Published in Wiley Interdiscip Rev Syst Biol Med on September 13, 2010
Integrative approaches for finding modular structure in biological networks. Nat Rev Genet (2013) 2.19
Structure-based systems biology for analyzing off-target binding. Curr Opin Struct Biol (2011) 1.25
Reverse engineering cellular networks with information theoretic methods. Cells (2013) 1.18
A network-based approach to classify the three domains of life. Biol Direct (2011) 0.84
How do oncoprotein mutations rewire protein-protein interaction networks? Expert Rev Proteomics (2015) 0.83
Identification of rifampin-regulated functional modules and related microRNAs in human hepatocytes based on the protein interaction network. BMC Genomics (2016) 0.81
Construction and analyses of human large-scale tissue specific networks. PLoS One (2014) 0.79
NIBBS-search for fast and accurate prediction of phenotype-biased metabolic systems. PLoS Comput Biol (2012) 0.77
Basic local alignment search tool. J Mol Biol (1990) 659.07
Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet (2000) 336.52
Clustal W and Clustal X version 2.0. Bioinformatics (2007) 126.47
Emergence of scaling in random networks Science (1999) 89.38
The COG database: an updated version includes eukaryotes. BMC Bioinformatics (2003) 60.98
The Pfam protein families database. Nucleic Acids Res (2004) 56.46
Transcriptional regulatory networks in Saccharomyces cerevisiae. Science (2002) 43.52
Network biology: understanding the cell's functional organization. Nat Rev Genet (2004) 36.62
Network motifs: simple building blocks of complex networks. Science (2002) 35.80
Causal protein-signaling networks derived from multiparameter single-cell data. Science (2005) 34.28
Global analysis of protein expression in yeast. Nature (2003) 34.15
A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc Natl Acad Sci U S A (2001) 33.71
An efficient algorithm for large-scale detection of protein families. Nucleic Acids Res (2002) 25.81
Comparative assessment of large-scale data sets of protein-protein interactions. Nature (2002) 24.25
From molecular to modular cell biology. Nature (1999) 23.51
Assigning protein functions by comparative genome analysis: protein phylogenetic profiles. Proc Natl Acad Sci U S A (1999) 22.80
The human disease network. Proc Natl Acad Sci U S A (2007) 19.58
A gene-coexpression network for global discovery of conserved genetic modules. Science (2003) 18.75
Large-scale identification, mapping, and genotyping of single-nucleotide polymorphisms in the human genome. Science (1998) 18.23
Protein interaction maps for complete genomes based on gene fusion events. Nature (1999) 16.48
Using Bayesian networks to analyze expression data. J Comput Biol (2000) 15.98
An automated method for finding molecular complexes in large protein interaction networks. BMC Bioinformatics (2003) 15.42
The tandem affinity purification (TAP) method: a general procedure of protein complex purification. Methods (2001) 15.37
Genome-wide analysis of DNA copy-number changes using cDNA microarrays. Nat Genet (1999) 14.96
Systems biology: a brief overview. Science (2002) 14.69
Discovering regulatory and signalling circuits in molecular interaction networks. Bioinformatics (2002) 12.88
Network-based classification of breast cancer metastasis. Mol Syst Biol (2007) 12.18
Next-generation sequencing transforms today's biology. Nat Methods (2007) 11.93
From patterns to pathways: gene expression data analysis comes of age. Nat Genet (2002) 10.35
Inferring cellular networks using probabilistic graphical models. Science (2004) 9.91
A human phenome-interactome network of protein complexes implicated in genetic disorders. Nat Biotechnol (2007) 9.90
Genomic analysis of regulatory network dynamics reveals large topological changes. Nature (2004) 9.32
Protein complexes and functional modules in molecular networks. Proc Natl Acad Sci U S A (2003) 9.03
A probabilistic functional network of yeast genes. Science (2004) 8.35
A genome-wide scalable SNP genotyping assay using microarray technology. Nat Genet (2005) 7.64
Comparing protein abundance and mRNA expression levels on a genomic scale. Genome Biol (2003) 6.98
Probabilistic Boolean Networks: a rule-based uncertainty model for gene regulatory networks. Bioinformatics (2002) 6.90
Global protein function prediction from protein-protein interaction networks. Nat Biotechnol (2003) 6.28
Genetic network inference: from co-expression clustering to reverse engineering. Bioinformatics (2000) 6.16
Network-based prediction of protein function. Mol Syst Biol (2007) 6.13
Biclustering algorithms for biological data analysis: a survey. IEEE/ACM Trans Comput Biol Bioinform (2006) 5.91
Relating whole-genome expression data with protein-protein interactions. Genome Res (2002) 5.78
Protein networks in disease. Genome Res (2008) 5.65
Methods and strategies for analyzing copy number variation using DNA microarrays. Nat Genet (2007) 5.64
Systematic interpretation of genetic interactions using protein networks. Nat Biotechnol (2005) 5.38
Modeling cellular machinery through biological network comparison. Nat Biotechnol (2006) 5.01
Conserved pathways within bacteria and yeast as revealed by global protein network alignment. Proc Natl Acad Sci U S A (2003) 4.68
Network-based prediction of human tissue-specific metabolism. Nat Biotechnol (2008) 4.39
Inferring domain-domain interactions from protein-protein interactions. Genome Res (2002) 4.36
Improved detection of overrepresentation of Gene-Ontology annotations with parent child analysis. Bioinformatics (2007) 4.32
Predicting disease genes using protein-protein interactions. J Med Genet (2006) 4.10
Principles of transcriptional control in the metabolic network of Saccharomyces cerevisiae. Nat Biotechnol (2003) 4.06
Evolutionary conservation of motif constituents in the yeast protein interaction network. Nat Genet (2003) 4.04
Biclustering of expression data. Proc Int Conf Intell Syst Mol Biol (2000) 3.97
The model organism as a system: integrating 'omics' data sets. Nat Rev Mol Cell Biol (2006) 3.69
Reconstruction of cellular signalling networks and analysis of their properties. Nat Rev Mol Cell Biol (2005) 3.46
Similarity of phylogenetic trees as indicator of protein-protein interaction. Protein Eng (2001) 3.36
Computational methods for the prediction of protein interactions. Curr Opin Struct Biol (2002) 3.35
Identification of genetic networks from a small number of gene expression patterns under the Boolean network model. Pac Symp Biocomput (1999) 3.27
Modeling interactome: scale-free or geometric? Bioinformatics (2004) 3.20
Navigating gene expression using microarrays--a technology review. Nat Cell Biol (2001) 3.20
Tissue specificity and the human protein interaction network. Mol Syst Biol (2009) 3.20
Identification of functional modules using network topology and high-throughput data. BMC Syst Biol (2007) 3.00
Evolving protein interaction networks through gene duplication. J Theor Biol (2003) 2.98
Whole-genome annotation by using evidence integration in functional-linkage networks. Proc Natl Acad Sci U S A (2004) 2.93
Graemlin: general and robust alignment of multiple large interaction networks. Genome Res (2006) 2.92
Topological structure analysis of the protein-protein interaction network in budding yeast. Nucleic Acids Res (2003) 2.90
Global alignment of multiple protein interaction networks with application to functional orthology detection. Proc Natl Acad Sci U S A (2008) 2.85
Biological network comparison using graphlet degree distribution. Bioinformatics (2007) 2.79
Subgraphs in random networks. Phys Rev E Stat Nonlin Soft Matter Phys (2003) 2.65
Predicting protein functions from redundancies in large-scale protein interaction networks. Proc Natl Acad Sci U S A (2003) 2.63
Structural systems biology: modelling protein interactions. Nat Rev Mol Cell Biol (2006) 2.61
Dynamic properties of network motifs contribute to biological network organization. PLoS Biol (2005) 2.58
Metabolic pathways in the post-genome era. Trends Biochem Sci (2003) 2.57
Network-based analysis of affected biological processes in type 2 diabetes models. PLoS Genet (2007) 2.54
Systems biology. Less is more in modeling large genetic networks. Science (2005) 2.44
Functional topology in a network of protein interactions. Bioinformatics (2004) 2.38
Post-transcriptional control of gene expression: a genome-wide perspective. Trends Biochem Sci (2005) 2.33
Identification of functional links between genes using phylogenetic profiles. Bioinformatics (2003) 2.33
Inferring network mechanisms: the Drosophila melanogaster protein interaction network. Proc Natl Acad Sci U S A (2005) 2.28
Prediction of protein function using protein-protein interaction data. J Comput Biol (2003) 2.15
Co-clustering of biological networks and gene expression data. Bioinformatics (2002) 2.12
Binary analysis and optimization-based normalization of gene expression data. Bioinformatics (2002) 2.10
Inferring gene networks from time series microarray data using dynamic Bayesian networks. Brief Bioinform (2003) 2.08
In silico two-hybrid system for the selection of physically interacting protein pairs. Proteins (2002) 2.05
Identification of protein complexes by comparative analysis of yeast and bacterial protein interaction data. J Comput Biol (2005) 2.02
Inferring protein domain interactions from databases of interacting proteins. Genome Biol (2005) 1.97
VAMPIRE microarray suite: a web-based platform for the interpretation of gene expression data. Nucleic Acids Res (2005) 1.97
Computational analysis of the synergy among multiple interacting genes. Mol Syst Biol (2007) 1.92
Gene expression network analysis and applications to immunology. Bioinformatics (2007) 1.87
Pairwise alignment of protein interaction networks. J Comput Biol (2006) 1.85
Duplication models for biological networks. J Comput Biol (2003) 1.70
Local modeling of global interactome networks. Bioinformatics (2005) 1.66
Co-evolutionary analysis of domains in interacting proteins reveals insights into domain-domain interactions mediating protein-protein interactions. J Mol Biol (2006) 1.60
Greedily building protein networks with confidence. Bioinformatics (2003) 1.53
An integrated approach to the prediction of domain-domain interactions. BMC Bioinformatics (2006) 1.52
PathFinder: mining signal transduction pathway segments from protein-protein interaction networks. BMC Bioinformatics (2007) 1.48
QPath: a method for querying pathways in a protein-protein interaction network. BMC Bioinformatics (2006) 1.46
Proteome analysis by mass spectrometry. Annu Rev Biophys Biomol Struct (2003) 1.44
Discovery and scoring of protein interaction subnetworks discriminative of late stage human colon cancer. Mol Cell Proteomics (2008) 1.43