Protein complex analysis: From raw protein lists to protein interaction networks (Q38681085)

5 September 2017

title

Protein complex analysis: From raw protein lists to protein interaction networks (English)

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5 September 2017

1

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5 September 2017

Kevin Titeca

2

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Bart Goethals

object named as

Bart Goethals

5

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Kris Laukens

object named as

Kris Laukens

8

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Lennart Martens

6

object named as

Lennart Martens

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5 September 2017

Sven Eyckerman

3

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5 September 2017

Jan Tavernier

4

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5 September 2017

Dirk Valkenborg

7

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5 September 2017

publication date

28 December 2015

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Mass Spectrometry Reviews

5 September 2017

published in

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5 September 2017

volume

36

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5 September 2017

issue

5

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5 September 2017

page(s)

600-614

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InterPreTS: protein interaction prediction through tertiary structure.

5 September 2017

cites work

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Kernel methods for predicting protein-protein interactions

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iMonDB: Mass Spectrometry Quality Control through Instrument Monitoring

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Predicting protein--protein interactions from primary structure

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An experimentally derived confidence score for binary protein-protein interactions

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NAViGaTOR: Network Analysis, Visualization and Graphing Toronto

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Interaction network containing conserved and essential protein complexes in Escherichia coli

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The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases

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Prediction of protein-protein interactions using random decision forest framework

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Predicting and validating protein interactions using network structure

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Analysis of protein complexes through model-based biclustering of label-free quantitative AP-MS data

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21 January 2018

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A review on models and algorithms for motif discovery in protein-protein interaction networks

21 January 2018

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High-resolution mapping of the protein interaction network for the human transcription machinery and affinity purification of RNA polymerase II-associated complexes

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Mapping multiprotein complexes by affinity purification and mass spectrometry

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Toward a comprehensive atlas of the physical interactome of Saccharomyces cerevisiae

21 January 2018

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

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ClusPro: an automated docking and discrimination method for the prediction of protein complexes

21 January 2018

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Protein interaction network of the mammalian Hippo pathway reveals mechanisms of kinase-phosphatase interactions

21 January 2018

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MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification

21 January 2018

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Conservation of gene order: a fingerprint of proteins that physically interact

21 January 2018

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Prediction of kinase-specific phosphorylation sites using conditional random fields

21 January 2018

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Topology-function conservation in protein-protein interaction networks

21 January 2018

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Protein interactions: two methods for assessment of the reliability of high throughput observations

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Affinity-purification coupled to mass spectrometry: basic principles and strategies

21 January 2018

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An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database

21 January 2018

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An efficient algorithm for large-scale detection of protein families

21 January 2018

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A comparative analysis of biclustering algorithms for gene expression data

21 January 2018

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Large-scale mapping of human protein-protein interactions by mass spectrometry

21 January 2018

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Design and application of a cytokine-receptor-based interaction trap

21 January 2018

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LuciPHOr2: site localization of generic post-translational modifications from tandem mass spectrometry data.

21 January 2018

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Targeted tandem affinity purification of PSD-95 recovers core postsynaptic complexes and schizophrenia susceptibility proteins

21 January 2018

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X-ray structure of a bifunctional protein kinase in complex with its protein substrate HPr

21 January 2018

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STRING v9.1: protein-protein interaction networks, with increased coverage and integration

21 January 2018

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Functional and evolutionary implications of gene orthology.

21 January 2018

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Expanded microbial genome coverage and improved protein family annotation in the COG database

21 January 2018

1 reference

Proteome survey reveals modularity of the yeast cell machinery

21 January 2018

1 reference

Recent advances in charting protein-protein interaction: mass spectrometry-based approaches

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Correlation between transcriptome and interactome mapping data from Saccharomyces cerevisiae

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Visualization of omics data for systems biology

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The transience of transient overexpression

21 January 2018

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Targeted data extraction of the MS/MS spectra generated by data-independent acquisition: a new concept for consistent and accurate proteome analysis

21 January 2018

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Analysis of protein complexes using mass spectrometry

21 January 2018

1 reference

An integrated workflow for charting the human interaction proteome: insights into the PP2A system

21 January 2018

1 reference

Co-evolution of proteins with their interaction partners

21 January 2018

1 reference

Assessing experimentally derived interactions in a small world

21 January 2018

1 reference

BioLayout(Java): versatile network visualisation of structural and functional relationships

21 January 2018

1 reference

Learning to predict protein-protein interactions from protein sequences

21 January 2018

1 reference

Phospho-tyrosine dependent protein-protein interaction network

21 January 2018

1 reference

Using support vector machine combined with auto covariance to predict protein-protein interactions from protein sequences

21 January 2018

1 reference

PRED_PPI: a server for predicting protein-protein interactions based on sequence data with probability assignment

21 January 2018

1 reference

A protein complex network of Drosophila melanogaster

21 January 2018

1 reference

A high-accuracy consensus map of yeast protein complexes reveals modular nature of gene essentiality.

21 January 2018

1 reference

A census of human soluble protein complexes

21 January 2018

1 reference

Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry

21 January 2018

1 reference

Genevestigator v3: a reference expression database for the meta-analysis of transcriptomes

21 January 2018

1 reference

VisANT 3.5: multi-scale network visualization, analysis and inference based on the gene ontology.

21 January 2018

1 reference

Search strategies and evaluation in protein-protein docking: principles, advances and challenges

21 January 2018

1 reference

Extracting gene function from protein-protein interactions using Quantitative BAC InteraCtomics (QUBIC).

21 January 2018

1 reference

Large-scale prediction of protein-protein interactions from structures

21 January 2018

1 reference

The BioPlex Network: A Systematic Exploration of the Human Interactome

21 January 2018

1 reference

Predicting protein function by genomic context: quantitative evaluation and qualitative inferences

21 January 2018

1 reference

Genome-wide studies of protein-protein interaction

21 January 2018

1 reference

Relating whole-genome expression data with protein-protein interactions

21 January 2018

1 reference

A Bayesian Networks Approach for Predicting Protein-Protein Interactions from Genomic Data

21 January 2018

1 reference

High-confidence prediction of global interactomes based on genome-wide coevolutionary networks

21 January 2018

1 reference

Proteome organization in a genome-reduced bacterium

21 January 2018

1 reference

KEGG for integration and interpretation of large-scale molecular data sets

21 January 2018

1 reference

The IntAct molecular interaction database in 2012

21 January 2018

1 reference

In silico prediction of physical protein interactions and characterization of interactome orphans

21 January 2018

1 reference

The RCSB PDB information portal for structural genomics

21 January 2018

1 reference

How good is automated protein docking?

21 January 2018

1 reference

Computational methods for Gene Orthology inference

21 January 2018

1 reference

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

21 January 2018

1 reference

ProCope--protein complex prediction and evaluation

21 January 2018

1 reference

RNA-Seq Atlas--a reference database for gene expression profiling in normal tissue by next-generation sequencing.

21 January 2018

1 reference

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

21 January 2018

1 reference

Bioinformatics approaches for the functional interpretation of protein lists: from ontology term enrichment to network analysis

21 January 2018

1 reference

Modeling contaminants in AP-MS/MS experiments

21 January 2018

1 reference

Docking, scoring, and affinity prediction in CAPRI.

21 January 2018

1 reference

OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes

21 January 2018

1 reference

Mammalian two-hybrids come of age.

21 January 2018

1 reference

Heterogeneous data integration by tree-augmented naïve Bayes for protein-protein interactions prediction

21 January 2018

1 reference

Analysis of the human endogenous coregulator complexome.

21 January 2018

1 reference

A combined algorithm for genome-wide prediction of protein function

21 January 2018

1 reference

Predicting protein-protein interactions using signature products

21 January 2018

1 reference

Identification of potential interaction networks using sequence-based searches for conserved protein-protein interactions or "interologs".

21 January 2018

1 reference

The CRAPome: a contaminant repository for affinity purification-mass spectrometry data

21 January 2018

1 reference

Next challenges in protein-protein docking: from proteome to interactome and beyond

21 January 2018

1 reference

COLOMBOS v2.0: an ever expanding collection of bacterial expression compendia

21 January 2018

1 reference

InteroPORC: automated inference of highly conserved protein interaction networks

21 January 2018

1 reference

Protein complementation assays: approaches for the in vivo analysis of protein interactions

21 January 2018

1 reference

Sequence-based prediction of protein-protein interactions by means of codon usage.

21 January 2018

1 reference

A primer to frequent itemset mining for bioinformatics

21 January 2018

1 reference

Computational and informatics strategies for identification of specific protein interaction partners in affinity purification mass spectrometry experiments

21 January 2018

1 reference

Finding and evaluating community structure in networks

21 January 2018

1 reference

Structure of the alpha beta tubulin dimer by electron crystallography

21 January 2018

1 reference

Two steps forward--one step back: advances in affinity purification mass spectrometry of macromolecular complexes

21 January 2018

1 reference

Comparison of label-free methods for quantifying human proteins by shotgun proteomics.

21 January 2018

1 reference

InParanoid 7: new algorithms and tools for eukaryotic orthology analysis

21 January 2018

1 reference

Identification of protein partners in mycobacteria using a single-step affinity purification method

21 January 2018

1 reference

The MIPS mammalian protein-protein interaction database

21 January 2018

1 reference

A survey of visualization tools for biological network analysis

21 January 2018

1 reference

21 January 2018

1 reference

Assigning protein functions by comparative genome analysis: Protein phylogenetic profiles

21 January 2018

1 reference

Probability-based protein identification by searching sequence databases using mass spectrometry data

21 January 2018

1 reference

SIMPATIQCO: a server-based software suite which facilitates monitoring the time course of LC-MS performance metrics on Orbitrap instruments

21 January 2018

1 reference

ZDOCK server: interactive docking prediction of protein-protein complexes and symmetric multimers

21 January 2018

1 reference

PIPE: a protein-protein interaction prediction engine based on the re-occurring short polypeptide sequences between known interacting protein pairs

21 January 2018

1 reference

eggNOG v4.0: nested orthology inference across 3686 organisms

21 January 2018

1 reference

Modeling interactome: scale-free or geometric?

21 January 2018

1 reference

Extracting high confidence protein interactions from affinity purification data: at the crossroads

21 January 2018

1 reference

The Pfam protein families database

21 January 2018

1 reference

iRefIndex: a consolidated protein interaction database with provenance

21 January 2018

1 reference

A proteome-scale map of the human interactome network

21 January 2018

1 reference

A promiscuous biotin ligase fusion protein identifies proximal and interacting proteins in mammalian cells

21 January 2018

1 reference

Performance metrics for liquid chromatography-tandem mass spectrometry systems in proteomics analyses

21 January 2018

1 reference

A structural perspective on protein-protein interactions.

21 January 2018

1 reference

ArrayExpress update--trends in database growth and links to data analysis tools

21 January 2018

1 reference

Probabilistic assembly of human protein interaction networks from label-free quantitative proteomics

21 January 2018

1 reference

Protein interaction screening by quantitative immunoprecipitation combined with knockdown (QUICK).

21 January 2018

1 reference

Escherichia coli σ⁷⁰ senses sequence and conformation of the promoter spacer region

21 January 2018

1 reference

Label-free quantitative proteomics and SAINT analysis enable interactome mapping for the human Ser/Thr protein phosphatase 5

21 January 2018

1 reference

The Negatome database: a reference set of non-interacting protein pairs

21 January 2018

1 reference

Prediction of protein-protein interactions by docking methods.

21 January 2018

1 reference

Stoichiometry of chromatin-associated protein complexes revealed by label-free quantitative mass spectrometry-based proteomics

21 January 2018

1 reference

Cytoscape 2.8: new features for data integration and network visualization

21 January 2018

1 reference

Defining the human deubiquitinating enzyme interaction landscape

21 January 2018

1 reference

21 January 2018

1 reference

OpenMS - an open-source software framework for mass spectrometry

21 January 2018

1 reference

A gene atlas of the mouse and human protein-encoding transcriptomes

21 January 2018

1 reference

Tools for visually exploring biological networks.

21 January 2018

1 reference

Two-hybrid technologies in proteomics research

21 January 2018

1 reference

Conserved clusters of functionally related genes in two bacterial genomes.

21 January 2018

1 reference

An in vivo map of the yeast protein interactome

21 January 2018

1 reference

SAINTexpress: improvements and additional features in Significance Analysis of INTeractome software

21 January 2018

1 reference

Structural basis of protein phosphatase 1 regulation

21 January 2018

1 reference

SFINX: Straightforward Filtering Index for Affinity Purification-Mass Spectrometry Data Analysis

21 January 2018

1 reference

SwarmDock: a server for flexible protein-protein docking.

21 January 2018

1 reference

DIA-Umpire: comprehensive computational framework for data-independent acquisition proteomics

21 January 2018

1 reference

Towards a knowledge-based Human Protein Atlas

21 January 2018

1 reference

Information-driven protein-DNA docking using HADDOCK: it is a matter of flexibility

21 January 2018

1 reference

Targeted interactomics reveals a complex core cell cycle machinery in Arabidopsis thaliana

21 January 2018

1 reference

Quantitative dissection and stoichiometry determination of the human SET1/MLL histone methyltransferase complexes

21 January 2018

1 reference

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

21 January 2018

1 reference

PeptideShaker enables reanalysis of MS-derived proteomics data sets.

21 January 2018

1 reference

qcML: an exchange format for quality control metrics from mass spectrometry experiments

21 January 2018

1 reference

Mass spectrometry supported determination of protein complex structure

21 January 2018

1 reference

Alternative isoform regulation in human tissue transcriptomes

21 January 2018

1 reference

Towards the prediction of protein interaction partners using physical docking

21 January 2018

1 reference

TRANSFAC: a database on transcription factors and their DNA binding sites

21 January 2018

1 reference

Topology and weights in a protein domain interaction network--a novel way to predict protein interactions

21 January 2018

1 reference

Sequence-based prediction of protein-protein interactions by means of rotation forest and autocorrelation descriptor.

21 January 2018

1 reference

GPS 2.0, a tool to predict kinase-specific phosphorylation sites in hierarchy

21 January 2018

1 reference

Network motifs in integrated cellular networks of transcription-regulation and protein-protein interaction

21 January 2018

1 reference

Predicting interactions in protein networks by completing defective cliques.

21 January 2018

1 reference

DroID: the Drosophila Interactions Database, a comprehensive resource for annotated gene and protein interactions

21 January 2018

1 reference

Predicting protein-protein interactions in unbalanced data using the primary structure of proteins

21 January 2018

1 reference

From pull-down data to protein interaction networks and complexes with biological relevance

21 January 2018

1 reference

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

21 January 2018

1 reference

Bridging structural biology and genomics: assessing protein interaction data with known complexes

21 January 2018

1 reference

The 4th meeting on the Critical Assessment of Predicted Interaction (CAPRI) held at the Mare Nostrum, Barcelona

21 January 2018

1 reference

Probabilistic model of the human protein-protein interaction network

21 January 2018

1 reference

21 January 2018

Identifiers

DOI

10.1002/MAS.21485

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5 September 2017

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