Published in Bioinformatics on August 27, 2007
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Exploring the human genome with functional maps. Genome Res (2009) 2.69
Probabilistic retrieval and visualization of biologically relevant microarray experiments. Bioinformatics (2009) 2.24
Mutation in TACO1, encoding a translational activator of COX I, results in cytochrome c oxidase deficiency and late-onset Leigh syndrome. Nat Genet (2009) 1.95
Identification of small RNA pathway genes using patterns of phylogenetic conservation and divergence. Nature (2012) 1.92
YeastMine--an integrated data warehouse for Saccharomyces cerevisiae data as a multipurpose tool-kit. Database (Oxford) (2012) 1.92
Boolean implication networks derived from large scale, whole genome microarray datasets. Genome Biol (2008) 1.91
Computationally driven, quantitative experiments discover genes required for mitochondrial biogenesis. PLoS Genet (2009) 1.90
Yeast: an experimental organism for 21st Century biology. Genetics (2011) 1.88
Bayesian approach to transforming public gene expression repositories into disease diagnosis databases. Proc Natl Acad Sci U S A (2010) 1.84
Systematic planning of genome-scale experiments in poorly studied species. PLoS Comput Biol (2010) 1.66
An intrinsically disordered yeast prion arrests the cell cycle by sequestering a spindle pole body component. J Cell Biol (2012) 1.60
A computational screen for regulators of oxidative phosphorylation implicates SLIRP in mitochondrial RNA homeostasis. PLoS Genet (2009) 1.56
Tissue-specific functional networks for prioritizing phenotype and disease genes. PLoS Comput Biol (2012) 1.54
Saccharomyces genome database provides new regulation data. Nucleic Acids Res (2013) 1.52
Rational diversification of a promoter providing fine-tuned expression and orthogonal regulation for synthetic biology. PLoS One (2012) 1.52
Mining for coexpression across hundreds of datasets using novel rank aggregation and visualization methods. Genome Biol (2009) 1.52
"Guilt by association" is the exception rather than the rule in gene networks. PLoS Comput Biol (2012) 1.45
Natural Variation in plep-1 Causes Male-Male Copulatory Behavior in C. elegans. Curr Biol (2015) 1.41
Independent component analysis: mining microarray data for fundamental human gene expression modules. J Biomed Inform (2010) 1.39
Loss of a conserved tRNA anticodon modification perturbs cellular signaling. PLoS Genet (2013) 1.37
Curated collection of yeast transcription factor DNA binding specificity data reveals novel structural and gene regulatory insights. Genome Biol (2011) 1.32
Structural biochemistry of nuclear actin-related proteins 4 and 8 reveals their interaction with actin. EMBO J (2011) 1.28
YeTFaSCo: a database of evaluated yeast transcription factor sequence specificities. Nucleic Acids Res (2011) 1.26
Genetic interactions reveal the evolutionary trajectories of duplicate genes. Mol Syst Biol (2010) 1.22
The impact of incomplete knowledge on evaluation: an experimental benchmark for protein function prediction. Bioinformatics (2009) 1.21
Directing experimental biology: a case study in mitochondrial biogenesis. PLoS Comput Biol (2009) 1.20
Multi-dimensional correlations for gene coexpression and application to the large-scale data of Arabidopsis. Bioinformatics (2009) 1.17
The role of indirect connections in gene networks in predicting function. Bioinformatics (2011) 1.10
Content-based microarray search using differential expression profiles. BMC Bioinformatics (2010) 1.07
Identification of molecular pathways affected by pterostilbene, a natural dimethylether analog of resveratrol. BMC Med Genomics (2008) 1.06
Mapping yeast transcriptional networks. Genetics (2013) 1.06
Systematically differentiating functions for alternatively spliced isoforms through integrating RNA-seq data. PLoS Comput Biol (2013) 1.04
A comprehensive performance evaluation on the prediction results of existing cooperative transcription factors identification algorithms. BMC Syst Biol (2014) 1.00
Meta Analysis of Gene Expression Data within and Across Species. Curr Genomics (2008) 0.95
Ontology-aware classification of tissue and cell-type signals in gene expression profiles across platforms and technologies. Bioinformatics (2013) 0.95
Targeted exploration and analysis of large cross-platform human transcriptomic compendia. Nat Methods (2015) 0.95
Assessing the functional structure of genomic data. Bioinformatics (2008) 0.93
A quick guide to large-scale genomic data mining. PLoS Comput Biol (2010) 0.93
Precise genetic mapping and integrative bioinformatics in Diversity Outbred mice reveals Hydin as a novel pain gene. Mamm Genome (2014) 0.91
A rapid and massive gene expression shift marking adolescent transition in C. elegans. Sci Rep (2014) 0.89
Using pre-existing microarray datasets to increase experimental power: application to insulin resistance. PLoS Comput Biol (2010) 0.89
Genome-wide matching of genes to cellular roles using guilt-by-association models derived from single sample analysis. BMC Res Notes (2012) 0.88
Using the Saccharomyces Genome Database (SGD) for analysis of genomic information. Curr Protoc Bioinformatics (2011) 0.88
SCS3 and YFT2 link transcription of phospholipid biosynthetic genes to ER stress and the UPR. PLoS Genet (2012) 0.87
PCTFPeval: a web tool for benchmarking newly developed algorithms for predicting cooperative transcription factor pairs in yeast. BMC Bioinformatics (2015) 0.86
Generalized random set framework for functional enrichment analysis using primary genomics datasets. Bioinformatics (2010) 0.86
Prosecutor: parameter-free inference of gene function for prokaryotes using DNA microarray data, genomic context and multiple gene annotation sources. BMC Genomics (2008) 0.85
Beyond tissueInfo: functional prediction using tissue expression profile similarity searches. Nucleic Acids Res (2008) 0.85
Proceedings of the 2008 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) Conference. BMC Bioinformatics (2008) 0.85
High-precision high-coverage functional inference from integrated data sources. BMC Bioinformatics (2008) 0.85
Progress and challenges in the computational prediction of gene function using networks. F1000Res (2012) 0.84
What's that gene (or protein)? Online resources for exploring functions of genes, transcripts, and proteins. Mol Biol Cell (2014) 0.84
Xbp1 directs global repression of budding yeast transcription during the transition to quiescence and is important for the longevity and reversibility of the quiescent state. PLoS Genet (2013) 0.84
Transcription factor binding to Caenorhabditis elegans first introns reveals lack of redundancy with gene promoters. Nucleic Acids Res (2013) 0.84
Comparative genomic analysis of the DUF71/COG2102 family predicts roles in diphthamide biosynthesis and B12 salvage. Biol Direct (2012) 0.82
MIsoMine: a genome-scale high-resolution data portal of expression, function and networks at the splice isoform level in the mouse. Database (Oxford) (2015) 0.82
Discovering biological connections between experimental conditions based on common patterns of differential gene expression. BMC Bioinformatics (2011) 0.81
Saccharomyces cerevisiae genes involved in survival of heat shock. G3 (Bethesda) (2013) 0.81
Decoupling of divergent gene regulation by sequence-specific DNA binding factors. Nucleic Acids Res (2015) 0.81
Web resources for model organism studies. Genomics Proteomics Bioinformatics (2015) 0.81
Multiple small RNA pathways regulate the silencing of repeated and foreign genes in C. elegans. Genes Dev (2013) 0.81
Interactive Big Data Resource to Elucidate Human Immune Pathways and Diseases. Immunity (2015) 0.81
A new system for comparative functional genomics of Saccharomyces yeasts. Genetics (2013) 0.81
A lysine-rich region within fungal BAG domain-containing proteins mediates a novel association with ribosomes. Eukaryot Cell (2012) 0.80
Evolutionary engineering of a wine yeast strain revealed a key role of inositol and mannoprotein metabolism during low-temperature fermentation. BMC Genomics (2015) 0.80
Metabolic and chaperone gene loss marks the origin of animals: evidence for Hsp104 and Hsp78 chaperones sharing mitochondrial enzymes as clients. PLoS One (2015) 0.80
Query-based biclustering of gene expression data using Probabilistic Relational Models. BMC Bioinformatics (2011) 0.80
Structural and functional study of YER067W, a new protein involved in yeast metabolism control and drug resistance. PLoS One (2010) 0.79
The novel component Kgd4 recruits the E3 subunit to the mitochondrial α-ketoglutarate dehydrogenase. Mol Biol Cell (2014) 0.79
Cell-type-specific predictive network yields novel insights into mouse embryonic stem cell self-renewal and cell fate. PLoS One (2013) 0.79
Query large scale microarray compendium datasets using a model-based bayesian approach with variable selection. PLoS One (2009) 0.79
Deriving transcriptional programs and functional processes from gene expression databases. Bioinformatics (2012) 0.79
Biocuration at the Saccharomyces genome database. Genesis (2015) 0.78
Saccharomyces cerevisiae Forms d-2-Hydroxyglutarate and Couples Its Degradation to d-Lactate Formation via a Cytosolic Transhydrogenase. J Biol Chem (2016) 0.78
The YeastGenome app: the Saccharomyces Genome Database at your fingertips. Database (Oxford) (2013) 0.78
Topoisomerase II regulates yeast genes with singular chromatin architectures. Nucleic Acids Res (2013) 0.77
Polyglutamine toxicity in yeast induces metabolic alterations and mitochondrial defects. BMC Genomics (2015) 0.77
Evolution of cis-regulatory elements in yeast de novo and duplicated new genes. BMC Genomics (2012) 0.77
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yStreX: yeast stress expression database. Database (Oxford) (2014) 0.76
CellMapper: rapid and accurate inference of gene expression in difficult-to-isolate cell types. Genome Biol (2016) 0.76
Turning publicly available gene expression data into discoveries using gene set context analysis. Nucleic Acids Res (2015) 0.76
Nuclear actin-related proteins take shape. Bioarchitecture (2011) 0.76
A combined binary interaction and phenotypic map of C. elegans cell polarity proteins. Nat Cell Biol (2016) 0.76
Application of biclustering of gene expression data and gene set enrichment analysis methods to identify potentially disease causing nanomaterials. Beilstein J Nanotechnol (2015) 0.76
Identifying functional transcription factor binding sites in yeast by considering their positional preference in the promoters. PLoS One (2013) 0.76
Construction and evaluation of yeast expression networks by database-guided predictions. Microb Cell (2016) 0.75
Integrating in silico resources to map a signaling network. Methods Mol Biol (2014) 0.75
Computational discovery of transcriptional regulatory modules in fungal ribosome biogenesis genes reveals novel sequence and function patterns. PLoS One (2013) 0.75
Identification of under-detected periodicity in time-series microarray data by using empirical mode decomposition. PLoS One (2014) 0.75
Cellobionic acid utilization: from Neurospora crassa to Saccharomyces cerevisiae. Biotechnol Biofuels (2015) 0.75
Comparative analyses of homocitrate synthase genes of ascomycetous yeasts. Int J Evol Biol (2012) 0.75
NP-MuScL: unsupervised global prediction of interaction networks from multiple data sources. J Comput Biol (2013) 0.75
The Hsp90 cochaperones Cpr6, Cpr7, and Cns1 interact with the intact ribosome. Eukaryot Cell (2014) 0.75
Proceedings of the 2009 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) conference. Introduction. BMC Bioinformatics (2009) 0.75
Regulation of cell-to-cell variability in divergent gene expression. Nat Commun (2016) 0.75
YAGM: a web tool for mining associated genes in yeast based on diverse biological associations. BMC Syst Biol (2015) 0.75
The genetic landscape of a cell. Science (2010) 16.52
Metagenomic biomarker discovery and explanation. Genome Biol (2011) 11.29
Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. Nat Biotechnol (2013) 11.05
Metagenomic microbial community profiling using unique clade-specific marker genes. Nat Methods (2012) 8.37
Metabolic reconstruction for metagenomic data and its application to the human microbiome. PLoS Comput Biol (2012) 6.27
Genomic analysis identifies association of Fusobacterium with colorectal carcinoma. Genome Res (2011) 5.97
Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment. Genome Biol (2012) 5.66
Expansion of intestinal Prevotella copri correlates with enhanced susceptibility to arthritis. Elife (2013) 5.49
Microbial co-occurrence relationships in the human microbiome. PLoS Comput Biol (2012) 5.35
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
A critical assessment of Mus musculus gene function prediction using integrated genomic evidence. Genome Biol (2008) 4.78
Composition of the adult digestive tract bacterial microbiome based on seven mouth surfaces, tonsils, throat and stool samples. Genome Biol (2012) 4.68
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
Finding function: evaluation methods for functional genomic data. BMC Genomics (2006) 3.10
A guide to enterotypes across the human body: meta-analysis of microbial community structures in human microbiome datasets. PLoS Comput Biol (2013) 2.96
Systemic and cell type-specific gene expression patterns in scleroderma skin. Proc Natl Acad Sci U S A (2003) 2.87
Colorectal cancer: a tale of two sides or a continuum? Gut (2012) 2.85
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
Pediatric Crohn disease patients exhibit specific ileal transcriptome and microbiome signature. J Clin Invest (2014) 2.39
Growth hormone enhances thymic function in HIV-1-infected adults. J Clin Invest (2008) 2.35
Prognostic significance of microscopic positive margins for gastric cancer patients with potentially curative resection. Ann Surg Oncol (2009) 2.31
PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes. Nat Commun (2013) 2.28
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
The Human Microbiome Project: a community resource for the healthy human microbiome. PLoS Biol (2012) 2.17
Remote evaluation of acute ischemic stroke: reliability of National Institutes of Health Stroke Scale via telestroke. Stroke (2003) 2.17
Steroid-resistant kaposiform hemangioendothelioma: a retrospective study of 37 patients treated with vincristine and long-term follow-up. Pediatr Blood Cancer (2014) 2.14
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
A metagenomic approach to characterization of the vaginal microbiome signature in pregnancy. PLoS One (2012) 1.98
The genome of th17 cell-inducing segmented filamentous bacteria reveals extensive auxotrophy and adaptations to the intestinal environment. Cell Host Microbe (2011) 1.97
Tryptophan biosynthesis protects mycobacteria from CD4 T-cell-mediated killing. Cell (2013) 1.96
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
Global assessment of genomic regions required for growth in Mycobacterium tuberculosis. PLoS Pathog (2012) 1.85
Computational meta'omics for microbial community studies. Mol Syst Biol (2013) 1.84
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
MiR-150 promotes gastric cancer proliferation by negatively regulating the pro-apoptotic gene EGR2. Biochem Biophys Res Commun (2010) 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
Acute respiratory distress syndrome induced by avian influenza A (H5N1) virus in mice. Am J Respir Crit Care Med (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
Wnt pathway activation in mesothelioma: evidence of Dishevelled overexpression and transcriptional activity of beta-catenin. Cancer Res (2003) 1.70
Antibacterial drug leads targeting isoprenoid biosynthesis. Proc Natl Acad Sci U S A (2012) 1.69
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
Genome-wide association study for vitiligo identifies susceptibility loci at 6q27 and the MHC. Nat Genet (2010) 1.69
Establishment of clonal colony-forming assay for propagation of pancreatic cancer cells with stem cell properties. Pancreas (2007) 1.68
Compact Hinfinity robust rebalance loop controller design for a micromachined electrostatically suspended gyroscope. ISA Trans (2009) 1.64
An integrated approach to characterize genetic interaction networks in yeast metabolism. Nat Genet (2011) 1.62
STAT3 expression, molecular features, inflammation patterns, and prognosis in a database of 724 colorectal cancers. Clin Cancer Res (2011) 1.62
Who's in favor of translational cell therapy for stroke: STEPS forward please? Cell Transplant (2009) 1.60
Early microbial and metabolomic signatures predict later onset of necrotizing enterocolitis in preterm infants. Microbiome (2013) 1.58
Variation in gene expression patterns in follicular lymphoma and the response to rituximab. Proc Natl Acad Sci U S A (2003) 1.58
Experimental occlusal interference induces long-term masticatory muscle hyperalgesia in rats. Pain (2009) 1.58
Tissue-specific functional networks for prioritizing phenotype and disease genes. PLoS Comput Biol (2012) 1.54
Optimal schedule of bacillus calmette-guerin for non-muscle-invasive bladder cancer: a meta-analysis of comparative studies. BMC Cancer (2013) 1.54
Biodiversity and functional genomics in the human microbiome. Trends Genet (2012) 1.52
Epigenomic diversity of colorectal cancer indicated by LINE-1 methylation in a database of 869 tumors. Mol Cancer (2010) 1.50
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