Publications

Journal Article
Benoit JB, Adelman ZN, Reinhardt K, Dolan A, Poelchau M, Jennings EC, Szuter EM, Hagan RW, Gujar H, Shukla JNath, Zhu F, Mohan M, Nelson DR, Rosendale AJ, Derst C, Resnik V, Wernig S, Menegazzi P, Wegener C, Peschel N, Hendershot JM, Blenau W, Predel R, Johnston PR, Ioannidis P, Waterhouse RM, Nauen R, Schorn C, Ott M-C, Maiwald F, J Johnston S, Gondhalekar AD, Scharf ME, Peterson BF, Raje KR, Hottel BA, Armisén D, Crumière AJean Johan, Refki PNagui, Santos MEmilia, Sghaier E, Viala S, Khila A, Ahn S-J, Childers C, Lee C-Y, Lin H, Hughes DST, Duncan EJ, Murali SC, Qu J, Dugan S, Lee SL, Chao H, Dinh H, Han Y, Doddapaneni H, Worley KC, Muzny DM, Wheeler D, Panfilio KA, Jentzsch IMVargas, Vargo EL, Booth W, Friedrich M, Weirauch MT, Anderson MAE, Jones JW, Mittapalli O, Zhao C, Zhou J-J, Evans JD, Attardo GM, Robertson HM, Zdobnov EM, Ribeiro JMC, Gibbs RA, Werren JH, Palli SR, Schal C, Richards S. Unique features of a global human ectoparasite identified through sequencing of the bed bug genome. Nat Commun. 2016 ;7:10165.
Tellam RL, Lemay DG, Van Tassell CP, Lewin HA, Worley KC, Elsik CG. Unlocking the bovine genome. BMC Genomics. 2009 ;10:193.
Vogelaar IP, van der Post RS, J van Krieken HJm, Spruijt L, van Zelst-Stams WAg, C Kets M, Lubinski J, Jakubowska A, Teodorczyk U, Aalfs CM, van Hest LP, Pinheiro H, Oliveira C, Jhangiani SN, Muzny DM, Gibbs RA, Lupski JR, de Ligt J, Vissers LELM, Hoischen A, Gilissen C, van de Vorst M, Goeman JJ, Schackert HK, Ranzani GN, Molinaro V, García EBGómez, Hes FJ, Holinski-Feder E, Genuardi M, Ausems MGEM, Sijmons RH, Wagner A, van der Kolk LE, Bjørnevoll I, Høberg-Vetti H, van Kessel AGeurts, Kuiper RP, Ligtenberg MJL, Hoogerbrugge N. Unraveling genetic predisposition to familial or early onset gastric cancer using germline whole-exome sequencing. Eur J Hum Genet. 2017 ;25(11):1246-1252.
Yee SWah, Stecula A, Chien H-C, Zou L, Feofanova EV, van Borselen M, Cheung KWun Kathy, Yousri NA, Suhre K, Kinchen JM, Boerwinkle E, Irannejad R, Yu B, Giacomini KM. Unraveling the functional role of the orphan solute carrier, SLC22A24 in the transport of steroid conjugates through metabolomic and genome-wide association studies. PLoS Genet. 2019 ;15(9):e1008208.
Doyle VP, Andersen JJ, Nelson BJ, Metzker ML, Brown JM. Untangling the influences of unmodeled evolutionary processes on phylogenetic signal in a forensically important HIV-1 transmission cluster. Mol Phylogenet Evol. 2014 ;75:126-37.
Harris RA, Raveendran M, Worley KC, Rogers J. Unusual sequence characteristics of human chromosome 19 are conserved across 11 nonhuman primates. BMC Evol Biol. 2020 ;20(1):33.
Agustinho DP, Fu Y, Menon VK, Metcalf GA, Treangen TJ, Sedlazeck FJ. Unveiling microbial diversity: harnessing long-read sequencing technology. Nat Methods. 2024 ;21(6):954-966.
Ji Y, Zhao J, Gong J, Sedlazeck FJ, Fan S. Unveiling novel genetic variants in 370 challenging medically relevant genes using the long read sequencing data of 41 samples from 19 global populations. Mol Genet Genomics. 2024 ;299(1):65.
Jünemann S, Sedlazeck FJ, Prior K, Albersmeier A, John U, Kalinowski J, Mellmann A, Goesmann A, von Haeseler A, Stoye J, Harmsen D. Updating benchtop sequencing performance comparison. Nat Biotechnol. 2013 ;31(4):294-6.
Kowalski MH, Qian H, Hou Z, Rosen JD, Tapia AL, Shan Y, Jain D, Argos M, Arnett DK, Avery C, Barnes KC, Becker LC, Bien SA, Bis JC, Blangero J, Boerwinkle E, Bowden DW, Buyske S, Cai J, Cho MH, Choi SHoan, Choquet H, L Cupples A, Cushman M, Daya M, de Vries PS, Ellinor PT, Faraday N, Fornage M, Gabriel S, Ganesh SK, Graff M, Gupta N, He J, Heckbert SR, Hidalgo B, Hodonsky CJ, Irvin MR, Johnson AD, Jorgenson E, Kaplan R, Kardia SLR, Kelly TN, Kooperberg C, Lasky-Su JA, Loos RJF, Lubitz SA, Mathias RA, McHugh CP, Montgomery C, Moon J-Y, Morrison AC, Palmer ND, Pankratz N, Papanicolaou GJ, Peralta JM, Peyser PA, Rich SS, Rotter JI, Silverman EK, Smith JA, Smith NL, Taylor KD, Thornton TA, Tiwari HK, Tracy RP, Wang T, Weiss ST, Weng L-C, Wiggins KL, Wilson JG, Yanek LR, Zöllner S, North KE, Auer PL, Raffield LM, Reiner AP, Li Y. Use of >100,000 NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium whole genome sequences improves imputation quality and detection of rare variant associations in admixed African and Hispanic/Latino populations. PLoS Genet. 2019 ;15(12):e1008500.
Meng L, Pammi M, Saronwala A, Magoulas P, Ghazi ARay, Vetrini F, Zhang J, He W, Dharmadhikari AV, Qu C, Ward P, Braxton A, Narayanan S, Ge X, Tokita MJ, Santiago-Sim T, Dai H, Chiang T, Smith H, Azamian MS, Robak L, Bostwick BL, Schaaf CP, Potocki L, Scaglia F, Bacino CA, Hanchard NA, Wangler MF, Scott D, Brown C, Hu J, Belmont JW, Burrage LC, Graham BH, Sutton VReid, Craigen WJ, Plon SE, Lupski JR, Beaudet AL, Gibbs RA, Muzny DM, Miller MJ, Wang X, Leduc MS, Xiao R, Liu P, Shaw C, Walkiewicz M, Bi W, Xia F, Lee B, Eng CM, Yang Y, Lalani SR. Use of Exome Sequencing for Infants in Intensive Care Units: Ascertainment of Severe Single-Gene Disorders and Effect on Medical Management. JAMA Pediatr. 2017 ;171(12):e173438.
Yang L, Wei Z, Chen X, Hu L, Peng X, Wang J, Lu C, Kong Y, Dong X, Ni Q, Lu Y, Wu B, Wang H, Meirelles K, Tian X, Zhang J, Chang F, Liu L, Li C, You W, Cheng G, Wang L, Cao Y, Chen C, Fang P, Tang S, Zhou W. Use of medical exome sequencing for identification of underlying genetic defects in NICU: Experience in a cohort of 2303 neonates in China. Clin Genet. 2022 ;101(1):101-109.
Donehower LA, Bohannon RC, Ford RJ, Gibbs RA. The use of primers from highly conserved pol regions to identify uncharacterized retroviruses by the polymerase chain reaction. J Virol Methods. 1990 ;28(1):33-46.
Rodin AS, Litvinenko A, Klos K, Morrison AC, Woodage T, Coresh J, Boerwinkle E. Use of wrapper algorithms coupled with a random forests classifier for variable selection in large-scale genomic association studies. J Comput Biol. 2009 ;16(12):1705-18.
Horvath JE, Gulden CL, Bailey JA, Yohn C, McPherson JD, Prescott A, Roe BA, de Jong PJ, Ventura M, Misceo D, Archidiacono N, Zhao S, Schwartz S, Rocchi M, Eichler EE. Using a pericentromeric interspersed repeat to recapitulate the phylogeny and expansion of human centromeric segmental duplications. Mol Biol Evol. 2003 ;20(9):1463-79.
Muzny DM, Metzker ML, Bouck J, Gorrell JH, Ding Y, Maxim E, Gibbs RA. Using BODIPY dye-primer chemistry in large-scale sequencing. IEEE Eng Med Biol Mag. 1998 ;17(6):88-93.
Monsivais D, Parks SE, Chandrashekar DS, Varambally S, Creighton CJ. Using cancer proteomics data to identify gene candidates for therapeutic targeting. Oncotarget. 2023 ;14:399-412.
Ober U, Ayroles JF, Stone EA, Richards S, Zhu D, Gibbs RA, Stricker C, Gianola D, Schlather M, Mackay TFC, Simianer H. Using whole-genome sequence data to predict quantitative trait phenotypes in Drosophila melanogaster. PLoS Genet. 2012 ;8(5):e1002685.
Mahmoud M, Huang Y, Garimella K, Audano PA, Wan W, Prasad N, Handsaker RE, Hall S, Pionzio A, Schatz MC, Talkowski ME, Eichler EE, Levy SE, Sedlazeck FJ. Utility of long-read sequencing for All of Us. Nat Commun. 2024 ;15(1):837.
Chandramohan R, Reuther J, Gandhi I, Voicu H, Alvarez KR, Plon SE, López-Terrada DH, Fisher KE, D Parsons W, Roy A. A Validation Framework for Somatic Copy Number Detection in Targeted Sequencing Panels. J Mol Diagn. 2022 ;24(7):760-774.
Grochowski CM, Gibbs RA, Doddapaneni H. Validation of Single-Nucleotide Mosaic Variants Through Droplet Digital PCR. Curr Protoc. 2024 ;4(5):e1041.
Worley KC, Richards S, Rogers J. The value of new genome references. Exp Cell Res. 2017 ;358(2):433-438.
Wang Z, Choi SWan, Chami N, Boerwinkle E, Fornage M, Redline S, Bis JC, Brody JA, Psaty BM, Kim W, McDonald M-LN, Regan EA, Silverman EK, Liu C-T, Vasan RS, Kalyani RR, Mathias RA, Yanek LR, Arnett DK, Justice AE, North KE, Kaplan R, Heckbert SR, de Andrade M, Guo X, Lange LA, Rich SS, Rotter JI, Ellinor PT, Lubitz SA, Blangero J, M Shoemaker B, Darbar D, Gladwin MT, Albert CM, Chasman DI, Jackson RD, Kooperberg C, Reiner AP, O'Reilly PF, Loos RJF. The Value of Rare Genetic Variation in the Prediction of Common Obesity in European Ancestry Populations. Front Endocrinol (Lausanne). 2022 ;13:863893.
Livak KJ, Rogers J, Lichter JB. Variability of dopamine D4 receptor (DRD4) gene sequence within and among nonhuman primate species. Proc Natl Acad Sci U S A. 1995 ;92(2):427-31.
da Palma MMatioli, Vargas ME, Burr A, Chen R, Pennesi ME, Weleber RG, Yang P. Variable expressivity of -associated autosomal dominant vitreoretinochoroidopathy (ADVIRC) in a three-generation pedigree. BMJ Open Ophthalmol. 2021 ;6(1):e000813.