2021
A fast likelihood approach for estimation of large phylogenies from continuous trait data
Peng J, Rajeevan H, Kubatko L, RoyChoudhury A. A fast likelihood approach for estimation of large phylogenies from continuous trait data. Molecular Phylogenetics And Evolution 2021, 161: 107142. PMID: 33713799, DOI: 10.1016/j.ympev.2021.107142.Peer-Reviewed Original ResearchMeSH KeywordsBayes TheoremGene FrequencyHumansLikelihood FunctionsPhenotypePhylogenyReproducibility of ResultsResearch DesignConceptsContinuous trait dataMaximum likelihood estimatorMaximum likelihood estimatesMathematical propertiesHundreds of taxaInternal branch lengthsFast approximationAddition of taxaLarge-scale genomic dataCollection of methodsBayesian frameworkLikelihood estimatorLikelihood estimatesLikelihood approachMaximum likelihoodIntensive calculationsModel-based methodApproximationLarge phylogeniesComparable accuracyPossible phylogenyInferenceBranch lengthsEstimatorSuch data
2020
FrogAncestryCalc: A standalone batch likelihood computation tool for ancestry inference panels catalogued in FROG-kb
Rajeevan H, Soundararajan U, Pakstis AJ, Kidd KK. FrogAncestryCalc: A standalone batch likelihood computation tool for ancestry inference panels catalogued in FROG-kb. Forensic Science International Genetics 2020, 46: 102237. PMID: 31991337, DOI: 10.1016/j.fsigen.2020.102237.Peer-Reviewed Original Research
2019
Population relationships based on 170 ancestry SNPs from the combined Kidd and Seldin panels
Pakstis AJ, Speed WC, Soundararajan U, Rajeevan H, Kidd JR, Li H, Kidd KK. Population relationships based on 170 ancestry SNPs from the combined Kidd and Seldin panels. Scientific Reports 2019, 9: 18874. PMID: 31827153, PMCID: PMC6906462, DOI: 10.1038/s41598-019-55175-x.Peer-Reviewed Original ResearchConceptsGenetic diversityPopulation relationshipsHuman populationAncestry informative SNP panelsInformative SNP panelsMajor continental regionsHuman reference populationsSNP panelIndividual populationsGenotype dataReference populationNative American populationsDiverse collectionAISNPsAllele frequency databasesWorldwide populationDiversityFrequency databaseAmerican populationReference population dataPopulationSNPsPrincipal component analysisCombined panelCluster patternsGenetic relationships of European, Mediterranean, and SW Asian populations using a panel of 55 AISNPs
Pakstis AJ, Gurkan C, Dogan M, Balkaya HE, Dogan S, Neophytou PI, Cherni L, Boussetta S, Khodjet-El-Khil H, Ben Ammar ElGaaied A, Salvo NM, Janssen K, Olsen GH, Hadi S, Almohammed EK, Pereira V, Truelsen DM, Bulbul O, Soundararajan U, Rajeevan H, Kidd JR, Kidd KK. Genetic relationships of European, Mediterranean, and SW Asian populations using a panel of 55 AISNPs. European Journal Of Human Genetics 2019, 27: 1885-1893. PMID: 31285530, PMCID: PMC6871633, DOI: 10.1038/s41431-019-0466-6.Peer-Reviewed Original Research
2018
Improving ancestry distinctions among Southwest Asian populations
Bulbul O, Speed WC, Gurkan C, Soundararajan U, Rajeevan H, Pakstis AJ, Kidd KK. Improving ancestry distinctions among Southwest Asian populations. Forensic Science International Genetics 2018, 35: 14-20. PMID: 29625264, DOI: 10.1016/j.fsigen.2018.03.010.Peer-Reviewed Original Research
2017
The redesigned Forensic Research/Reference on Genetics-knowledge base, FROG-kb
Kidd KK, Soundararajan U, Rajeevan H, Pakstis AJ, Moore KN, Ropero-Miller JD. The redesigned Forensic Research/Reference on Genetics-knowledge base, FROG-kb. Forensic Science International Genetics 2017, 33: 33-37. PMID: 29175726, DOI: 10.1016/j.fsigen.2017.11.009.Peer-Reviewed Original ResearchConceptsWeb interfaceFROG-kbAccessible web interfaceDatabase interfaceEasy navigationNew reference panelsWeb sitesGenetic knowledge baseIndividual identification single nucleotide polymorphismsExtensive redesignExtensive documentationOngoing updatesComprehensive toolInterfaceOngoing researchForensicsNavigationIndividual identification SNPsFunctional enhancementReference population dataPrototypeDocumentationIncreasing the reference populations for the 55 AISNP panel: the need and benefits
Pakstis AJ, Kang L, Liu L, Zhang Z, Jin T, Grigorenko EL, Wendt FR, Budowle B, Hadi S, Al Qahtani MS, Morling N, Mogensen HS, Themudo GE, Soundararajan U, Rajeevan H, Kidd JR, Kidd KK. Increasing the reference populations for the 55 AISNP panel: the need and benefits. International Journal Of Legal Medicine 2017, 131: 913-917. PMID: 28070634, PMCID: PMC5491587, DOI: 10.1007/s00414-016-1524-z.Peer-Reviewed Original Research
2014
Application of six IrisPlex SNPs and comparison of two eye color prediction systems in diverse Eurasia populations
Yun L, Gu Y, Rajeevan H, Kidd KK. Application of six IrisPlex SNPs and comparison of two eye color prediction systems in diverse Eurasia populations. International Journal Of Legal Medicine 2014, 128: 447-453. PMID: 24395150, DOI: 10.1007/s00414-013-0953-1.Peer-Reviewed Original Research
2011
ALFRED: an allele frequency resource for research and teaching
Rajeevan H, Soundararajan U, Kidd JR, Pakstis AJ, Kidd KK. ALFRED: an allele frequency resource for research and teaching. Nucleic Acids Research 2011, 40: d1010-d1015. PMID: 22039151, PMCID: PMC3245092, DOI: 10.1093/nar/gkr924.Peer-Reviewed Original Research
2003
ALFRED: the ALelle FREquency Database. Update
Rajeevan H, Osier MV, Cheung KH, Deng H, Druskin L, Heinzen R, Kidd JR, Stein S, Pakstis AJ, Tosches NP, Yeh CC, Miller PL, Kidd KK. ALFRED: the ALelle FREquency Database. Update. Nucleic Acids Research 2003, 31: 270-271. PMID: 12519999, PMCID: PMC165490, DOI: 10.1093/nar/gkg043.Peer-Reviewed Original ResearchMeSH KeywordsAllelesComputer GraphicsDatabases, Nucleic AcidGene FrequencyGenetics, PopulationHumansPolymorphism, GeneticSoftwareConceptsAccessibility of data