Publications

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E
Jacobs DI, Fukumura K, Bainbridge MN, Armstrong GN, Tsavachidis S, Gu X, Doddapaneni H, Hu J, Jayaseelan JC, Muzny DM, Huse JT, Bondy ML. Elucidating the molecular pathogenesis of glioma: integrated germline and somatic profiling of a familial glioma case series. Neuro Oncol. 2018 ;20(12):1625-1633.
D
Criss ZK, Bhasin N, Di Rienzi SC, Rajan A, Deans-Fielder K, Swaminathan G, Kamyabi N, Zeng X-L, Doddapaneni H, Menon VK, Chakravarti D, Estrella C, Yu X, Patil K, Petrosino JF, Fleet JC, Verzi MP, Christakos S, Helmrath MA, Arimura S, DePinho RA, Britton RA, Maresso AW, K Grande-Allen J, Blutt SE, Crawford SE, Estes MK, Ramani S, Shroyer NF. Drivers of transcriptional variance in human intestinal epithelial organoids. Physiol Genomics. 2021 ;53(11):486-508.
Doddapaneni H, Yadav JS. Differential regulation and xenobiotic induction of tandem P450 monooxygenase genes pc-1 (CYP63A1) and pc-2 (CYP63A2) in the white-rot fungus Phanerochaete chrysosporium. Appl Microbiol Biotechnol. 2004 ;65(5):559-65.
C
Price DC, Chan CXin, Yoon HSu, Yang EChan, Qiu H, Weber APM, Schwacke R, Gross J, Blouin NA, Lane C, Reyes-Prieto A, Durnford DG, Neilson JAD, B Lang F, Burger G, Steiner JM, Löffelhardt W, Meuser JE, Posewitz MC, Ball S, Arias MCecilia, Henrissat B, Coutinho PM, Rensing SA, Symeonidi A, Doddapaneni H, Green BR, Rajah VD, Boore J, Bhattacharya D. Cyanophora paradoxa genome elucidates origin of photosynthesis in algae and plants. Science. 2012 ;335(6070):843-7.
Rotenberg D, Baumann AA, Ben-Mahmoud S, Christiaens O, Dermauw W, Ioannidis P, Jacobs CGC, Jentzsch IMVargas, Oliver JE, Poelchau MF, Rajarapu SPriya, Schneweis DJ, Snoeck S, Taning CNT, Wei D, Gamage SMKWidana, Hughes DST, Murali SC, Bailey ST, Bejerman NE, Holmes CJ, Jennings EC, Rosendale AJ, Rosselot A, Hervey K, Schneweis BA, Cheng S, Childers C, Simão FA, Dietzgen RG, Chao H, Dinh H, Doddapaneni H, Dugan S, Han Y, Lee SL, Muzny DM, Qu J, Worley KC, Benoit JB, Friedrich M, Jones JW, Panfilio KA, Park Y, Robertson HM, Smagghe G, Ullman DE, Van der Zee M, Van Leeuwen T, Veenstra JA, Waterhouse RM, Weirauch MT, Werren JH, Whitfield AE, Zdobnov EM, Gibbs RA, Richards S. Correction to: Genome-enabled insights into the biology of thrips as crop pests. BMC Biol. 2020 ;18(1):169.
Harris RA, Raveendran M, Lyfoung DT, Sedlazeck FJ, Mahmoud M, Prall TM, Karl JA, Doddapaneni H, Meng Q, Han Y, Muzny DM, Wiseman RW, O'Connor DH, Rogers J. Construction of a new chromosome-scale, long-read reference genome assembly for the Syrian hamster, Mesocricetus auratus. Gigascience. 2022 ;11.
Duan Y, Zhou L, Hall DG, Li W, Doddapaneni H, Lin H, Liu L, Vahling CM, Gabriel DW, Williams KP, Dickerman A, Sun Y, Gottwald T. Complete genome sequence of citrus huanglongbing bacterium, 'Candidatus Liberibacter asiaticus' obtained through metagenomics. Mol Plant Microbe Interact. 2009 ;22(8):1011-20.
Lin H, Lou B, Glynn JM, Doddapaneni H, Civerolo EL, Chen C, Duan Y, Zhou L, Vahling CM. The complete genome sequence of 'Candidatus Liberibacter solanacearum', the bacterium associated with potato zebra chip disease. PLoS One. 2011 ;6(4):e19135.
Doddapaneni H, Liao H, Lin H, Bai X, Zhao X, Civerolo EL, Irey M, Coletta-Filho H, Pietersen G. Comparative phylogenomics and multi-gene cluster analyses of the Citrus Huanglongbing (HLB)-associated bacterium Candidatus Liberibacter. BMC Res Notes. 2008 ;1:72.
Fernandez-Fueyo E, Ruiz-Duenas FJ, Ferreira P, Floudas D, Hibbett DS, Canessa P, Larrondo LF, James TY, Seelenfreund D, Lobos S, Polanco R, Tello M, Honda Y, Watanabe T, Watanabe T, San Ryu J, Kubicek CP, Schmoll M, Gaskell J, Hammel KE, St John FJ, Wymelenberg AVanden, Sabat G, BonDurant SSplinter, Syed K, Yadav JS, Doddapaneni H, Subramanian V, Lavín JL, Oguiza JA, Perez G, Pisabarro AG, Ramirez L, Santoyo F, Master E, Coutinho PM, Henrissat B, Lombard V, Magnuson JKarl, Kües U, Hori C, Igarashi K, Samejima M, Held BW, Barry KW, LaButti KM, Lapidus A, Lindquist EA, Lucas SM, Riley R, Salamov AA, Hoffmeister D, Schwenk D, Hadar Y, Yarden O, de Vries RP, Wiebenga A, Stenlid J, Eastwood D, Grigoriev IV, Berka RM, Blanchette RA, Kersten P, Martinez AT, Vicuna R, Cullen D. Comparative genomics of Ceriporiopsis subvermispora and Phanerochaete chrysosporium provide insight into selective ligninolysis. Proc Natl Acad Sci U S A. 2012 ;109(14):5458-63.
Doddapaneni H, Subramanian V, Fu B, Cullen D. A comparative genomic analysis of the oxidative enzymes potentially involved in lignin degradation by Agaricus bisporus. Fungal Genet Biol. 2013 ;55:22-31.
Lin H, Doddapaneni H, Takahashi Y, M Walker A. Comparative analysis of ESTs involved in grape responses to Xylella fastidiosa infection. BMC Plant Biol. 2007 ;7:8.
Bielinski SJ, St Sauver JL, Olson JE, Larson NB, Black JL, Scherer SE, Bernard ME, Boerwinkle E, Borah BJ, Caraballo PJ, Curry TB, Doddapaneni H, Formea CM, Freimuth RR, Gibbs RA, Giri J, Hathcock MA, Hu J, Jacobson DJ, Jones LA, Kalla SE, Koep TH, Korchina V, Kovar CL, Lee S, Liu H, Matey ET, McGree ME, McAllister TM, Moyer AM, Muzny DM, Nicholson WT, Oyen LJ, Qin X, Raj R, Roger VL, Vitek CRRohrer, Ross JL, Sharp RR, Takahashi PY, Venner E, Walker K, Wang L, Wang Q, Wright JA, Wu T-J, Wang L, Weinshilboum RM. Cohort Profile: The Right Drug, Right Dose, Right Time: Using Genomic Data to Individualize Treatment Protocol (RIGHT Protocol). Int J Epidemiol. 2020 ;49(1):23-24k.
Natarajan P, Pampana A, Graham SE, Ruotsalainen SE, Perry JA, de Vries PS, Broome JG, Pirruccello JP, Honigberg MC, Aragam K, Wolford B, Brody JA, Antonacci-Fulton L, Arden M, Aslibekyan S, Assimes TL, Ballantyne CM, Bielak LF, Bis JC, Cade BE, Do R, Doddapaneni H, Emery LS, Hung Y-J, Irvin MR, Khan AT, Lange L, Lee J, Lemaitre RN, Martin LW, Metcalf GA, Montasser ME, Moon J-Y, Muzny DM, O'Connell JR, Palmer ND, Peralta JM, Peyser PA, Stilp AM, Tsai M, Wang FFei, Weeks DE, Yanek LR, Wilson JG, Abecasis G, Arnett DK, Becker LC, Blangero J, Boerwinkle E, Bowden DW, Chang Y-C, Chen Y-DI, Choi WJung, Correa A, Curran JE, Daly MJ, Dutcher SK, Ellinor PT, Fornage M, Freedman BI, Gabriel S, Germer S, Gibbs RA, He J, Hveem K, Jarvik GP, Kaplan RC, Kardia SLR, Kenny E, Kim RW, Kooperberg C, Laurie CC, Lee S, Lloyd-Jones DM, Loos RJF, Lubitz SA, Mathias RA, Martinez KAViaud, McGarvey ST, Mitchell BD, Nickerson DA, North KE, Palotie A, Park CJoo, Psaty BM, Rao DC, Redline S, Reiner AP, Seo D, Seo J-S, Smith AV, Tracy RP, Vasan RS, Kathiresan S, L Cupples A, Rotter JI, Morrison AC, Rich SS, Ripatti S, Willer C, Peloso GM. Chromosome Xq23 is associated with lower atherogenic lipid concentrations and favorable cardiometabolic indices. Nat Commun. 2021 ;12(1):2182.
Wilton PR, Sloan DB, Logsdon JM, Doddapaneni H, Neiman M. Characterization of transcriptomes from sexual and asexual lineages of a New Zealand snail (Potamopyrgus antipodarum). Mol Ecol Resour. 2013 ;13(2):289-94.
B
Sparks ME, Bansal R, Benoit JB, Blackburn MB, Chao H, Chen M, Cheng S, Childers C, Dinh H, Doddapaneni H, Dugan S, Elpidina EN, Farrow DW, Friedrich M, Gibbs RA, Hall B, Han Y, Hardy RW, Holmes CJ, Hughes DST, Ioannidis P, Jarvela AMCheatle, J Johnston S, Jones JW, Kronmiller BA, Kung F, Lee SL, Martynov AG, Masterson P, Maumus F, Munoz-Torres M, Murali SC, Murphy TD, Muzny DM, Nelson DR, Oppert B, Panfilio KA, Paula DPires, Pick L, Poelchau MF, Qu J, Reding K, Rhoades JH, Rhodes A, Richards S, Richter R, Robertson HM, Rosendale AJ, Tu ZJake, Velamuri AS, Waterhouse RM, Weirauch MT, Wells JT, Werren JH, Worley KC, Zdobnov EM, Gundersen-Rindal DE. Brown marmorated stink bug, Halyomorpha halys (Stål), genome: putative underpinnings of polyphagy, insecticide resistance potential and biology of a top worldwide pest. BMC Genomics. 2020 ;21(1):227.
Burrage LC, Reynolds JJ, Baratang NVida, Phillips JB, Wegner J, McFarquhar A, Higgs MR, Christiansen AE, Lanza DG, Seavitt JR, Jain M, Li X, Parry DA, Raman V, Chitayat D, Chinn IK, Bertuch AA, Karaviti L, Schlesinger AE, Earl D, Bamshad M, Savarirayan R, Doddapaneni H, Muzny DM, Jhangiani SN, Eng CM, Gibbs RA, Bi W, Emrick L, Rosenfeld JA, Postlethwait J, Westerfield M, Dickinson ME, Beaudet AL, Ranza E, Huber C, Cormier-Daire V, Shen W, Mao R, Heaney JD, Orange JS, Bertola D, Yamamoto GL, Baratela WAR, Butler MG, Ali A, Adeli M, Cohn DH, Krakow D, Jackson AP, Lees M, Offiah AC, Carlston CM, Carey JC, Stewart GS, Bacino CA, Campeau PM, Lee B. Bi-allelic Variants in TONSL Cause SPONASTRIME Dysplasia and a Spectrum of Skeletal Dysplasia Phenotypes. Am J Hum Genet. 2019 ;104(3):422-438.
Peters TL, Kumar V, Polikepahad S, Lin FY, Sarabia SF, Liang Y, Wang W-L, Lazar AJ, Doddapaneni H, Chao H, Muzny DM, Wheeler DA, M Okcu F, Plon SE, M Hicks J, López-Terrada D, D Parsons W, Roy A. BCOR-CCNB3 fusions are frequent in undifferentiated sarcomas of male children. Mod Pathol. 2015 ;28(4):575-86.
A
Doddapaneni H, Yao J, Lin H, M Walker A, Civerolo EL. Analysis of the genome-wide variations among multiple strains of the plant pathogenic bacterium Xylella fastidiosa. BMC Genomics. 2006 ;7:225.
Raffield LM, Iyengar AK, Wang B, Gaynor SM, Spracklen CN, Zhong X, Kowalski MH, Salimi S, Polfus LM, Benjamin EJ, Bis JC, Bowler R, Cade BE, Choi WJung, Comellas AP, Correa A, Cruz P, Doddapaneni H, Durda P, Gogarten SM, Jain D, Kim RW, Kral BG, Lange LA, Larson MG, Laurie C, Lee J, Lee S, Lewis JP, Metcalf GA, Mitchell BD, Momin Z, Muzny DM, Pankratz N, Park CJoo, Rich SS, Rotter JI, Ryan K, Seo D, Tracy RP, Viaud-Martinez KA, Yanek LR, Zhao LPing, Lin X, Li B, Li Y, Dupuis J, Reiner AP, Mohlke KL, Auer PL. Allelic Heterogeneity at the CRP Locus Identified by Whole-Genome Sequencing in Multi-ancestry Cohorts. Am J Hum Genet. 2020 ;106(1):112-120.
Lin H, Doddapaneni H, Bai X, Yao J, Zhao X, Civerolo EL. Acquisition of uncharacterized sequences from Candidatus liberibacter, an unculturable bacterium, using an improved genomic walking method. Mol Cell Probes. 2008 ;22(1):30-7.
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Pomerantz MM, Ahmadiyeh N, Jia L, Herman P, Verzi MP, Doddapaneni H, Beckwith CA, Chan JA, Hills A, Davis M, Yao K, Kehoe SM, Lenz H-J, Haiman CA, Yan C, Henderson BE, Frenkel B, Barretina J, Bass A, Tabernero J, Baselga J, Regan MM, J Manak R, Shivdasani R, Coetzee GA, Freedman ML. The 8q24 cancer risk variant rs6983267 shows long-range interaction with MYC in colorectal cancer. Nat Genet. 2009 ;41(8):882-4.