Published in Proc Natl Acad Sci U S A on October 17, 2003
Conserved patterns of protein interaction in multiple species. Proc Natl Acad Sci U S A (2005) 7.48
Network-based prediction of protein function. Mol Syst Biol (2007) 6.13
How complete are current yeast and human protein-interaction networks? Genome Biol (2006) 3.50
A Drosophila protein-interaction map centered on cell-cycle regulators. Genome Biol (2004) 2.95
Ribosome biogenesis in the yeast Saccharomyces cerevisiae. Genetics (2013) 2.70
A high-accuracy consensus map of yeast protein complexes reveals modular nature of gene essentiality. BMC Bioinformatics (2007) 2.51
Toward a comprehensive temperature-sensitive mutant repository of the essential genes of Saccharomyces cerevisiae. Mol Cell (2008) 2.39
Uncovering biological network function via graphlet degree signatures. Cancer Inform (2008) 1.80
How and when should interactome-derived clusters be used to predict functional modules and protein function? Bioinformatics (2009) 1.71
The small subunit processome in ribosome biogenesis—progress and prospects. Wiley Interdiscip Rev RNA (2011) 1.66
Systems approach to explore components and interactions in the presynapse. Proteomics (2009) 1.61
SPICi: a fast clustering algorithm for large biological networks. Bioinformatics (2010) 1.60
Semantic integration to identify overlapping functional modules in protein interaction networks. BMC Bioinformatics (2007) 1.43
Recent advances in clustering methods for protein interaction networks. BMC Genomics (2010) 1.40
Clustering proteins from interaction networks for the prediction of cellular functions. BMC Bioinformatics (2004) 1.38
RNA-binding proteins that inhibit RNA virus infection. Proc Natl Acad Sci U S A (2007) 1.35
The PINc domain protein Utp24, a putative nuclease, is required for the early cleavage steps in 18S rRNA maturation. Proc Natl Acad Sci U S A (2006) 1.31
A novel functional module detection algorithm for protein-protein interaction networks. Algorithms Mol Biol (2006) 1.25
A large scale analysis of protein-protein interactions in the nitrogen-fixing bacterium Mesorhizobium loti. DNA Res (2008) 1.20
Novel genes exhibit distinct patterns of function acquisition and network integration. Genome Biol (2010) 1.19
Gene function prediction using labeled and unlabeled data. BMC Bioinformatics (2008) 1.19
Using indirect protein interactions for the prediction of Gene Ontology functions. BMC Bioinformatics (2007) 1.13
Systems-level analyses identify extensive coupling among gene expression machines. Mol Syst Biol (2006) 1.12
Proteasomal ATPase-associated factor 1 negatively regulates proteasome activity by interacting with proteasomal ATPases. Mol Cell Biol (2005) 1.09
Revisiting the Saccharomyces cerevisiae predicted ORFeome. Genome Res (2008) 1.07
Characterization of protein hubs by inferring interacting motifs from protein interactions. PLoS Comput Biol (2007) 1.01
A Mep2-dependent transcriptional profile links permease function to gene expression during pseudohyphal growth in Saccharomyces cerevisiae. Mol Biol Cell (2008) 0.99
Integration of relational and hierarchical network information for protein function prediction. BMC Bioinformatics (2008) 0.99
Replication-independent long-distance trafficking by viral RNAs in Nicotiana benthamiana. Plant Cell (2007) 0.98
Gene annotation and network inference by phylogenetic profiling. BMC Bioinformatics (2006) 0.98
Spectral affinity in protein networks. BMC Syst Biol (2009) 0.94
Detecting remotely related proteins by their interactions and sequence similarity. Proc Natl Acad Sci U S A (2005) 0.93
A novel plasmid-based microarray screen identifies suppressors of rrp6Delta in Saccharomyces cerevisiae. Mol Cell Biol (2006) 0.92
Vps9 family protein Muk1 is the second Rab5 guanosine nucleotide exchange factor in budding yeast. J Biol Chem (2013) 0.91
Charting gene regulatory networks: strategies, challenges and perspectives. Biochem J (2004) 0.90
Prediction of enzyme function by combining sequence similarity and protein interactions. BMC Bioinformatics (2008) 0.90
Interaction of the Saccharomyces cerevisiae cortical actin patch protein Rvs167p with proteins involved in ER to Golgi vesicle trafficking. Genetics (2005) 0.88
The drug cocktail network. BMC Syst Biol (2012) 0.88
Algorithmic and analytical methods in network biology. Wiley Interdiscip Rev Syst Biol Med (2010) 0.87
Role-similarity based functional prediction in networked systems: application to the yeast proteome. J R Soc Interface (2005) 0.87
An iterative approach of protein function prediction. BMC Bioinformatics (2011) 0.86
Consistent dissection of the protein interaction network by combining global and local metrics. Genome Biol (2007) 0.86
A protein network-guided screen for cell cycle regulators in Drosophila. BMC Syst Biol (2011) 0.86
AVID: an integrative framework for discovering functional relationships among proteins. BMC Bioinformatics (2005) 0.86
Assembly and nuclear export of pre-ribosomal particles in budding yeast. Chromosoma (2014) 0.85
High-precision high-coverage functional inference from integrated data sources. BMC Bioinformatics (2008) 0.85
Local network topology in human protein interaction data predicts functional association. PLoS One (2009) 0.85
Comparison of protein interaction networks reveals species conservation and divergence. BMC Bioinformatics (2006) 0.84
Identification of novel proteins associated with yeast snR30 small nucleolar RNA. Nucleic Acids Res (2011) 0.83
Investigating the validity of current network analysis on static conglomerate networks by protein network stratification. BMC Bioinformatics (2010) 0.81
Defining a modular signalling network from the fly interactome. BMC Syst Biol (2008) 0.81
Removing bias against membrane proteins in interaction networks. BMC Syst Biol (2011) 0.81
CASCADE: a novel quasi all paths-based network analysis algorithm for clustering biological interactions. BMC Bioinformatics (2008) 0.81
The yeast kinome displays scale free topology with functional hub clusters. BMC Bioinformatics (2005) 0.81
Enhancing the functional content of eukaryotic protein interaction networks. PLoS One (2014) 0.81
Topology-function conservation in protein-protein interaction networks. Bioinformatics (2015) 0.81
Accuracy improvement in protein complex prediction from protein interaction networks by refining cluster overlaps. Proteome Sci (2012) 0.80
Gene ontology function prediction in mollicutes using protein-protein association networks. BMC Syst Biol (2011) 0.80
A systems biology approach to the global analysis of transcription factors in colorectal cancer. BMC Cancer (2012) 0.80
An integrated quantitative proteomics and systems biology approach to explore synaptic protein profile changes during morphine exposure. Neuropsychopharmacology (2013) 0.79
Nonparametric simulation of signal transduction networks with semi-synchronized update. PLoS One (2012) 0.78
Extracting the abstraction pyramid from complex networks. BMC Bioinformatics (2010) 0.77
Identifying responsive modules by mathematical programming: an application to budding yeast cell cycle. PLoS One (2012) 0.77
Neighbor overlap is enriched in the yeast interaction network: analysis and implications. PLoS One (2012) 0.76
Pet10p is a yeast perilipin that stabilizes lipid droplets and promotes their assembly. J Cell Biol (2017) 0.76
MicroRNA-integrated and network-embedded gene selection with diffusion distance. PLoS One (2010) 0.75
A Two-Step Approach for Clustering Proteins based on Protein Interaction Profile. Proc IEEE Comput Syst Bioinform Conf (2005) 0.75
Enhancement of protein production via the strong DIT1 terminator and two RNA-binding proteins in Saccharomyces cerevisiae. Sci Rep (2016) 0.75
Survey of network-based approaches to research of cardiovascular diseases. Biomed Res Int (2014) 0.75
Interlog protein network: an evolutionary benchmark of protein interaction networks for the evaluation of clustering algorithms. BMC Bioinformatics (2015) 0.75
Prediction of Growth Factor-Dependent Cleft Formation During Branching Morphogenesis Using A Dynamic Graph-Based Growth Model. IEEE/ACM Trans Comput Biol Bioinform (2016) 0.75
Illuminating drug action by network integration of disease genes: a case study of myocardial infarction. Mol Biosyst (2016) 0.75
PAND: A Distribution to Identify Functional Linkage from Networks with Preferential Attachment Property. PLoS One (2015) 0.75
Predicting Abdominal Aortic Aneurysm Target Genes by Level-2 Protein-Protein Interaction. PLoS One (2015) 0.75
Identification of Saccharomyces cerevisiae Genes Whose Deletion Causes Synthetic Effects in Cells with Reduced Levels of the Nuclear Pif1 DNA Helicase. G3 (Bethesda) (2015) 0.75
Analysis of transcriptional profiles of Saccharomyces cerevisiae exposed to bisphenol A. Curr Genet (2016) 0.75
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Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature (2002) 45.19
Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature (2002) 37.66
A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc Natl Acad Sci U S A (2001) 33.71
Lethality and centrality in protein networks. Nature (2001) 29.64
The large-scale organization of metabolic networks. Nature (2000) 27.57
Systematic genetic analysis with ordered arrays of yeast deletion mutants. Science (2001) 24.48
Comparative assessment of large-scale data sets of protein-protein interactions. Nature (2002) 24.25
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Specificity and stability in topology of protein networks. Science (2002) 21.07
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Molecular evidence for an ancient duplication of the entire yeast genome. Nature (1997) 13.86
Global analysis of protein activities using proteome chips. Science (2001) 13.74
Protein interactions: two methods for assessment of the reliability of high throughput observations. Mol Cell Proteomics (2002) 8.11
Analyzing yeast protein-protein interaction data obtained from different sources. Nat Biotechnol (2002) 7.06
Expanding protein universe and its origin from the biological Big Bang. Proc Natl Acad Sci U S A (2002) 2.92
Systematic and large-scale two-hybrid screens. Curr Opin Microbiol (2000) 2.34
Functional fingerprints of folds: evidence for correlated structure-function evolution. J Mol Biol (2003) 1.80
Treasures and traps in genome-wide data sets: case examples from yeast. Nat Rev Genet (2002) 1.57
Dnmt3a is essential for hematopoietic stem cell differentiation. Nat Genet (2011) 4.85
Identification of transcribed sequences in Arabidopsis thaliana by using high-resolution genome tiling arrays. Proc Natl Acad Sci U S A (2005) 3.21
Widespread and tissue specific age-related DNA methylation changes in mice. Genome Res (2010) 2.99
TDRD3 is an effector molecule for arginine-methylated histone marks. Mol Cell (2010) 1.80
Molecular mechanism by which the nucleoid occlusion factor, SlmA, keeps cytokinesis in check. EMBO J (2010) 1.72
Genome architecture marked by retrotransposons modulates predisposition to DNA methylation in cancer. Genome Res (2010) 1.53
The postnatal role of Sox9 in cartilage. J Bone Miner Res (2012) 1.31
Identification of SOX9 interaction sites in the genome of chondrocytes. PLoS One (2010) 1.26
Detection of bladder cancer using novel DNA methylation biomarkers in urine sediments. Cancer Epidemiol Biomarkers Prev (2011) 1.19
Modeling a lethal prostate cancer variant with small-cell carcinoma features. Clin Cancer Res (2011) 1.15
Aberrant DNA methylation is associated with disease progression, resistance to imatinib and shortened survival in chronic myelogenous leukemia. PLoS One (2011) 1.13
BM-map: Bayesian mapping of multireads for next-generation sequencing data. Biometrics (2011) 1.11
Age-related epigenetic drift in the pathogenesis of MDS and AML. Genome Res (2014) 1.08
Conserved DNA methylation patterns in healthy blood cells and extensive changes in leukemia measured by a new quantitative technique. Epigenetics (2012) 1.02
SINE retrotransposons cause epigenetic reprogramming of adjacent gene promoters. Mol Cancer Res (2012) 1.01
fREDUCE: detection of degenerate regulatory elements using correlation with expression. BMC Bioinformatics (2007) 1.01
REST regulates oncogenic properties of glioblastoma stem cells. Stem Cells (2012) 1.00
Architecture of epigenetic reprogramming following Twist1-mediated epithelial-mesenchymal transition. Genome Biol (2013) 0.95
The role of antigen cross-presentation from leukemia blasts on immunity to the leukemia-associated antigen PR1. J Immunother (2012) 0.94
Accuracy of RNA-Seq and its dependence on sequencing depth. BMC Bioinformatics (2012) 0.94
Stabilization of the promoter nucleosomes in nucleosome-free regions by the yeast Cyc8-Tup1 corepressor. Genome Res (2012) 0.93
On differential gene expression using RNA-Seq data. Cancer Inform (2011) 0.91
The epigenome of AML stem and progenitor cells. Epigenetics (2012) 0.87
Local network topology in human protein interaction data predicts functional association. PLoS One (2009) 0.85
Common minor histocompatibility antigen discovery based upon patient clinical outcomes and genomic data. PLoS One (2011) 0.84
Potentiation of colon cancer susceptibility in mice by colonic epithelial PPAR-δ/β overexpression. J Natl Cancer Inst (2014) 0.83
Dynamic status of REST in the mouse ESC pluripotency network. PLoS One (2012) 0.80
dsPIG: a tool to predict imprinted genes from the deep sequencing of whole transcriptomes. BMC Bioinformatics (2012) 0.80
BM-BC: a Bayesian method of base calling for Solexa sequence data. BMC Bioinformatics (2012) 0.79
Access to the nucleus and functional association with c-Myc is required for the full oncogenic potential of ΔEGFR/EGFRvIII. J Biol Chem (2012) 0.78
Correction: SOX9 Regulates Multiple Genes in Chondrocytes, Including Genes Encoding ECM Proteins, ECM Modification Enzymes, Receptors, and Transporters. PLoS One (2015) 0.77
Cyclic neutropenia associated with T cell immunity to granulocyte proteases and a double de novo mutation in GFI1, a transcriptional regulator of ELANE. Br J Haematol (2010) 0.76
Intragenomic evolution of a transcriptional enhancer in the genome of Strongylocentrotus purpuratus. Mar Genomics (2009) 0.75
Cell cycle-dependent nucleosome occupancy at cohesin binding sites in yeast chromosomes. Genomics (2008) 0.75
Toward breaking the histone code: bayesian graphical models for histone modifications. Circ Cardiovasc Genet (2013) 0.75
BM-SNP: A Bayesian Model for SNP Calling Using High Throughput Sequencing Data. IEEE/ACM Trans Comput Biol Bioinform (2015) 0.75