Use of mechanistic models to integrate and analyze multiple proteomic datasets (Q35333673)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25863072%20AND%20SRC:MED&resulttype=core&format=json

5 March 2020

title

Use of mechanistic models to integrate and analyze multiple proteomic datasets (English)

1 reference

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5 March 2020

1 reference

6

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5 March 2020

author name string

Edward C Stites

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25863072%20AND%20SRC:MED&resulttype=core&format=json

5 March 2020

Meraj Aziz

2

1 reference

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5 March 2020

Matthew S Creamer

3

1 reference

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5 March 2020

Daniel D Von Hoff

4

1 reference

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5 March 2020

Richard G Posner

5

1 reference

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5 March 2020

language of work or name

English

0 references

publication date

1 April 2015

1 reference

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5 March 2020

1 reference

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5 March 2020

volume

108

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5 March 2020

issue

7

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5 March 2020

page(s)

1819-1829

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Multi-state modeling of biomolecules

5 March 2020

cites work

1 reference

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Structural bioinformatics of the interactome.

12 July 2018

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Proteomic analysis of the epidermal growth factor receptor (EGFR) interactome and post-translational modifications associated with receptor endocytosis in response to EGF and stress

12 July 2018

1 reference

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Recruitment of the adaptor protein Grb2 to EGFR tetramers

12 July 2018

1 reference

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Analyzing protein-protein interactions in the post-interactomic era. Are we ready for the endgame?

12 July 2018

1 reference

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Minimal, encapsulated proteomic-sample processing applied to copy-number estimation in eukaryotic cells

12 July 2018

1 reference

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Using optogenetics to interrogate the dynamic control of signal transmission by the Ras/Erk module.

12 July 2018

1 reference

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Rule-based modeling: a computational approach for studying biomolecular site dynamics in cell signaling systems.

12 July 2018

1 reference

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Complexity of receptor tyrosine kinase signal processing

12 July 2018

1 reference

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Threshold-controlled ubiquitination of the EGFR directs receptor fate

12 July 2018

1 reference

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BioModels Database: a repository of mathematical models of biological processes

12 July 2018

1 reference

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Endocytosis of receptor tyrosine kinases

12 July 2018

1 reference

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Exploring higher-order EGFR oligomerisation and phosphorylation--a combined experimental and theoretical approach

12 July 2018

1 reference

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The SH2 domain interaction landscape

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4390817

Structure and dynamics of molecular networks: a novel paradigm of drug discovery: a comprehensive review

12 July 2018

1 reference

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Conformational coupling across the plasma membrane in activation of the EGF receptor

12 July 2018

1 reference

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Phosphotyrosine signaling proteins that drive oncogenesis tend to be highly interconnected

12 July 2018

1 reference

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The BioGRID interaction database: 2013 update

12 July 2018

1 reference

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

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4390817

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

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4390817

Comprehensive binary interaction mapping of SH2 domains via fluorescence polarization reveals novel functional diversification of ErbB receptors

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4390817

Integrated experimental and model-based analysis reveals the spatial aspects of EGFR activation dynamics

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4390817

Specification, annotation, visualization and simulation of a large rule-based model for ERBB receptor signaling.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4390817

Constructing structural networks of signaling pathways on the proteome scale

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4390817

Computational approaches for analyzing information flow in biological networks

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4390817

Network analysis of epidermal growth factor signaling using integrated genomic, proteomic and phosphorylation data

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4390817

Yes and Lyn play a role in nuclear translocation of the epidermal growth factor receptor

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4390817

Comparative proteomic analysis of eleven common cell lines reveals ubiquitous but varying expression of most proteins

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4390817

ErbB1 dimerization is promoted by domain co-confinement and stabilized by ligand binding

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4390817

Rapid phospho-turnover by receptor tyrosine kinases impacts downstream signaling and drug binding

12 July 2018

1 reference

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The efficiency of reactant site sampling in network-free simulation of rule-based models for biochemical systems

12 July 2018

1 reference

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

12 July 2018

1 reference

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Efficient modeling, simulation and coarse-graining of biological complexity with NFsim

12 July 2018

1 reference

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Protein binding specificity versus promiscuity.

12 July 2018

1 reference

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Phosphotyrosine Signaling: Evolving a New Cellular Communication System

12 July 2018

1 reference

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SnapShot: key numbers in biology

12 July 2018

1 reference

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Spatio-temporal modeling of signaling protein recruitment to EGFR.

12 July 2018

1 reference

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Signal transduction networks in cancer: quantitative parameters influence network topology

12 July 2018

1 reference

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NetPath: a public resource of curated signal transduction pathways

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4390817

Molecular machines or pleiomorphic ensembles: signaling complexes revisited

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4390817

Rule-based modeling of biochemical systems with BioNetGen

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4390817

Protein promiscuity and its implications for biotechnology

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4390817

Input-output behavior of ErbB signaling pathways as revealed by a mass action model trained against dynamic data

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4390817

Human Protein Reference Database--2009 update

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4390817

Kinetic Monte Carlo method for rule-based modeling of biochemical networks.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4390817

Heterogeneity in EGF-binding affinities arises from negative cooperativity in an aggregating system

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4390817

Tyrosine phosphorylated Par3 regulates epithelial tight junction assembly promoted by EGFR signaling

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4390817

Rules for modeling signal-transduction systems

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4390817

A comprehensive pathway map of epidermal growth factor receptor signaling

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4390817

Phosphotyrosine interactome of the ErbB-receptor kinase family

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4390817

A quantitative protein interaction network for the ErbB receptors using protein microarrays

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4390817

Ligand regulates epidermal growth factor receptor kinase specificity: activation increases preference for GAB1 and SHC versus autophosphorylation sites

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4390817

BioNetGen: software for rule-based modeling of signal transduction based on the interactions of molecular domains

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4390817

The complexity of complexes in signal transduction.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4390817

Grb2 regulates internalization of EGF receptors through clathrin-coated pits

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4390817

Rewiring MAP kinase pathways using alternative scaffold assembly mechanisms

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4390817

Searching for specificity in SH domains

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4390817

Effect of epidermal growth factor receptor internalization on regulation of the phospholipase C-gamma1 signaling pathway

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4390817

Interactions between SH2 domains and tyrosine-phosphorylated platelet-derived growth factor beta-receptor sequences: analysis of kinetic parameters by a novel biosensor-based approach

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4390817

Implications of epidermal growth factor (EGF) induced egf receptor aggregation

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4390817

Do low-affinity ErbB receptor protein interactions represent the base of a cell signaling iceberg?

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4390817

Therapeutically targeting ErbB3: a key node in ligand-induced activation of the ErbB receptor-PI3K axis.

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4390817

A network model of early events in epidermal growth factor receptor signaling that accounts for combinatorial complexity

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4390817

Specificity is complex and time consuming: mutual exclusivity in tyrosine kinase-mediated signaling

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4390817

Real-time measurements of kinetics of EGF binding to soluble EGF receptor monomers and dimers support the dimerization model for receptor activation

26 September 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/25863072

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Quantification of Short Term Signaling by the Epidermal Growth Factor Receptor

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/25863072

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

The coming age of complete, accurate, and ubiquitous proteomes

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/25863072

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1016/J.BPJ.2015.02.030

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25863072%20AND%20SRC:MED&resulttype=core&format=json

5 March 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25863072%20AND%20SRC:MED&resulttype=core&format=json

5 March 2020

PubMed publication ID

25863072

1 reference