Human Protein Reference Database and Human Proteinpedia as Discovery Resources for Molecular Biotechnology

The power of protein interaction networks for associating genes with diseases

(2010) Saket Navlakha et al.   BIOINFORMATICS

Modular composition predicts kinase/substrate interactions

(2010) Yichuan Liu et al.   BMC BIOINFORMATICS

Extracting consistent knowledge from highly inconsistent cancer gene data sources

(2010) Xue Gong et al.   BMC BIOINFORMATICS

Identifying differentially regulated subnetworks from phosphoproteomic data

(2010) Martin Klammer et al.   BMC BIOINFORMATICS

AutoSOME: a clustering method for identifying gene expression modules without prior knowledge of cluster number

(2010) Aaron M Newman et al.   BMC BIOINFORMATICS

Dynamic cross-talk analysis among TNF-R, TLR-4 and IL-1R signalings in TNFα-induced inflammatory responses

(2010) Shih-Kuang Yang et al.   BMC Medical Genomics

Identifying potential survival strategies of HIV-1 through virus-host protein interaction networks

(2010) David van Dijk et al.   BMC Systems Biology

Mutation@A Glance: An Integrative Web Application for Analysing Mutations from Human Genetic Diseases

(2010) A. Hijikata et al.   DNA RESEARCH

Literature-Based Discovery of IFN-γand Vaccine-Mediated Gene Interaction Networks

(2010) Arzucan Özgür et al.   JOURNAL OF BIOMEDICINE AND BIOTECHNOLOGY

Network-Based Relating Pharmacological and Genomic Spaces for Drug Target Identification

(2010) Shiwen Zhao et al.   PLoS One

Transcription Profiling of Epstein-Barr Virus Nuclear Antigen (EBNA)-1 Expressing Cells Suggests Targeting of Chromatin Remodeling Complexes

(2010) Ramakrishna Sompallae et al.   PLoS One

Divergence of human and mouse brain transcriptome highlights Alzheimer disease pathways

(2010) Jeremy A. Miller et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Network-Based Elucidation of Human Disease Similarities Reveals Common Functional Modules Enriched for Pluripotent Drug Targets

(2010) Silpa Suthram et al.   PLoS Computational Biology

NetPath: a public resource of curated signal transduction pathways

(2010) Kumaran Kandasamy et al.   GENOME BIOLOGY

MatrixDB, a database focused on extracellular protein–protein and protein–carbohydrate interactions

(2009) Emilie Chautard et al.   BIOINFORMATICS

Functionally guided alignment of protein interaction networks for module detection

(2009) Waqar Ali et al.   BIOINFORMATICS

DASMI: exchanging, annotating and assessing molecular interaction data

(2009) Hagen Blankenburg et al.   BIOINFORMATICS

Algorithms for effective querying of compound graph-based pathway databases

(2009) Ugur Dogrusoz et al.   BMC BIOINFORMATICS

POINeT: protein interactome with sub-network analysis and hub prioritization

(2009) Sheng-An Lee et al.   BMC BIOINFORMATICS

Identification of functionally related genes using data mining and data integration: a breast cancer case study

(2009) Ettore Mosca et al.   BMC BIOINFORMATICS

PDbase: a database of Parkinson's Disease-related genes and genetic variation using substantia nigra ESTs

(2009) Jin Ok Yang et al.   BMC GENOMICS

Prediction of Candidate Primary Immunodeficiency Disease Genes Using a Support Vector Machine Learning Approach

(2009) S. Keerthikumar et al.   DNA RESEARCH

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

Defining Elastic Fiber Interactions by Molecular Fishing

(2009) Stuart A. Cain et al.   MOLECULAR & CELLULAR PROTEOMICS

Multiple Reaction Monitoring-based, Multiplexed, Absolute Quantitation of 45 Proteins in Human Plasma

(2009) Michael A. Kuzyk et al.   MOLECULAR & CELLULAR PROTEOMICS

High-throughput generation of selected reaction-monitoring assays for proteins and proteomes

(2009) Paola Picotti et al.   NATURE METHODS

HLungDB: an integrated database of human lung cancer research

(2009) Lishan Wang et al.   NUCLEIC ACIDS RESEARCH

DASMIweb: online integration, analysis and assessment of distributed protein interaction data

(2009) H. Blankenburg et al.   NUCLEIC ACIDS RESEARCH

ELM: the status of the 2010 eukaryotic linear motif resource

(2009) Cathryn M. Gould et al.   NUCLEIC ACIDS RESEARCH

Network of Cancer Genes: a web resource to analyze duplicability, orthology and network properties of cancer genes

(2009) Adnan S. Syed et al.   NUCLEIC ACIDS RESEARCH

MINT, the molecular interaction database: 2009 update

(2009) Arnaud Ceol et al.   NUCLEIC ACIDS RESEARCH

The IntAct molecular interaction database in 2010

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

Proteomic and Phospho-Proteomic Profile of Human Platelets in Basal, Resting State: Insights into Integrin Signaling

(2009) Amir H. Qureshi et al.   PLoS One

Combining selected reaction monitoring with discovery proteomics in limited biological samples

(2009) Mukesh Kumar Gupta et al.   PROTEOMICS

Applications of Proteomics to Lab Diagnosis

(2008) Raghothama Chaerkady et al.   Annual Review of Pathology-Mechanisms of Disease

PhosphoPOINT: a comprehensive human kinase interactome and phospho-protein database

(2008) Chia-Ying Yang et al.   BIOINFORMATICS

CompariMotif: quick and easy comparisons of sequence motifs

(2008) R. J. Edwards et al.   BIOINFORMATICS

VisANT: an integrative framework for networks in systems biology

(2008) Z. Hu et al.   BRIEFINGS IN BIOINFORMATICS

High confidence determination of specific protein–protein interactions using quantitative mass spectrometry

(2008) Michiel Vermeulen et al.   CURRENT OPINION IN BIOTECHNOLOGY

A Quantitative Proteomic Approach for Identification of Potential Biomarkers in Hepatocellular Carcinoma

(2008) Raghothama Chaerkady et al.   JOURNAL OF PROTEOME RESEARCH

GPS 2.0, a Tool to Predict Kinase-specific Phosphorylation Sites in Hierarchy

(2008) Yu Xue et al.   MOLECULAR & CELLULAR PROTEOMICS

Human Proteinpedia enables sharing of human protein data

(2008) Suresh Mathivanan et al.   NATURE BIOTECHNOLOGY

A forward chemical genetic screen reveals an inhibitor of the Mre11–Rad50–Nbs1 complex

(2008) Aude Dupré et al.   Nature Chemical Biology

Thou shalt share your data

(2008)   NATURE METHODS

OKCAM: an ontology-based, human-centered knowledgebase for cell adhesion molecules

(2008) Chuan-Yun Li et al.   NUCLEIC ACIDS RESEARCH

Human Proteinpedia: a unified discovery resource for proteomics research

(2008) Kumaran Kandasamy et al.   NUCLEIC ACIDS RESEARCH

MoKCa database—mutations of kinases in cancer

(2008) Christopher J. Richardson et al.   NUCLEIC ACIDS RESEARCH

ConsensusPathDB—a database for integrating human functional interaction networks

(2008) Atanas Kamburov et al.   NUCLEIC ACIDS RESEARCH

RAPID: Resource of Asian Primary Immunodeficiency Diseases

(2008) S. Keerthikumar et al.   NUCLEIC ACIDS RESEARCH

Human Protein Reference Database--2009 update

(2008) T. S. Keshava Prasad et al.   NUCLEIC ACIDS RESEARCH

CentrosomeDB: a human centrosomal proteins database

(2008) R. Nogales-Cadenas et al.   NUCLEIC ACIDS RESEARCH

STRING 8--a global view on proteins and their functional interactions in 630 organisms

(2008) L. J. Jensen et al.   NUCLEIC ACIDS RESEARCH

High-Quality Binary Protein Interaction Map of the Yeast Interactome Network

(2008) H. Yu et al.   SCIENCE

Introducing meta-services for biomedical information extraction

(2008) Florian Leitner et al.   GENOME BIOLOGY