Related references
Note: Only part of the references are listed.Finding consistent disease subnetworks across microarray datasets
Donny Soh et al.
BMC BIOINFORMATICS (2011)
Network-Based Pipeline for Analyzing MS Data: An Application toward Liver Cancer
Wilson Wen Bin Goh et al.
JOURNAL OF PROTEOME RESEARCH (2011)
Parallel Proteomics to Improve Coverage and Confidence in the Partially Annotated Oryctolagus cuniculus Mitochondrial Proteome
Melanie Y. White et al.
MOLECULAR & CELLULAR PROTEOMICS (2011)
Pathway Commons, a web resource for biological pathway data
Ethan G. Cerami et al.
NUCLEIC ACIDS RESEARCH (2011)
The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored
Damian Szklarczyk et al.
NUCLEIC ACIDS RESEARCH (2011)
Concurrency and Network Disassortativity
Susan Khor
ARTIFICIAL LIFE (2010)
Using manifold embedding for assessing and predicting protein interactions from high-throughput experimental data
Zhu-Hong You et al.
BIOINFORMATICS (2010)
Consistency, comprehensiveness, and compatibility of pathway databases
Donny Soh et al.
BMC BIOINFORMATICS (2010)
Recent advances in clustering methods for protein interaction networks
Jianxin Wang et al.
BMC GENOMICS (2010)
Network-based Identification of Novel Cancer Genes
Gabriel Ostlund et al.
MOLECULAR & CELLULAR PROTEOMICS (2010)
Sequence signatures and mRNA concentration can explain two-thirds of protein abundance variation in a human cell line
Christine Vogel et al.
MOLECULAR SYSTEMS BIOLOGY (2010)
KEGG for representation and analysis of molecular networks involving diseases and drugs
Minoru Kanehisa et al.
NUCLEIC ACIDS RESEARCH (2010)
CORUM: the comprehensive resource of mammalian protein complexes-2009
Andreas Ruepp et al.
NUCLEIC ACIDS RESEARCH (2010)
The IntAct molecular interaction database in 2010
B. Aranda et al.
NUCLEIC ACIDS RESEARCH (2010)
Revisiting Date and Party Hubs: Novel Approaches to Role Assignment in Protein Interaction Networks
Sumeet Agarwal et al.
PLOS COMPUTATIONAL BIOLOGY (2010)
ADDITIVE RISK ANALYSIS OF MICROARRAY GENE EXPRESSION DATA VIA CORRELATION PRINCIPAL COMPONENT REGRESSION
YICHUAN ZHAO et al.
Journal of Bioinformatics and Computational Biology (2010)
A MULTI-STRATEGY APPROACH TO INFORMATIVE GENE IDENTIFICATION FROM GENE EXPRESSION DATA
ZIYING LIU et al.
Journal of Bioinformatics and Computational Biology (2010)
ADEPTS: ADVANCED PEPTIDE DE NOVO SEQUENCING WITH A PAIR OF TANDEM MASS SPECTRA
LIN HE et al.
Journal of Bioinformatics and Computational Biology (2010)
Systematic Mapping of Genetic Interaction Networks
Scott J. Dixon et al.
ANNUAL REVIEW OF GENETICS (2009)
Evaluating reproducibility of differential expression discoveries in microarray studies by considering correlated molecular changes
Min Zhang et al.
BIOINFORMATICS (2009)
Complex discovery from weighted PPI networks
Guimei Liu et al.
BIOINFORMATICS (2009)
Global networks of functional coupling in eukaryotes from comprehensive data integration
Andrey Alexeyenko et al.
GENOME RESEARCH (2009)
MRMaid, the Web-based Tool for Designing Multiple Reaction Monitoring (MRM) Transitions
Jennifer A. Mead et al.
MOLECULAR & CELLULAR PROTEOMICS (2009)
Tissue specificity and the human protein interaction network
Alice Bossi et al.
MOLECULAR SYSTEMS BIOLOGY (2009)
Network-assisted protein identification and data interpretation in shotgun proteomics
Jing Li et al.
MOLECULAR SYSTEMS BIOLOGY (2009)
Empirically controlled mapping of the Caenorhabditis elegans protein-protein interactome network
Nicolas Simonis et al.
NATURE METHODS (2009)
A HUPO test sample study reveals common problems in mass spectrometry-based proteomics
Alexander W. Bell et al.
NATURE METHODS (2009)
Up-to-date catalogues of yeast protein complexes
Shuye Pu et al.
NUCLEIC ACIDS RESEARCH (2009)
Mining Biological Pathways Using WikiPathways Web Services
Thomas Kelder et al.
PLOS ONE (2009)
Comparative Functional Analysis of the Caenorhabditis elegans and Drosophila melanogaster Proteomes
Sabine P. Schrimpf et al.
PLOS BIOLOGY (2009)
ProLoc-GO: Utilizing informative Gene Ontology terms for sequence-based prediction of protein subcellular localization
Wen-Lin Huang et al.
BMC BIOINFORMATICS (2008)
Correlation of mRNA and protein levels: Cell type-specific gene expression of cluster designation antigens in the prostate
Laura E. Pascal et al.
BMC GENOMICS (2008)
Increasing the reliability of protein interactomes
Hon Nian Chua et al.
DRUG DISCOVERY TODAY (2008)
A Genecentric Human Protein Atlas for Expression Profiles Based on Antibodies
Lisa Berglund et al.
MOLECULAR & CELLULAR PROTEOMICS (2008)
Comprehensive mass-spectrometry-based proteome quantification of haploid versus diploid yeast
Lyris M. F. de Godoy et al.
NATURE (2008)
GOEAST: a web-based software toolkit for Gene Ontology enrichment analysis
Qi Zheng et al.
NUCLEIC ACIDS RESEARCH (2008)
Shortest-Path Network Analysis Is a Useful Approach toward Identifying Genetic Determinants of Longevity
J. R. Managbanag et al.
PLOS ONE (2008)
High-confidence prediction of global interactomes based on genome-wide coevolutionary networks
David Juan et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2008)
Precision proteomics: The case for high resolution and high mass accuracy
Matthias Mann et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2008)
Why Do Hubs in the Yeast Protein Interaction Network Tend To Be Essential: Reexamining the Connection between the Network Topology and Essentiality
Elena Zotenko et al.
PLOS COMPUTATIONAL BIOLOGY (2008)
ON PREPROCESSING AND ANTISYMMETRY IN DE NOVO PEPTIDE SEQUENCING: IMPROVING EFFICIENCY AND ACCURACY
KANG NING et al.
Journal of Bioinformatics and Computational Biology (2008)
DESIGN AND ANALYSIS OF QUANTITATIVE DIFFERENTIAL PROTEOMICS INVESTIGATIONS USING LC-MS TECHNOLOGY
YURY V. BUKHMAN et al.
Journal of Bioinformatics and Computational Biology (2008)
USING INDIRECT PROTEIN–PROTEIN INTERACTIONS FOR PROTEIN COMPLEX PREDICTION
HON NIAN CHUA et al.
Journal of Bioinformatics and Computational Biology (2008)
Improved detection of overrepresentation of Gene-Ontology annotations with parentchild analysis
Steffen Grossmann et al.
BIOINFORMATICS (2007)
Network-based classification of breast cancer metastasis
Han-Yu Chuang et al.
MOLECULAR SYSTEMS BIOLOGY (2007)
The paragon algorithm, a next generation search engine that uses sequence temperature values and feature probabilities to identify peptides from tandem mass spectra
Ignat V. Shilov et al.
MOLECULAR & CELLULAR PROTEOMICS (2007)
Is proteomics the new genomics?
Juergen Cox et al.
CELL (2007)
Network-based analysis of affected biological processes in type 2 diabetes models
Manway Liu et al.
PLOS GENETICS (2007)
MOLECULAR NETWORKS IN MICROARRAY ANALYSIS
Andrey Y. Sivachenko et al.
JOURNAL OF BIOINFORMATICS AND COMPUTATIONAL BIOLOGY (2007)
Deciphering protein-protein interactions. Part II. Computational methods to predict protein and domain interaction partners
Benjamin A. Shoemaker et al.
PLOS COMPUTATIONAL BIOLOGY (2007)
Identification of conserved protein complexes based on a model of protein network evolution
Eitan Hirsh et al.
BIOINFORMATICS (2007)
MINT: the molecular INTeraction database
Andrew Chatr-aryamontri et al.
NUCLEIC ACIDS RESEARCH (2007)
Reactome: a knowledge base of biologic pathways and processes
Imre Vastrik et al.
GENOME BIOLOGY (2007)
Using indirect protein interactions for the prediction of Gene Ontology functions
Hon Nian Chua et al.
BMC BIOINFORMATICS (2007)
Predicting aging/longevity-related genes in the nematode Caenorhabditis elegans
Tarynn M. Witten et al.
CHEMISTRY & BIODIVERSITY (2007)
Detecting functional modules in the yeast protein-protein interaction network
Jingchun Chen et al.
BIOINFORMATICS (2006)
Increasing confidence of protein interactomes using network topological metrics
Jin Chen et al.
BIOINFORMATICS (2006)
A molecular-properties-based approach to understanding PDZ domain proteins and PDZ ligands
Cosmas Giallourakis et al.
GENOME RESEARCH (2006)
A computational approach toward label-free protein quantification using predicted peptide detectability
Haixu Tang et al.
BIOINFORMATICS (2006)
Exploiting indirect neighbours and topological weight to predict protein function from protein-protein interactions
Hon Nian Chua et al.
BIOINFORMATICS (2006)
Discovering motif pairs at interaction sites from protein sequences on a proteome-wide scale
HQ Li et al.
BIOINFORMATICS (2006)
CFinder:: locating cliques and overlapping modules in biological networks
B Adamcsek et al.
BIOINFORMATICS (2006)
Thousands of samples are needed to generate a robust gene list for predicting outcome in cancer
L Ein-Dor et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2006)
On methods for gene function scoring as a means of facilitating the interpretation of microarray results
N. Raghavan et al.
JOURNAL OF COMPUTATIONAL BIOLOGY (2006)
BioGRID: a general repository for interaction datasets
Chris Stark et al.
NUCLEIC ACIDS RESEARCH (2006)
Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles
A Subramanian et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2005)
Towards a proteome-scale map of the human protein-protein interaction network
JF Rual et al.
NATURE (2005)
A human protein-protein interaction network:: A resource for annotating the proteome
U Stelzl et al.
CELL (2005)
Ontological analysis of gene expression data: current tools, limitations, and open problems
P Khatri et al.
BIOINFORMATICS (2005)
Querying and computing with BioCyc databases
M Krummenacker et al.
BIOINFORMATICS (2005)
PRIDE: The proteomics identifications database
L Martens et al.
PROTEOMICS (2005)
Uncovering the overlapping community structure of complex networks in nature and society
G Palla et al.
NATURE (2005)
Whole-proteome prediction of protein function via graph-theoretic analysis of interaction maps
E Nabieva et al.
BIOINFORMATICS (2005)
Intact-protein-based high-resolution three-dimensional quantitative analysis system for proteome profiling of biological fluids
H Wang et al.
MOLECULAR & CELLULAR PROTEOMICS (2005)
PepNovo: De novo peptide sequencing via probabilistic network modeling
A Frank et al.
ANALYTICAL CHEMISTRY (2005)
Finding and evaluating community structure in networks
MEJ Newman et al.
PHYSICAL REVIEW E (2004)
Gene expression profiling identifies clinically relevant subtypes of prostate cancer
J Lapointe et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2004)
GO::TermFinder - open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes
EI Boyle et al.
BIOINFORMATICS (2004)
A model for random sampling and estimation of relative protein abundance in shotgun proteomics
HB Liu et al.
ANALYTICAL CHEMISTRY (2004)
New methods for joint analysis of biological networks and expression data
F Sohler et al.
BIOINFORMATICS (2004)
Evidence for dynamically organized modularity in the yeast protein-protein interaction network
JDJ Han et al.
NATURE (2004)
Protein complex prediction via cost-based clustering
AD King et al.
BIOINFORMATICS (2004)
A global test for groups of genes: testing association with a clinical outcome
JJ Goeman et al.
BIOINFORMATICS (2004)
MIPS: analysis and annotation of proteins from whole genomes
HW Mewes et al.
NUCLEIC ACIDS RESEARCH (2004)
What do we learn from high-throughput protein interaction data?
B Titz et al.
EXPERT REVIEW OF PROTEOMICS (2004)
Open source system for analyzing, validating, and storing protein identification data
R Craig et al.
JOURNAL OF PROTEOME RESEARCH (2004)
A gene-coexpression network for global discovery of conserved genetic modules
JM Stuart et al.
SCIENCE (2003)
How reliable are experimental protein-protein interaction data?
E Sprinzak et al.
JOURNAL OF MOLECULAR BIOLOGY (2003)
An automated method for finding molecular complexes in large protein interaction networks
GD Bader et al.
BMC BIOINFORMATICS (2003)
PEAKS: powerful software for peptide de novo sequencing by tandem mass spectrometry
B Ma et al.
RAPID COMMUNICATIONS IN MASS SPECTROMETRY (2003)
Pathway studio - the analysis and navigation of molecular networks
A Nikitin et al.
BIOINFORMATICS (2003)
Prediction of protein function using protein-protein interaction data
MH Deng et al.
JOURNAL OF COMPUTATIONAL BIOLOGY (2003)
Hierarchical organization of modularity in metabolic networks
E Ravasz et al.
SCIENCE (2002)
Comparative assessment of large-scale data sets of protein-protein interactions
C von Mering et al.
NATURE (2002)
Protein interactions - Two methods for assessment of the reliability of high throughput observations
CM Deane et al.
MOLECULAR & CELLULAR PROTEOMICS (2002)
An efficient algorithm for large-scale detection of protein families
AJ Enright et al.
NUCLEIC ACIDS RESEARCH (2002)
DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions
I Xenarios et al.
NUCLEIC ACIDS RESEARCH (2002)
Gene expression correlates of clinical prostate cancer behavior
D Singh et al.
CANCER CELL (2002)
Correlated sequence-signatures as markers of protein-protein interaction
E Sprinzak et al.
JOURNAL OF MOLECULAR BIOLOGY (2001)
Predicting protein-protein interactions from primary structure
JR Bock et al.
BIOINFORMATICS (2001)
Significance analysis of microarrays applied to the ionizing radiation response
VG Tusher et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2001)
Assessment of prediction accuracy of protein function from protein-protein interaction data
H Hishigaki et al.
YEAST (2001)
A network of protein-protein interactions in yeast
B Schwikowski et al.
NATURE BIOTECHNOLOGY (2000)
Error and attack tolerance of complex networks
R Albert et al.
NATURE (2000)
Share Paper
