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Ratan, Aakrosh

Aakrosh Ratan

Primary Appointment

Public Health Sciences

Contact Information

MSB-6131F; West Complex, 1300 JPA
Charlottesville, VA 22908
Telephone: 434-982-6583
Fax: 434-982-1815
Email: ar7jq@virginia.edu

Research Interests

Genomics, Molecular Evolution, Algorithm Design and Analysis

Research Description

My research is focused on study of genome variation and genetic diversity, and its consequences on species health and survival. I am interested in local changes consisting of substitutions and small indels that alter a few base pairs, as well as large-scale changes that consist of larger indels, rearrangements and copy number variations. My efforts are concentrated in the following areas: 1. Identification of variants: We are developing methods to identify and map variants (SNPs, indels, and large-scale rearrangements) from large-scale sequencing datasets. This includes identification of variants in species with a haploid representation (reference genome), species with multiple representations, as well as species where we lack a reference genome. 2. Study of genetic diversity: Genome-wide assessments of genetic diversity provide a powerful analytical tool that informs of the similarities, differences, origins and the evolutionary history of a species. We apply methods developed in (1) to identify variants among and between members of several species. The observed allele frequencies are then used to calculate metrics of population differentiation such as the fixation index, and can be correlated with phenotypes to identify adaptations, or used to detect the causative mutations for a genetic trait. 3. Cancer Genomics: Tumor sequencing experiments can provide insight into the changes driving tumorigenesis. The current sequencing platforms provide (given adequate coverage of the genomes) the high level of sensitivity and accuracy required to properly characterize the differences between a tumor/normal pair. We use the methods developed in (1) to view the unique somatic mutations accrued by a tumor, and germline mutations in the matched normal tissue. We are currently applying our methods to understand how genomic changes contribute to the pathogenesis of the T-cell form of Large Granular Lymphocyte (LGL) leukemia in collaboration with the Loughran lab at University of Virginia.

Selected Publications

Kistler L, Johnson SM, Irwin MT, Louis EE, Ratan A, Perry GH, A massively parallel strategy for STR marker development, capture, and genotyping., 2017; Nucleic acids research. 45(15) e142 PMID: 28666376 | PMCID: PMC5587753

Carpi G, Kitchen A, Kim HL, Ratan A, Drautz-Moses DI, McGraw JJ, Kazimirova M, Rizzoli A, Schuster SC, Mitogenomes reveal diversity of the European Lyme borreliosis vector Ixodes ricinus in Italy., 2016; Molecular phylogenetics and evolution. 101() 194-202 PMID: 27165938 |

Welch AJ, Collins K, Ratan A, Drautz-Moses DI, Schuster SC, Lindqvist C, Data characterizing the chloroplast genomes of extinct and endangered Hawaiian endemic mints (Lamiaceae) and their close relatives., 2016; Data in brief. 7() 900-22 PMID: 27077093 | PMCID: PMC4816906

Welch AJ, Collins K, Ratan A, Drautz-Moses DI, Schuster SC, Lindqvist C, The quest to resolve recent radiations: Plastid phylogenomics of extinct and endangered Hawaiian endemic mints (Lamiaceae)., 2016; Molecular phylogenetics and evolution. 99() 16-33 PMID: 26953739 |

Agaba M, Ishengoma E, Miller WC, McGrath BC, Hudson CN, Bedoya Reina OC, Ratan A, Burhans R, Chikhi R, Medvedev P, Praul CA, Wu-Cavener L, Wood B, Robertson H, Penfold L, Cavener DR, Giraffe genome sequence reveals clues to its unique morphology and physiology., 2016; Nature communications. 7() 11519 PMID: 27187213 | PMCID: PMC4873664

Junqueira AC, Azeredo-Espin AM, Paulo DF, Marinho MA, Tomsho LP, Drautz-Moses DI, Purbojati RW, Ratan A, Schuster SC, Large-scale mitogenomics enables insights into Schizophora (Diptera) radiation and population diversity., 2016; Scientific reports. 6() 21762 PMID: 26912394 | PMCID: PMC4766414

Lynch VJ, Bedoya-Reina OC, Ratan A, Sulak M, Drautz-Moses DI, Perry GH, Miller W, Schuster SC, Elephantid Genomes Reveal the Molecular Bases of Woolly Mammoth Adaptations to the Arctic., 2015; Cell reports. 12(2) 217-28 PMID: 26146078 |

Fuller ZL, Ni?o EL, Patch HM, Bedoya-Reina OC, Baumgarten T, Muli E, Mumoki F, Ratan A, McGraw J, Frazier M, Masiga D, Schuster S, Grozinger CM, Miller W, Genome-wide analysis of signatures of selection in populations of African honey bees (Apis mellifera) using new web-based tools., 2015; BMC genomics. 16() 518 PMID: 26159619 | PMCID: PMC4496815

Kim HL, Ratan A, Perry GH, Montenegro A, Miller W, Schuster SC, Khoisan hunter-gatherers have been the largest population throughout most of modern-human demographic history., 2014; Nature communications. 5() 5692 PMID: 25471224 | PMCID: PMC4268704

Bedoya-Reina OC, Ratan A, Burhans R, Kim HL, Giardine B, Riemer C, Li Q, Olson TL, Loughran TP, Vonholdt BM, Perry GH, Schuster SC, Miller W, Galaxy tools to study genome diversity., 2014; GigaScience. 2(1) 17 PMID: 24377391 | PMCID: PMC3877877

Kistler L, Ratan A, Godfrey LR, Crowley BE, Hughes CE, Lei R, Cui Y, Wood ML, Muldoon KM, Andriamialison H, McGraw JJ, Tomsho LP, Schuster SC, Miller W, Louis EE, Yoder AD, Malhi RS, Perry GH, Comparative and population mitogenomic analyses of Madagascar's extinct, giant 'subfossil' lemurs., 2014; Journal of human evolution. 79() 45-54 PMID: 25523037 |

Perry GH, Louis EE, Ratan A, Bedoya-Reina OC, Burhans RC, Lei R, Johnson SE, Schuster SC, Miller W, Aye-aye population genomic analyses highlight an important center of endemism in northern Madagascar., 2013; Proceedings of the National Academy of Sciences of the United States of America. 110(15) 5823-8 PMID: 23530231 | PMCID: PMC3625347

Ratan A, Miller W, Guillory J, Stinson J, Seshagiri S, Schuster SC, Comparison of sequencing platforms for single nucleotide variant calls in a human sample., 2013; PloS one. 8(2) e55089 PMID: 23405114 | PMCID: PMC3566181

Miller W, Schuster SC, Welch AJ, Ratan A, Bedoya-Reina OC, Zhao F, Kim HL, Burhans RC, Drautz DI, Wittekindt NE, Tomsho LP, Ibarra-Laclette E, Herrera-Estrella L, Peacock E, Farley S, Sage GK, Rode K, Obbard M, Montiel R, Bachmann L, Ing?lfsson O,..., Polar and brown bear genomes reveal ancient admixture and demographic footprints of past climate change., 2012; Proceedings of the National Academy of Sciences of the United States of America. 109(36) E2382-90 PMID: 22826254 | PMCID: PMC3437856

Giardine BM, Riemer C, Burhans R, Ratan A, Miller W, Some phenotype association tools in Galaxy: looking for disease SNPs in a full genome., 2012; Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.]. 0() Unit15.2 PMID: 22948727 | PMCID: PMC3548453

Gupta R, Ratan A, Rajesh C, Chen R, Kim HL, Burhans R, Miller W, Santhosh S, Davuluri RV, Butte AJ, Schuster SC, Seshagiri S, Thomas G, Sequencing and analysis of a South Asian-Indian personal genome., 2012; BMC genomics. 13() 440 PMID: 22938532 | PMCID: PMC3534380

Miller W, Hayes VM, Ratan A, Petersen DC, Wittekindt NE, Miller J, Walenz B, Knight J, Qi J, Zhao F, Wang Q, Bedoya-Reina OC, Katiyar N, Tomsho LP, Kasson LM, Hardie RA, Woodbridge P, Tindall EA, Bertelsen MF, Dixon D, Pyecroft S, Helgen KM, Lesk ..., Genetic diversity and population structure of the endangered marsupial Sarcophilus harrisii (Tasmanian devil)., 2011; Proceedings of the National Academy of Sciences of the United States of America. 108(30) 12348-53 PMID: 21709235 | PMCID: PMC3145710

Perry GH, Reeves D, Melsted P, Ratan A, Miller W, Michelini K, Louis EE, Pritchard JK, Mason CE, Gilad Y, A genome sequence resource for the aye-aye (Daubentonia madagascariensis), a nocturnal lemur from Madagascar., 2011; Genome biology and evolution. 4(2) 126-35 PMID: 22155688 | PMCID: PMC3273163

Ratan A, Zhang Y, Hayes VM, Schuster SC, Miller W, Calling SNPs without a reference sequence., 2010; BMC bioinformatics. 11() 130 PMID: 20230626 | PMCID: PMC2851604

Lindqvist C, Schuster SC, Sun Y, Talbot SL, Qi J, Ratan A, Tomsho LP, Kasson L, Zeyl E, Aars J, Miller W, Ing?lfsson O, Bachmann L, Wiig O, Complete mitochondrial genome of a Pleistocene jawbone unveils the origin of polar bear., 2010; Proceedings of the National Academy of Sciences of the United States of America. 107(11) 5053-7 PMID: 20194737 | PMCID: PMC2841953

Schuster SC, Miller W, Ratan A, Tomsho LP, Giardine B, Kasson LR, Harris RS, Petersen DC, Zhao F, Qi J, Alkan C, Kidd JM, Sun Y, Drautz DI, Bouffard P, Muzny DM, Reid JG, Nazareth LV, Wang Q, Burhans R, Riemer C, Wittekindt NE, Moorjani P, Tindall..., Complete Khoisan and Bantu genomes from southern Africa., 2010; Nature. 463(7283) 943-7 PMID: 20164927 | PMCID: PMC3890430

Willerslev E, Gilbert MT, Binladen J, Ho SY, Campos PF, Ratan A, Tomsho LP, da Fonseca RR, Sher A, Kuznetsova TV, Nowak-Kemp M, Roth TL, Miller W, Schuster SC, Analysis of complete mitochondrial genomes from extinct and extant rhinoceroses reveals lack of phylogenetic resolution., 2009; BMC evolutionary biology. 9() 95 PMID: 19432984 | PMCID: PMC2694787

Miller W, Drautz DI, Janecka JE, Lesk AM, Ratan A, Tomsho LP, Packard M, Zhang Y, McClellan LR, Qi J, Zhao F, Gilbert MT, Dal?n L, Arsuaga JL, Ericson PG, Huson DH, Helgen KM, Murphy WJ, G?therstr?m A, Schuster SC, The mitochondrial genome sequence of the Tasmanian tiger (Thylacinus cynocephalus)., 2009; Genome research. 19(2) 213-20 PMID: 19139089 | PMCID: PMC2652203

Miller W, Drautz DI, Ratan A, Pusey B, Qi J, Lesk AM, Tomsho LP, Packard MD, Zhao F, Sher A, Tikhonov A, Raney B, Patterson N, Lindblad-Toh K, Lander ES, Knight JR, Irzyk GP, Fredrikson KM, Harkins TT, Sheridan S, Pringle T, Schuster SC, Sequencing the nuclear genome of the extinct woolly mammoth., 2008; Nature. 456(7220) 387-90 PMID: 19020620 |

Ma J, Ratan A, Raney BJ, Suh BB, Miller W, Haussler D, The infinite sites model of genome evolution., 2008; Proceedings of the National Academy of Sciences of the United States of America. 105(38) 14254-61 PMID: 18787111 | PMCID: PMC2533685

Ma J, Ratan A, Raney BJ, Suh BB, Zhang L, Miller W, Haussler D, DUPCAR: reconstructing contiguous ancestral regions with duplications., 2008; Journal of computational biology : a journal of computational molecular cell biology. 15(8) 1007-27 PMID: 18774902 | PMCID: PMC3205822