Published in Bioinformatics on June 26, 2009
Computational tools for prioritizing candidate genes: boosting disease gene discovery. Nat Rev Genet (2012) 2.92
Issues in bioinformatics benchmarking: the case study of multiple sequence alignment. Nucleic Acids Res (2010) 2.05
Yeast: an experimental organism for 21st Century biology. Genetics (2011) 1.88
Systems biology of the autophagy-lysosomal pathway. Autophagy (2011) 1.15
A comprehensive assessment of methods for de-novo reverse-engineering of genome-scale regulatory networks. Genomics (2010) 1.07
Accurate evaluation and analysis of functional genomics data and methods. Ann N Y Acad Sci (2012) 0.94
The impact of incomplete knowledge on the evaluation of protein function prediction: a structured-output learning perspective. Bioinformatics (2014) 0.94
Mining GO annotations for improving annotation consistency. PLoS One (2012) 0.94
A quick guide to large-scale genomic data mining. PLoS Comput Biol (2010) 0.93
Negative example selection for protein function prediction: the NoGO database. PLoS Comput Biol (2014) 0.84
Hierarchical ensemble methods for protein function prediction. ISRN Bioinform (2014) 0.84
Parametric Bayesian priors and better choice of negative examples improve protein function prediction. Bioinformatics (2013) 0.83
Novel insights into embryonic stem cell self-renewal revealed through comparative human and mouse systems biology networks. Stem Cells (2014) 0.80
Cell-type-specific predictive network yields novel insights into mouse embryonic stem cell self-renewal and cell fate. PLoS One (2013) 0.79
De-novo learning of genome-scale regulatory networks in S. cerevisiae. PLoS One (2014) 0.78
PHENOstruct: Prediction of human phenotype ontology terms using heterogeneous data sources. F1000Res (2015) 0.77
The CRIT framework for identifying cross patterns in systems biology and application to chemogenomics. Genome Biol (2011) 0.75
Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet (2000) 336.52
KEGG for linking genomes to life and the environment. Nucleic Acids Res (2007) 49.37
Causal protein-signaling networks derived from multiparameter single-cell data. Science (2005) 34.28
NCBI GEO: mining tens of millions of expression profiles--database and tools update. Nucleic Acids Res (2006) 19.42
A Bayesian networks approach for predicting protein-protein interactions from genomic data. Science (2003) 12.07
Alternative splicing: new insights from global analyses. Cell (2006) 10.31
Gene Ontology annotations at SGD: new data sources and annotation methods. Nucleic Acids Res (2007) 9.03
ArrayExpress--a public database of microarray experiments and gene expression profiles. Nucleic Acids Res (2006) 8.92
The FunCat, a functional annotation scheme for systematic classification of proteins from whole genomes. Nucleic Acids Res (2004) 8.79
A probabilistic functional network of yeast genes. Science (2004) 8.35
A Bayesian framework for combining heterogeneous data sources for gene function prediction (in Saccharomyces cerevisiae). Proc Natl Acad Sci U S A (2003) 6.19
Tetrazolium overlay technique for population studies of respiration deficiency in yeast. Science (1957) 4.52
Synthetic genetic array analysis in Saccharomyces cerevisiae. Methods Mol Biol (2006) 4.45
Discovery of biological networks from diverse functional genomic data. Genome Biol (2005) 3.73
Whole-proteome prediction of protein function via graph-theoretic analysis of interaction maps. Bioinformatics (2005) 3.70
The Stanford Microarray Database: implementation of new analysis tools and open source release of software. Nucleic Acids Res (2006) 3.66
A statistical framework for genomic data fusion. Bioinformatics (2004) 3.64
Exploring the functional landscape of gene expression: directed search of large microarray compendia. Bioinformatics (2007) 3.59
Finding function: evaluation methods for functional genomic data. BMC Genomics (2006) 3.10
Whole-genome annotation by using evidence integration in functional-linkage networks. Proc Natl Acad Sci U S A (2004) 2.93
Hierarchical multi-label prediction of gene function. Bioinformatics (2006) 2.62
The yeast actin cytoskeleton: from cellular function to biochemical mechanism. Microbiol Mol Biol Rev (2006) 2.55
A scalable method for integration and functional analysis of multiple microarray datasets. Bioinformatics (2006) 2.10
Computationally driven, quantitative experiments discover genes required for mitochondrial biogenesis. PLoS Genet (2009) 1.90
Context-sensitive data integration and prediction of biological networks. Bioinformatics (2007) 1.72
Directing experimental biology: a case study in mitochondrial biogenesis. PLoS Comput Biol (2009) 1.20
The genetic landscape of a cell. Science (2010) 16.52
Short hairpin RNAs (shRNAs) induce sequence-specific silencing in mammalian cells. Genes Dev (2002) 10.71
Measuring differential gene expression by short read sequencing: quantitative comparison to 2-channel gene expression microarrays. BMC Genomics (2009) 6.41
Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry. Proc Natl Acad Sci U S A (2007) 5.09
Stable suppression of gene expression by RNAi in mammalian cells. Proc Natl Acad Sci U S A (2002) 5.05
A critical assessment of Mus musculus gene function prediction using integrated genomic evidence. Genome Biol (2008) 4.78
Visualization of omics data for systems biology. Nat Methods (2010) 4.59
Dissection of genetically complex traits with extremely large pools of yeast segregants. Nature (2010) 4.32
Coordination of growth rate, cell cycle, stress response, and metabolic activity in yeast. Mol Biol Cell (2007) 4.27
Endothelial cell diversity revealed by global expression profiling. Proc Natl Acad Sci U S A (2003) 3.98
Discovery of biological networks from diverse functional genomic data. Genome Biol (2005) 3.73
Exploring the functional landscape of gene expression: directed search of large microarray compendia. Bioinformatics (2007) 3.59
Metabolomic analysis via reversed-phase ion-pairing liquid chromatography coupled to a stand alone orbitrap mass spectrometer. Anal Chem (2010) 3.22
Finding function: evaluation methods for functional genomic data. BMC Genomics (2006) 3.10
Systemic and cell type-specific gene expression patterns in scleroderma skin. Proc Natl Acad Sci U S A (2003) 2.87
Systems-level dynamic analyses of fate change in murine embryonic stem cells. Nature (2009) 2.70
Exploring the human genome with functional maps. Genome Res (2009) 2.69
Quantitative analysis of fitness and genetic interactions in yeast on a genome scale. Nat Methods (2010) 2.67
Hierarchical multi-label prediction of gene function. Bioinformatics (2006) 2.62
A simple, assumption-free, and clinically interpretable approach for analysis of modified Rankin outcomes. Stroke (2012) 2.57
GOLEM: an interactive graph-based gene-ontology navigation and analysis tool. BMC Bioinformatics (2006) 2.46
Remote ischemic perconditioning is effective alone and in combination with intravenous tissue-type plasminogen activator in murine model of embolic stroke. Stroke (2012) 2.46
Chapter 2: Data-driven view of disease biology. PLoS Comput Biol (2012) 2.40
Variation in gene expression patterns in human gastric cancers. Mol Biol Cell (2003) 2.39
Modeling complex genetic interactions in a simple eukaryotic genome: actin displays a rich spectrum of complex haploinsufficiencies. Genes Dev (2006) 2.26
Systematic exploration of essential yeast gene function with temperature-sensitive mutants. Nat Biotechnol (2011) 2.26
A genomewide functional network for the laboratory mouse. PLoS Comput Biol (2008) 2.25
Remote evaluation of acute ischemic stroke: reliability of National Institutes of Health Stroke Scale via telestroke. Stroke (2003) 2.17
A scalable method for integration and functional analysis of multiple microarray datasets. Bioinformatics (2006) 2.10
Significant conservation of synthetic lethal genetic interaction networks between distantly related eukaryotes. Proc Natl Acad Sci U S A (2008) 2.01
IMP: a multi-species functional genomics portal for integration, visualization and prediction of protein functions and networks. Nucleic Acids Res (2012) 2.01
Defining cell-type specificity at the transcriptional level in human disease. Genome Res (2013) 1.96
Functional analysis of gene duplications in Saccharomyces cerevisiae. Genetics (2006) 1.96
SDF-1 (CXCL12) is upregulated in the ischemic penumbra following stroke: association with bone marrow cell homing to injury. J Neuropathol Exp Neurol (2004) 1.94
Computationally driven, quantitative experiments discover genes required for mitochondrial biogenesis. PLoS Genet (2009) 1.90
Accurate detection of aneuploidies in array CGH and gene expression microarray data. Bioinformatics (2004) 1.89
Systematic exploration of synergistic drug pairs. Mol Syst Biol (2011) 1.89
Targets for vascular protection after acute ischemic stroke. Stroke (2004) 1.88
Element 1360 and RNAi components contribute to HP1-dependent silencing of a pericentric reporter. Curr Biol (2006) 1.85
Nested effects models for high-dimensional phenotyping screens. Bioinformatics (2007) 1.84
Epigenetic and genetic influences on DNA methylation variation in maize populations. Plant Cell (2013) 1.83
Phospholipase A2 group IIA expression in gastric adenocarcinoma is associated with prolonged survival and less frequent metastasis. Proc Natl Acad Sci U S A (2002) 1.81
Matrix metalloproteinase-9 in an exploratory trial of intravenous minocycline for acute ischemic stroke. Stroke (2011) 1.80
Minocycline up-regulates Bcl-2 and protects against cell death in mitochondria. J Biol Chem (2004) 1.79
Integrated molecular profiles of invasive breast tumors and ductal carcinoma in situ (DCIS) reveal differential vascular and interleukin signaling. Proc Natl Acad Sci U S A (2011) 1.78
Predicting gene function in a hierarchical context with an ensemble of classifiers. Genome Biol (2008) 1.78
Global analysis of gene function in yeast by quantitative phenotypic profiling. Mol Syst Biol (2006) 1.77
Synthetic genetic array (SGA) analysis in Saccharomyces cerevisiae and Schizosaccharomyces pombe. Methods Enzymol (2010) 1.73
Context-sensitive data integration and prediction of biological networks. Bioinformatics (2007) 1.72
Minocycline to improve neurologic outcome in stroke (MINOS): a dose-finding study. Stroke (2010) 1.69
Delayed minocycline inhibits ischemia-activated matrix metalloproteinases 2 and 9 after experimental stroke. BMC Neurosci (2006) 1.69
An integrated approach to characterize genetic interaction networks in yeast metabolism. Nat Genet (2011) 1.62
Who's in favor of translational cell therapy for stroke: STEPS forward please? Cell Transplant (2009) 1.60
Variation in gene expression patterns in follicular lymphoma and the response to rituximab. Proc Natl Acad Sci U S A (2003) 1.58
Tissue-specific functional networks for prioritizing phenotype and disease genes. PLoS Comput Biol (2012) 1.54
Improving modified Rankin Scale assessment with a simplified questionnaire. Stroke (2010) 1.50
Predicting cellular growth from gene expression signatures. PLoS Comput Biol (2009) 1.50
Global prediction of tissue-specific gene expression and context-dependent gene networks in Caenorhabditis elegans. PLoS Comput Biol (2009) 1.48
Low dose intravenous minocycline is neuroprotective after middle cerebral artery occlusion-reperfusion in rats. BMC Neurol (2004) 1.47
Coordinated concentration changes of transcripts and metabolites in Saccharomyces cerevisiae. PLoS Comput Biol (2009) 1.47
Riboneogenesis in yeast. Cell (2011) 1.43
DRYGIN: a database of quantitative genetic interaction networks in yeast. Nucleic Acids Res (2009) 1.41
Enhanced yeast one-hybrid assays for high-throughput gene-centered regulatory network mapping. Nat Methods (2011) 1.41
Optimal delivery of minocycline to the brain: implication for human studies of acute neuroprotection. Exp Neurol (2004) 1.40
Maize gene atlas developed by RNA sequencing and comparative evaluation of transcriptomes based on RNA sequencing and microarrays. PLoS One (2013) 1.40
Bone marrow grafts restore cerebral blood flow and blood brain barrier in stroke rats. Brain Res (2004) 1.40
Pathophysiology and treatment of stroke in sickle-cell disease: present and future. Lancet Neurol (2006) 1.39
The neuroblast and angioblast chemotaxic factor SDF-1 (CXCL12) expression is briefly up regulated by reactive astrocytes in brain following neonatal hypoxic-ischemic injury. BMC Neurosci (2005) 1.38
Detailing regulatory networks through large scale data integration. Bioinformatics (2009) 1.38
The Sleipnir library for computational functional genomics. Bioinformatics (2008) 1.36
Endogenous DNA replication stress results in expansion of dNTP pools and a mutator phenotype. EMBO J (2012) 1.35
Bringing order to protein disorder through comparative genomics and genetic interactions. Genome Biol (2011) 1.34
Uniform nomenclature for the mitochondrial contact site and cristae organizing system. J Cell Biol (2014) 1.34
Rural-urban differences in acute stroke management practices: a modifiable disparity. Arch Neurol (2008) 1.33
Therapeutic targets and limits of minocycline neuroprotection in experimental ischemic stroke. BMC Neurosci (2009) 1.33
Using networks to measure similarity between genes: association index selection. Nat Methods (2013) 1.30
Minocycline and tissue-type plasminogen activator for stroke: assessment of interaction potential. Stroke (2009) 1.30
Charting the genetic interaction map of a cell. Curr Opin Biotechnol (2010) 1.28
Short hairpin activated gene silencing in mammalian cells. Methods Mol Biol (2004) 1.28