Dual proteome-scale networks reveal cell-specific remodeling of the human interactome

Quantitative Proteomics of the Cancer Cell Line Encyclopedia

(2020) David P. Nusinow et al.   CELL

A reference map of the human binary protein interactome

(2020) Katja Luck et al.   NATURE

CryoEM structures of human CMG–ATPγS–DNA and CMG–AND-1 complexes

(2020) Neil J Rzechorzek et al.   NUCLEIC ACIDS RESEARCH

TGF-β Signaling

(2020) Kalliopi Tzavlaki et al.   Biomolecules

SECAT: Quantifying Protein Complex Dynamics across Cell States by Network-Centric Analysis of SEC-SWATH-MS Profiles

(2020) George Rosenberger et al.   Cell Systems

Active instrument engagement combined with a real-time database search for improved performance of sample multiplexing workflows

(2019) Brian K Erickson et al.   JOURNAL OF PROTEOME RESEARCH

SubCellBarCode: Proteome-wide Mapping of Protein Localization and Relocalization

(2019) Lukas Minus Orre et al.   MOLECULAR CELL

Complex‐centric proteome profiling by SEC‐SWATH‐MS

(2019) Moritz Heusel et al.   Molecular Systems Biology

The multiple mechanisms that regulate p53 activity and cell fate

(2019) Antonina Hafner et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

A deep proteome and transcriptome abundance atlas of 29 healthy human tissues

(2019) Dongxue Wang et al.   Molecular Systems Biology

Disentangling Genetic and Environmental Effects on the Proteotypes of Individuals

(2019) Natalie Romanov et al.   CELL

The complete structure of the human TFIIH core complex

(2019) Basil J Greber et al.   eLife

Streamlined Tandem Mass Tag (SL-TMT) Protocol: An Efficient Strategy for Quantitative (Phospho)proteome Profiling Using Tandem Mass Tag-Synchronous Precursor Selection-MS3

(2018) José Navarrete-Perea et al.   JOURNAL OF PROTEOME RESEARCH

High-Density Proximity Mapping Reveals the Subcellular Organization of mRNA-Associated Granules and Bodies

(2018) Ji-Young Youn et al.   MOLECULAR CELL

GeneMANIA update 2018

(2018) Max Franz et al.   NUCLEIC ACIDS RESEARCH

Interrogation of Mammalian Protein Complex Structure, Function, and Membership Using Genome-Scale Fitness Screens

(2018) Joshua Pan et al.   Cell Systems

Context-specific interactions in literature-curated protein interaction databases

(2018) R. Greg Stacey et al.   BMC GENOMICS

Cryo-EM Structure of the Human Ribonuclease P Holoenzyme

(2018) Jian Wu et al.   CELL

High‐resolution mapping of cancer cell networks using co‐functional interactions

(2018) Evan A Boyle et al.   Molecular Systems Biology

CORUM: the comprehensive resource of mammalian protein complexes—2019

(2018) Madalina Giurgiu et al.   NUCLEIC ACIDS RESEARCH

The BioGRID interaction database: 2019 update

(2018) Rose Oughtred et al.   NUCLEIC ACIDS RESEARCH

SIFTS: updated Structure Integration with Function, Taxonomy and Sequences resource allows 40-fold increase in coverage of structure-based annotations for proteins

(2018) Jose M Dana et al.   NUCLEIC ACIDS RESEARCH

The Pfam protein families database in 2019

(2018) Sara El-Gebali et al.   NUCLEIC ACIDS RESEARCH

Glucose deprivation induces primary cilium formation through mTORC1 inactivation

(2017) Kengo Takahashi et al.   JOURNAL OF CELL SCIENCE

A Compendium of RNA-Binding Proteins that Regulate MicroRNA Biogenesis

(2017) Thomas Treiber et al.   MOLECULAR CELL

Integration of over 9,000 mass spectrometry experiments builds a global map of human protein complexes

(2017) Kevin Drew et al.   Molecular Systems Biology

Architecture of the human interactome defines protein communities and disease networks

(2017) Edward L. Huttlin et al.   NATURE

Computational correction of copy number effect improves specificity of CRISPR–Cas9 essentiality screens in cancer cells

(2017) Robin M Meyers et al.   NATURE GENETICS

The Reactome Pathway Knowledgebase

(2017) Antonio Fabregat et al.   NUCLEIC ACIDS RESEARCH

SAMTOR is anS-adenosylmethionine sensor for the mTORC1 pathway

(2017) Xin Gu et al.   SCIENCE

A subcellular map of the human proteome

(2017) Peter J. Thul et al.   SCIENCE

A Compendium of Co-regulated Protein Complexes in Breast Cancer Reveals Collateral Loss Events

(2017) Colm J. Ryan et al.   Cell Systems

The CASTOR Proteins Are Arginine Sensors for the mTORC1 Pathway

(2016) Lynne Chantranupong et al.   CELL

Towards Consensus Gene Ages

(2016) Benjamin J. Liebeskind et al.   Genome Biology and Evolution

A Triple Knockout (TKO) Proteomics Standard for Diagnosing Ion Interference in Isobaric Labeling Experiments

(2016) Joao A. Paulo et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

Mechanisms of ephrin–Eph signalling in development, physiology and disease

(2016) Artur Kania et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Integration of TP53, DREAM, MMB-FOXM1 and RB-E2F target gene analyses identifies cell cycle gene regulatory networks

(2016) Martin Fischer et al.   NUCLEIC ACIDS RESEARCH

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

(2016) Janet Piñero et al.   NUCLEIC ACIDS RESEARCH

The STRING database in 2017: quality-controlled protein–protein association networks, made broadly accessible

(2016) Damian Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

An organelle-specific protein landscape identifies novel diseases and molecular mechanisms

(2016) Karsten Boldt et al.   Nature Communications

A Dynamic Protein Interaction Landscape of the Human Centrosome-Cilium Interface

(2015) Gagan D. Gupta et al.   CELL

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

(2015) Marco Y. Hein et al.   CELL

The BioPlex Network: A Systematic Exploration of the Human Interactome

(2015) Edward L. Huttlin et al.   CELL

HEK293 in cell biology and cancer research: phenotype, karyotype, tumorigenicity, and stress-induced genome-phenotype evolution

(2015) A.A. Stepanenko et al.   GENE

Cell-fate determination by ubiquitin-dependent regulation of translation

(2015) Achim Werner et al.   NATURE

Panorama of ancient metazoan macromolecular complexes

(2015) Cuihong Wan et al.   NATURE

Gene essentiality and synthetic lethality in haploid human cells

(2015) V. A. Blomen et al.   SCIENCE

Identification and characterization of essential genes in the human genome

(2015) T. Wang et al.   SCIENCE

NDEx, the Network Data Exchange

(2015) Dexter Pratt et al.   Cell Systems

MultiNotch MS3 Enables Accurate, Sensitive, and Multiplexed Detection of Differential Expression across Cancer Cell Line Proteomes

(2014) Graeme C. McAlister et al.   ANALYTICAL CHEMISTRY

A Proteome-Scale Map of the Human Interactome Network

(2014) Thomas Rolland et al.   CELL

UniProt: a hub for protein information

(2014)   NUCLEIC ACIDS RESEARCH

ABRO1 suppresses tumourigenesis and regulates the DNA damage response by stabilizing p53

(2014) Jianhong Zhang et al.   Nature Communications

Interlaboratory reproducibility of large-scale human protein-complex analysis by standardized AP-MS

(2013) Markku Varjosalo et al.   NATURE METHODS

Cancer Genome Landscapes

(2013) B. Vogelstein et al.   SCIENCE

Epigenetic and genetic features of 24 colon cancer cell lines

(2013) D Ahmed et al.   Oncogenesis

The large tumor antigen: A “Swiss Army knife” protein possessing the functions required for the polyomavirus life cycle

(2012) D. Topalis et al.   ANTIVIRAL RESEARCH

A Census of Human Soluble Protein Complexes

(2012) Pierre C. Havugimana et al.   CELL

Fiji: an open-source platform for biological-image analysis

(2012) Johannes Schindelin et al.   NATURE METHODS

Comet: An open-source MS/MS sequence database search tool

(2012) Jimmy K. Eng et al.   PROTEOMICS

A Protein Complex Network of Drosophila melanogaster

(2011) K.G. Guruharsha et al.   CELL

MS3 eliminates ratio distortion in isobaric multiplexed quantitative proteomics

(2011) Lily Ting et al.   NATURE METHODS

A public genome-scale lentiviral expression library of human ORFs

(2011) Xiaoping Yang et al.   NATURE METHODS

A Tissue-Specific Atlas of Mouse Protein Phosphorylation and Expression

(2010) Edward L. Huttlin et al.   CELL

Functional organization of the Sm core in the crystal structure of human U1 snRNP

(2010) Gert Weber et al.   EMBO JOURNAL

Network organization of the human autophagy system

(2010) Christian Behrends et al.   NATURE

Defining the Human Deubiquitinating Enzyme Interaction Landscape

(2009) Mathew E. Sowa et al.   CELL

TGF-β-induced epithelial to mesenchymal transition

(2009) Jian Xu et al.   CELL RESEARCH

Loss of Nephrocystin-3 Function Can Cause Embryonic Lethality, Meckel-Gruber-like Syndrome, Situs Inversus, and Renal-Hepatic-Pancreatic Dysplasia

(2008) Carsten Bergmann et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Polyglutamylation: a fine-regulator of protein function? ‘Protein Modifications: Beyond the Usual Suspects’ Review Series

(2008) Carsten Janke et al.   EMBO REPORTS