2024
F67. CHARACTERIZING THE IMPACT OF AUTOZYGOSITY AND RUNS OF HOMOZYGOSITY ON PSYCHIATRIC DISEASE RISK IN INDIAN POPULATION
Kandasamy K, Ganesh S, Sachdeva P, Mahadevan J, Holla B, Benegal V, Purushottam M, Jain S, Viswanath B. F67. CHARACTERIZING THE IMPACT OF AUTOZYGOSITY AND RUNS OF HOMOZYGOSITY ON PSYCHIATRIC DISEASE RISK IN INDIAN POPULATION. European Neuropsychopharmacology 2024, 87: 242. DOI: 10.1016/j.euroneuro.2024.08.478.Peer-Reviewed Original ResearchGenetic architecture of psychiatric disordersIllumina Global Screening ArrayGlobal Screening ArrayContinental populationsGenetic architectureInbreeding coefficientRecessive locusAutozygosityFROHObsessive compulsive disorderScreening ArrayPLINK v.GenomeInbreedingBipolar disorderDisease-riskPsychiatric diagnosisPsychiatric disordersDisease riskEndogamyIlluminaCase-control differencesLociPLINKROHCombining short- and long-read sequencing unveils geographically structured diversity in Borrelia miyamotoi
Hoornstra D, Kuleshov K, Fingerle V, Hepner S, Wagemakers A, Strube C, Castillo-Ramírez S, Bockenstedt L, Telford S, Sprong H, Platonov A, Margos G, Hovius J. Combining short- and long-read sequencing unveils geographically structured diversity in Borrelia miyamotoi. IScience 2024, 27: 110616. PMID: 39262806, PMCID: PMC11388275, DOI: 10.1016/j.isci.2024.110616.Peer-Reviewed Original ResearchComparative whole-genome sequencingCombination of IlluminaLong-read sequencingGenetically distinct populationsGenome assemblyPacBio platformPlasmid typesCore plasmidHuman pathogensGenetic basisDistinct populationsExpression sitesPlasmidGeographical originIxodes speciesGenomeIsolatesTick-borne human pathogenVector competenceStructural diversityNorth AmericaBorrelia miyamotoiPacBioIlluminaVirulence
2020
Data Sanitization to Reduce Private Information Leakage from Functional Genomics
Gürsoy G, Emani P, Brannon CM, Jolanki OA, Harmanci A, Strattan JS, Cherry JM, Miranker AD, Gerstein M. Data Sanitization to Reduce Private Information Leakage from Functional Genomics. Cell 2020, 183: 905-917.e16. PMID: 33186529, PMCID: PMC7672785, DOI: 10.1016/j.cell.2020.09.036.Peer-Reviewed Original ResearchConceptsFunctional genomicsSingle-cell RNA sequencingAccurate reference genomesFunctional genomics datasetsFunctional genomics experimentsOrganismal phenotypesGene regulationReference genomeNext-generation sequencingRaw readsGenomics experimentsRNA sequencingGenomic datasetsGenetic variantsGenomicsKnown individualsSequencingReadsEnvironmental samplesGenomeIlluminaPhenotypeGood statistical powerRegulationStatistical power
2017
Temporal Variations in Cigarette Tobacco Bacterial Community Composition and Tobacco-Specific Nitrosamine Content Are Influenced by Brand and Storage Conditions
Chopyk J, Chattopadhyay S, Kulkarni P, Smyth E, Hittle L, Paulson J, Pop M, Buehler S, Clark P, Mongodin E, Sapkota A. Temporal Variations in Cigarette Tobacco Bacterial Community Composition and Tobacco-Specific Nitrosamine Content Are Influenced by Brand and Storage Conditions. Frontiers In Microbiology 2017, 08: 358. PMID: 28326071, PMCID: PMC5339245, DOI: 10.3389/fmicb.2017.00358.Peer-Reviewed Original ResearchOperational taxonomic unitsCore bacterial operational taxonomic unitsStorage conditionsBacterial operational taxonomic unitsV3V4 hypervariable regionBacterial community compositionTaxonomic unitsDay 0Illumina MiSeqRRNA geneCommunity compositionMicrobial ecosystemBacterial communitiesHypervariable regionTobacco-specific nitrosamine contentTime series experimentsBacillus pumilusNitrosamine contentAbundanceRelative humidityStorageIlluminaMiSeqLiquid chromatographyV3V4
2015
Sex difference of autosomal alleles in populations of European and African descent
Zuo L, Wang T, Lin X, Wang J, Tan Y, Wang X, Yu X, Luo X. Sex difference of autosomal alleles in populations of European and African descent. Genes & Genomics 2015, 37: 1007-1016. PMID: 26702338, PMCID: PMC4684836, DOI: 10.1007/s13258-015-0332-z.Peer-Reviewed Original Research
2014
Using ancestry-informative markers to identify fine structure across 15 populations of European origin
Huckins L, Boraska V, Franklin C, Floyd J, Southam L, Sullivan P, Bulik C, Collier D, Tyler-Smith C, Zeggini E, Tachmazidou I. Using ancestry-informative markers to identify fine structure across 15 populations of European origin. European Journal Of Human Genetics 2014, 22: 1190-1200. PMID: 24549058, PMCID: PMC4169539, DOI: 10.1038/ejhg.2014.1.Peer-Reviewed Original ResearchConceptsMinor allele frequencyPopulations of European originGenome-wide association scanAncestry-informative markersEuropean-descent populationsAxes of variationEuropean originGenetic structureAssociation scansPopulation structurePopulation stratificationK chipAllele frequenciesAssociation resultsSNPsInformative axesIlluminaMarkersPopulationVariantsPrincipal component analysisConsortiaComparative methodOriginWellcome
2010
PositionMatcher: A Fast Custom-Annotation Tool for Short DNA Sequences.
Pitzer E, Kim J, Patel K, Galante P, Ohno-Machado L. PositionMatcher: A Fast Custom-Annotation Tool for Short DNA Sequences. AMIA Joint Summits On Translational Science Proceedings 2010, 2010: 25-9. PMID: 21347141, PMCID: PMC3041550.Peer-Reviewed Original ResearchParallel sequencing technologiesShort DNA sequencesTranscriptome studiesGenomic positionsDNA sequencesSequencing technologiesGenomic tagsExpression technologySequencing readsRapid AnnotationGene levelMicroarray probesShort readsCustom annotationsAbundance valuesAnnotationNovel alignment algorithmReadsBiological referenceTagsIlluminaAffymetrixSequenceMore insightProbe
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