The Perseus computational platform for comprehensive analysis of (prote)omics data
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Title
The Perseus computational platform for comprehensive analysis of (prote)omics data
Authors
Keywords
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Journal
NATURE METHODS
Volume 13, Issue 9, Pages 731-740
Publisher
Springer Nature
Online
2016-06-28
DOI
10.1038/nmeth.3901
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- Ensembl 2016
- (2015) Andrew Yates et al. NUCLEIC ACIDS RESEARCH
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- 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
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- (2014) Jürgen Cox et al. MOLECULAR & CELLULAR PROTEOMICS
- Periodic mRNA synthesis and degradation co-operate during cell cycle gene expression
- (2014) P. Eser et al. Molecular Systems Biology
- ProteomeXchange provides globally coordinated proteomics data submission and dissemination
- (2014) Juan A Vizcaíno et al. NATURE BIOTECHNOLOGY
- PhosphoSitePlus, 2014: mutations, PTMs and recalibrations
- (2014) Peter V. Hornbeck et al. NUCLEIC ACIDS RESEARCH
- Gene Ontology Consortium: going forward
- (2014) NUCLEIC ACIDS RESEARCH
- UniProt: a hub for protein information
- (2014) NUCLEIC ACIDS RESEARCH
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- (2014) Maria S. Robles et al. PLoS Genetics
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- The Reactome pathway knowledgebase
- (2013) David Croft et al. NUCLEIC ACIDS RESEARCH
- Molecular architecture of the mammalian circadian clock
- (2013) Carrie L. Partch et al. TRENDS IN CELL BIOLOGY
- Phosphorylation Variation during the Cell Cycle Scales with Structural Propensities of Proteins
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- TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions
- (2013) Daehwan Kim et al. GENOME BIOLOGY
- STAR: ultrafast universal RNA-seq aligner
- (2012) Alexander Dobin et al. BIOINFORMATICS
- 1D and 2D annotation enrichment: a statistical method integrating quantitative proteomics with complementary high-throughput data
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- The Proteomics Identifications (PRIDE) database and associated tools: status in 2013
- (2012) Juan Antonio Vizcaíno et al. NUCLEIC ACIDS RESEARCH
- LIBSVM
- (2012) Chih-Chung Chang et al. ACM Transactions on Intelligent Systems and Technology
- Quantitative, High-Resolution Proteomics for Data-Driven Systems Biology
- (2011) Jürgen Cox et al. Annual Review of Biochemistry
- Andromeda: A Peptide Search Engine Integrated into the MaxQuant Environment
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- (2011) J. Munoz et al. Molecular Systems Biology
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- (2011) N. Nagaraj et al. Molecular Systems Biology
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- (2011) M. Beck et al. Molecular Systems Biology
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- (2010) A. W.-C. Liew et al. BRIEFINGS IN BIOINFORMATICS
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