CELL

A Systematic Mammalian Genetic Interaction Map Reveals Pathways Underlying Ricin Susceptibility

(2013) Michael C. Bassik et al.   CELL

Population Genetics of Rare Variants and Complex Diseases

(2013) M. Cyrus Maher et al.   HUMAN HEREDITY

Analyses of the Effects of All Ubiquitin Point Mutants on Yeast Growth Rate

(2013) Benjamin P. Roscoe et al.   JOURNAL OF MOLECULAR BIOLOGY

From Systems to Structure: Bridging Networks and Mechanism

(2013) James S. Fraser et al.   MOLECULAR CELL

Signatures of mutational processes in human cancer

(2013) Ludmil B. Alexandrov et al.   NATURE

Mapping genetic interactions in human cancer cells with RNAi and multiparametric phenotyping

(2013) Christina Laufer et al.   NATURE METHODS

Quantitative genetic-interaction mapping in mammalian cells

(2013) Assen Roguev et al.   NATURE METHODS

Integrative approaches for finding modular structure in biological networks

(2013) Koyel Mitra et al.   NATURE REVIEWS GENETICS

Integrative Structural Biology

(2013) A. B. Ward et al.   SCIENCE

RNA-Guided Human Genome Engineering via Cas9

(2013) P. Mali et al.   SCIENCE

Multiplex Genome Engineering Using CRISPR/Cas Systems

(2013) L. Cong et al.   SCIENCE

Systematic Triple-Mutant Analysis Uncovers Functional Connectivity between Pathways Involved in Chromosome Regulation

(2013) James E. Haber et al.   Cell Reports

Synthetic Lethal Interaction of Combined BCL-XL and MEK Inhibition Promotes Tumor Regressions in KRAS Mutant Cancer Models

(2012) Ryan B. Corcoran et al.   CANCER CELL

Systematic Functional Prioritization of Protein Posttranslational Modifications

(2012) Pedro Beltrao et al.   CELL

A Census of Human Soluble Protein Complexes

(2012) Pierre C. Havugimana et al.   CELL

A TALEN Genome-Editing System for Generating Human Stem Cell-Based Disease Models

(2012) Qiurong Ding et al.   Cell Stem Cell

Go hybrid: EM, crystallography, and beyond

(2012) Gabriel C Lander et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Domain-mediated protein interaction prediction: From genome to network

(2012) Jüri Reimand et al.   FEBS LETTERS

Comparative analysis of virus–host interactomes with a mammalian high-throughput protein complementation assay based on Gaussia princeps luciferase

(2012) Grégory Neveu et al.   METHODS

Hierarchical Modularity and the Evolution of Genetic Interactomes across Species

(2012) Colm J. Ryan et al.   MOLECULAR CELL

Differential network biology

(2012) Trey Ideker et al.   Molecular Systems Biology

Systematic identification of genomic markers of drug sensitivity in cancer cells

(2012) Mathew J. Garnett et al.   NATURE

Structure-based prediction of protein–protein interactions on a genome-wide scale

(2012) Qiangfeng Cliff Zhang et al.   NATURE

Functional dissection of lysine deacetylases reveals that HDAC1 and p300 regulate AMPK

(2012) Yu-yi Lin et al.   NATURE

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

(2012) Jordi Barretina et al.   NATURE

An integrated map of genetic variation from 1,092 human genomes

(2012)   NATURE

Interpreting noncoding genetic variation in complex traits and human disease

(2012) Lucas D Ward et al.   NATURE BIOTECHNOLOGY

Three-dimensional reconstruction of protein networks provides insight into human genetic disease

(2012) Xiujuan Wang et al.   NATURE BIOTECHNOLOGY

Fitness analyses of all possible point mutations for regions of genes in yeast

(2012) Ryan Hietpas et al.   Nature Protocols

ChIP–seq and beyond: new and improved methodologies to detect and characterize protein–DNA interactions

(2012) Terrence S. Furey   NATURE REVIEWS GENETICS

The BioGRID interaction database: 2013 update

(2012) Andrew Chatr-aryamontri et al.   NUCLEIC ACIDS RESEARCH

Molecular architecture of the 26S proteasome holocomplex determined by an integrative approach

(2012) K. Lasker et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Putting the Pieces Together: Integrative Modeling Platform Software for Structure Determination of Macromolecular Assemblies

(2012) Daniel Russel et al.   PLOS BIOLOGY

A Genome-Scale RNA–Interference Screen Identifies RRAS Signaling as a Pathologic Feature of Huntington's Disease

(2012) John P. Miller et al.   PLoS Genetics

A Protein Complex Network of Drosophila melanogaster

(2011) K.G. Guruharsha et al.   CELL

Genetic Interactions in Cancer Progression and Treatment

(2011) Alan Ashworth et al.   CELL

RNA Polymerase II Carboxyl-terminal Domain Phosphorylation Regulates Protein Stability of the Set2 Methyltransferase and Histone H3 Di- and Trimethylation at Lysine 36

(2011) Stephen M. Fuchs et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Key Functional Regions in the Histone Variant H2A.Z C-Terminal Docking Domain

(2011) A. Y. Wang et al.   MOLECULAR AND CELLULAR BIOLOGY

Predicting selective drug targets in cancer through metabolic networks

(2011) O. Folger et al.   Molecular Systems Biology

Genetic engineering of human pluripotent cells using TALE nucleases

(2011) Dirk Hockemeyer et al.   NATURE BIOTECHNOLOGY

A systematic RNAi synthetic interaction screen reveals a link between p53 and snoRNP assembly

(2011) Dragomir B. Krastev et al.   NATURE CELL BIOLOGY

A chemical-genetic screen reveals a mechanism of resistance to PI3K inhibitors in cancer

(2011) Markus K Muellner et al.   Nature Chemical Biology

Mapping of signaling networks through synthetic genetic interaction analysis by RNAi

(2011) Thomas Horn et al.   NATURE METHODS

MINT, the molecular interaction database: 2012 update

(2011) Luana Licata et al.   NUCLEIC ACIDS RESEARCH

The Pfam protein families database

(2011) M. Punta et al.   NUCLEIC ACIDS RESEARCH

Demographic history and rare allele sharing among human populations

(2011) S. Gravel et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Site-specific acetylation mark on an essential chromatin-remodeling complex promotes resistance to replication stress

(2011) G. M. Charles et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Systematic investigation of genetic vulnerabilities across cancer cell lines reveals lineage-specific dependencies in ovarian cancer

(2011) H. W. Cheung et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genetic Interaction Maps in Escherichia coli Reveal Functional Crosstalk among Cell Envelope Biogenesis Pathways

(2011) Mohan Babu et al.   PLoS Genetics

Missing value imputation for epistatic MAPs

(2010) Colm Ryan et al.   BMC BIOINFORMATICS

Quantitative Genetic Interactions Reveal Biological Modularity

(2010) Pedro Beltrao et al.   CELL

Predicting genetic modifier loci using functional gene networks

(2010) I. Lee et al.   GENOME RESEARCH

Individual Lysine Acetylations on the N Terminus ofSaccharomyces cerevisiaeH2A.Z Are Highly but Not Differentially Regulated

(2010) Monika Mehta et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

It's the machine that matters: Predicting gene function and phenotype from protein networks

(2010) Peggy I. Wang et al.   Journal of Proteomics

Cross-species chemogenomic profiling reveals evolutionarily conserved drug mode of action

(2010) Laura Kapitzky et al.   Molecular Systems Biology

A map of human genome variation from population-scale sequencing

(2010) Richard M. Durbin et al.   NATURE

A method and server for predicting damaging missense mutations

(2010) Ivan A Adzhubei et al.   NATURE METHODS

Signalling ballet in space and time

(2010) Boris N. Kholodenko et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Decoding signalling networks by mass spectrometry-based proteomics

(2010) Chunaram Choudhary et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

The three-dimensional folding of the α-globin gene domain reveals formation of chromatin globules

(2010) Davide Baù et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

DOMINE: a comprehensive collection of known and predicted domain-domain interactions

(2010) Sailu Yellaboina et al.   NUCLEIC ACIDS RESEARCH

The BioGRID Interaction Database: 2011 update

(2010) C. Stark et al.   NUCLEIC ACIDS RESEARCH

Critical role for transcriptional repressor Snail2 in transformation by oncogenic RAS in colorectal carcinoma cells

(2010) Y Wang et al.   ONCOGENE

Detailed structural and assembly model of the type II secretion pilus from sparse data

(2010) M. Campos et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Genetic Landscape of a Cell

(2010) M. Costanzo et al.   SCIENCE

An Integrative Multi-Network and Multi-Classifier Approach to Predict Genetic Interactions

(2010) Gaurav Pandey et al.   PLoS Computational Biology

Systematic analysis of genome-wide fitness data in yeast reveals novel gene function and drug action

(2010) Maureen E Hillenmeyer et al.   GENOME BIOLOGY

Global fitness profiling of fission yeast deletion strains by barcode sequencing

(2010) Tian Xu Han et al.   GENOME BIOLOGY

A Physical and Regulatory Map of Host-Influenza Interactions Reveals Pathways in H1N1 Infection

(2009) Sagi D. Shapira et al.   CELL

A Genome-wide RNAi Screen Identifies Multiple Synthetic Lethal Interactions with the Ras Oncogene

(2009) Ji Luo et al.   CELL

HistoneHits: A database for histone mutations and their phenotypes

(2009) H. Huang et al.   GENOME RESEARCH

Inferential Optimization for Simultaneous Fitting of Multiple Components into a CryoEM Map of Their Assembly

(2009) Keren Lasker et al.   JOURNAL OF MOLECULAR BIOLOGY

Edgetic perturbation models of human inherited disorders

(2009) Quan Zhong et al.   Molecular Systems Biology

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

(2009) David A. Barbie et al.   NATURE

'Edgetic' perturbation of a C. elegans BCL2 ortholog

(2009) Matija Dreze et al.   NATURE METHODS

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

(2009) Prateek Kumar et al.   Nature Protocols

An acetylated form of histone H2A.Z regulates chromosome architecture in Schizosaccharomyces pombe

(2009) Hyun-Soo Kim et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

DRYGIN: a database of quantitative genetic interaction networks in yeast

(2009) Judice L. Y. Koh et al.   NUCLEIC ACIDS RESEARCH

Structural domain-domain interactions: Assessment and comparison with protein-protein interaction data to improve the interactome

(2009) C. Prieto et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Scale-Free Networks: A Decade and Beyond

(2009) Albert-László Barabási   SCIENCE

Mutant p53 Gain-of-Function in Cancer

(2009) M. Oren et al.   Cold Spring Harbor Perspectives in Biology

Global Functional Atlas of Escherichia coli Encompassing Previously Uncharacterized Proteins

(2009) Pingzhao Hu et al.   PLOS BIOLOGY

Integrating Diverse Data for Structure Determination of Macromolecular Assemblies

(2008) Frank Alber et al.   Annual Review of Biochemistry

A Protein Domain-Based Interactome Network for C. elegans Early Embryogenesis

(2008) Mike Boxem et al.   CELL

Probing Nucleosome Function: A Highly Versatile Library of Synthetic Histone H3 and H4 Mutants

(2008) Junbiao Dai et al.   CELL

Challenges and Rewards of Interaction Proteomics

(2008) Shoshana J. Wodak et al.   MOLECULAR & CELLULAR PROTEOMICS

Tumour maintenance is mediated by eNOS

(2008) Kian-Huat Lim et al.   NATURE

A comprehensive strategy enabling high-resolution functional analysis of the yeast genome

(2008) David K Breslow et al.   NATURE METHODS

Empirically controlled mapping of the Caenorhabditis elegans protein-protein interactome network

(2008) Nicolas Simonis et al.   NATURE METHODS

eSGA: E. coli synthetic genetic array analysis

(2008) Gareth Butland et al.   NATURE METHODS

High-throughput, quantitative analyses of genetic interactions in E. coli

(2008) Athanasios Typas et al.   NATURE METHODS

Literature-curated protein interaction datasets

(2008) Michael E Cusick et al.   NATURE METHODS

Epistasis — the essential role of gene interactions in the structure and evolution of genetic systems

(2008) Patrick C. Phillips   NATURE REVIEWS GENETICS

Modelling and analysis of gene regulatory networks

(2008) Guy Karlebach et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

A comprehensive library of histone mutants identifies nucleosomal residues required for H3K4 methylation

(2008) Shima Nakanishi et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Significant conservation of synthetic lethal genetic interaction networks between distantly related eukaryotes

(2008) S. J. Dixon et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

High-Quality Binary Protein Interaction Map of the Yeast Interactome Network

(2008) H. Yu et al.   SCIENCE

Phosphorylation Networks Regulating JNK Activity in Diverse Genetic Backgrounds

(2008) C. Bakal et al.   SCIENCE

The Chemical Genomic Portrait of Yeast: Uncovering a Phenotype for All Genes

(2008) M. E. Hillenmeyer et al.   SCIENCE

Conservation and Rewiring of Functional Modules Revealed by an Epistasis Map in Fission Yeast

(2008) A. Roguev et al.   SCIENCE

An in Vivo Map of the Yeast Protein Interactome

(2008) K. Tarassov et al.   SCIENCE

Functional Maps of Protein Complexes from Quantitative Genetic Interaction Data

(2008) Sourav Bandyopadhyay et al.   PLoS Computational Biology

Protein interactions in human genetic diseases

(2008) Benjamin Schuster-Böckler et al.   GENOME BIOLOGY