Publications

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2024
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.
2022
Pan B, Ren L, Onuchic V, Guan M, Kusko R, Bruinsma S, Trigg L, Scherer A, Ning B, Zhang C, Glidewell-Kenney C, Xiao C, Donaldson E, Sedlazeck FJ, Schroth G, Yavas G, Grunenwald H, Chen H, Meinholz H, Meehan J, Wang J, Yang J, Foox J, Shang J, Miclaus K, Dong L, Shi L, Mohiyuddin M, Pirooznia M, Gong P, Golshani R, Wolfinger R, Lababidi S, Sahraeian SMohammad E, Sherry S, Han T, Chen T, Shi T, Hou W, Ge W, Zou W, Guo W, Bao W, Xiao W, Fan X, Gondo Y, Yu Y, Zhao Y, Su Z, Liu Z, Tong W, Xiao W, Zook JM, Zheng Y, Hong H. Assessing reproducibility of inherited variants detected with short-read whole genome sequencing. Genome Biol. 2022 ;23(1):2.
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.
Farek J, Hughes D, Salerno W, Zhu Y, Pisupati A, Mansfield A, Krasheninina O, English AC, Metcalf GA, Boerwinkle E, Muzny DM, Gibbs RA, Khan Z, Sedlazeck FJ. xAtlas: scalable small variant calling across heterogeneous next-generation sequencing experiments. Gigascience. 2022 ;12.
2021
Taliun D, Harris DN, Kessler MD, Carlson J, Szpiech ZA, Torres R, Taliun SAGagliano, Corvelo A, Gogarten SM, Kang HMin, Pitsillides AN, LeFaive J, Lee S-B, Tian X, Browning BL, Das S, Emde A-K, Clarke WE, Loesch DP, Shetty AC, Blackwell TW, Smith AV, Wong Q, Liu X, Conomos MP, Bobo DM, Aguet F, Albert C, Alonso A, Ardlie KG, Arking DE, Aslibekyan S, Auer PL, Barnard J, R Barr G, Barwick L, Becker LC, Beer RL, Benjamin EJ, Bielak LF, Blangero J, Boehnke M, Bowden DW, Brody JA, Burchard EG, Cade BE, Casella JF, Chalazan B, Chasman DI, Chen Y-DIda, Cho MH, Choi SHoan, Chung MK, Clish CB, Correa A, Curran JE, Custer B, Darbar D, Daya M, de Andrade M, DeMeo DL, Dutcher SK, Ellinor PT, Emery LS, Eng C, Fatkin D, Fingerlin T, Forer L, Fornage M, Franceschini N, Fuchsberger C, Fullerton SM, Germer S, Gladwin MT, Gottlieb DJ, Guo X, Hall ME, He J, Heard-Costa NL, Heckbert SR, Irvin MR, Johnsen JM, Johnson AD, Kaplan R, Kardia SLR, Kelly T, Kelly S, Kenny EE, Kiel DP, Klemmer R, Konkle BA, Kooperberg C, Köttgen A, Lange LA, Lasky-Su J, Levy D, Lin X, Lin K-H, Liu C, Loos RJF, Garman L, Gerszten R, Lubitz SA, Lunetta KL, C Y Mak A, Manichaikul A, Manning AK, Mathias RA, McManus DD, McGarvey ST, Meigs JB, Meyers DA, Mikulla JL, Minear MA, Mitchell BD, Mohanty S, Montasser ME, Montgomery C, Morrison AC, Murabito JM, Natale A, Natarajan P, Nelson SC, North KE, O'Connell JR, Palmer ND, Pankratz N, Peloso GM, Peyser PA, Pleiness J, Post WS, Psaty BM, Rao DC, Redline S, Reiner AP, Roden D, Rotter JI, Ruczinski I, Sarnowski C, Schoenherr S, Schwartz DA, Seo J-S, Seshadri S, Sheehan VA, Sheu WH, M Shoemaker B, Smith NL, Smith JA, Sotoodehnia N, Stilp AM, Tang W, Taylor KD, Telen M, Thornton TA, Tracy RP, Van Den Berg DJ, Vasan RS, Viaud-Martinez KA, Vrieze S, Weeks DE, Weir BS, Weiss ST, Weng L-C, Willer CJ, Zhang Y, Zhao X, Arnett DK, Ashley-Koch AE, Barnes KC, Boerwinkle E, Gabriel S, Gibbs RA, Rice KM, Rich SS, Silverman EK, Qasba P, Gan W, Papanicolaou GJ, Nickerson DA, Browning SR, Zody MC, Zöllner S, Wilson JG, L Cupples A, Laurie CC, Jaquish CE, Hernandez RD, O'Connor TD, Abecasis GR. Sequencing of 53,831 diverse genomes from the NHLBI TOPMed Program. Nature. 2021 ;590(7845):290-299.
Gingras M-C, Sabo A, Cardenas M, Rana A, Dhingra S, Meng Q, Hu J, Muzny DM, Doddapaneni H, Perez L, Korchina V, Nessner C, Liu X, Chao H, Goss J, Gibbs RA. Sequencing of a central nervous system tumor demonstrates cancer transmission in an organ transplant. Life Sci Alliance. 2021 ;4(9).
2020
Rheinbay E, Nielsen MMuhlig, Abascal F, Wala JA, Shapira O, Tiao G, Hornshøj H, Hess JM, Juul RIstrup, Lin Z, Feuerbach L, Sabarinathan R, Madsen T, Kim J, Mularoni L, Shuai S, Lanzós A, Herrmann C, Maruvka YE, Shen C, Amin SB, Bandopadhayay P, Bertl J, Boroevich KA, Busanovich J, Carlevaro-Fita J, Chakravarty D, Chan CWing Yiu, Craft D, Dhingra P, Diamanti K, Fonseca NA, Gonzalez-Perez A, Guo Q, Hamilton MP, Haradhvala NJ, Hong C, Isaev K, Johnson TA, Juul M, Kahles A, Kahraman A, Kim Y, Komorowski J, Kumar K, Kumar S, Lee D, Van Lehmann K-, Li Y, Liu EMinwei, Lochovsky L, Park K, Pich O, Roberts ND, Saksena G, Schumacher SE, Sidiropoulos N, Sieverling L, Sinnott-Armstrong N, Stewart C, Tamborero D, Tubio JMC, Umer HM, Uusküla-Reimand L, Wadelius C, Wadi L, Yao X, Zhang C-Z, Zhang J, Haber JE, Hobolth A, Imielinski M, Kellis M, Lawrence MS, von Mering C, Nakagawa H, Raphael BJ, Rubin MA, Sander C, Stein LD, Stuart JM, Tsunoda T, Wheeler DA, Johnson R, Reimand J, Gerstein M, Khurana E, Campbell PJ, Lopez-Bigas N, Weischenfeldt J, Beroukhim R, Martincorena I, Pedersen JSkou, Getz G. Analyses of non-coding somatic drivers in 2,658 cancer whole genomes. Nature. 2020 ;578(7793):102-111.
Yuan B, Wang L, Liu P, Shaw C, Dai H, Cooper L, Zhu W, Anderson SA, Meng L, Wang X, Wang Y, Xia F, Xiao R, Braxton A, Peacock S, Schmitt E, Ward PA, Vetrini F, He W, Chiang T, Muzny DM, Gibbs RA, Beaudet AL, Breman AM, Smith J, Cheung SWai, Bacino CA, Eng CM, Yang Y, Lupski JR, Bi W. CNVs cause autosomal recessive genetic diseases with or without involvement of SNV/indels. Genet Med. 2020 ;22(10):1633-1641.
Zook JM, Hansen NF, Olson ND, Chapman L, Mullikin JC, Xiao C, Sherry S, Koren S, Phillippy AM, Boutros PC, Sahraeian SMohammad E, Huang V, Rouette A, Alexander N, Mason CE, Hajirasouliha I, Ricketts C, Lee J, Tearle R, Fiddes IT, Barrio AMartinez, Wala J, Carroll A, Ghaffari N, Rodriguez OL, Bashir A, Jackman S, Farrell JJ, Wenger AM, Alkan C, Soylev A, Schatz MC, Garg S, Church G, Marschall T, Chen K, Fan X, English AC, Rosenfeld JA, Zhou W, Mills RE, Sage JM, Davis JR, Kaiser MD, Oliver JS, Catalano AP, Chaisson MJP, Spies N, Sedlazeck FJ, Salit M. A robust benchmark for detection of germline large deletions and insertions. Nat Biotechnol. 2020 ;38(11):1347-1355.
2019
Yuan B, Neira J, Pehlivan D, Santiago-Sim T, Song X, Rosenfeld J, Posey JE, Patel V, Jin W, Adam MP, Baple EL, Dean J, Fong C-T, Hickey SE, Hudgins L, Leon E, Madan-Khetarpal S, Rawlins L, Rustad CF, Stray-Pedersen A, Tveten K, Wenger O, Diaz J, Jenkins L, Martin L, McGuire M, Pietryga M, Ramsdell L, Slattery L, Abid F, Bertuch AA, Grange D, Immken L, Schaaf CP, Van Esch H, Bi W, Cheung SWai, Breman AM, Smith JL, Shaw C, Crosby AH, Eng CM, Yang Y, Lupski JR, Xiao R, Liu P. Clinical exome sequencing reveals locus heterogeneity and phenotypic variability of cohesinopathies. Genet Med. 2019 ;21(3):663-675.
Vetrini F, McKee S, Rosenfeld JA, Suri M, Lewis AM, Nugent KMargaret, Roeder E, Littlejohn RO, Holder S, Zhu W, Alaimo JT, Graham B, Harris JM, Gibson JB, Pastore M, McBride KL, Komara M, Al-Gazali L, Shamsi AAl, Fanning EA, Wierenga KJ, Scott DA, Ben-Neriah Z, Meiner V, Cassuto H, Elpeleg O, J Holder L, Burrage LC, Seaver LH, Van Maldergem L, Mahida S, Soul JS, Marlatt M, Matyakhina L, Vogt J, Gold J-A, Park S-M, Varghese V, Lampe AK, Kumar A, Lees M, Holder-Espinasse M, McConnell V, Bernhard B, Blair E, Harrison V, Muzny DM, Gibbs RA, Elsea SH, Posey JE, Bi W, Lalani S, Xia F, Yang Y, Eng CM, Lupski JR, Liu P. De novo and inherited TCF20 pathogenic variants are associated with intellectual disability, dysmorphic features, hypotonia, and neurological impairments with similarities to Smith-Magenis syndrome. Genome Med. 2019 ;11(1):12.
Beck CR, Carvalho CMB, Akdemir ZC, Sedlazeck FJ, Song X, Meng Q, Hu J, Doddapaneni H, Chong Z, Chen ES, Thornton PC, Liu P, Yuan B, Withers M, Jhangiani SN, Kalra D, Walker K, English AC, Han Y, Chen K, Muzny DM, Ira G, Shaw CA, Gibbs RA, Hastings PJ, Lupski JR. Megabase Length Hypermutation Accompanies Human Structural Variation at 17p11.2. Cell. 2019 ;176(6):1310-1324.e10.
Luo R, Sedlazeck FJ, Lam T-W, Schatz MC. A multi-task convolutional deep neural network for variant calling in single molecule sequencing. Nat Commun. 2019 ;10(1):998.
2015
Li JN, Carrero IG, Dong JF, Yu FL. Complexity and diversity of F8 genetic variations in the 1000 genomes. J Thromb Haemost. 2015 ;13(11):2031-40.
Challis D, Antunes L, Garrison E, Banks E, Evani US, Muzny DM, Poplin R, Gibbs RA, Marth G, Yu F. The distribution and mutagenesis of short coding INDELs from 1,128 whole exomes. BMC Genomics. 2015 ;16(1):143.
Ritter DI, Haines K, Cheung H, Davis CF, Lau CC, Berg JS, Brown CW, Thompson PA, Gibbs RA, Wheeler DA, Plon SE. Identifying gene disruptions in novel balanced de novo constitutional translocations in childhood cancer patients by whole-genome sequencing. Genet Med. 2015 ;17(10):831-5.
2014
Huang W, Massouras A, Inoue Y, Peiffer J, Ràmia M, Tarone AM, Turlapati L, Zichner T, Zhu D, Lyman RF, Magwire MM, Blankenburg K, Carbone MAnna, Chang K, Ellis LL, Fernandez S, Han Y, Highnam G, Hjelmen CE, Jack JR, Javaid M, Jayaseelan J, Kalra D, Lee S, Lewis L, Munidasa M, Ongeri F, Patel S, Perales L, Perez A, Pu LL, Rollmann SM, Ruth R, Saada N, Warner C, Williams A, Wu Y-Q, Yamamoto A, Zhang Y, Zhu Y, Anholt RRH, Korbel JO, Mittelman D, Muzny DM, Gibbs RA, Barbadilla A, J Johnston S, Stone EA, Richards S, Deplancke B, Mackay TFC. Natural variation in genome architecture among 205 Drosophila melanogaster Genetic Reference Panel lines. Genome Res. 2014 ;24(7):1193-208.
English AC, Salerno WJ, Reid JG. PBHoney: identifying genomic variants via long-read discordance and interrupted mapping. BMC Bioinformatics. 2014 ;15:180.
2012
Lu JT, Wang Y, Gibbs RA, Yu F. Characterizing linkage disequilibrium and evaluating imputation power of human genomic insertion-deletion polymorphisms. Genome Biol. 2012 ;13(2):R15.
Challis D, Yu J, Evani US, Jackson AR, Paithankar S, Coarfa C, Milosavljevic A, Gibbs RA, Yu F. An integrative variant analysis suite for whole exome next-generation sequencing data. BMC Bioinformatics. 2012 ;13:8.
2011
Agrawal N, Frederick MJ, Pickering CR, Bettegowda C, Chang K, Li RJ, Fakhry C, Xie T-X, Zhang J, Wang J, Zhang N, El-Naggar AK, Jasser SA, Weinstein JN, Treviño L, Drummond JA, Muzny DM, Wu Y, Wood LD, Hruban RH, Westra WH, Koch WM, Califano JA, Gibbs RA, Sidransky D, Vogelstein B, Velculescu VE, Papadopoulos N, Wheeler DA, Kinzler KW, Myers JN. Exome sequencing of head and neck squamous cell carcinoma reveals inactivating mutations in NOTCH1. Science. 2011 ;333(6046):1154-7.
Totoki Y, Tatsuno K, Yamamoto S, Arai Y, Hosoda F, Ishikawa S, Tsutsumi S, Sonoda K, Totsuka H, Shirakihara T, Sakamoto H, Wang L, Ojima H, Shimada K, Kosuge T, Okusaka T, Kato K, Kusuda J, Yoshida T, Aburatani H, Shibata T. High-resolution characterization of a hepatocellular carcinoma genome. Nat Genet. 2011 ;43(5):464-9.