How advancement in biological network analysis methods empowers proteomics (Q37975999)

26 August 2017

How advancement in biological network analysis methods empowers proteomics (English)

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26 August 2017

Wilson W B Goh

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26 August 2017

Yie H Lee

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2

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26 August 2017

Maxey Chung

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3

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26 August 2017

Limsoon Wong

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4

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26 August 2017

19 January 2012

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26 August 2017

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26 August 2017

12

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26 August 2017

4-5

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26 August 2017

550-563

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Is proteomics the new genomics?

26 August 2017

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https://api.crossref.org/works/10.1002%2FPMIC.201100321

Correlation of mRNA and protein levels: cell type-specific gene expression of cluster designation antigens in the prostate

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100321

A HUPO test sample study reveals common problems in mass spectrometry-based proteomics

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100321

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100321

Parallel proteomics to improve coverage and confidence in the partially annotated Oryctolagus cuniculus mitochondrial proteome

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100321

Intact-protein-based High-resolution Three-dimensional Quantitative Analysis System for Proteome Profiling of Biological Fluids

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100321

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100321

Comparative functional analysis of the Caenorhabditis elegans and Drosophila melanogaster proteomes

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100321

Integration with the human genome of peptide sequences obtained by high-throughput mass spectrometry

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100321

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100321

PRIDE: the proteomics identifications database

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100321

Scale-free networks in cell biology

21 January 2018

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https://api.crossref.org/works/10.1002%2FPMIC.201100321

Taking the mystery out of biological networks.

21 January 2018

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https://api.crossref.org/works/10.1002%2FPMIC.201100321

Concurrency and network disassortativity.

21 January 2018

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https://api.crossref.org/works/10.1002%2FPMIC.201100321

Error and attack tolerance of complex networks

21 January 2018

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https://api.crossref.org/works/10.1002%2FPMIC.201100321

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

21 January 2018

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https://api.crossref.org/works/10.1002%2FPMIC.201100321

Revisiting date and party hubs: novel approaches to role assignment in protein interaction networks

21 January 2018

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https://api.crossref.org/works/10.1002%2FPMIC.201100321

Why do hubs in the yeast protein interaction network tend to be essential: reexamining the connection between the network topology and essentiality

21 January 2018

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https://api.crossref.org/works/10.1002%2FPMIC.201100321

Hierarchical organization of modularity in metabolic networks

21 January 2018

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https://api.crossref.org/works/10.1002%2FPMIC.201100321

Empirically controlled mapping of the Caenorhabditis elegans protein-protein interactome network

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100321

Precision proteomics: the case for high resolution and high mass accuracy

21 January 2018

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https://api.crossref.org/works/10.1002%2FPMIC.201100321

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

21 January 2018

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https://api.crossref.org/works/10.1002%2FPMIC.201100321

Role of accurate mass measurement (+/- 10 ppm) in protein identification strategies employing MS or MS/MS and database searching.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100321

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100321

The Paragon Algorithm, a next generation search engine that uses sequence temperature values and feature probabilities to identify peptides from tandem mass spectra.

21 January 2018

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https://api.crossref.org/works/10.1002%2FPMIC.201100321

PEAKS: powerful software for peptide de novo sequencing by tandem mass spectrometry

21 January 2018

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https://api.crossref.org/works/10.1002%2FPMIC.201100321

ADEPTS: advanced peptide de novo sequencing with a pair of tandem mass spectra

21 January 2018

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https://api.crossref.org/works/10.1002%2FPMIC.201100321

Sequence database searches via de novo peptide sequencing by tandem mass spectrometry

21 January 2018

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https://api.crossref.org/works/10.1002%2FPMIC.201100321

PepNovo: de novo peptide sequencing via probabilistic network modeling

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100321

On preprocessing and antisymmetry in de novo peptide sequencing: improving efficiency and accuracy.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100321

KEGG for representation and analysis of molecular networks involving diseases and drugs

21 January 2018

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https://api.crossref.org/works/10.1002%2FPMIC.201100321

Querying and computing with BioCyc databases

21 January 2018

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https://api.crossref.org/works/10.1002%2FPMIC.201100321

Mining biological pathways using WikiPathways web services

21 January 2018

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https://api.crossref.org/works/10.1002%2FPMIC.201100321

Reactome: a knowledge base of biologic pathways and processes

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100321

Pathway Commons, a web resource for biological pathway data

21 January 2018

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https://api.crossref.org/works/10.1002%2FPMIC.201100321

Consistency, comprehensiveness, and compatibility of pathway databases

21 January 2018

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https://api.crossref.org/works/10.1002%2FPMIC.201100321

Systematic mapping of genetic interaction networks

21 January 2018

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https://api.crossref.org/works/10.1002%2FPMIC.201100321

BioGRID: a general repository for interaction datasets

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100321

DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100321

Human Protein Reference Database and Human Proteinpedia as discovery tools for systems biology.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100321

The IntAct molecular interaction database in 2010

21 January 2018

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https://api.crossref.org/works/10.1002%2FPMIC.201100321

MINT: the Molecular INTeraction database

21 January 2018

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https://api.crossref.org/works/10.1002%2FPMIC.201100321

The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100321

Creating the gene ontology resource: design and implementation

21 January 2018

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https://api.crossref.org/works/10.1002%2FPMIC.201100321

CORUM: the comprehensive resource of mammalian protein complexes--2009

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100321

MIPS: analysis and annotation of proteins from whole genomes

21 January 2018

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https://api.crossref.org/works/10.1002%2FPMIC.201100321

Up-to-date catalogues of yeast protein complexes

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100321

MRMaid, the web-based tool for designing multiple reaction monitoring (MRM) transitions

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100321

A computational approach toward label-free protein quantification using predicted peptide detectability.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100321

Design and analysis of quantitative differential proteomics investigations using LC-MS technology.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100321

Network-based classification of breast cancer metastasis

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100321

Network-based analysis of affected biological processes in type 2 diabetes models

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100321

New methods for joint analysis of biological networks and expression data

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100321

Molecular networks in microarray analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100321

Network-assisted protein identification and data interpretation in shotgun proteomics

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100321

Network-based Identification of novel cancer genes

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100321

Shortest-path network analysis is a useful approach toward identifying genetic determinants of longevity

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100321

Network-based pipeline for analyzing MS data: an application toward liver cancer

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100321

A genecentric Human Protein Atlas for expression profiles based on antibodies

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100321

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100321

What do we learn from high-throughput protein interaction data?

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100321

A network of protein-protein interactions in yeast

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100321

Using indirect protein interactions for the prediction of Gene Ontology functions

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100321

An efficient algorithm for large-scale detection of protein families

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100321

Protein complex prediction via cost-based clustering

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100321

Uncovering the overlapping community structure of complex networks in nature and society

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100321

Using indirect protein-protein interactions for protein complex prediction.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100321

Complex discovery from weighted PPI networks.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100321

Towards a proteome-scale map of the human protein–protein interaction network

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100321

A human protein-protein interaction network: a resource for annotating the proteome

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100321

Comparative assessment of large-scale data sets of protein-protein interactions

21 January 2018

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https://api.crossref.org/works/10.1002%2FPMIC.201100321

Global networks of functional coupling in eukaryotes from comprehensive data integration

21 January 2018

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https://api.crossref.org/works/10.1002%2FPMIC.201100321

Detecting functional modules in the yeast protein-protein interaction network.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100321

Predicting aging/longevity-related genes in the nematode Caenorhabditis elegans

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100321

Whole-proteome prediction of protein function via graph-theoretic analysis of interaction maps

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100321

Exploiting indirect neighbours and topological weight to predict protein function from protein-protein interactions

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100321

Prediction of protein function using protein-protein interaction data

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100321

Identification of conserved protein complexes based on a model of protein network evolution.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100321

A gene-coexpression network for global discovery of conserved genetic modules

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100321

A multi-strategy approach to informative gene identification from gene expression data

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100321

Significance analysis of microarrays applied to the ionizing radiation response

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100321

Thousands of samples are needed to generate a robust gene list for predicting outcome in cancer

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100321

Gene expression profiling identifies clinically relevant subtypes of prostate cancer

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100321

Evaluating reproducibility of differential expression discoveries in microarray studies by considering correlated molecular changes

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100321

Sequence signatures and mRNA concentration can explain two-thirds of protein abundance variation in a human cell line

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100321

A molecular-properties-based approach to understanding PDZ domain proteins and PDZ ligands

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100321

Ontological analysis of gene expression data: current tools, limitations, and open problems

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100321

A global test for groups of genes: testing association with a clinical outcome

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100321

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100321

Finding consistent disease subnetworks across microarray datasets

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100321

Recent advances in clustering methods for protein interaction networks

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100321

Finding and evaluating community structure in networks

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100321

GOEAST: a web-based software toolkit for Gene Ontology enrichment analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100321

GO::TermFinder--open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100321

Improved detection of overrepresentation of Gene-Ontology annotations with parent child analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100321

ProLoc-GO: utilizing informative Gene Ontology terms for sequence-based prediction of protein subcellular localization

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100321

Protein interactions: two methods for assessment of the reliability of high throughput observations

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100321

Tissue specificity and the human protein interaction network

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100321

Increasing the reliability of protein interactomes

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100321

How reliable are experimental protein-protein interaction data?

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100321

Using manifold embedding for assessing and predicting protein interactions from high-throughput experimental data

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100321

Predicting functions from protein sequences--where are the bottlenecks?

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100321

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100321

Predicting protein--protein interactions from primary structure

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100321

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100321

Discovering motif pairs at interaction sites from protein sequences on a proteome-wide scale

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100321

Detecting protein function and protein-protein interactions from genome sequences

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100321

High-confidence prediction of global interactomes based on genome-wide coevolutionary networks

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100321

Increasing confidence of protein interactomes using network topological metrics.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201100321

21 January 2018

Identifiers

DOI

10.1002/PMIC.201100321

1 reference

26 August 2017

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