Computational methods and opportunities for phosphorylation network medicine (Q34742859)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25530950 AND SRC:MED&resulttype=core&format=json

25 February 2020

title

Computational methods and opportunities for phosphorylation network medicine (English)

1 reference

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25 February 2020

0 references

1 reference

Yian Ann Chen

1

1 reference

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25 February 2020

Steven A Eschrich

series ordinal

2

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25 February 2020

publication date

1 June 2014

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Translational cancer research

25 February 2020

published in

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25 February 2020

volume

3

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25 February 2020

issue

3

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25 February 2020

page(s)

266-278

1 reference

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Comparison of alternative MS/MS and bioinformatics approaches for confident phosphorylation site localization

25 February 2020

cites work

1 reference

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Status of large-scale analysis of post-translational modifications by mass spectrometry

7 July 2018

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K-Map: connecting kinases with therapeutics for drug repurposing and development

7 July 2018

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A BAYESIAN GRAPHICAL MODELING APPROACH TO MICRORNA REGULATORY NETWORK INFERENCE.

7 July 2018

1 reference

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PKIS: computational identification of protein kinases for experimentally discovered protein phosphorylation sites

7 July 2018

1 reference

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Large-scale gene function analysis with the PANTHER classification system

7 July 2018

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Dissection of TBK1 signaling via phosphoproteomics in lung cancer cells

7 July 2018

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INCORPORATING BIOLOGICAL INFORMATION INTO LINEAR MODELS: A BAYESIAN APPROACH TO THE SELECTION OF PATHWAYS AND GENES.

7 July 2018

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Iterative rank-order normalization of gene expression microarray data

7 July 2018

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Construction of human activity-based phosphorylation networks.

7 July 2018

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Informatics confronts drug-drug interactions

7 July 2018

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An automated pipeline for high-throughput label-free quantitative proteomics

7 July 2018

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Signaling network prediction by the Ontology Fingerprint enhanced Bayesian network

7 July 2018

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PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees

7 July 2018

1 reference

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Normalization and missing value imputation for label-free LC-MS analysis

7 July 2018

1 reference

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Estimating relative abundances of proteins from shotgun proteomics data

7 July 2018

1 reference

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Measurement of phospholipids may improve diagnostic accuracy in ovarian cancer

7 July 2018

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LFQuant: a label-free fast quantitative analysis tool for high-resolution LC-MS/MS proteomics data

7 July 2018

1 reference

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A comparative analysis of computational approaches to relative protein quantification using peptide peak intensities in label-free LC-MS proteomics experiments.

7 July 2018

1 reference

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Systematic analysis of protein phosphorylation networks from phosphoproteomic data

7 July 2018

1 reference

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ATM and MET kinases are synthetic lethal with nongenotoxic activation of p53.

7 July 2018

1 reference

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Phosphosignature predicts dasatinib response in non-small cell lung cancer.

7 July 2018

1 reference

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From modules to medicine: How modular domains and their associated networks can enable personalized medicine

7 July 2018

1 reference

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Discovery and explanation of drug-drug interactions via text mining.

7 July 2018

1 reference

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Human Protein Reference Database and Human Proteinpedia as resources for phosphoproteome analysis.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4271781

PhosphoSitePlus: a comprehensive resource for investigating the structure and function of experimentally determined post-translational modifications in man and mouse

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4271781

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

7 July 2018

1 reference

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Comprehensive analysis of kinase inhibitor selectivity

7 July 2018

1 reference

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Comprehensive assay of kinase catalytic activity reveals features of kinase inhibitor selectivity

7 July 2018

1 reference

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In Situ Kinase Profiling Reveals Functionally Relevant Properties of Native Kinases

7 July 2018

1 reference

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Comparative evaluation of label-free SINQ normalized spectral index quantitation in the central proteomics facilities pipeline

7 July 2018

1 reference

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Andromeda: a peptide search engine integrated into the MaxQuant environment

7 July 2018

1 reference

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Phospho.ELM: a database of phosphorylation sites--update 2011

7 July 2018

1 reference

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Proof of Concept: Network and Systems Biology Approaches Aid in the Discovery of Potent Anticancer Drug Combinations

7 July 2018

1 reference

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Tackling the widespread and critical impact of batch effects in high-throughput data

7 July 2018

1 reference

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Computational analysis of tissue-specific gene networks: application to murine retinal functional studies.

7 July 2018

1 reference

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A summary of computational resources for protein phosphorylation.

7 July 2018

1 reference

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Targeted cancer therapies in the twenty-first century: lessons from imatinib

7 July 2018

1 reference

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Role of spectral counting in quantitative proteomics.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4271781

Normalization and statistical analysis of quantitative proteomics data generated by metabolic labeling

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4271781

Normalization of peak intensities in bottom-up MS-based proteomics using singular value decomposition

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4271781

Evaluation of genome-wide association study results through development of ontology fingerprints

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4271781

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4271781

A statistical model for iTRAQ data analysis

7 July 2018

1 reference

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4271781

Comparative LC-MS: a landscape of peaks and valleys

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4271781

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4271781

An assessment of software solutions for the analysis of mass spectrometry based quantitative proteomics data

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4271781

Global survey of phosphotyrosine signaling identifies oncogenic kinases in lung cancer

7 July 2018

1 reference

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NetworKIN: a resource for exploring cellular phosphorylation networks

7 July 2018

1 reference

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Capturing heterogeneity in gene expression studies by surrogate variable analysis

7 July 2018

1 reference

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SuperHirn - a novel tool for high resolution LC-MS-based peptide/protein profiling

7 July 2018

1 reference

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Systematic Discovery of In Vivo Phosphorylation Networks

7 July 2018

1 reference

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Functional interrogation of the kinome using nucleotide acyl phosphates

7 July 2018

1 reference

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The Connectivity Map: using gene-expression signatures to connect small molecules, genes, and disease

7 July 2018

1 reference

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Phosphoproteomic analysis of Her2/neu signaling and inhibition

7 July 2018

1 reference

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Normalization approaches for removing systematic biases associated with mass spectrometry and label-free proteomics

7 July 2018

1 reference

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A systems model of signaling identifies a molecular basis set for cytokine-induced apoptosis

7 July 2018

1 reference

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An iterative statistical approach to the identification of protein phosphorylation motifs from large-scale data sets

7 July 2018

1 reference

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Bayesian network analysis of signaling networks: a primer

7 July 2018

1 reference

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Src kinase regulation by phosphorylation and dephosphorylation

7 July 2018

1 reference

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STRING: known and predicted protein-protein associations, integrated and transferred across organisms

7 July 2018

1 reference

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Optimized LOWESS normalization parameter selection for DNA microarray data

7 July 2018

1 reference

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Src protein-tyrosine kinase structure and regulation

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4271781

Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents

7 July 2018

1 reference

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Advances to Bayesian network inference for generating causal networks from observational biological data

7 July 2018

1 reference

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A model for random sampling and estimation of relative protein abundance in shotgun proteomics

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4271781

Identification of phosphorylation sites in protein kinase A substrates using artificial neural networks and mass spectrometry

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4271781

Phospho.ELM: a database of experimentally verified phosphorylation sites in eukaryotic proteins

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4271781

Network component analysis: reconstruction of regulatory signals in biological systems

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4271781

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

7 July 2018

1 reference

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Scansite 2.0: Proteome-wide prediction of cell signaling interactions using short sequence motifs

7 July 2018

1 reference

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ELM server: A new resource for investigating short functional sites in modular eukaryotic proteins

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4271781

Properties of 13C-Substituted Arginine in Stable Isotope Labeling by Amino Acids in Cell Culture (SILAC)

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4271781

Mass spectrometry-based proteomics

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4271781

A comparison of normalization methods for high density oligonucleotide array data based on variance and bias

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4271781

Protein kinases--the major drug targets of the twenty-first century?

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4271781

Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4271781

PlantsP: a functional genomics database for plant phosphorylation

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4271781

HyperModules: identifying clinically and phenotypically significant network modules with disease mutations for biomarker discovery

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4271781

PhosphoSiteAnalyzer: a bioinformatic platform for deciphering phospho proteomes using kinase predictions retrieved from NetworKIN.

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4271781

Phospho.ELM: a database of phosphorylation sites--update 2008.

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4271781

Inference in Bayesian networks

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4271781

Bayesian analysis of signaling networks governing embryonic stem cell fate decisions

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4271781

David A. Karnofsky Award lecture. Imatinib as a paradigm of targeted therapies

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4271781

Direct comparison of MS-based label-free and SILAC quantitative proteome profiling strategies in primary retinal Müller cells

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4271781

9 December 2018

Identifiers

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25530950 AND SRC:MED&resulttype=core&format=json

25 February 2020

PubMed publication ID

25530950

1 reference