Protein networks in disease.

Network medicine: a network-based approach to human disease. Nat Rev Genet (2011) 14.07

Prioritizing candidate disease genes by network-based boosting of genome-wide association data. Genome Res (2011) 4.39

Automated network analysis identifies core pathways in glioblastoma. PLoS One (2010) 3.64

Network link prediction by global silencing of indirect correlations. Nat Biotechnol (2013) 3.27

Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins. PLoS Biol (2009) 3.03

ConsensusPathDB: toward a more complete picture of cell biology. Nucleic Acids Res (2010) 2.79

Genome-wide prioritization of disease genes and identification of disease-disease associations from an integrated human functional linkage network. Genome Biol (2009) 2.43

Psychosis genetics: modeling the relationship between schizophrenia, bipolar disorder, and mixed (or "schizoaffective") psychoses. Schizophr Bull (2009) 2.39

Integrative approaches for finding modular structure in biological networks. Nat Rev Genet (2013) 2.19

Mining biological pathways using WikiPathways web services. PLoS One (2009) 2.17

Reproducible quantification of cancer-associated proteins in body fluids using targeted proteomics. Sci Transl Med (2012) 2.06

A comprehensive benchmark of kernel methods to extract protein-protein interactions from literature. PLoS Comput Biol (2010) 2.03

The power of protein interaction networks for associating genes with diseases. Bioinformatics (2010) 1.96

Supergenomic network compression and the discovery of EXP1 as a glutathione transferase inhibited by artesunate. Cell (2014) 1.91

Systems approaches to polypharmacology and drug discovery. Curr Opin Drug Discov Devel (2010) 1.74

Schizophrenia gene networks and pathways and their applications for novel candidate gene selection. PLoS One (2010) 1.67

It's the machine that matters: Predicting gene function and phenotype from protein networks. J Proteomics (2010) 1.57

An integrative -omics approach to identify functional sub-networks in human colorectal cancer. PLoS Comput Biol (2010) 1.54

Enhancing the prioritization of disease-causing genes through tissue specific protein interaction networks. PLoS Comput Biol (2012) 1.51

A system-level pathway-phenotype association analysis using synthetic feature random forest. Genet Epidemiol (2014) 1.46

DADA: Degree-Aware Algorithms for Network-Based Disease Gene Prioritization. BioData Min (2011) 1.44

Improving disease gene prioritization using the semantic similarity of Gene Ontology terms. Bioinformatics (2010) 1.37

Prioritization of disease microRNAs through a human phenome-microRNAome network. BMC Syst Biol (2010) 1.37

Disease-aging network reveals significant roles of aging genes in connecting genetic diseases. PLoS Comput Biol (2009) 1.32

The proteostasis boundary in misfolding diseases of membrane traffic. FEBS Lett (2009) 1.31

Network properties of human disease genes with pleiotropic effects. BMC Syst Biol (2010) 1.31

Gene module level analysis: identification to networks and dynamics. Curr Opin Biotechnol (2008) 1.29

Protein interaction network underpins concordant prognosis among heterogeneous breast cancer signatures. J Biomed Inform (2010) 1.28

Identifying dysfunctional crosstalk of pathways in various regions of Alzheimer's disease brains. BMC Syst Biol (2010) 1.24

A comparative study of cancer proteins in the human protein-protein interaction network. BMC Genomics (2010) 1.23

Identification of candidate disease genes by integrating Gene Ontologies and protein-interaction networks: case study of primary immunodeficiencies. Nucleic Acids Res (2008) 1.23

Subnetwork state functions define dysregulated subnetworks in cancer. J Comput Biol (2011) 1.21

Evidence mining and novelty assessment of protein-protein interactions with the ConsensusPathDB plugin for Cytoscape. Bioinformatics (2010) 1.19

Systems-level cancer gene identification from protein interaction network topology applied to melanogenesis-related functional genomics data. J R Soc Interface (2009) 1.19

Dominating biological networks. PLoS One (2011) 1.19

The role of the interactome in the maintenance of deleterious variability in human populations. Mol Syst Biol (2014) 1.18

Functional analysis of multiple genomic signatures demonstrates that classification algorithms choose phenotype-related genes. Pharmacogenomics J (2010) 1.16

Comparison of an expanded ataxia interactome with patient medical records reveals a relationship between macular degeneration and ataxia. Hum Mol Genet (2010) 1.16

Edgotype: a fundamental link between genotype and phenotype. Curr Opin Genet Dev (2013) 1.12

Network-based Identification of novel cancer genes. Mol Cell Proteomics (2009) 1.12

How cytokines co-occur across asthma patients: from bipartite network analysis to a molecular-based classification. J Biomed Inform (2011) 1.12

Transcriptome profiling of citrus fruit response to huanglongbing disease. PLoS One (2012) 1.11

Chapter 4: Protein interactions and disease. PLoS Comput Biol (2012) 1.10

Dual- and triple-acting agents for treating core and co-morbid symptoms of major depression: novel concepts, new drugs. Neurotherapeutics (2009) 1.10

Benchmarking of the 2010 BioCreative Challenge III text-mining competition by the BioGRID and MINT interaction databases. BMC Bioinformatics (2011) 1.09

Structural influence of gene networks on their inference: analysis of C3NET. Biol Direct (2011) 1.09

Inferring gene-phenotype associations via global protein complex network propagation. PLoS One (2011) 1.08

GenRev: exploring functional relevance of genes in molecular networks. Genomics (2011) 1.07

Bimodal gene expression patterns in breast cancer. BMC Genomics (2010) 1.07

A network-based, integrative study to identify core biological pathways that drive breast cancer clinical subtypes. Br J Cancer (2012) 1.05

Computational analysis of tissue-specific gene networks: application to murine retinal functional studies. Bioinformatics (2010) 1.05

Rac2 controls tumor growth, metastasis and M1-M2 macrophage differentiation in vivo. PLoS One (2014) 1.05

A novel link prediction algorithm for reconstructing protein-protein interaction networks by topological similarity. Bioinformatics (2012) 1.05

Inhibitors of the anti-apoptotic Bcl-2 proteins: a patent review. Expert Opin Ther Pat (2011) 1.04

Systems biology of fungal infection. Front Microbiol (2012) 1.04

The role of complementary bipartite visual analytical representations in the analysis of SNPs: a case study in ancestral informative markers. J Am Med Inform Assoc (2012) 1.04

Biana: a software framework for compiling biological interactions and analyzing networks. BMC Bioinformatics (2010) 1.03

A network-based approach to prioritize results from genome-wide association studies. PLoS One (2011) 1.03

Coordinated modular functionality and prognostic potential of a heart failure biomarker-driven interaction network. BMC Syst Biol (2010) 1.03

Topology of molecular interaction networks. BMC Syst Biol (2013) 1.03

Integrating literature-constrained and data-driven inference of signalling networks. Bioinformatics (2012) 1.03

Network-based model weighting to detect multiple loci influencing complex diseases. Hum Genet (2008) 1.02

Combining multiple positive training sets to generate confidence scores for protein-protein interactions. Bioinformatics (2008) 1.02

iCTNet: a Cytoscape plugin to produce and analyze integrative complex traits networks. BMC Bioinformatics (2011) 1.01

Negative feedback confers mutational robustness in yeast transcription factor regulation. Proc Natl Acad Sci U S A (2012) 1.01

Distinguishing between driver and passenger mutations in individual cancer genomes by network enrichment analysis. BMC Bioinformatics (2014) 1.00

Concerted perturbation observed in a hub network in Alzheimer's disease. PLoS One (2012) 1.00

Graphlet-based edge clustering reveals pathogen-interacting proteins. Bioinformatics (2012) 0.99

Vavien: an algorithm for prioritizing candidate disease genes based on topological similarity of proteins in interaction networks. J Comput Biol (2011) 0.99

Genotype to phenotype via network analysis. Curr Opin Genet Dev (2013) 0.99

Network-based genomic discovery: application and comparison of Markov random field models. J R Stat Soc Ser C Appl Stat (2010) 0.98

Reverse-engineering human regulatory networks. Wiley Interdiscip Rev Syst Biol Med (2012) 0.98

Exploiting protein-protein interaction networks for genome-wide disease-gene prioritization. PLoS One (2012) 0.98

Positive-unlabeled learning for disease gene identification. Bioinformatics (2012) 0.98

Revealing missing parts of the interactome via link prediction. PLoS One (2014) 0.96

Mechanisms of tumor resistance to EGFR-targeted therapies. Expert Opin Ther Targets (2009) 0.96

A novel network model identified a 13-gene lung cancer prognostic signature. Int J Comput Biol Drug Des (2011) 0.96

Network analysis of genes regulated in renal diseases: implications for a molecular-based classification. BMC Bioinformatics (2009) 0.96

Network topology reveals key cardiovascular disease genes. PLoS One (2013) 0.96

Fundamentals of protein interaction network mapping. Mol Syst Biol (2015) 0.93

A disease module in the interactome explains disease heterogeneity, drug response and captures novel pathways and genes in asthma. Hum Mol Genet (2015) 0.93

Analysis of AML genes in dysregulated molecular networks. BMC Bioinformatics (2009) 0.93

Increasing alternative promoter repertories is positively associated with differential expression and disease susceptibility. PLoS One (2010) 0.93

Omics-based molecular target and biomarker identification. Methods Mol Biol (2011) 0.93

Structural bioinformatics of the interactome. Annu Rev Biophys (2014) 0.93

Protein-protein interaction networks (PPI) and complex diseases. Gastroenterol Hepatol Bed Bench (2014) 0.93

Systems biology approaches for discovering biomarkers for traumatic brain injury. J Neurotrauma (2013) 0.92

Integrated network analysis of transcriptomic and proteomic data in psoriasis. BMC Syst Biol (2010) 0.91

The MI bundle: enabling network and structural biology in genome visualization tools. Bioinformatics (2015) 0.91

Network-based analysis of vaccine-related associations reveals consistent knowledge with the vaccine ontology. J Biomed Semantics (2013) 0.91

Complex biomarker discovery in neuroimaging data: Finding a needle in a haystack. Neuroimage Clin (2013) 0.91

Integrative analysis reveals disease-associated genes and biomarkers for prostate cancer progression. BMC Med Genomics (2014) 0.91

ResponseNet2.0: Revealing signaling and regulatory pathways connecting your proteins and genes--now with human data. Nucleic Acids Res (2013) 0.90

Chemical-genetic profile analysis in yeast suggests that a previously uncharacterized open reading frame, YBR261C, affects protein synthesis. BMC Genomics (2008) 0.90

Biomine: predicting links between biological entities using network models of heterogeneous databases. BMC Bioinformatics (2012) 0.90

A network-based approach for predicting missing pathway interactions. PLoS Comput Biol (2012) 0.90

Genome and network visualization facilitates the analyses of the effects of drugs and mutations on protein-protein and drug-protein networks. BMC Bioinformatics (2016) 0.90

Systems pharmacology. Mt Sinai J Med (2010) 0.90

A generally applicable translational strategy identifies S100A4 as a candidate gene in allergy. Sci Transl Med (2014) 0.89

Discovering the hidden sub-network component in a ranked list of genes or proteins derived from genomic experiments. Nucleic Acids Res (2012) 0.89

The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res (2004) 54.37

A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature (2000) 47.15

Network biology: understanding the cell's functional organization. Nat Rev Genet (2004) 36.62

A census of human cancer genes. Nat Rev Cancer (2004) 36.20

Network motifs: simple building blocks of complex networks. Science (2002) 35.80

A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc Natl Acad Sci U S A (2001) 33.71

Functional discovery via a compendium of expression profiles. Cell (2000) 31.39

Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders. Nucleic Acids Res (2005) 30.44

Lethality and centrality in protein networks. Nature (2001) 29.64

Transcriptional regulatory code of a eukaryotic genome. Nature (2004) 27.21

Towards a proteome-scale map of the human protein-protein interaction network. Nature (2005) 24.76

Population genomics of human gene expression. Nat Genet (2007) 24.49

Systematic genetic analysis with ordered arrays of yeast deletion mutants. Science (2001) 24.48

Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature (2006) 24.29

From molecular to modular cell biology. Nature (1999) 23.51

A genome-wide association study of global gene expression. Nat Genet (2007) 22.98

Global mapping of the yeast genetic interaction network. Science (2004) 21.34

Proteome survey reveals modularity of the yeast cell machinery. Nature (2006) 20.77

The human disease network. Proc Natl Acad Sci U S A (2007) 19.58

A human protein-protein interaction network: a resource for annotating the proteome. Cell (2005) 18.97

BIND: the Biomolecular Interaction Network Database. Nucleic Acids Res (2003) 18.75

Integrated genomic and proteomic analyses of a systematically perturbed metabolic network. Science (2001) 17.11

Discovering regulatory and signalling circuits in molecular interaction networks. Bioinformatics (2002) 12.88

A network-based analysis of systemic inflammation in humans. Nature (2005) 12.60

Structure and function of the feed-forward loop network motif. Proc Natl Acad Sci U S A (2003) 12.50

Network-based classification of breast cancer metastasis. Mol Syst Biol (2007) 12.18

A Bayesian networks approach for predicting protein-protein interactions from genomic data. Science (2003) 12.07

MINT: the Molecular INTeraction database. Nucleic Acids Res (2006) 11.90

Drug-target network. Nat Biotechnol (2007) 11.15

Discovery of expression QTLs using large-scale transcriptional profiling in human lymphocytes. Nat Genet (2007) 11.09

Exploration of the function and organization of the yeast early secretory pathway through an epistatic miniarray profile. Cell (2005) 10.41

A human phenome-interactome network of protein complexes implicated in genetic disorders. Nat Biotechnol (2007) 9.90

The landscape of genetic complexity across 5,700 gene expression traits in yeast. Proc Natl Acad Sci U S A (2005) 9.66

STRING: a database of predicted functional associations between proteins. Nucleic Acids Res (2003) 9.45

Functional dissection of protein complexes involved in yeast chromosome biology using a genetic interaction map. Nature (2007) 9.25

The protein-protein interaction map of Helicobacter pylori. Nature (2001) 8.71

A protein-protein interaction network for human inherited ataxias and disorders of Purkinje cell degeneration. Cell (2006) 8.61

Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities. Nat Biotechnol (2006) 8.38

The 1.2-megabase genome sequence of Mimivirus. Science (2004) 8.37

A probabilistic functional network of yeast genes. Science (2004) 8.35

Large-scale mapping of human protein-protein interactions by mass spectrometry. Mol Syst Biol (2007) 8.16

The protein network of HIV budding. Cell (2003) 7.82

Global analysis of protein phosphorylation in yeast. Nature (2005) 7.46

Correlation between transcriptome and interactome mapping data from Saccharomyces cerevisiae. Nat Genet (2001) 7.16

Analysis of the human protein interactome and comparison with yeast, worm and fly interaction datasets. Nat Genet (2006) 6.74

A DNA integrity network in the yeast Saccharomyces cerevisiae. Cell (2006) 6.61

Global protein function prediction from protein-protein interaction networks. Nat Biotechnol (2003) 6.28

Reconstruction of a functional human gene network, with an application for prioritizing positional candidate genes. Am J Hum Genet (2006) 6.10

Integrating genetic and network analysis to characterize genes related to mouse weight. PLoS Genet (2006) 5.82

Integration of chemical-genetic and genetic interaction data links bioactive compounds to cellular target pathways. Nat Biotechnol (2003) 5.60

Gaining confidence in high-throughput protein interaction networks. Nat Biotechnol (2003) 5.15

Identification of potential interaction networks using sequence-based searches for conserved protein-protein interactions or "interologs". Genome Res (2001) 5.10

Modeling cellular machinery through biological network comparison. Nat Biotechnol (2006) 5.01

Evaluation of clustering algorithms for protein-protein interaction networks. BMC Bioinformatics (2006) 4.85

Herpesviral protein networks and their interaction with the human proteome. Science (2005) 4.74

Taking gene-expression profiling to the clinic: when will molecular signatures become relevant to patient care? Nat Rev Cancer (2007) 4.74

Network modeling links breast cancer susceptibility and centrosome dysfunction. Nat Genet (2007) 4.69

Genetic reconstruction of a functional transcriptional regulatory network. Nat Genet (2007) 4.62

Functional and topological characterization of protein interaction networks. Proteomics (2004) 4.57

Global topological features of cancer proteins in the human interactome. Bioinformatics (2006) 4.17

Predicting disease genes using protein-protein interactions. J Med Genet (2006) 4.10

The modular nature of genetic diseases. Clin Genet (2007) 4.06

Exploring the mode-of-action of bioactive compounds by chemical-genetic profiling in yeast. Cell (2006) 4.03

A protein interaction network of the malaria parasite Plasmodium falciparum. Nature (2005) 3.81

Consolidating the set of known human protein-protein interactions in preparation for large-scale mapping of the human interactome. Genome Biol (2005) 3.79

A systems approach to mapping DNA damage response pathways. Science (2006) 3.55

Epstein-Barr virus and virus human protein interaction maps. Proc Natl Acad Sci U S A (2007) 3.50

Microarray analysis and tumor classification. N Engl J Med (2006) 3.35

An evaluation of human protein-protein interaction data in the public domain. BMC Bioinformatics (2006) 3.33

A protein interaction network links GIT1, an enhancer of huntingtin aggregation, to Huntington's disease. Mol Cell (2004) 3.26

Predicting protein function from protein/protein interaction data: a probabilistic approach. Bioinformatics (2003) 3.24

Automated modelling of signal transduction networks. BMC Bioinformatics (2002) 2.92

Interactome-transcriptome analysis reveals the high centrality of genes differentially expressed in lung cancer tissues. Bioinformatics (2005) 2.82

Genome-wide analysis of vaccinia virus protein-protein interactions. Proc Natl Acad Sci U S A (2000) 2.81

Pivotal role of oligomerization in expanded polyglutamine neurodegenerative disorders. Nature (2003) 2.60

Systematic identification of functional orthologs based on protein network comparison. Genome Res (2006) 2.47

eQED: an efficient method for interpreting eQTL associations using protein networks. Mol Syst Biol (2008) 2.45

Physical network models. J Comput Biol (2004) 2.44

Analysis of gene expression data with pathway scores. Proc Int Conf Intell Syst Mol Biol (2000) 2.30

Identification of key processes underlying cancer phenotypes using biologic pathway analysis. PLoS One (2007) 2.18

A proteome-wide protein interaction map for Campylobacter jejuni. Genome Biol (2007) 2.13

Co-clustering of biological networks and gene expression data. Bioinformatics (2002) 2.12

Protein interactions and disease: computational approaches to uncover the etiology of diseases. Brief Bioinform (2007) 2.10

Validation and refinement of gene-regulatory pathways on a network of physical interactions. Genome Biol (2005) 2.03

Global network analysis of phenotypic effects: protein networks and toxicity modulation in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A (2004) 1.90

An integrative approach for causal gene identification and gene regulatory pathway inference. Bioinformatics (2006) 1.82

Where have all the interactions gone? Estimating the coverage of two-hybrid protein interaction maps. PLoS Comput Biol (2007) 1.81

Efficient algorithms for detecting signaling pathways in protein interaction networks. J Comput Biol (2006) 1.81

The Plasmodium protein network diverges from those of other eukaryotes. Nature (2005) 1.76

Context-sensitive data integration and prediction of biological networks. Bioinformatics (2007) 1.72

A genomic approach of the hepatitis C virus generates a protein interaction map. Gene (2000) 1.72

Diffusion kernel-based logistic regression models for protein function prediction. OMICS (2006) 1.63

SPINE: a framework for signaling-regulatory pathway inference from cause-effect experiments. Bioinformatics (2007) 1.60

CGI: a new approach for prioritizing genes by combining gene expression and protein-protein interaction data. Bioinformatics (2006) 1.55

A systems-level approach to mapping the telomere length maintenance gene circuitry. Mol Syst Biol (2008) 1.27

Characterizing disease states from topological properties of transcriptional regulatory networks. BMC Bioinformatics (2006) 1.27

Predicting protein functions with message passing algorithms. Bioinformatics (2004) 1.13

Detecting remotely related proteins by their interactions and sequence similarity. Proc Natl Acad Sci U S A (2005) 0.93

Transcriptional regulation of protein complexes within and across species. Proc Natl Acad Sci U S A (2007) 7.07

Discovering statistically significant biclusters in gene expression data. Bioinformatics (2002) 6.17

Medical sequencing at the extremes of human body mass. Am J Hum Genet (2007) 5.61

Conserved pathways within bacteria and yeast as revealed by global protein network alignment. Proc Natl Acad Sci U S A (2003) 4.68

An initial blueprint for myogenic differentiation. Genes Dev (2005) 4.22

Genome-wide in silico identification of transcriptional regulators controlling the cell cycle in human cells. Genome Res (2003) 3.79

Associating genes and protein complexes with disease via network propagation. PLoS Comput Biol (2010) 3.65

Revealing modularity and organization in the yeast molecular network by integrated analysis of highly heterogeneous genomewide data. Proc Natl Acad Sci U S A (2004) 3.49

EXPANDER--an integrative program suite for microarray data analysis. BMC Bioinformatics (2005) 3.43

PREDICT: a method for inferring novel drug indications with application to personalized medicine. Mol Syst Biol (2011) 3.22

PathBLAST: a tool for alignment of protein interaction networks. Nucleic Acids Res (2004) 3.20

Systematic identification of functional orthologs based on protein network comparison. Genome Res (2006) 2.47

A genome-scale computational study of the interplay between transcriptional regulation and metabolism. Mol Syst Biol (2007) 2.15

Expander: from expression microarrays to networks and functions. Nat Protoc (2010) 2.12

Efficient algorithms for detecting signaling pathways in protein interaction networks. J Comput Biol (2006) 1.81

The large-scale organization of the bacterial network of ecological co-occurrence interactions. Nucleic Acids Res (2010) 1.75

Competitive and cooperative metabolic interactions in bacterial communities. Nat Commun (2011) 1.75

Simultaneous identification of multiple driver pathways in cancer. PLoS Comput Biol (2013) 1.71

Genome-scale metabolic modeling elucidates the role of proliferative adaptation in causing the Warburg effect. PLoS Comput Biol (2011) 1.66

SPINE: a framework for signaling-regulatory pathway inference from cause-effect experiments. Bioinformatics (2007) 1.60

A direct comparison of protein interaction confidence assignment schemes. BMC Bioinformatics (2006) 1.56

SIGMA: a set-cover-based inexact graph matching algorithm. J Bioinform Comput Biol (2010) 1.53

Enhancing the prioritization of disease-causing genes through tissue specific protein interaction networks. PLoS Comput Biol (2012) 1.51

A network-based method for predicting disease-causing genes. J Comput Biol (2009) 1.49

QPath: a method for querying pathways in a protein-protein interaction network. BMC Bioinformatics (2006) 1.46

Metabolic-network-driven analysis of bacterial ecological strategies. Genome Biol (2009) 1.44

Translation efficiency in humans: tissue specificity, global optimization and differences between developmental stages. Nucleic Acids Res (2010) 1.42

MAPK signaling to the early secretory pathway revealed by kinase/phosphatase functional screening. J Cell Biol (2010) 1.41

Toward accurate reconstruction of functional protein networks. Mol Syst Biol (2009) 1.40

INDI: a computational framework for inferring drug interactions and their associated recommendations. Mol Syst Biol (2012) 1.40

An algorithmic framework for predicting side effects of drugs. J Comput Biol (2011) 1.39

NetworkBLAST: comparative analysis of protein networks. Bioinformatics (2008) 1.37

QNet: a tool for querying protein interaction networks. J Comput Biol (2008) 1.32

Epitope mapping using combinatorial phage-display libraries: a graph-based algorithm. Nucleic Acids Res (2006) 1.29

A systems-level approach to mapping the telomere length maintenance gene circuitry. Mol Syst Biol (2008) 1.27

Identification of conserved protein complexes based on a model of protein network evolution. Bioinformatics (2007) 1.24

Combining drug and gene similarity measures for drug-target elucidation. J Comput Biol (2011) 1.23

A genome-wide screen for essential yeast genes that affect telomere length maintenance. Nucleic Acids Res (2009) 1.20

Increased microRNA activity in human cancers. PLoS One (2009) 1.18

Systematic identification of gene annotation errors in the widely used yeast mutation collections. Nat Methods (2012) 1.17

A discriminative model for identifying spatial cis-regulatory modules. J Comput Biol (2005) 1.17

Pepitope: epitope mapping from affinity-selected peptides. Bioinformatics (2007) 1.16

Fast and accurate alignment of multiple protein networks. J Comput Biol (2009) 1.14

ANAT: a tool for constructing and analyzing functional protein networks. Sci Signal (2011) 1.11

Identification of protein complexes from co-immunoprecipitation data. Bioinformatics (2010) 1.09

t4 workshop report: Pathways of Toxicity. ALTEX (2013) 1.06

A sequence-based filtering method for ncRNA identification and its application to searching for riboswitch elements. Bioinformatics (2006) 1.04

Alternative splicing regulates biogenesis of miRNAs located across exon-intron junctions. Mol Cell (2013) 1.03

Genetic variation in putative regulatory loci controlling gene expression in breast cancer. Proc Natl Acad Sci U S A (2006) 1.03

Gene loss rate: a probabilistic measure for the conservation of eukaryotic genes. Nucleic Acids Res (2006) 1.02

Gene expression in the rodent brain is associated with its regional connectivity. PLoS Comput Biol (2011) 1.02

Environmental stresses disrupt telomere length homeostasis. PLoS Genet (2013) 1.00

Topology-free querying of protein interaction networks. J Comput Biol (2010) 0.99

Decoupling Environment-Dependent and Independent Genetic Robustness across Bacterial Species. PLoS Comput Biol (2010) 0.99

Constraint-based functional similarity of metabolic genes: going beyond network topology. Bioinformatics (2007) 0.98

Systematic condition-dependent annotation of metabolic genes. Genome Res (2007) 0.97

Large-scale elucidation of drug response pathways in humans. J Comput Biol (2012) 0.93

A method for inferring medical diagnoses from patient similarities. BMC Med (2013) 0.93

A note on phasing long genomic regions using local haplotype predictions. J Bioinform Comput Biol (2006) 0.93

DEFOG: a practical scheme for deciphering families of genes. Genomics (2002) 0.92

Comprehensive analysis of co-occurring domain sets in yeast proteins. BMC Genomics (2007) 0.89

Improved network-based identification of protein orthologs. Bioinformatics (2008) 0.88

Bayesian haplotype inference via the Dirichlet process. J Comput Biol (2007) 0.87

Pathway-based analysis of genomic variation data. Curr Opin Genet Dev (2013) 0.87

Analysis of SNP-expression association matrices. Proc IEEE Comput Syst Bioinform Conf (2005) 0.87

Network-free inference of knockout effects in yeast. PLoS Comput Biol (2010) 0.87

Optimally orienting physical networks. J Comput Biol (2011) 0.86

TP53 cancerous mutations exhibit selection for translation efficiency. Cancer Res (2009) 0.86

A supervised approach for identifying discriminating genotype patterns and its application to breast cancer data. Bioinformatics (2007) 0.86

A complex-centric view of protein network evolution. Nucleic Acids Res (2009) 0.85

Detecting excess radical replacements in phylogenetic trees. Gene (2003) 0.85

Transcriptional regulation by CHIP/LDB complexes. PLoS Genet (2010) 0.83

A linearized constraint-based approach for modeling signaling networks. J Comput Biol (2012) 0.83

Network-based interpretation of genomic variation data. J Mol Biol (2013) 0.83

Analysis of SNP-expression association matrices. J Bioinform Comput Biol (2006) 0.83

TORQUE: topology-free querying of protein interaction networks. Nucleic Acids Res (2009) 0.81

Genetic interactions in yeast: is robustness going bust? Mol Syst Biol (2007) 0.81

PRINCIPLE: a tool for associating genes with diseases via network propagation. Bioinformatics (2011) 0.80

iPoint: an integer programming based algorithm for inferring protein subnetworks. Mol Biosyst (2013) 0.80

Evolution of domain promiscuity in eukaryotic genomes--a perspective from the inferred ancestral domain architectures. Mol Biosyst (2010) 0.79

Structural similarity of genetically interacting proteins. BMC Syst Biol (2008) 0.79

Met kinetic signature derived from the response to HGF/SF in a cellular model predicts breast cancer patient survival. PLoS One (2012) 0.78

A novel HMM-based method for detecting enriched transcription factor binding sites reveals RUNX3 as a potential target in pancreatic cancer biology. PLoS One (2010) 0.78

Network orientation via shortest paths. Bioinformatics (2014) 0.78

Processes of fungal proteome evolution and gain of function: gene duplication and domain rearrangement. Phys Biol (2011) 0.77

A genetic screen for high copy number suppressors of the synthetic lethality between elg1Δ and srs2Δ in yeast. G3 (Bethesda) (2013) 0.77

Elucidating influenza inhibition pathways via network reconstruction. J Comput Biol (2014) 0.76

INFERENCE OF PERSONALIZED DRUG TARGETS VIA NETWORK PROPAGATION. Pac Symp Biocomput (2016) 0.75

Estimating population size via line graph reconstruction. Algorithms Mol Biol (2013) 0.75

The approximability of shortest path-based graph orientations of protein-protein interaction networks. J Comput Biol (2013) 0.75

Introduction. These two issues contain a selected subset of the papers presented at RECOMB 2014. J Comput Biol (2015) 0.75

Towards optimally multiplexed applications of universal arrays. J Comput Biol (2004) 0.75

Global alignment of protein-protein interaction networks. Methods Mol Biol (2013) 0.75

Genome Rearrangement with ILP. IEEE/ACM Trans Comput Biol Bioinform (2017) 0.75