2022
Sequencing and Analysis of the Entire Genome of the Mycoparasitic Bioeffector Fungus Trichoderma asperelloides Strain T 203 (Hypocreales)
Gortikov M, Wang Z, Steindorff AS, Grigoriev IV, Druzhinina IS, Townsend JP, Yarden O. Sequencing and Analysis of the Entire Genome of the Mycoparasitic Bioeffector Fungus Trichoderma asperelloides Strain T 203 (Hypocreales). Microbiology Resource Announcements 2022, 11: e00995-21. PMID: 35175124, PMCID: PMC8852338, DOI: 10.1128/mra.00995-21.Peer-Reviewed Original Research
2017
Chapter One Maximizing Power in Phylogenetics and Phylogenomics: A Perspective Illuminated by Fungal Big Data
Dornburg A, Townsend JP, Wang Z. Chapter One Maximizing Power in Phylogenetics and Phylogenomics: A Perspective Illuminated by Fungal Big Data. Advances In Genetics 2017, 100: 1-47. PMID: 29153398, DOI: 10.1016/bs.adgen.2017.09.007.ChaptersConceptsTree of lifeFungal evolutionary biologyGenomic-scale dataHundreds of lociGenome-scale analysisFungal phylogenomicsFungal treeSpecies delimitationPhenotypic diversificationFirst genomeEvolutionary biologyPhylogenetic treePhylogenetic inferencePhylogenetic analysisEntire genomeTree inferenceReview of considerationsEvolutionary problemsPhylogenomicsGenomeTreesLociCentral roleExperimental designBiodiversity
2016
Effects of Physical Activity on DNA Methylation and Associations with Breast Cancer
Yu H, Irwin M. Effects of Physical Activity on DNA Methylation and Associations with Breast Cancer. Energy Balance And Cancer 2016, 11: 251-264. DOI: 10.1007/978-3-319-41610-6_11.Peer-Reviewed Original ResearchDNA methylationTumor suppressor genePhysical activityEpigenetic regulationSuppressor geneCancer riskGenome-wide methylationBetter patient survivalBreast cancer patientsPro-inflammatory cytokinesBreast cancer riskSex steroid hormonesLower cancer riskMitogenic growth factorsEntire genomeMolecular mechanismsInsulin resistancePatient survivalCancer patientsMethylationMore profound impactsCancer preventionBreast cancerDisease outcomeHealthy individuals
2012
Crohn's Disease Risk Alleles on the NOD2 Locus Have Been Maintained by Natural Selection on Standing Variation
Nakagome S, Mano S, Kozlowski L, Bujnicki JM, Shibata H, Fukumaki Y, Kidd JR, Kidd KK, Kawamura S, Oota H. Crohn's Disease Risk Alleles on the NOD2 Locus Have Been Maintained by Natural Selection on Standing Variation. Molecular Biology And Evolution 2012, 29: 1569-1585. PMID: 22319155, PMCID: PMC3697811, DOI: 10.1093/molbev/mss006.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SubstitutionCrohn DiseaseGene FrequencyGenetic Predisposition to DiseaseGenotyping TechniquesHaplotypesHumansModels, GeneticModels, MolecularNod2 Signaling Adaptor ProteinPhylogenyPolymorphism, Single NucleotideProtein Structure, SecondaryProtein Structure, TertiaryRisk FactorsSelection, GeneticSequence Analysis, DNAConceptsDisease risk allelesNatural selectionCD risk allelesGenome-wide association studiesClassical linkage analysisMost recent common ancestorPhylogenetic network analysisRecent common ancestorNOD2 proteinProtein structural predictionRecent genome-wide association studiesHigh-frequency haplotypesSerious conformational changesEuropean populationsAmino acid substitutionsRisk allelesStanding variationDeleterious haplotypesEvolutionary studiesCoalescent simulationsCommon ancestorGenomic regionsNon-European populationsEntire genomeDiploid individuals
2011
S6-4: Protein Kinase Mutation Patterns in Human Breast Cancer.
Pusztai L, Qi Y, Shi W, Liu C, Wang B, Liu X, Booser D, Esteva F, Symmans F, Hortobagyi G. S6-4: Protein Kinase Mutation Patterns in Human Breast Cancer. Cancer Research 2011, 71: s6-4-s6-4. DOI: 10.1158/0008-5472.sabcs11-s6-4.Peer-Reviewed Original ResearchGene expression profilingBiological pathwaysExpression profilingHuman protein kinasesImportant regulatory genesCanonical biological pathwaysDNA copy number variationsDNA copy number alterationsArray CGHSOLiD sequencing platformTarget base pairCopy number variationsFunctional impact scoresCopy number alterationsProtein functionAffymetrix U133A chipsMAPK familyRegulatory genesBMP2KEntire genomeProtein kinaseSequence dataGerm-line variantsGenomic dataBiological functions
2007
Analysis of the RPE transcriptome reveals dynamic changes during the development of the outer blood-retinal barrier.
Rizzolo LJ, Chen X, Weitzman M, Sun R, Zhang H. Analysis of the RPE transcriptome reveals dynamic changes during the development of the outer blood-retinal barrier. Molecular Vision 2007, 13: 1259-73. PMID: 17679949.Peer-Reviewed Original ResearchMeSH KeywordsActinsAnimalsBlood-Retinal BarrierCell Cycle ProteinsChick EmbryoCluster AnalysisCollagenExtracellular MatrixGene Expression ProfilingIntercellular JunctionsLamininMembrane ProteinsMicrotubule-Associated ProteinsMyosinsOligonucleotide Array Sequence AnalysisPhagocytosisPigment Epithelium of EyeProtein SubunitsProteinsReceptors, Cell SurfaceReverse Transcriptase Polymerase Chain ReactionRNA, MessengerTranscription, GeneticConceptsPattern of expressionExtensive remodelingAffymetrix microarray chipsCell-cell junctionsSignal transduction pathwaysExtracellular matrix interactionsAdherens junction proteinsTranscellular ion transportCell surface receptorsGenomic approachesEntire genomeGene OntologyTransduction pathwaysSTEM softwareZO-3Biological pathwaysFunctional clusteringMatrix interactionsExtracellular matrixSurface receptorsJunctional complexesMicroarray chipContinuous remodelingFalse discovery rateAffymetrix software
2005
Linkage analysis and association analysis in the presence of linkage using age at onset of COGA alcoholism data
Zhong X, Zhang H. Linkage analysis and association analysis in the presence of linkage using age at onset of COGA alcoholism data. BMC Genomic Data 2005, 6: s31. PMID: 16451641, PMCID: PMC1866754, DOI: 10.1186/1471-2156-6-s1-s31.Peer-Reviewed Original ResearchConceptsLinkage analysisAssociation analysisSusceptibility genesGenetic Analysis Workshop 14Alcoholism dataCombination of linkageComplex disease mappingDisease susceptibility genesEntire genomeMean identityLinkage disequilibriumTransmission/disequilibrium testAssociation TestGenesPresence of linkageDisequilibrium testGenomeChromosomesGeneticsLinkageDisequilibriumAssociation strategyGreater numberRegion
2004
Genome-Wide Linkage Scan for Loci Predisposing to Social Phobia: Evidence for a Chromosome 16 Risk Locus
Gelernter J, Page GP, Stein MB, Woods SW. Genome-Wide Linkage Scan for Loci Predisposing to Social Phobia: Evidence for a Chromosome 16 Risk Locus. American Journal Of Psychiatry 2004, 161: 59-66. PMID: 14702251, DOI: 10.1176/appi.ajp.161.1.59.Peer-Reviewed Original ResearchConceptsGenome-wide linkage scanLinkage scanChromosome 16LOD scoreGenetic linkage analysisNorepinephrine transporter proteinLinkage genome scanGenomic locationEntire genomeChromosome 16 markersGenome scanMultipoint LOD scoreRisk lociTransporter proteinsGenetic markersLinkage analysisSusceptibility lociChromosome 9Physiological candidatesLocus predisposingLociZlr scoreAmerican pedigreesX softwareD16S415
1986
Nucleotide sequence and genome organization of human parvovirus B19 isolated from the serum of a child during aplastic crisis
Shade R, Blundell M, Cotmore S, Tattersall P, Astell C. Nucleotide sequence and genome organization of human parvovirus B19 isolated from the serum of a child during aplastic crisis. Journal Of Virology 1986, 58: 921-936. PMID: 3701931, PMCID: PMC253001, DOI: 10.1128/jvi.58.3.921-936.1986.Peer-Reviewed Original ResearchConceptsNucleotide sequenceLarge open reading frameMajor nonstructural proteinOpen reading frameFull-length cloneMajor structural polypeptidesGenome organizationGenomic clonesPutative polypeptideTranscription unitEntire genomeReading frameDNA sequencesFourth promoterParvovirus genomeSequence informationNonstructural proteinsGenomeTerminal repeatDependovirus genusStructural polypeptidesViral DNAB19 genomePolypeptideSequence
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