Published in Nucleic Acids Res on January 21, 2010
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EXPANDER--an integrative program suite for microarray data analysis. BMC Bioinformatics (2005) 3.43
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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
Regulatory on/off minimization of metabolic flux changes after genetic perturbations. Proc Natl Acad Sci U S A (2005) 2.99
Computational reconstruction of tissue-specific metabolic models: application to human liver metabolism. Mol Syst Biol (2010) 2.60
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Efficient algorithms for detecting signaling pathways in protein interaction networks. J Comput Biol (2006) 1.81
The average common substring approach to phylogenomic reconstruction. J Comput Biol (2006) 1.79
The large-scale organization of the bacterial network of ecological co-occurrence interactions. Nucleic Acids Res (2010) 1.75
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Simultaneous identification of multiple driver pathways in cancer. PLoS Comput Biol (2013) 1.71
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SPINE: a framework for signaling-regulatory pathway inference from cause-effect experiments. Bioinformatics (2007) 1.60
Direct evolution of genetic robustness in microRNA. Proc Natl Acad Sci U S A (2006) 1.59
Predicting metabolic biomarkers of human inborn errors of metabolism. Mol Syst Biol (2009) 1.59
A direct comparison of protein interaction confidence assignment schemes. BMC Bioinformatics (2006) 1.56
Glutamine-driven oxidative phosphorylation is a major ATP source in transformed mammalian cells in both normoxia and hypoxia. Mol Syst Biol (2013) 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
Predicting metabolic engineering knockout strategies for chemical production: accounting for competing pathways. Bioinformatics (2009) 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
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MAPK signaling to the early secretory pathway revealed by kinase/phosphatase functional screening. J Cell Biol (2010) 1.41
INDI: a computational framework for inferring drug interactions and their associated recommendations. Mol Syst Biol (2012) 1.40
Toward accurate reconstruction of functional protein networks. Mol Syst Biol (2009) 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
From E-MAPs to module maps: dissecting quantitative genetic interactions using physical interactions. Mol Syst Biol (2008) 1.35
iMAT: an integrative metabolic analysis tool. Bioinformatics (2010) 1.32
QNet: a tool for querying protein interaction networks. J Comput Biol (2008) 1.32
Inferring phylogenetic networks by the maximum parsimony criterion: a case study. Mol Biol Evol (2006) 1.30
Epitope mapping using combinatorial phage-display libraries: a graph-based algorithm. Nucleic Acids Res (2006) 1.29
Genome-scale analysis of translation elongation with a ribosome flow model. PLoS Comput Biol (2011) 1.29
A systems-level approach to mapping the telomere length maintenance gene circuitry. Mol Syst Biol (2008) 1.27
Maximum likelihood of phylogenetic networks. Bioinformatics (2006) 1.26
Efficient parsimony-based methods for phylogenetic network reconstruction. Bioinformatics (2007) 1.24
Identification of conserved protein complexes based on a model of protein network evolution. Bioinformatics (2007) 1.24
Association between translation efficiency and horizontal gene transfer within microbial communities. Nucleic Acids Res (2011) 1.24
Combining drug and gene similarity measures for drug-target elucidation. J Comput Biol (2011) 1.23
Determinants of translation elongation speed and ribosomal profiling biases in mouse embryonic stem cells. PLoS Comput Biol (2012) 1.23
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A genome-wide screen for essential yeast genes that affect telomere length maintenance. Nucleic Acids Res (2009) 1.20