How advancement in biological network analysis methods empowers proteomics

Finding consistent disease subnetworks across microarray datasets

(2011) Donny Soh et al.   BMC BIOINFORMATICS

Network-Based Pipeline for Analyzing MS Data: An Application toward Liver Cancer

(2011) Wilson Wen Bin Goh et al.   JOURNAL OF PROTEOME RESEARCH

Concurrency and Network Disassortativity

(2010) Susan Khor   ARTIFICIAL LIFE

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

(2010) Z.-H. You et al.   BIOINFORMATICS

Consistency, comprehensiveness, and compatibility of pathway databases

(2010) Donny Soh et al.   BMC BIOINFORMATICS

Recent advances in clustering methods for protein interaction networks

(2010) Jianxin Wang et al.   BMC GENOMICS

Parallel Proteomics to Improve Coverage and Confidence in the Partially AnnotatedOryctolagus cuniculusMitochondrial Proteome

(2010) Melanie Y. White et al.   MOLECULAR & CELLULAR PROTEOMICS

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

(2010) Christine Vogel et al.   Molecular Systems Biology

Pathway Commons, a web resource for biological pathway data

(2010) E. G. Cerami et al.   NUCLEIC ACIDS RESEARCH

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

(2010) D. Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

Revisiting Date and Party Hubs: Novel Approaches to Role Assignment in Protein Interaction Networks

(2010) Sumeet Agarwal et al.   PLoS Computational Biology

ADDITIVE RISK ANALYSIS OF MICROARRAY GENE EXPRESSION DATA VIA CORRELATION PRINCIPAL COMPONENT REGRESSION

(2010) YICHUAN ZHAO et al.   Journal of Bioinformatics and Computational Biology

A MULTI-STRATEGY APPROACH TO INFORMATIVE GENE IDENTIFICATION FROM GENE EXPRESSION DATA

(2010) ZIYING LIU et al.   Journal of Bioinformatics and Computational Biology

ADEPTS: ADVANCED PEPTIDE DE NOVO SEQUENCING WITH A PAIR OF TANDEM MASS SPECTRA

(2010) LIN HE et al.   Journal of Bioinformatics and Computational Biology

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

(2009) Min Zhang et al.   BIOINFORMATICS

Complex discovery from weighted PPI networks

(2009) Guimei Liu et al.   BIOINFORMATICS

Global networks of functional coupling in eukaryotes from comprehensive data integration

(2009) A. Alexeyenko et al.   GENOME RESEARCH

Network-based Identification of Novel Cancer Genes

(2009) Gabriel Östlund et al.   MOLECULAR & CELLULAR PROTEOMICS

Tissue specificity and the human protein interaction network

(2009) Alice Bossi et al.   Molecular Systems Biology

Network-assisted protein identification and data interpretation in shotgun proteomics

(2009) Jing Li et al.   Molecular Systems Biology

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

(2009) Alexander W Bell et al.   NATURE METHODS

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

(2009) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

CORUM: the comprehensive resource of mammalian protein complexes—2009

(2009) Andreas Ruepp et al.   NUCLEIC ACIDS RESEARCH

The IntAct molecular interaction database in 2010

(2009) B. Aranda et al.   NUCLEIC ACIDS RESEARCH

Mining Biological Pathways Using WikiPathways Web Services

(2009) Thomas Kelder et al.   PLoS One

Comparative Functional Analysis of the Caenorhabditis elegans and Drosophila melanogaster Proteomes

(2009) Sabine P Schrimpf et al.   PLOS BIOLOGY

Systematic Mapping of Genetic Interaction Networks

(2008) Scott J. Dixon et al.   Annual Review of Genetics

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

(2008) Wen-Lin Huang et al.   BMC BIOINFORMATICS

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

(2008) Laura E Pascal et al.   BMC GENOMICS

Increasing the reliability of protein interactomes

(2008) Hon Nian Chua et al.   DRUG DISCOVERY TODAY

A Genecentric Human Protein Atlas for Expression Profiles Based on Antibodies

(2008) Lisa Berglund et al.   MOLECULAR & CELLULAR PROTEOMICS

MRMaid, the Web-based Tool for Designing Multiple Reaction Monitoring (MRM) Transitions

(2008) Jennifer A. Mead et al.   MOLECULAR & CELLULAR PROTEOMICS

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

(2008) Lyris M. F. de Godoy et al.   NATURE

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

(2008) Nicolas Simonis et al.   NATURE METHODS

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

(2008) Qi Zheng et al.   NUCLEIC ACIDS RESEARCH

Up-to-date catalogues of yeast protein complexes

(2008) Shuye Pu et al.   NUCLEIC ACIDS RESEARCH

Shortest-Path Network Analysis Is a Useful Approach toward Identifying Genetic Determinants of Longevity

(2008) J. R. Managbanag et al.   PLoS One

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

(2008) D. Juan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2008) M. Mann et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Why Do Hubs in the Yeast Protein Interaction Network Tend To Be Essential: Reexamining the Connection between the Network Topology and Essentiality

(2008) Elena Zotenko et al.   PLoS Computational Biology

ON PREPROCESSING AND ANTISYMMETRY IN DE NOVO PEPTIDE SEQUENCING: IMPROVING EFFICIENCY AND ACCURACY

(2008) KANG NING et al.   Journal of Bioinformatics and Computational Biology

DESIGN AND ANALYSIS OF QUANTITATIVE DIFFERENTIAL PROTEOMICS INVESTIGATIONS USING LC-MS TECHNOLOGY

(2008) YURY V. BUKHMAN et al.   Journal of Bioinformatics and Computational Biology

USING INDIRECT PROTEIN–PROTEIN INTERACTIONS FOR PROTEIN COMPLEX PREDICTION

(2008) HON NIAN CHUA et al.   Journal of Bioinformatics and Computational Biology