Published in Methods Enzymol on January 01, 2002
Extensive association of functionally and cytotopically related mRNAs with Puf family RNA-binding proteins in yeast. PLoS Biol (2004) 6.38
The functional landscape of mouse gene expression. J Biol (2004) 5.65
The proteome of Saccharomyces cerevisiae mitochondria. Proc Natl Acad Sci U S A (2003) 5.13
GOtcha: a new method for prediction of protein function assessed by the annotation of seven genomes. BMC Bioinformatics (2004) 4.76
Genome-wide analysis of mRNA stability using transcription inhibitors and microarrays reveals posttranscriptional control of ribosome biogenesis factors. Mol Cell Biol (2004) 3.72
Data preparation and interannotator agreement: BioCreAtIvE task 1B. BMC Bioinformatics (2005) 3.19
Judging the quality of gene expression-based clustering methods using gene annotation. Genome Res (2002) 2.76
Profiling condition-specific, genome-wide regulation of mRNA stability in yeast. Proc Natl Acad Sci U S A (2005) 2.57
Computational identification of non-coding RNAs in Saccharomyces cerevisiae by comparative genomics. Nucleic Acids Res (2003) 2.15
Global gene expression profiling reveals widespread yet distinctive translational responses to different eukaryotic translation initiation factor 2B-targeting stress pathways. Mol Cell Biol (2005) 2.13
Genome-wide occupancy profile of the RNA polymerase III machinery in Saccharomyces cerevisiae reveals loci with incomplete transcription complexes. Mol Cell Biol (2004) 2.13
Computationally driven, quantitative experiments discover genes required for mitochondrial biogenesis. PLoS Genet (2009) 1.90
Global analysis of Pub1p targets reveals a coordinate control of gene expression through modulation of binding and stability. Mol Cell Biol (2005) 1.50
Genome-wide deletion mutant analysis reveals genes required for respiratory growth, mitochondrial genome maintenance and mitochondrial protein synthesis in Saccharomyces cerevisiae. Genome Biol (2009) 1.49
QPath: a method for querying pathways in a protein-protein interaction network. BMC Bioinformatics (2006) 1.46
dictyBase: a new Dictyostelium discoideum genome database. Nucleic Acids Res (2004) 1.42
Genomewide identification of Sko1 target promoters reveals a regulatory network that operates in response to osmotic stress in Saccharomyces cerevisiae. Eukaryot Cell (2005) 1.42
Retroviruses and yeast retrotransposons use overlapping sets of host genes. Genome Res (2005) 1.38
Simultaneous reconstruction of multiple signaling pathways via the prize-collecting steiner forest problem. J Comput Biol (2013) 1.10
Genome-wide screen for inositol auxotrophy in Saccharomyces cerevisiae implicates lipid metabolism in stress response signaling. Mol Genet Genomics (2010) 1.07
Mining experimental evidence of molecular function claims from the literature. Bioinformatics (2007) 1.07
The DEAD-box RNA helicase-like Utp25 is an SSU processome component. RNA (2010) 1.04
Shedding genomic ballast: extensive parallel loss of ancestral gene families in animals. J Mol Evol (2004) 1.04
Transformation and other factors of the peptide mass spectrometry pairwise peak-list comparison process. BMC Bioinformatics (2005) 1.01
Whi3, a developmental regulator of budding yeast, binds a large set of mRNAs functionally related to the endoplasmic reticulum. J Biol Chem (2008) 0.96
A protein domain co-occurrence network approach for predicting protein function and inferring species phylogeny. PLoS One (2011) 0.96
Novel role for checkpoint Rad53 protein kinase in the initiation of chromosomal DNA replication in Saccharomyces cerevisiae. Genetics (2006) 0.91
Assembling a protein-protein interaction map of the SSU processome from existing datasets. PLoS One (2011) 0.90
Interaction networks in yeast define and enumerate the signaling steps of the vertebrate aryl hydrocarbon receptor. PLoS Biol (2004) 0.87
ESF1 is required for 18S rRNA synthesis in Saccharomyces cerevisiae. Nucleic Acids Res (2004) 0.87
Different mechanisms for pseudouridine formation in yeast 5S and 5.8S rRNAs. Mol Cell Biol (2008) 0.84
Multi-targeted priming for genome-wide gene expression assays. BMC Genomics (2010) 0.83
Towards classifying species in systems biology papers using text mining. BMC Res Notes (2011) 0.81
Mitochondrial heat shock protein (Hsp) 70 and Hsp10 cooperate in the formation of Hsp60 complexes. J Biol Chem (2015) 0.80
Gene regulatory networks modelling using a dynamic evolutionary hybrid. BMC Bioinformatics (2010) 0.80
Alternative cytoskeletal landscapes: cytoskeletal novelty and evolution in basal excavate protists. Curr Opin Cell Biol (2013) 0.79
Elongator-dependent modification of cytoplasmic tRNALysUUU is required for mitochondrial function under stress conditions. Nucleic Acids Res (2015) 0.77
Information-based methods for predicting gene function from systematic gene knock-downs. BMC Bioinformatics (2008) 0.77
From networks of protein interactions to networks of functional dependencies. BMC Syst Biol (2012) 0.76
Identifying hierarchical and overlapping protein complexes based on essential protein-protein interactions and "seed-expanding" method. Biomed Res Int (2014) 0.75
A New Method for Identifying Essential Proteins Based on Network Topology Properties and Protein Complexes. PLoS One (2016) 0.75
A new computational strategy for identifying essential proteins based on network topological properties and biological information. PLoS One (2017) 0.75
Repeated observation of breast tumor subtypes in independent gene expression data sets. Proc Natl Acad Sci U S A (2003) 34.68
GO::TermFinder--open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes. Bioinformatics (2004) 20.23
Mutational evolution in a lobular breast tumour profiled at single nucleotide resolution. Nature (2009) 18.08
Genome sequence of the palaeopolyploid soybean. Nature (2010) 17.82
Identification of genes periodically expressed in the human cell cycle and their expression in tumors. Mol Biol Cell (2002) 17.32
Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data. Nat Genet (2003) 14.56
ARID1A mutations in endometriosis-associated ovarian carcinomas. N Engl J Med (2010) 13.07
Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project. Nat Biotechnol (2008) 12.96
Microarray analysis reveals a major direct role of DNA copy number alteration in the transcriptional program of human breast tumors. Proc Natl Acad Sci U S A (2002) 12.68
The clonal and mutational evolution spectrum of primary triple-negative breast cancers. Nature (2012) 11.91
The BioGRID Interaction Database: 2008 update. Nucleic Acids Res (2007) 11.83
Annotation of functional variation in personal genomes using RegulomeDB. Genome Res (2012) 11.47
Gene expression profiling identifies clinically relevant subtypes of prostate cancer. Proc Natl Acad Sci U S A (2004) 10.99
Saccharomyces Genome Database (SGD) provides secondary gene annotation using the Gene Ontology (GO). Nucleic Acids Res (2002) 10.65
SOURCE: a unified genomic resource of functional annotations, ontologies, and gene expression data. Nucleic Acids Res (2003) 10.28
Saccharomyces Genome Database (SGD) provides tools to identify and analyze sequences from Saccharomyces cerevisiae and related sequences from other organisms. Nucleic Acids Res (2004) 10.18
Frequent mutation of histone-modifying genes in non-Hodgkin lymphoma. Nature (2011) 9.71
Gene expression signature of fibroblast serum response predicts human cancer progression: similarities between tumors and wounds. PLoS Biol (2004) 9.38
Gene Ontology annotations at SGD: new data sources and annotation methods. Nucleic Acids Res (2007) 9.03
Saccharomyces Genome Database: the genomics resource of budding yeast. Nucleic Acids Res (2011) 8.57
The BioGRID Interaction Database: 2011 update. Nucleic Acids Res (2010) 8.46
Repeatability of published microarray gene expression analyses. Nat Genet (2008) 8.24
Introductory science and mathematics education for 21st-Century biologists. Science (2004) 7.69
A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB. BMC Bioinformatics (2006) 7.53
Molecular characterisation of soft tissue tumours: a gene expression study. Lancet (2002) 7.05
Diversity, topographic differentiation, and positional memory in human fibroblasts. Proc Natl Acad Sci U S A (2002) 6.98
Gene expression patterns in human liver cancers. Mol Biol Cell (2002) 6.93
Prediction of survival in diffuse large-B-cell lymphoma based on the expression of six genes. N Engl J Med (2004) 6.91
Gene expression profiling reveals molecularly and clinically distinct subtypes of glioblastoma multiforme. Proc Natl Acad Sci U S A (2005) 6.54
The Stanford Microarray Database: data access and quality assessment tools. Nucleic Acids Res (2003) 6.31
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
The BioGRID interaction database: 2013 update. Nucleic Acids Res (2012) 6.09
Saccharomyces Genome Database (SGD) provides biochemical and structural information for budding yeast proteins. Nucleic Acids Res (2003) 5.69
Macronuclear genome sequence of the ciliate Tetrahymena thermophila, a model eukaryote. PLoS Biol (2006) 5.44
Expression of cytokeratins 17 and 5 identifies a group of breast carcinomas with poor clinical outcome. Am J Pathol (2002) 5.20
Predicting expression patterns from regulatory sequence in Drosophila segmentation. Nature (2008) 5.08
Use and misuse of the gene ontology annotations. Nat Rev Genet (2008) 5.01
Characteristic genome rearrangements in experimental evolution of Saccharomyces cerevisiae. Proc Natl Acad Sci U S A (2002) 4.97
A standardized kinesin nomenclature. J Cell Biol (2004) 4.43
Genetic alterations activating kinase and cytokine receptor signaling in high-risk acute lymphoblastic leukemia. Cancer Cell (2012) 4.41
Coordination of growth rate, cell cycle, stress response, and metabolic activity in yeast. Mol Biol Cell (2007) 4.27
The Rice Annotation Project Database (RAP-DB): 2008 update. Nucleic Acids Res (2007) 4.23
Standards for microarray data. Science (2002) 4.11
Decay rates of human mRNAs: correlation with functional characteristics and sequence attributes. Genome Res (2003) 4.07
Endothelial cell diversity revealed by global expression profiling. Proc Natl Acad Sci U S A (2003) 3.98
Stereotyped and specific gene expression programs in human innate immune responses to bacteria. Proc Natl Acad Sci U S A (2002) 3.85
The novel marker, DOG1, is expressed ubiquitously in gastrointestinal stromal tumors irrespective of KIT or PDGFRA mutation status. Am J Pathol (2004) 3.84
Different gene expression patterns in invasive lobular and ductal carcinomas of the breast. Mol Biol Cell (2004) 3.73
Discovery of biological networks from diverse functional genomic data. Genome Biol (2005) 3.73
The Stanford Microarray Database: implementation of new analysis tools and open source release of software. Nucleic Acids Res (2006) 3.66