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

SciPy 1.0: fundamental algorithms for scientific computing in Python

(2020) Pauli Virtanen et al.   NATURE METHODS

A Global Screen for Assembly State Changes of the Mitotic Proteome by SEC-SWATH-MS

(2020) Moritz Heusel et al.   Cell Systems

A reference map of the human binary protein interactome

(2020) Katja Luck et al.   NATURE

Complex‐centric proteome profiling by SEC‐SWATH‐MS

(2019) Moritz Heusel et al.   Molecular Systems Biology

EPIC: software toolkit for elution profile-based inference of protein complexes

(2019) Lucas ZhongMing Hu et al.   NATURE METHODS

Structural insights into the functional diversity of the CDK–cyclin family

(2018) Daniel J. Wood et al.   Open Biology

CORUM: the comprehensive resource of mammalian protein complexes—2019

(2018) Madalina Giurgiu et al.   NUCLEIC ACIDS RESEARCH

IID 2018 update: context-specific physical protein–protein interactions in human, model organisms and domesticated species

(2018) Max Kotlyar et al.   NUCLEIC ACIDS RESEARCH

STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets

(2018) Damian Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

The BioGRID interaction database: 2019 update

(2018) Rose Oughtred et al.   NUCLEIC ACIDS RESEARCH

Interactome disassembly during apoptosis occurs independent of caspase cleavage

(2017) Nichollas E Scott et al.   Molecular Systems Biology

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

Statistical control of peptide and protein error rates in large-scale targeted data-independent acquisition analyses

(2017) George Rosenberger et al.   NATURE METHODS

Combining dependentP-values with an empirical adaptation of Brown’s method

(2016) William Poole et al.   BIOINFORMATICS

ARACNe-AP: gene network reverse engineering through adaptive partitioning inference of mutual information

(2016) Alexander Lachmann et al.   BIOINFORMATICS

Mass-spectrometric exploration of proteome structure and function

(2016) Ruedi Aebersold et al.   NATURE

Functional characterization of somatic mutations in cancer using network-based inference of protein activity

(2016) Mariano J Alvarez et al.   NATURE GENETICS

A computational interactome and functional annotation for the human proteome

(2016) José Ignacio Garzón et al.   eLife

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

Development of a computational framework for the analysis of protein correlation profiling and spatial proteomics experiments

(2015) Nichollas E. Scott et al.   Journal of Proteomics

Peptide-Centric Proteome Analysis: An Alternative Strategy for the Analysis of Tandem Mass Spectrometry Data

(2015) Ying S. Ting et al.   MOLECULAR & CELLULAR PROTEOMICS

Panorama of ancient metazoan macromolecular complexes

(2015) Cuihong Wan et al.   NATURE

xTract: software for characterizing conformational changes of protein complexes by quantitative cross-linking mass spectrometry

(2015) Thomas Walzthoeni et al.   NATURE METHODS

Distinct domains in Bub1 localize RZZ and BubR1 to kinetochores to regulate the checkpoint

(2015) Gang Zhang et al.   Nature Communications

aLFQ: an R-package for estimating absolute protein quantities from label-free LC-MS/MS proteomics data

(2014) George Rosenberger et al.   BIOINFORMATICS

DIANA—algorithmic improvements for analysis of data-independent acquisition MS data

(2014) Johan Teleman et al.   BIOINFORMATICS

Accurate Protein Complex Retrieval by Affinity Enrichment Mass Spectrometry (AE-MS) Rather than Affinity Purification Mass Spectrometry (AP-MS)

(2014) Eva C. Keilhauer et al.   MOLECULAR & CELLULAR PROTEOMICS

OpenSWATH enables automated, targeted analysis of data-independent acquisition MS data

(2014) Hannes L Röst et al.   NATURE BIOTECHNOLOGY

Statistical power and significance testing in large-scale genetic studies

(2014) Pak C. Sham et al.   NATURE REVIEWS GENETICS

The function of spliceosome components in open mitosis

(2014) Jennifer C. Hofmann et al.   Nucleus

Characterization of Native Protein Complexes and Protein Isoform Variation Using Size-fractionation-based Quantitative Proteomics

(2013) Kathryn J. Kirkwood et al.   MOLECULAR & CELLULAR PROTEOMICS

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

(2013) Markku Varjosalo et al.   NATURE METHODS

Quantifying protein interaction dynamics by SWATH mass spectrometry: application to the 14-3-3 system

(2013) Ben C Collins et al.   NATURE METHODS

Mapping differential interactomes by affinity purification coupled with data-independent mass spectrometry acquisition

(2013) Jean-Philippe Lambert et al.   NATURE METHODS

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

(2013) Sandra Orchard et al.   NUCLEIC ACIDS RESEARCH

Critical assessment of proteome-wide label-free absolute abundance estimation strategies

(2013) Erik Ahrné et al.   PROTEOMICS

minerva and minepy: a C engine for the MINE suite and its R, Python and MATLAB wrappers

(2012) Davide Albanese et al.   BIOINFORMATICS

A Census of Human Soluble Protein Complexes

(2012) Pierre C. Havugimana et al.   CELL

ComplexQuant: High-throughput computational pipeline for the global quantitative analysis of endogenous soluble protein complexes using high resolution protein HPLC and precision label-free LC/MS/MS

(2012) Cuihong Wan et al.   Journal of Proteomics

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

(2012) Qiangfeng Cliff Zhang et al.   NATURE

A high-throughput approach for measuring temporal changes in the interactome

(2012) Anders R Kristensen et al.   NATURE METHODS

Proteomics meets the scientific method

(2012) Paola Picotti et al.   NATURE METHODS

PrePPI: a structure-informed database of protein–protein interactions

(2012) Qiangfeng Cliff Zhang et al.   NUCLEIC ACIDS RESEARCH

Structural Probing of a Protein Phosphatase 2A Network by Chemical Cross-Linking and Mass Spectrometry

(2012) F. Herzog et al.   SCIENCE

Selected reaction monitoring mass spectrometry reveals the dynamics of signaling through the GRB2 adaptor

(2011) Nicolas Bisson et al.   NATURE BIOTECHNOLOGY

mProphet: automated data processing and statistical validation for large-scale SRM experiments

(2011) Lukas Reiter et al.   NATURE METHODS

Progressive Activation of CyclinB1-Cdk1 Coordinates Entry to Mitosis

(2010) Olivier Gavet et al.   DEVELOPMENTAL CELL

Phenotypic profiling of the human genome by time-lapse microscopy reveals cell division genes

(2010) Beate Neumann et al.   NATURE

Options and considerations when selecting a quantitative proteomics strategy

(2010) Bruno Domon et al.   NATURE BIOTECHNOLOGY

SAINT: probabilistic scoring of affinity purification–mass spectrometry data

(2010) Hyungwon Choi et al.   NATURE METHODS

Spliceosome Structure and Function

(2010) C. L. Will et al.   Cold Spring Harbor Perspectives in Biology

Defining the Human Deubiquitinating Enzyme Interaction Landscape

(2009) Mathew E. Sowa et al.   CELL