(Q36364750)

13 August 2017

1 reference

title

From protein-protein interactions to protein co-expression networks: a new perspective to evaluate large-scale proteomic data (English)

1 reference

protein-protein interaction

13 August 2017

1 reference

Danila Vella

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28477207%20AND%20SRC:MED&resulttype=core&format=json

9 June 2020

Italo Zoppis

series ordinal

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28477207%20AND%20SRC:MED&resulttype=core&format=json

9 June 2020

Pierluigi Mauri

series ordinal

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28477207%20AND%20SRC:MED&resulttype=core&format=json

9 June 2020

publication date

20 March 2017

1 reference

Eurasip Journal on Bioinformatics and Systems Biology

13 August 2017

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28477207%20AND%20SRC:MED&resulttype=core&format=json

9 June 2020

volume

2017

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28477207%20AND%20SRC:MED&resulttype=core&format=json

9 June 2020

issue

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28477207%20AND%20SRC:MED&resulttype=core&format=json

9 June 2020

page(s)

6

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28477207%20AND%20SRC:MED&resulttype=core&format=json

Creative Commons Attribution 4.0 International

9 June 2020

copyright license

start time

20 March 2017

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

describes a project that uses

WGCNA

object named as

WGCNA

1 reference

CZ Software Mentions: A large dataset of software mentions in the biomedical literature

Cytoscape

object named as

Cytoscape

1 reference

CZ Software Mentions: A large dataset of software mentions in the biomedical literature

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30 September 2017

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30 September 2017

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Network-based proteomic analysis for postmenopausal osteoporosis in Caucasian females.

30 September 2017

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30 September 2017

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30 September 2017

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A null model for Pearson coexpression networks

30 September 2017

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Experimental and Computational Analysis of a Large Protein Network That Controls Fat Storage Reveals the Design Principles of a Signaling Network

30 September 2017

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A density-based clustering approach for identifying overlapping protein complexes with functional preferences

30 September 2017

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Reverse Engineering of Genome-wide Gene Regulatory Networks from Gene Expression Data

30 September 2017

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Integrating -Omics: Systems Biology as Explored Through C. elegans Research

30 September 2017

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

30 September 2017

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cytoHubba: identifying hub objects and sub-networks from complex interactome

30 September 2017

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Modules, networks and systems medicine for understanding disease and aiding diagnosis.

30 September 2017

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Altered glutamate protein co-expression network topology linked to spine loss in the auditory cortex of schizophrenia.

30 September 2017

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30 September 2017

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30 September 2017

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30 September 2017

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Detecting overlapping protein complexes based on a generative model with functional and topological properties

30 September 2017

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30 September 2017

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Network analysis of inflammatory genes and their transcriptional regulators in coronary artery disease

30 September 2017

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Combined analysis of chromosomal instabilities and gene expression for colon cancer progression inference

30 September 2017

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30 September 2017

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30 September 2017

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Integrating protein-protein interaction networks with phenotypes reveals signs of interactions.

30 September 2017

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Utilizing both topological and attribute information for protein complex identification in PPI networks.

30 September 2017

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30 September 2017

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30 September 2017

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A survey of computational methods for protein complex prediction from protein interaction networks

30 September 2017

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30 September 2017

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30 September 2017

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Predicting permanent and transient protein-protein interfaces

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5359264

Comparison of co-expression measures: mutual information, correlation, and model based indices

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5359264

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

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5359264

Investigation of stable and transient protein-protein interactions: Past, present, and future

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5359264

A travel guide to Cytoscape plugins

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5359264

Network enrichment analysis: extension of gene-set enrichment analysis to gene networks

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5359264

atBioNet--an integrated network analysis tool for genomics and biomarker discovery

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5359264

Filtering Gene Ontology semantic similarity for identifying protein complexes in large protein interaction networks

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5359264

Detecting overlapping protein complexes in protein-protein interaction networks

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5359264

Topological analysis and interactive visualization of biological networks and protein structures

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5359264

Central dogma at the single-molecule level in living cells

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5359264

Global quantification of mammalian gene expression control

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5359264

Interactome networks and human disease

30 September 2017

1 reference

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Network medicine: a network-based approach to human disease

30 September 2017

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Protein-protein interactions essentials: key concepts to building and analyzing interactome networks

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5359264

Coordinated modular functionality and prognostic potential of a heart failure biomarker-driven interaction network

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5359264

A general co-expression network-based approach to gene expression analysis: comparison and applications

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5359264

An integrative -omics approach to identify functional sub-networks in human colorectal cancer

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5359264

Global signatures of protein and mRNA expression levels

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5359264

MINT, the molecular interaction database: 2009 update

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5359264

Correlation of mRNA and protein in complex biological samples.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5359264

Co-expression tools for plant biology: opportunities for hypothesis generation and caveats

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5359264

Applying mass spectrometry-based proteomics to genetics, genomics and network biology

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5359264

A core-attachment based method to detect protein complexes in PPI networks

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5359264

WGCNA: an R package for weighted correlation network analysis

30 September 2017

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Human Protein Reference Database--2009 update

30 September 2017

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Identifying differences in protein expression levels by spectral counting and feature selection

30 September 2017

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Eigengene networks for studying the relationships between co-expression modules

30 September 2017

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An Arabidopsis gene network based on the graphical Gaussian model.

30 September 2017

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Constructing gene co-expression networks and predicting functions of unknown genes by random matrix theory

30 September 2017

1 reference

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Integrative analysis of transcriptomic and proteomic data: challenges, solutions and applications

30 September 2017

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Systematic construction of gene coexpression networks with applications to human T helper cell differentiation process

30 September 2017

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Deciphering Protein–Protein Interactions. Part II. Computational Methods to Predict Protein and Domain Interaction Partners

30 September 2017

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5359264

The importance of bottlenecks in protein networks: correlation with gene essentiality and expression dynamics

30 September 2017

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Graph theory and networks in Biology.

30 September 2017

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5359264

IntAct--open source resource for molecular interaction data

30 September 2017

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5359264

30 September 2017

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5359264

Why do hubs tend to be essential in protein networks?

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5359264

Integrated biclustering of heterogeneous genome-wide datasets for the inference of global regulatory networks

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5359264

Modularity and community structure in networks

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5359264

A general framework for weighted gene co-expression network analysis

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5359264

The model organism as a system: integrating 'omics' data sets

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5359264

Pathguide: a pathway resource list

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5359264

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

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5359264

Systematic survey reveals general applicability of "guilt-by-association" within gene coexpression networks

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5359264

Structure, function, and evolution of transient and obligate protein-protein interactions

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5359264

Bayesian network analysis of signaling networks: a primer

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5359264

Fast algorithm for detecting community structure in networks

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5359264

Evidence for dynamically organized modularity in the yeast protein-protein interaction network

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5359264

VisANT: an online visualization and analysis tool for biological interaction data

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5359264

Finding and evaluating community structure in networks

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5359264

Protein complexes and functional modules in molecular networks

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5359264

Statistical significance for genomewide studies

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5359264

An automated method for finding molecular complexes in large protein interaction networks

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5359264

Network motifs: simple building blocks of complex networks

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5359264

Community structure in social and biological networks

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5359264

Lethality and centrality in protein networks

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5359264

Error and attack tolerance of complex networks

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5359264

From molecular to modular cell biology

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5359264

Emergence of Scaling in Random Networks

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5359264

Collective dynamics of 'small-world' networks

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5359264

CytoNCA: a cytoscape plugin for centrality analysis and evaluation of protein interaction networks

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5359264

Proteomics of bronchial biopsies: galectin-3 as a predictive biomarker of airway remodelling modulation in omalizumab-treated severe asthma patients

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5359264

Fast R Functions for Robust Correlations and Hierarchical Clustering

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5359264

Analyzing biological network parameters with CentiScaPe

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5359264

Weighted gene co-expression network analysis of pneumocytes under exposure to a carcinogenic dose of chloroprene.

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5359264

Comprehensive network analysis of genes expressed in human oropharyngeal cancer

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5359264

Characterization of protein species and weighted protein co-expression network regulation of Escherichia coli in response to serum killing using a 2-DE based proteomics approach

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5359264

Combination of gene expression and genome copy number alteration has a prognostic value for breast cancer

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5359264

Shotgun protein profile of human adipose tissue and its changes in relation to systemic amyloidoses.

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5359264

Identification of essential proteins based on edge clustering coefficient

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5359264

Reliable typing of systemic amyloidoses through proteomic analysis of subcutaneous adipose tissue.

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5359264

How perfect can protein interactomes be?

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5359264

Integrated network analysis platform for protein-protein interactions

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5359264

Biological network comparison using graphlet degree distribution

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5359264

Modeling interactome: scale-free or geometric?

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5359264

Gene co-expression network topology provides a framework for molecular characterization of cellular state

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5359264

Effect of sampling on topology predictions of protein-protein interaction networks

22 September 2018

1 reference

Crossref

https://api.crossref.org/works/10.1186%2FS13637-017-0059-Z

Using matrix of thresholding partial correlation coefficients to infer regulatory network

21 January 2018

1 reference

12 December 2020

Network analysis reveals roles of inflammatory factors in different phenotypes of kidney transplant patients

1 reference

12 December 2020

CFinder: locating cliques and overlapping modules in biological networks

1 reference

12 December 2020

Betweenness centrality in a weighted network

1 reference

12 December 2020

10.1186/S13637-017-0059-Z

Identifiers

DOI

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28477207%20AND%20SRC:MED&resulttype=core&format=json

journals/ejbsb/VellaZMMS17

9 June 2020

DBLP publication ID

1 reference

DBLP Dataset 2021-01-02

Dimensions Publication ID

28 January 2021

0 references

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28477207%20AND%20SRC:MED&resulttype=core&format=json

9 June 2020

PubMed publication ID

28477207

1 reference