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Items: 46


Identification of African-Specific Admixture between Modern and Archaic Humans.

Wall JD, Ratan A, Stawiski E; GenomeAsia 100K Consortium.

Am J Hum Genet. 2019 Dec 5;105(6):1254-1261. doi: 10.1016/j.ajhg.2019.11.005.


Data and replication supplement for double auction markets with snipers.

Brewer P, Ratan A.

Data Brief. 2019 Oct 30;27:104729. doi: 10.1016/j.dib.2019.104729. eCollection 2019 Dec.


Genomics of LGL leukemia and select other rare leukemia/lymphomas.

Moosic KB, Paila U, Olson KC, Dziewulska K, Wang TT, Xing JC, Ratan A, Feith DJ, Loughran TP Jr, Olson TL.

Best Pract Res Clin Haematol. 2019 Sep;32(3):196-206. doi: 10.1016/j.beha.2019.06.003. Epub 2019 Jun 6. Review.


Biogenic synthesis and thermo-magnetic study of highly porous carbon nanotubes.

Ranu R, Chauhan Y, Ratan A, Singh PK, Bhattacharya B, Tomar SK.

IET Nanobiotechnol. 2019 Jun;13(4):363-367. doi: 10.1049/iet-nbt.2018.5105.


Augmented Interval List: a novel data structure for efficient genomic interval search.

Feng J, Ratan A, Sheffield NC.

Bioinformatics. 2019 Dec 1;35(23):4907-4911. doi: 10.1093/bioinformatics/btz407.


Changing Aspects in the Management of Splenic Injury Patients: Experience of 129 Isolated Splenic Injury Patients at Level 1 Trauma Center from India.

Bagaria D, Kumar A, Ratan A, Gupta A, Kumar A, Kumar S, Mishra B, Sagar S.

J Emerg Trauma Shock. 2019 Jan-Mar;12(1):35-39. doi: 10.4103/JETS.JETS_1_18.


Genomic Variants Among Threatened Acropora Corals.

Kitchen SA, Ratan A, Bedoya-Reina OC, Burhans R, Fogarty ND, Miller W, Baums IB.

G3 (Bethesda). 2019 May 7;9(5):1633-1646. doi: 10.1534/g3.119.400125.


Severe hypertriglyceridemia-induced pancreatitis successfully managed with therapeutic plasma exchange: Report from India.

Mehta SP, Tiwari AK, Puri R, Arora D, Aggarwal G, Ratan A.

Asian J Transfus Sci. 2018 Jul-Dec;12(2):154-156. doi: 10.4103/ajts.AJTS_86_17.


The Germline Variants rs61757955 and rs34988193 Are Predictive of Survival in Lower Grade Glioma Patients.

Chatrath A, Kiran M, Kumar P, Ratan A, Dutta A.

Mol Cancer Res. 2019 May;17(5):1075-1086. doi: 10.1158/1541-7786.MCR-18-0996. Epub 2019 Jan 16.


Genomic analysis of DNA repair genes and androgen signaling in prostate cancer.

Jividen K, Kedzierska KZ, Yang CS, Szlachta K, Ratan A, Paschal BM.

BMC Cancer. 2018 Oct 10;18(1):960. doi: 10.1186/s12885-018-4848-x.


Improved molecular karyotyping in glioblastoma.

Burbulis IE, Wierman MB, Wolpert M, Haakenson M, Lopes MB, Schiff D, Hicks J, Loe J, Ratan A, McConnell MJ.

Mutat Res. 2018 Sep;811:16-26. doi: 10.1016/j.mrfmmm.2018.06.002. Epub 2018 Jul 8.


SONiCS: PCR stutter noise correction in genome-scale microsatellites.

Kedzierska KZ, Gerber L, Cagnazzi D, Krützen M, Ratan A, Kistler L.

Bioinformatics. 2018 Dec 1;34(23):4115-4117. doi: 10.1093/bioinformatics/bty485.


Evaluation of new indigenous "point-of-care" ABO and Rh grouping device.

Tiwari AK, Setya D, Aggarwal G, Arora D, Dara RC, Ratan A, Bhardwaj G, Acharya DP.

J Lab Physicians. 2018 Jan-Mar;10(1):80-84. doi: 10.4103/JLP.JLP_71_17.


The microbiomes of blowflies and houseflies as bacterial transmission reservoirs.

Junqueira ACM, Ratan A, Acerbi E, Drautz-Moses DI, Premkrishnan BNV, Costea PI, Linz B, Purbojati RW, Paulo DF, Gaultier NE, Subramanian P, Hasan NA, Colwell RR, Bork P, Azeredo-Espin AML, Bryant DA, Schuster SC.

Sci Rep. 2017 Nov 24;7(1):16324. doi: 10.1038/s41598-017-16353-x.


Missed diaphragmatic injury after blunt trauma presenting with colonic strangulation: a rare scenario.

Kumar A, Bagaria D, Ratan A, Gupta A.

BMJ Case Rep. 2017 Aug 7;2017. pii: bcr-2017-221220. doi: 10.1136/bcr-2017-221220.


A massively parallel strategy for STR marker development, capture, and genotyping.

Kistler L, Johnson SM, Irwin MT, Louis EE, Ratan A, Perry GH.

Nucleic Acids Res. 2017 Sep 6;45(15):e142. doi: 10.1093/nar/gkx574.


A facile synthesis of sulfonylureas via water assisted preparation of carbamates.

Tanwar DK, Ratan A, Gill MS.

Org Biomol Chem. 2017 Jun 14;15(23):4992-4999. doi: 10.1039/c7ob00872d.


Giraffe genome sequence reveals clues to its unique morphology and physiology.

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.

Nat Commun. 2016 May 17;7:11519. doi: 10.1038/ncomms11519.


Mitogenomes reveal diversity of the European Lyme borreliosis vector Ixodes ricinus in Italy.

Carpi G, Kitchen A, Kim HL, Ratan A, Drautz-Moses DI, McGraw JJ, Kazimirova M, Rizzoli A, Schuster SC.

Mol Phylogenet Evol. 2016 Aug;101:194-202. doi: 10.1016/j.ympev.2016.05.009. Epub 2016 May 7.


Data characterizing the chloroplast genomes of extinct and endangered Hawaiian endemic mints (Lamiaceae) and their close relatives.

Welch AJ, Collins K, Ratan A, Drautz-Moses DI, Schuster SC, Lindqvist C.

Data Brief. 2016 Mar 14;7:900-22. doi: 10.1016/j.dib.2016.03.037. eCollection 2016 Jun.


The quest to resolve recent radiations: Plastid phylogenomics of extinct and endangered Hawaiian endemic mints (Lamiaceae).

Welch AJ, Collins K, Ratan A, Drautz-Moses DI, Schuster SC, Lindqvist C.

Mol Phylogenet Evol. 2016 Jun;99:16-33. doi: 10.1016/j.ympev.2016.02.024. Epub 2016 Mar 5.


Large-scale mitogenomics enables insights into Schizophora (Diptera) radiation and population diversity.

Junqueira AC, Azeredo-Espin AM, Paulo DF, Marinho MA, Tomsho LP, Drautz-Moses DI, Purbojati RW, Ratan A, Schuster SC.

Sci Rep. 2016 Feb 25;6:21762. doi: 10.1038/srep21762.


Genome-wide analysis of signatures of selection in populations of African honey bees (Apis mellifera) using new web-based tools.

Fuller ZL, Niño 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.

BMC Genomics. 2015 Jul 10;16:518. doi: 10.1186/s12864-015-1712-0.


Elephantid Genomes Reveal the Molecular Bases of Woolly Mammoth Adaptations to the Arctic.

Lynch VJ, Bedoya-Reina OC, Ratan A, Sulak M, Drautz-Moses DI, Perry GH, Miller W, Schuster SC.

Cell Rep. 2015 Jul 14;12(2):217-28. doi: 10.1016/j.celrep.2015.06.027. Epub 2015 Jul 2.


Identification of indels in next-generation sequencing data.

Ratan A, Olson TL, Loughran TP Jr, Miller W.

BMC Bioinformatics. 2015 Feb 13;16:42. doi: 10.1186/s12859-015-0483-6.



Karlan D, Ratan AL, Zinman J.

Rev Income Wealth. 2014 Mar;60(1):36-78.


Comparative and population mitogenomic analyses of Madagascar's extinct, giant 'subfossil' lemurs.

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.

J Hum Evol. 2015 Feb;79:45-54. doi: 10.1016/j.jhevol.2014.06.016. Epub 2014 Dec 16.


Khoisan hunter-gatherers have been the largest population throughout most of modern-human demographic history.

Kim HL, Ratan A, Perry GH, Montenegro A, Miller W, Schuster SC.

Nat Commun. 2014 Dec 4;5:5692. doi: 10.1038/ncomms6692.


Galaxy tools to study genome diversity.

Bedoya-Reina OC, Ratan A, Burhans R, Kim HL, Giardine B, Riemer C, Li Q, Olson TL, Loughran TP Jr, Vonholdt BM, Perry GH, Schuster SC, Miller W.

Gigascience. 2013 Dec 30;2(1):17. doi: 10.1186/2047-217X-2-17.


Aye-aye population genomic analyses highlight an important center of endemism in northern Madagascar.

Perry GH, Louis EE Jr, Ratan A, Bedoya-Reina OC, Burhans RC, Lei R, Johnson SE, Schuster SC, Miller W.

Proc Natl Acad Sci U S A. 2013 Apr 9;110(15):5823-8. doi: 10.1073/pnas.1211990110. Epub 2013 Mar 25.


Comparison of sequencing platforms for single nucleotide variant calls in a human sample.

Ratan A, Miller W, Guillory J, Stinson J, Seshagiri S, Schuster SC.

PLoS One. 2013;8(2):e55089. doi: 10.1371/journal.pone.0055089. Epub 2013 Feb 6.


Some phenotype association tools in Galaxy: looking for disease SNPs in a full genome.

Giardine BM, Riemer C, Burhans R, Ratan A, Miller W.

Curr Protoc Bioinformatics. 2012 Sep;Chapter 15:Unit15.2. doi: 10.1002/0471250953.bi1502s39.


Sequencing and analysis of a South Asian-Indian personal genome.

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.

BMC Genomics. 2012 Aug 31;13:440. doi: 10.1186/1471-2164-13-440.


Polar and brown bear genomes reveal ancient admixture and demographic footprints of past climate change.

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, Ingólfsson O, Aars J, Mailund T, Wiig O, Talbot SL, Lindqvist C.

Proc Natl Acad Sci U S A. 2012 Sep 4;109(36):E2382-90. doi: 10.1073/pnas.1210506109. Epub 2012 Jul 23.


A genome sequence resource for the aye-aye (Daubentonia madagascariensis), a nocturnal lemur from Madagascar.

Perry GH, Reeves D, Melsted P, Ratan A, Miller W, Michelini K, Louis EE Jr, Pritchard JK, Mason CE, Gilad Y.

Genome Biol Evol. 2012;4(2):126-35. doi: 10.1093/gbe/evr132. Epub 2011 Dec 7.


Genetic diversity and population structure of the endangered marsupial Sarcophilus harrisii (Tasmanian devil).

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 AM, Pringle TH, Patterson N, Zhang Y, Kreiss A, Woods GM, Jones ME, Schuster SC.

Proc Natl Acad Sci U S A. 2011 Jul 26;108(30):12348-53. doi: 10.1073/pnas.1102838108. Epub 2011 Jun 27. Erratum in: Proc Natl Acad Sci U S A. 2012 Nov 6;109(45):18625.


Comparative and demographic analysis of orang-utan genomes.

Locke DP, Hillier LW, Warren WC, Worley KC, Nazareth LV, Muzny DM, Yang SP, Wang Z, Chinwalla AT, Minx P, Mitreva M, Cook L, Delehaunty KD, Fronick C, Schmidt H, Fulton LA, Fulton RS, Nelson JO, Magrini V, Pohl C, Graves TA, Markovic C, Cree A, Dinh HH, Hume J, Kovar CL, Fowler GR, Lunter G, Meader S, Heger A, Ponting CP, Marques-Bonet T, Alkan C, Chen L, Cheng Z, Kidd JM, Eichler EE, White S, Searle S, Vilella AJ, Chen Y, Flicek P, Ma J, Raney B, Suh B, Burhans R, Herrero J, Haussler D, Faria R, Fernando O, Darré F, Farré D, Gazave E, Oliva M, Navarro A, Roberto R, Capozzi O, Archidiacono N, Della Valle G, Purgato S, Rocchi M, Konkel MK, Walker JA, Ullmer B, Batzer MA, Smit AF, Hubley R, Casola C, Schrider DR, Hahn MW, Quesada V, Puente XS, Ordoñez GR, López-Otín C, Vinar T, Brejova B, Ratan A, Harris RS, Miller W, Kosiol C, Lawson HA, Taliwal V, Martins AL, Siepel A, Roychoudhury A, Ma X, Degenhardt J, Bustamante CD, Gutenkunst RN, Mailund T, Dutheil JY, Hobolth A, Schierup MH, Ryder OA, Yoshinaga Y, de Jong PJ, Weinstock GM, Rogers J, Mardis ER, Gibbs RA, Wilson RK.

Nature. 2011 Jan 27;469(7331):529-33. doi: 10.1038/nature09687.


Calling SNPs without a reference sequence.

Ratan A, Zhang Y, Hayes VM, Schuster SC, Miller W.

BMC Bioinformatics. 2010 Mar 15;11:130. doi: 10.1186/1471-2105-11-130.


Complete mitochondrial genome of a Pleistocene jawbone unveils the origin of polar bear.

Lindqvist C, Schuster SC, Sun Y, Talbot SL, Qi J, Ratan A, Tomsho LP, Kasson L, Zeyl E, Aars J, Miller W, Ingólfsson O, Bachmann L, Wiig O.

Proc Natl Acad Sci U S A. 2010 Mar 16;107(11):5053-7. doi: 10.1073/pnas.0914266107. Epub 2010 Mar 1. Erratum in: Proc Natl Acad Sci U S A. 2010 Mar 30;107(13):6118.


Complete Khoisan and Bantu genomes from southern Africa.

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 EA, Danko CG, Teo WS, Buboltz AM, Zhang Z, Ma Q, Oosthuysen A, Steenkamp AW, Oostuisen H, Venter P, Gajewski J, Zhang Y, Pugh BF, Makova KD, Nekrutenko A, Mardis ER, Patterson N, Pringle TH, Chiaromonte F, Mullikin JC, Eichler EE, Hardison RC, Gibbs RA, Harkins TT, Hayes VM.

Nature. 2010 Feb 18;463(7283):943-7. doi: 10.1038/nature08795.


Analysis of complete mitochondrial genomes from extinct and extant rhinoceroses reveals lack of phylogenetic resolution.

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.

BMC Evol Biol. 2009 May 11;9:95. doi: 10.1186/1471-2148-9-95.


The mitochondrial genome sequence of the Tasmanian tiger (Thylacinus cynocephalus).

Miller W, Drautz DI, Janecka JE, Lesk AM, Ratan A, Tomsho LP, Packard M, Zhang Y, McClellan LR, Qi J, Zhao F, Gilbert MT, Dalén L, Arsuaga JL, Ericson PG, Huson DH, Helgen KM, Murphy WJ, Götherström A, Schuster SC.

Genome Res. 2009 Feb;19(2):213-20. doi: 10.1101/gr.082628.108. Epub 2009 Jan 12.


Sequencing the nuclear genome of the extinct woolly mammoth.

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.

Nature. 2008 Nov 20;456(7220):387-90. doi: 10.1038/nature07446.


The infinite sites model of genome evolution.

Ma J, Ratan A, Raney BJ, Suh BB, Miller W, Haussler D.

Proc Natl Acad Sci U S A. 2008 Sep 23;105(38):14254-61. doi: 10.1073/pnas.0805217105. Epub 2008 Sep 11.


DUPCAR: reconstructing contiguous ancestral regions with duplications.

Ma J, Ratan A, Raney BJ, Suh BB, Zhang L, Miller W, Haussler D.

J Comput Biol. 2008 Oct;15(8):1007-27. doi: 10.1089/cmb.2008.0069.


Intraspecific phylogenetic analysis of Siberian woolly mammoths using complete mitochondrial genomes.

Gilbert MT, Drautz DI, Lesk AM, Ho SY, Qi J, Ratan A, Hsu CH, Sher A, Dalén L, Götherström A, Tomsho LP, Rendulic S, Packard M, Campos PF, Kuznetsova TV, Shidlovskiy F, Tikhonov A, Willerslev E, Iacumin P, Buigues B, Ericson PG, Germonpré M, Kosintsev P, Nikolaev V, Nowak-Kemp M, Knight JR, Irzyk GP, Perbost CS, Fredrikson KM, Harkins TT, Sheridan S, Miller W, Schuster SC.

Proc Natl Acad Sci U S A. 2008 Jun 17;105(24):8327-32. doi: 10.1073/pnas.0802315105. Epub 2008 Jun 9.

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