The Perseus computational platform for comprehensive analysis of (prote)omics data (Q31110953)

28 June 2017

title

The Perseus computational platform for comprehensive analysis of (prote)omics data (English)

1 reference

28 June 2017

Pavel Sinitcyn

0 references

Marco Y Hein

0 references

Jürgen Cox

1 reference

28 June 2017

Matthias Mann

1 reference

28 June 2017

Stefka Tyanova

1 reference

28 June 2017

Tikira Temu

series ordinal

1 reference

28 June 2017

Arthur Carlson

series ordinal

1 reference

28 June 2017

Tamar Geiger

series ordinal

1 reference

28 June 2017

publication date

27 June 2016

1 reference

28 June 2017

1 reference

28 June 2017

1 reference

28 June 2017

1 reference

28 June 2017

page(s)

731-740

1 reference

Next-generation proteomics: towards an integrative view of proteome dynamics.

28 June 2017

cites work

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3901

7 January 2021

Quantitative, high-resolution proteomics for data-driven systems biology

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3901

7 January 2021

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

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3901

7 January 2021

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

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3901

7 January 2021

Open mass spectrometry search algorithm

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3901

7 January 2021

TANDEM: matching proteins with tandem mass spectra

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3901

7 January 2021

Lookup peaks: a hybrid of de novo sequencing and database search for protein identification by tandem mass spectrometry

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3901

7 January 2021

Open source system for analyzing, validating, and storing protein identification data

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3901

7 January 2021

Analysis and validation of proteomic data generated by tandem mass spectrometry

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3901

7 January 2021

Trans-Proteomic Pipeline, a standardized data processing pipeline for large-scale reproducible proteomics informatics

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3901

7 January 2021

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

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3901

7 January 2021

The PRoteomics IDEntifications (PRIDE) database and associated tools: status in 2013

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3901

7 January 2021

ProteomeXchange provides globally coordinated proteomics data submission and dissemination

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3901

7 January 2021

Comprehensive mass-spectrometry-based proteome quantification of haploid versus diploid yeast

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3901

7 January 2021

The one hour yeast proteome

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3901

7 January 2021

Deep proteome and transcriptome mapping of a human cancer cell line

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3901

7 January 2021

The quantitative proteome of a human cell line.

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3901

7 January 2021

The quantitative proteomes of human-induced pluripotent stem cells and embryonic stem cells

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3901

7 January 2021

The coming age of complete, accurate, and ubiquitous proteomes

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3901

7 January 2021

A "proteomic ruler" for protein copy number and concentration estimation without spike-in standards.

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3901

7 January 2021

Accurate proteome-wide label-free quantification by delayed normalization and maximal peptide ratio extraction, termed MaxLFQ.

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3901

7 January 2021

Super-SILAC mix for quantitative proteomics of human tumor tissue

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3901

7 January 2021

Significance analysis of microarrays applied to the ionizing radiation response

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3901

7 January 2021

Singular value decomposition for genome-wide expression data processing and modeling

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3901

7 January 2021

Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3901

7 January 2021

Orchestrating high-throughput genomic analysis with Bioconductor

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3901

7 January 2021

A probability-based approach for high-throughput protein phosphorylation analysis and site localization

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3901

7 January 2021

Andromeda: a peptide search engine integrated into the MaxQuant environment

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3901

7 January 2021

Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3901

7 January 2021

Ultradeep human phosphoproteome reveals a distinct regulatory nature of Tyr and Ser/Thr-based signaling

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3901

7 January 2021

Gene Ontology Consortium: going forward

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3901

7 January 2021

PhosphoSitePlus, 2014: mutations, PTMs and recalibrations

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3901

7 January 2021

Phosphorylation variation during the cell cycle scales with structural propensities of proteins

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3901

7 January 2021

A human interactome in three quantitative dimensions organized by stoichiometries and abundances

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3901

7 January 2021

The BioPlex Network: A Systematic Exploration of the Human Interactome

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3901

7 January 2021

Quantitative proteomics combined with BAC TransgeneOmics reveals in vivo protein interactions

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3901

7 January 2021

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

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3901

7 January 2021

Accurate protein complex retrieval by affinity enrichment mass spectrometry (AE-MS) rather than affinity purification mass spectrometry (AP-MS).

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3901

7 January 2021

Cytoscape: a software environment for integrated models of biomolecular interaction networks

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3901

7 January 2021

DNA repair. Proteomics reveals dynamic assembly of repair complexes during bypass of DNA cross-links

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3901

7 January 2021

Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3901

7 January 2021

Cyclebase.org a comprehensive multi-organism online database of cell-cycle experiments

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3901

7 January 2021

Periodic mRNA synthesis and degradation co-operate during cell cycle gene expression

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3901

7 January 2021

Molecular architecture of the mammalian circadian clock

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3901

7 January 2021

In-vivo quantitative proteomics reveals a key contribution of post-transcriptional mechanisms to the circadian regulation of liver metabolism.

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3901

7 January 2021

RNA-Seq: a revolutionary tool for transcriptomics

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3901

7 January 2021

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3901

7 January 2021

STAR: ultrafast universal RNA-seq aligner

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3901

7 January 2021

Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3901

7 January 2021

Mapping and quantifying mammalian transcriptomes by RNA-Seq

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3901

7 January 2021

Global quantification of mammalian gene expression control

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3901

7 January 2021

Uncovering Hidden Layers of Cell Cycle Regulation through Integrative Multi-omic Analysis

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3901

7 January 2021

https://api.crossref.org/works/10.1038%2FNMETH.3901

1 reference

7 January 2021

1D and 2D annotation enrichment: a statistical method integrating quantitative proteomics with complementary high-throughput data

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3901

7 January 2021

Machine Learning-based Classification of Diffuse Large B-cell Lymphoma Patients by Their Protein Expression Profiles

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3901

7 January 2021

The Proteome of Primary Prostate Cancer

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3901

7 January 2021

Proteomic maps of breast cancer subtypes

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3901

7 January 2021

https://api.crossref.org/works/10.1038%2FNMETH.3901

1 reference

7 January 2021

A general framework for weighted gene co-expression network analysis

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3901

7 January 2021

Differential network biology

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3901

7 January 2021

Pathway and network analysis of cancer genomes

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3901

7 January 2021

COPASI--a COmplex PAthway SImulator

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3901

7 January 2021

Computational modeling of cellular signaling processes embedded into dynamic spatial contexts

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3901

7 January 2021

Spatial modeling of cell signaling networks

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3901

7 January 2021

The Reactome pathway knowledgebase

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3901

7 January 2021

KEGG as a reference resource for gene and protein annotation

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3901

7 January 2021

Visualization of LC-MS/MS proteomics data in MaxQuant

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3901

7 January 2021

Missing value estimation methods for DNA microarrays

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3901

7 January 2021

Missing value imputation for gene expression data: computational techniques to recover missing data from available information.

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3901

7 January 2021

UniProt: a hub for protein information

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3901

7 January 2021

A Double-Barrel Liquid Chromatography-Tandem Mass Spectrometry (LC-MS/MS) System to Quantify 96 Interactomes per Day

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3901

7 January 2021

Global analysis of genome, transcriptome and proteome reveals the response to aneuploidy in human cells.

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3901

7 January 2021

Identifiers

DOI

10.1038/NMETH.3901

1 reference

Dimensions Publication ID

28 June 2017

1032398342

0 references

1 reference