Published in BMC Bioinformatics on June 29, 2010
Simultaneous reconstruction of multiple signaling pathways via the prize-collecting steiner forest problem. J Comput Biol (2013) 1.10
Perturbation biology: inferring signaling networks in cellular systems. PLoS Comput Biol (2013) 1.00
Passing messages between biological networks to refine predicted interactions. PLoS One (2013) 0.99
Reverse engineering and analysis of large genome-scale gene networks. Nucleic Acids Res (2012) 0.92
Differential network analysis reveals genetic effects on catalepsy modules. PLoS One (2013) 0.83
Revealing disease-associated pathways by network integration of untargeted metabolomics. Nat Methods (2016) 0.83
Optimization-based inference for temporally evolving networks with applications in biology. J Comput Biol (2012) 0.78
Construction and verification of the transcriptional regulatory response network of Streptococcus mutans upon treatment with the biofilm inhibitor carolacton. BMC Genomics (2014) 0.78
RegnANN: Reverse Engineering Gene Networks using Artificial Neural Networks. PLoS One (2011) 0.78
Network Modeling Identifies Patient-specific Pathways in Glioblastoma. Sci Rep (2016) 0.75
Predicting protein-ligand affinity with a random matrix framework. Proc Natl Acad Sci U S A (2016) 0.75
PTRcombiner: mining combinatorial regulation of gene expression from post-transcriptional interaction maps. BMC Genomics (2014) 0.75
A physarum-inspired prize-collecting steiner tree approach to identify subnetworks for drug repositioning. BMC Syst Biol (2016) 0.75
Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci U S A (1998) 192.97
Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science (1995) 88.48
Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol Biol Cell (1998) 62.20
Exploring the metabolic and genetic control of gene expression on a genomic scale. Science (1997) 60.15
Genomic expression programs in the response of yeast cells to environmental changes. Mol Biol Cell (2000) 36.09
Network motifs: simple building blocks of complex networks. Science (2002) 35.80
Network motifs in the transcriptional regulation network of Escherichia coli. Nat Genet (2002) 19.57
Correlation between protein and mRNA abundance in yeast. Mol Cell Biol (1999) 16.95
Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data. Nat Genet (2003) 14.56
ARACNE: an algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context. BMC Bioinformatics (2006) 14.49
Reverse engineering of regulatory networks in human B cells. Nat Genet (2005) 13.16
Stochastic kinetic analysis of developmental pathway bifurcation in phage lambda-infected Escherichia coli cells. Genetics (1998) 12.21
A genomic regulatory network for development. Science (2002) 9.67
Remodeling of yeast genome expression in response to environmental changes. Mol Biol Cell (2001) 9.63
Inferring genetic networks and identifying compound mode of action via expression profiling. Science (2003) 9.10
The Stanford Microarray Database. Nucleic Acids Res (2001) 7.77
The yeast cell-cycle network is robustly designed. Proc Natl Acad Sci U S A (2004) 6.76
Genetic network inference: from co-expression clustering to reverse engineering. Bioinformatics (2000) 6.16
The topology of the regulatory interactions predicts the expression pattern of the segment polarity genes in Drosophila melanogaster. J Theor Biol (2003) 5.85
Reverse engineering gene networks using singular value decomposition and robust regression. Proc Natl Acad Sci U S A (2002) 5.29
Reveal, a general reverse engineering algorithm for inference of genetic network architectures. Pac Symp Biocomput (1998) 4.99
Reverse engineering gene networks: integrating genetic perturbations with dynamical modeling. Proc Natl Acad Sci U S A (2003) 4.89
The YEASTRACT database: a tool for the analysis of transcription regulatory associations in Saccharomyces cerevisiae. Nucleic Acids Res (2006) 4.53
Topological and causal structure of the yeast transcriptional regulatory network. Nat Genet (2002) 4.22
Using graphical models and genomic expression data to statistically validate models of genetic regulatory networks. Pac Symp Biocomput (2001) 3.97
Inferring subnetworks from perturbed expression profiles. Bioinformatics (2001) 3.93
Candida parapsilosis, an emerging fungal pathogen. Clin Microbiol Rev (2008) 3.52
Global control of cell-cycle transcription by coupled CDK and network oscillators. Nature (2008) 3.32
Identifying cooperativity among transcription factors controlling the cell cycle in yeast. Nucleic Acids Res (2003) 2.50
Comprehensive analysis of combinatorial regulation using the transcriptional regulatory network of yeast. J Mol Biol (2006) 2.36
Statistical methods for identifying yeast cell cycle transcription factors. Proc Natl Acad Sci U S A (2005) 1.81
SIRENE: supervised inference of regulatory networks. Bioinformatics (2008) 1.79
Learning by message passing in networks of discrete synapses. Phys Rev Lett (2006) 1.70
A coordinated network of transporters with overlapping specificities provides a robust survival strategy. Proc Natl Acad Sci U S A (2009) 1.58
The proteasome: a proteolytic nanomachine of cell regulation and waste disposal. Biochim Biophys Acta (2004) 1.54
A semi-supervised method for predicting transcription factor-gene interactions in Escherichia coli. PLoS Comput Biol (2008) 1.40
Identification of transcription factor cooperativity via stochastic system model. Bioinformatics (2006) 1.25
New insights into the pleiotropic drug resistance network from genome-wide characterization of the YRR1 transcription factor regulation system. Mol Cell Biol (2002) 1.20
A post-translational modification code for transcription factors: sorting through a sea of signals. Trends Cell Biol (2009) 1.14
A general strategy to uncover transcription factor properties identifies a new regulator of drug resistance in yeast. J Biol Chem (2003) 1.11
The central role of PDR1 in the foundation of yeast drug resistance. J Biol Chem (2006) 1.10
Identifying cooperative transcriptional regulations using protein-protein interactions. Nucleic Acids Res (2005) 1.09
Function constrains network architecture and dynamics: a case study on the yeast cell cycle Boolean network. Phys Rev E Stat Nonlin Soft Matter Phys (2007) 1.08
Structure and properties of transcriptional networks driving selenite stress response in yeasts. BMC Genomics (2008) 1.07
Competitive promoter occupancy by two yeast paralogous transcription factors controlling the multidrug resistance phenomenon. J Biol Chem (2003) 1.03
Responses of pathogenic and nonpathogenic yeast species to steroids reveal the functioning and evolution of multidrug resistance transcriptional networks. Eukaryot Cell (2007) 0.97
Inferring regulatory networks. Front Biosci (2008) 0.95
Sparse combinatorial inference with an application in cancer biology. Bioinformatics (2008) 0.93
Transcription networks and cyclin/CDKs: the yin and yang of cell cycle oscillators. Cell Cycle (2008) 0.93
Topological comparison of methods for predicting transcriptional cooperativity in yeast. BMC Genomics (2008) 0.92
Inference of Boolean networks using sensitivity regularization. EURASIP J Bioinform Syst Biol (2008) 0.88
A critical assessment of Mus musculus gene function prediction using integrated genomic evidence. Genome Biol (2008) 4.78
Protein 3D structure computed from evolutionary sequence variation. PLoS One (2011) 4.71
Direct-coupling analysis of residue coevolution captures native contacts across many protein families. Proc Natl Acad Sci U S A (2011) 4.08
Improved contact prediction in proteins: using pseudolikelihoods to infer Potts models. Phys Rev E Stat Nonlin Soft Matter Phys (2013) 2.31
Integrated transcriptional and competitive endogenous RNA networks are cross-regulated in permissive molecular environments. Proc Natl Acad Sci U S A (2013) 2.13
Learning by message passing in networks of discrete synapses. Phys Rev Lett (2006) 1.70
Genomics-aided structure prediction. Proc Natl Acad Sci U S A (2012) 1.63
Structural basis of histidine kinase autophosphorylation deduced by integrating genomics, molecular dynamics, and mutagenesis. Proc Natl Acad Sci U S A (2012) 1.57
High-resolution protein complexes from integrating genomic information with molecular simulation. Proc Natl Acad Sci U S A (2009) 1.57
Genome-wide analysis identifies a functional association of Tet1 and Polycomb repressive complex 2 in mouse embryonic stem cells. Genome Biol (2013) 1.22
Modelling Competing Endogenous RNA Networks. PLoS One (2013) 1.21
Dissecting the specificity of protein-protein interaction in bacterial two-component signaling: orphans and crosstalks. PLoS One (2011) 1.20
Random K-satisfiability problem: from an analytic solution to an efficient algorithm. Phys Rev E Stat Nonlin Soft Matter Phys (2002) 1.17
Predicting protein functions with message passing algorithms. Bioinformatics (2004) 1.13
Simultaneous reconstruction of multiple signaling pathways via the prize-collecting steiner forest problem. J Comput Biol (2013) 1.10
Estimating the size of the solution space of metabolic networks. BMC Bioinformatics (2008) 1.09
Clustering by soft-constraint affinity propagation: applications to gene-expression data. Bioinformatics (2007) 1.04
From principal component to direct coupling analysis of coevolution in proteins: low-eigenvalue modes are needed for structure prediction. PLoS Comput Biol (2013) 1.03
Efficient supervised learning in networks with binary synapses. Proc Natl Acad Sci U S A (2007) 1.01
Shape similarity, better than semantic membership, accounts for the structure of visual object representations in a population of monkey inferotemporal neurons. PLoS Comput Biol (2013) 1.01
Inference of direct residue contacts in two-component signaling. Methods Enzymol (2010) 1.00
Computational modeling of phosphotransfer complexes in two-component signaling. Methods Enzymol (2010) 0.97
Threshold values, stability analysis, and high-q asymptotics for the coloring problem on random graphs. Phys Rev E Stat Nonlin Soft Matter Phys (2004) 0.94
Zero-temperature properties of RNA secondary structures. Phys Rev E Stat Nonlin Soft Matter Phys (2002) 0.91
Bridging the gaps in systems biology. Mol Genet Genomics (2014) 0.90
A stochastic local search algorithm for distance-based phylogeny reconstruction. Mol Biol Evol (2010) 0.85
An externally modulated, noise-driven switch for the regulation of SPI1 in Salmonella enterica serovar Typhimurium. J Math Biol (2010) 0.84
Source coding by efficient selection of ground-state clusters. Phys Rev E Stat Nonlin Soft Matter Phys (2005) 0.83
Solving satisfiability problems by fluctuations: the dynamics of stochastic local search algorithms. Phys Rev E Stat Nonlin Soft Matter Phys (2003) 0.83
Direct coupling analysis for protein contact prediction. Methods Mol Biol (2014) 0.80
Sharing information to reconstruct patient-specific pathways in heterogeneous diseases. Pac Symp Biocomput (2014) 0.79
Optimizing searches via rare events. Phys Rev Lett (2002) 0.78
Inter-individual variation in nucleotide excision repair pathway is modulated by non-synonymous polymorphisms in ERCC4 and MBD4 genes. Mutat Res (2013) 0.77
SLAMF1 regulation of chemotaxis and autophagy determines CLL patient response. J Clin Invest (2015) 0.77
Performance of a cavity-method-based algorithm for the prize-collecting Steiner tree problem on graphs. Phys Rev E Stat Nonlin Soft Matter Phys (2012) 0.77
Cavity approach to the random solid state. Phys Rev Lett (2005) 0.75
Computational complexity arising from degree correlations in networks. Phys Rev E Stat Nonlin Soft Matter Phys (2003) 0.75
Lossy data compression with random gates. Phys Rev Lett (2005) 0.75
Minimizing energy below the glass thresholds. Phys Rev E Stat Nonlin Soft Matter Phys (2004) 0.75
Statistical mechanics of combinatorial auctions. Phys Rev Lett (2006) 0.75