2007
The DART classification of unannotated transcription within the ENCODE regions: Associating transcription with known and novel loci
Rozowsky JS, Newburger D, Sayward F, Wu J, Jordan G, Korbel JO, Nagalakshmi U, Yang J, Zheng D, Guigó R, Gingeras TR, Weissman S, Miller P, Snyder M, Gerstein MB. The DART classification of unannotated transcription within the ENCODE regions: Associating transcription with known and novel loci. Genome Research 2007, 17: 732-745. PMID: 17567993, PMCID: PMC1891334, DOI: 10.1101/gr.5696007.Peer-Reviewed Original ResearchMeSH KeywordsBase SequenceChromosome MappingGene Expression ProfilingGene Expression RegulationGenome, HumanHumansMolecular Sequence DataQuantitative Trait LociTranscription, Genetic
2000
An integrated web interface for large-scale characterization of sequence data
Cheung K, Kumar A, Snyder M, Miller P. An integrated web interface for large-scale characterization of sequence data. Functional & Integrative Genomics 2000, 1: 70-75. PMID: 11793223, DOI: 10.1007/s101420000004.Peer-Reviewed Original ResearchMeSH KeywordsClinical Laboratory Information SystemsComputational BiologyDatabases, GeneticDatabases, ProteinDNA Transposable ElementsDNA, FungalGene Expression ProfilingGenomeGenome, FungalInternetMutagenesis, InsertionalOpen Reading FramesSaccharomyces cerevisiaeSequence Analysis, DNASequence Homology, Nucleic AcidSoftwareUser-Computer InterfaceConceptsWeb interfaceWeb front endGenomic data processingData filesLarge-scale genome projectsIndependent software programsSet of programsMultiple directoriesData directoryData processingRaw dataTransposon insertion eventsSoftware programFilesFront endDirectoryEfficient protocolLarge amountInterfaceLarge numberGeneral approachUsersSetDownloadNavigation
1999
Large-scale analysis of the yeast genome by transposon tagging and gene disruption
Ross-Macdonald P, Coelho P, Roemer T, Agarwal S, Kumar A, Jansen R, Cheung K, Sheehan A, Symoniatis D, Umansky L, Heidtman M, Nelson F, Iwasaki H, Hager K, Gerstein M, Miller P, Roeder G, Snyder M. Large-scale analysis of the yeast genome by transposon tagging and gene disruption. Nature 1999, 402: 413-418. PMID: 10586881, DOI: 10.1038/46558.Peer-Reviewed Original ResearchMeSH KeywordsAlgorithmsDNA Transposable ElementsEscherichia coliFungal ProteinsGene Expression ProfilingGenetic TechniquesGenome, FungalMolecular Sequence DataMutagenesisOligonucleotide Array Sequence AnalysisOpen Reading FramesPhenotypePolymerase Chain ReactionSaccharomyces cerevisiaeTransformation, GeneticConceptsGene functionDisruption phenotypesLarge-scale analysisNon-annotated open reading framesGenome-wide analysisOpen reading frameSingle genetic backgroundTransposon taggingYeast genomeYeast mutantsGenomic scaleYeast SaccharomycesDifferent growth conditionsProtein localizationGene disruptionReading frameGene expressionFunctional analysisVegetative growthGenetic backgroundGenesGenomeTransposonGrowth conditionsYeast