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On the Nature and Evolutionary Impact of Phenotypic Robustness Mechanisms. Annu Rev Ecol Evol Syst (2014) 0.94

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RSRE: RNA structural robustness evaluator. Nucleic Acids Res (2007) 0.84

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In silico genetic robustness analysis of secondary structural elements in the miRNA gene. J Mol Evol (2008) 0.83

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Sampled ensemble neutrality as a feature to classify potential structured RNAs. BMC Genomics (2015) 0.81

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RNAdualPF: software to compute the dual partition function with sample applications in molecular evolution theory. BMC Bioinformatics (2016) 0.76

Essential Genes Embody Increased Mutational Robustness to Compensate for the Lack of Backup Genetic Redundancy. PLoS One (2016) 0.75

EvoRSR: an integrated system for exploring evolution of RNA structural robustness. BMC Bioinformatics (2009) 0.75

Antigenic diversification is correlated with increased thermostability in a mammalian virus. Virology (2016) 0.75

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The nuclear RNase III Drosha initiates microRNA processing. Nature (2003) 35.49

An extensive class of small RNAs in Caenorhabditis elegans. Science (2001) 34.17

The microRNA Registry. Nucleic Acids Res (2004) 29.45

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Viral RNA and evolved mutational robustness. J Exp Zool (1999) 1.38

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Network-based prediction of human tissue-specific metabolism. Nat Biotechnol (2008) 4.39

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

Predicting selective drug targets in cancer through metabolic networks. Mol Syst Biol (2011) 3.65

Translation efficiency is determined by both codon bias and folding energy. Proc Natl Acad Sci U S A (2010) 3.40

Multiple knockout analysis of genetic robustness in the yeast metabolic network. Nat Genet (2006) 3.25

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

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

Large-scale reconstruction and phylogenetic analysis of metabolic environments. Proc Natl Acad Sci U S A (2008) 2.23

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

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The evolution of modularity in bacterial metabolic networks. Proc Natl Acad Sci U S A (2008) 1.96

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

Reconstruction of Arabidopsis metabolic network models accounting for subcellular compartmentalization and tissue-specificity. Proc Natl Acad Sci U S A (2011) 1.68

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

Integrating quantitative proteomics and metabolomics with a genome-scale metabolic network model. Bioinformatics (2010) 1.65

Composite effects of gene determinants on the translation speed and density of ribosomes. Genome Biol (2011) 1.61

Determinants of protein abundance and translation efficiency in S. cerevisiae. PLoS Comput Biol (2007) 1.60

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

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

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

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

Unsupervised learning of natural languages. Proc Natl Acad Sci U S A (2005) 1.44

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

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

iMAT: an integrative metabolic analysis tool. Bioinformatics (2010) 1.32

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

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

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

Gene expression of Caenorhabditis elegans neurons carries information on their synaptic connectivity. PLoS Comput Biol (2006) 1.21

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

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

Integrative genomic analysis identifies isoleucine and CodY as regulators of Listeria monocytogenes virulence. PLoS Genet (2012) 1.14

Metabolic associations of reduced proliferation and oxidative stress in advanced breast cancer. Cancer Res (2012) 1.13

Structural robustness of metabolic networks with respect to multiple knockouts. J Theor Biol (2007) 1.11

Feature selection via coalitional game theory. Neural Comput (2007) 1.11

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

Network-based prediction of metabolic enzymes' subcellular localization. Bioinformatics (2009) 1.10

Meta-analysis of gene expression data: a predictor-based approach. Bioinformatics (2007) 1.07

Selection for translation efficiency on synonymous polymorphisms in recent human evolution. Genome Biol Evol (2011) 1.05

Functional representation of enzymes by specific peptides. PLoS Comput Biol (2007) 1.05

Reconstructing ancestral gene content by coevolution. Genome Res (2009) 1.04

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

Model-based identification of drug targets that revert disrupted metabolism and its application to ageing. Nat Commun (2013) 1.01

Fair attribution of functional contribution in artificial and biological networks. Neural Comput (2004) 1.01

Conservation of expression and sequence of metabolic genes is reflected by activity across metabolic states. PLoS Comput Biol (2006) 1.00

Predicting drug targets and biomarkers of cancer via genome-scale metabolic modeling. Clin Cancer Res (2012) 1.00

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

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

p53 promotes the expression of gluconeogenesis-related genes and enhances hepatic glucose production. Cancer Metab (2013) 0.98

Metabolic modeling of endosymbiont genome reduction on a temporal scale. Mol Syst Biol (2011) 0.98

Properties of untranslated regions of the S. cerevisiae genome. BMC Genomics (2009) 0.98

Quantitative analysis of genetic and neuronal multi-perturbation experiments. PLoS Comput Biol (2005) 0.97

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

MuD: an interactive web server for the prediction of non-neutral substitutions using protein structural data. Nucleic Acids Res (2010) 0.96

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

Can single knockouts accurately single out gene functions? BMC Syst Biol (2008) 0.93

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

Evolutionary rate and gene expression across different brain regions. Genome Biol (2008) 0.90

Motif extraction and protein classification. Proc IEEE Comput Syst Bioinform Conf (2005) 0.90

Co-evolutionary networks of genes and cellular processes across fungal species. Genome Biol (2009) 0.89

Nucleotide variation of regulatory motifs may lead to distinct expression patterns. Bioinformatics (2007) 0.89

Evolutionary conservation and over-representation of functionally enriched network patterns in the yeast regulatory network. BMC Syst Biol (2007) 0.88

Computational evaluation of cellular metabolic costs successfully predicts genes whose expression is deleterious. Proc Natl Acad Sci U S A (2013) 0.88

Facial attractiveness: beauty and the machine. Neural Comput (2006) 0.88

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

Cooperation and cheating in microbial exoenzyme production--theoretical analysis for biotechnological applications. Biotechnol J (2010) 0.87

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

Glycan degradation (GlyDeR) analysis predicts mammalian gut microbiota abundance and host diet-specific adaptations. MBio (2014) 0.86

Fair localization of function via multi-lesion analysis. Neuroinformatics (2004) 0.85

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

Localization of function via lesion analysis. Neural Comput (2003) 0.85

Higher-order genomic organization of cellular functions in yeast. J Comput Biol (2009) 0.84

Inferring functional pathways from multi-perturbation data. Bioinformatics (2006) 0.84

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

Axiomatic scalable neurocontroller analysis via the Shapley value. Artif Life (2006) 0.83

Flux balance analysis accounting for metabolite dilution. Genome Biol (2010) 0.83

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

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

Hippocampus neuronal metabolic gene expression outperforms whole tissue data in accurately predicting Alzheimer's disease progression. Neurobiol Aging (2012) 0.80

Multiperturbation analysis of distributed neural networks: the case of spatial neglect. Hum Brain Mapp (2009) 0.80

A machine learning predictor of facial attractiveness revealing human-like psychophysical biases. Vision Res (2008) 0.80

A genome-wide systematic analysis reveals different and predictive proliferation expression signatures of cancerous vs. non-cancerous cells. PLoS Genet (2013) 0.80

Metabolically re-modeling the drug pipeline. Curr Opin Pharmacol (2013) 0.79

Global map of physical interactions among differentially expressed genes in multiple sclerosis relapses and remissions. Hum Mol Genet (2011) 0.79