2023
Search of a genomic sequence database for potential novel blood group antigens: Investigation into why some amino acid substitutions are not immunogenic
Howe J, Stack G. Search of a genomic sequence database for potential novel blood group antigens: Investigation into why some amino acid substitutions are not immunogenic. Transfusion 2023, 63: 1399-1411. PMID: 37386886, DOI: 10.1111/trf.17459.Peer-Reviewed Original ResearchConceptsBlood group antigensGroup antigensB-cell epitopesGenomic sequence databasesLinear B-cell epitopesLow prevalenceSequence databasesAtypical chemokine receptor 1Chemokine receptor 1New blood group antigensExtracellular domainHuman genome sequence databaseMissense mutationsGenome sequence databaseEpitope prediction programsTransfusion practiceProtein structural analysisPoor immunogenicityAmino acid substitutionsReceptor 1Phenotype prevalenceAntigenStudy designBlood groupPrevalence
2019
A potential nomenclature for the Immuno Polymorphism Database (IPD) of chicken MHC genes: progress and problems
Afrache H, Tregaskes C, Kaufman J. A potential nomenclature for the Immuno Polymorphism Database (IPD) of chicken MHC genes: progress and problems. Immunogenetics 2019, 72: 9-24. PMID: 31741010, PMCID: PMC6971145, DOI: 10.1007/s00251-019-01145-6.Peer-Reviewed Original ResearchConceptsChicken MHC genesImmuno Polymorphism DatabaseMajor histocompatibility complexIdentical sequencesNomenclature systemClass II B sequencesMHC genesHighest allelic polymorphismsIPD-MHC DatabaseMHC sequencesGeneral sequence databasesClass II lociClassical class IGene conversionPolymorphism databaseSequence diversitySequence databasesCurated sequencesB sequencesII lociHaplotypesAllelic polymorphismGenesAllelesSequencemetagenomeFeatures: an R package for working with 16S rRNA reference databases and marker-gene survey feature data
Olson N, Shah N, Kancherla J, Wagner J, Paulson J, Bravo H. metagenomeFeatures: an R package for working with 16S rRNA reference databases and marker-gene survey feature data. Bioinformatics 2019, 35: 3870-3872. PMID: 30821316, PMCID: PMC6761971, DOI: 10.1093/bioinformatics/btz136.Peer-Reviewed Original Research
2018
Search Effectiveness in Nonredundant Sequence Databases: Assessments and Solutions
Chen Q, Zhang X, Wan Y, Zobel J, Verspoor K. Search Effectiveness in Nonredundant Sequence Databases: Assessments and Solutions. Journal Of Computational Biology 2018, 26: 605-617. PMID: 30585742, DOI: 10.1089/cmb.2018.0198.Peer-Reviewed Original ResearchConceptsSearch effectivenessGroup similar sequencesBiological sequence databasesUser behaviorEvaluation metricsEffective search timeSearch timeClustering methodMatched clustersUsersAnnotation similarityMember recordsDatabaseIncreasing databaseSequence clustering methodsQueryAggregation sequenceRecallPrecisionNonredundant databaseSequence databasesSearchSimilar sequencesClustersNonredundant sequence database
2017
Comparative Analysis of Sequence Clustering Methods for Deduplication of Biological Databases
Chen Q, Wan Y, Zhang X, Lei Y, Zobel J, Verspoor K. Comparative Analysis of Sequence Clustering Methods for Deduplication of Biological Databases. Journal Of Data And Information Quality 2017, 9: 1-27. DOI: 10.1145/3131611.Peer-Reviewed Original ResearchVolume of dataClustering methodMassive volume of dataSequence clustering methodsClustering evaluation metricsBiological sequence databasesDetecting duplicate sequencesDatabase storageEvaluation metricsAnnotation consistencyMassive volumeDeduplicationSimilarity thresholdDetect duplicatesLevel of redundancyBiological case studyDatabase curationHeuristic approachDuplicated sequencesCD-HITBiological databasesSequence databasesBiological sequencesData qualityMultiple recordsDuplicates, redundancies and inconsistencies in the primary nucleotide databases: a descriptive study
Chen Q, Zobel J, Verspoor K. Duplicates, redundancies and inconsistencies in the primary nucleotide databases: a descriptive study. Database 2017, 2017: baw163. PMID: 28077566, PMCID: PMC5225397, DOI: 10.1093/database/baw163.Peer-Reviewed Original ResearchConceptsImpact of duplicationINSDC databasesInternational Nucleotide Sequence Database CollaborationDNA DataBank of JapanBioinformatics databasesEuropean Nucleotide ArchiveNucleotide sequence databasesPresence of duplicatesGC contentNucleotide databaseSequence databasesDuplicate pairsBiological databasesINSDCDNA databanksBioinformaticsDuplication typeAnnotation levelsDuplicationGenBankEMBLNucleotideDNA
2016
Supervised Learning for Detection of Duplicates in Genomic Sequence Databases
Chen Q, Zobel J, Zhang X, Verspoor K. Supervised Learning for Detection of Duplicates in Genomic Sequence Databases. PLOS ONE 2016, 11: e0159644. PMID: 27489953, PMCID: PMC4973881, DOI: 10.1371/journal.pone.0159644.Peer-Reviewed Original ResearchConceptsMulti-class modelSupervised learningMachine learningDe-duplicationGenome sequence databaseDetect duplicatesDuplicate detection methodsAutomatic systemAmount of dataDetection of duplicatesSequence databasesAblation studiesDetection contextMeta-dataDetection methodDatabase recordsExpert curationBiological databasesLearningCross-validationRecord featuresBinary modelSequence identityMachineDatabase
2013
Improved software detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of fungi and other eukaryotes for analysis of environmental sequencing data
Bengtsson‐Palme J, Ryberg M, Hartmann M, Branco S, Wang Z, Godhe A, De Wit P, Sánchez‐García M, Ebersberger I, de Sousa F, Amend A, Jumpponen A, Unterseher M, Kristiansson E, Abarenkov K, Bertrand Y, Sanli K, Eriksson K, Vik U, Veldre V, Nilsson R. Improved software detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of fungi and other eukaryotes for analysis of environmental sequencing data. Methods In Ecology And Evolution 2013, 4: 914-919. DOI: 10.1111/2041-210x.12073.Peer-Reviewed Original ResearchData setsLarge data setsSoftware detectionSequence analysis pipelineSoftware toolsProcess parallelizationSequence clusteringHigh-throughput sequencing data setsExpedient analysisSequence extractionNext-generation sequencing data setsAnalysis pipelineSequencing data setsLarge alignmentsNon-target sequencesMarkov modelEnvironmental data setsSequence databasesPublic sequence databasesEnvironmental sequencing dataSetExtractionParallelizationSearchSoftware
2012
Exploring ORFan Domains in Giant Viruses: Structure of Mimivirus Sulfhydryl Oxidase R596
Hakim M, Ezerina D, Alon A, Vonshak O, Fass D. Exploring ORFan Domains in Giant Viruses: Structure of Mimivirus Sulfhydryl Oxidase R596. PLOS ONE 2012, 7: e50649. PMID: 23209798, PMCID: PMC3509050, DOI: 10.1371/journal.pone.0050649.Peer-Reviewed Original ResearchConceptsSulfhydryl oxidaseViral sulfhydryl oxidasesCarboxy-terminal regionDouble-stranded DNA virusesBind target proteinsMimivirus genomeMimivirus genesDomain foldsGiant virusesEncode proteinsORFansVirus factoriesSequence databasesMimivirusDNA virusesERV familiesTarget proteinsBroad cleftStable structural unitsGenesProteinVirusOxidaseGenomeSide chains
2011
A note on the incidence of reverse complementary fungal ITS sequences in the public sequence databases and a software tool for their detection and reorientation
Nilsson R, Veldre V, Wang Z, Eckart M, Branco S, Hartmann M, Quince C, Godhe A, Bertrand Y, Alfredsson J, Larsson K, Kõljalg U, Abarenkov K. A note on the incidence of reverse complementary fungal ITS sequences in the public sequence databases and a software tool for their detection and reorientation. Mycoscience 2011, 52: 278-282. DOI: 10.1007/s10267-010-0086-z.Peer-Reviewed Original ResearchTasting Soil Fungal Diversity with Earth Tongues: Phylogenetic Test of SATé Alignments for Environmental ITS Data
Wang Z, Nilsson RH, Lopez-Giraldez F, Zhuang WY, Dai YC, Johnston PR, Townsend JP. Tasting Soil Fungal Diversity with Earth Tongues: Phylogenetic Test of SATé Alignments for Environmental ITS Data. PLOS ONE 2011, 6: e19039. PMID: 21533038, PMCID: PMC3080880, DOI: 10.1371/journal.pone.0019039.Peer-Reviewed Original ResearchConceptsFungal lineagesSoil fungal diversityNovel fungal lineagesTree estimationITS dataNuclear ribosomal ITS regionEnvironmental samplesRibosomal ITS regionFungal diversityPublic sequence databasesComplex communitiesDivergent taxaBasal classPhylogenetic testsNovel lineageITS phylogenyPhylogenetic analysisEctomycorrhizal isolatesITS sequencesITS regionEnvironmental samplingSequence databasesSATéFocal questionLineagesA note on the incidence of reverse complementary fungal ITS sequences in the public sequence databases and a software tool for their detection and reorientation
Nilsson R, Veldre V, Wang Z, Eckart M, Branco S, Hartmann M, Quince C, Godhe A, Bertrand Y, Alfredsson J, Larsson K, Kõljalg U, Abarenkov K. A note on the incidence of reverse complementary fungal ITS sequences in the public sequence databases and a software tool for their detection and reorientation. Mycoscience 2011, 52: 278-282. DOI: 10.47371/s10267-010-0086-z.Peer-Reviewed Original Research
2008
Effective suppression of HIV-1 by artificial bispecific miRNA targeting conserved sequences with tolerance for wobble base-pairing
Son J, Uchil PD, Kim YB, Shankar P, Kumar P, Lee SK. Effective suppression of HIV-1 by artificial bispecific miRNA targeting conserved sequences with tolerance for wobble base-pairing. Biochemical And Biophysical Research Communications 2008, 374: 214-218. PMID: 18619945, DOI: 10.1016/j.bbrc.2008.06.125.Peer-Reviewed Original ResearchConceptsFunctional RNAiHIV-1 isolatesHigh genetic diversityAntiviral therapyHIV replicationHIV-1Vif sequencesArtificial microRNAsGenetic diversityGenome sequenceSustained inhibitionVif geneHIV sequencesVariant residuesSequence databasesLuciferase constructSimultaneous targetingNatural variantsViral sequencesRNAiSequenceInhibitionAnalysis of Insertional Sites of the SIRE1 Retroelement Family from Glycine Max Using GenBank BAC-end Sequences
Flasch DA, Rebman EK, Olfson EH, Nguyen KK, Geirut LE, Garland MC, Lindorfer CM, Laten HM. Analysis of Insertional Sites of the SIRE1 Retroelement Family from Glycine Max Using GenBank BAC-end Sequences. In Silico Biology Journal Of Biological Systems Modeling And Multi-Scale Simulation 2008, 8: 531-543. PMID: 19374136, DOI: 10.3233/isb-00374.Peer-Reviewed Original ResearchConceptsRetroelement familiesGenome Survey Sequence databasesProtein-coding genesLow copy number sequencesClear consensus sequenceTy1/copia familyBAC end sequencesClass II transposable elementsSoybean genomeCopia familiesGenomic assembliesPlant membersSatellite DNATransposable elementsRepetitive elementsConsensus sequenceGlycine maxSequence databasesCopy numberReverse transcriptase geneInsertional siteGenomeGenesSIRE1Transcriptase gene
2005
The origin and evolution of human pathogens
Groisman EA, Casadesús J. The origin and evolution of human pathogens. Molecular Microbiology 2005, 56: 1-7. PMID: 15773974, DOI: 10.1111/j.1365-2958.2005.04564.x.Peer-Reviewed Original ResearchConceptsCreation of genesNon-host environmentsHuman pathogensRelated bacterial speciesCertain pathogensORFan genesHomologous genesCell surface modificationExpression of productsHousekeeping functionsRelated membersHost rangeColonization processTissue specificityPathogenicity islandSequence databasesCertain lociBacterial speciesGenesCell surfaceDisparate regulationGenetic originBacterial pathogensNew functionsGene variation
1999
A Novel Family of Divergent Seven-Transmembrane Proteins Candidate Odorant Receptors in Drosophila
Clyne P, Warr C, Freeman M, Lessing D, Kim J, Carlson J. A Novel Family of Divergent Seven-Transmembrane Proteins Candidate Odorant Receptors in Drosophila. Neuron 1999, 22: 327-338. PMID: 10069338, DOI: 10.1016/s0896-6273(00)81093-4.Peer-Reviewed Original ResearchConceptsOlfactory receptor neuronsPOU domain transcription factorLarge multigene familyCandidate odorant receptorsTransmembrane domain proteinGenomic sequence databasesSubset of ORNsDomain proteinsMultigene familyAntennal developmentOdorant receptorsTranscription factorsSequence databasesInitiate expressionOlfactory organOdorant specificityNovel familyDifferent membersReceptor neuronsReceptor moleculesInsectsMutantsValuable modelGenesOlfactory system
1998
Database tools for integrating and searching membrane property data correlated with neuronal morphology
Mirsky J, Nadkarni P, Healy M, Miller P, Shepherd G. Database tools for integrating and searching membrane property data correlated with neuronal morphology. Journal Of Neuroscience Methods 1998, 82: 105-121. PMID: 10223520, DOI: 10.1016/s0165-0270(98)00049-1.Peer-Reviewed Original ResearchConceptsDatabase toolsWeb resourcesSearch toolsCritical problemUsersSequence databasesSimple canonical modelFunctional operationDatabaseToolSearchDifferent neuronsInternetAnnotationEquivalent compartmentsModelersDataProperty dataCanonical modelDifferent typesInformationState of acceptanceResourcesVehiclesProperty space
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