Publications

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2014
Xia F, Bainbridge MN, Tan TYang, Wangler MF, Scheuerle AE, Zackai EH, Harr MH, V Sutton R, Nalam RL, Zhu W, Nash M, Ryan MM, Yaplito-Lee J, Hunter JV, Deardorff MA, Penney SJ, Beaudet AL, Plon SE, Boerwinkle E, Lupski JR, Eng CM, Muzny DM, Yang Y, Gibbs RA. De novo truncating mutations in AHDC1 in individuals with syndromic expressive language delay, hypotonia, and sleep apnea. Am J Hum Genet. 2014 ;94(5):784-9.
Boonma P, Spinler JK, Qin X, Jittaprasatsin C, Muzny DM, Doddapaneni H, Gibbs RA, Petrosino J, Tumwasorn S, Versalovic J. Draft genome sequences and description of Lactobacillus rhamnosus strains L31, L34, and L35. Stand Genomic Sci. 2014 ;9(3):744-54.
Yamamoto S, Jaiswal M, Charng W-L, Gambin T, Karaca E, Mirzaa G, Wiszniewski W, Sandoval H, Haelterman NA, Xiong B, Zhang K, Bayat V, David G, Li T, Chen K, Gala U, Harel T, Pehlivan D, Penney S, Vissers LELM, de Ligt J, Jhangiani SN, Xie Y, Tsang SH, Parman Y, Sivaci M, Battaloglu E, Muzny DM, Wan Y-W, Liu Z, Lin-Moore AT, Clark RD, Curry CJ, Link N, Schulze KL, Boerwinkle E, Dobyns WB, Allikmets R, Gibbs RA, Chen R, Lupski JR, Wangler MF, Bellen HJ. A drosophila genetic resource of mutants to study mechanisms underlying human genetic diseases. Cell. 2014 ;159(1):200-214.
Okamoto Y, Goksungur MTuba, Pehlivan D, Beck CR, Gonzaga-Jauregui C, Muzny DM, Atik MM, Carvalho CMB, Matur Z, Bayraktar S, Boone PM, Akyuz K, Gibbs RA, Battaloglu E, Parman Y, Lupski JR. Exonic duplication CNV of NDRG1 associated with autosomal-recessive HMSN-Lom/CMT4D. Genet Med. 2014 ;16(5):386-394.
Shinbrot E, Henninger EE, Weinhold N, Covington KR, A Göksenin Y, Schultz N, Chao H, Doddapaneni H, Muzny DM, Gibbs RA, Sander C, Pursell ZF, Wheeler DA. Exonuclease mutations in DNA polymerase epsilon reveal replication strand specific mutation patterns and human origins of replication. Genome Res. 2014 ;24(11):1740-50.
Chipman AD, Ferrier DEK, Brena C, Qu J, Hughes DST, Schröder R, Torres-Oliva M, Znassi N, Jiang H, Almeida FC, Alonso CR, Apostolou Z, Aqrawi P, Arthur W, Barna JCJ, Blankenburg KP, Brites D, Capella-Gutiérrez S, Coyle M, Dearden PK, Pasquier LDu, Duncan EJ, Ebert D, Eibner C, Erikson G, Evans PD, Extavour CG, Francisco L, Gabaldón T, Gillis WJ, Goodwin-Horn EA, Green JE, Griffiths-Jones S, Grimmelikhuijzen CJP, Gubbala S, Guigó R, Han Y, Hauser F, Havlak P, Hayden L, Helbing S, Holder M, Hui JHL, Hunn JP, Hunnekuhl VS, Jackson L, Javaid M, Jhangiani SN, Jiggins FM, Jones TE, Kaiser TS, Kalra D, Kenny NJ, Korchina V, Kovar CL, F Kraus B, Lapraz F, Lee SL, Lv J, Mandapat C, Manning G, Mariotti M, Mata R, Mathew T, Neumann T, Newsham I, Ngo DN, Ninova M, Okwuonu G, Ongeri F, Palmer WJ, Patil S, Patraquim P, Pham C, Pu L-L, Putman NH, Rabouille C, Ramos OMendivil, Rhodes AC, Robertson HE, Robertson HM, Ronshaugen M, Rozas J, Saada N, Sánchez-Gracia A, Scherer SE, Schurko AM, Siggens KW, Simmons DN, Stief A, Stolle E, Telford MJ, Tessmar-Raible K, Thornton R, Van der Zee M, von Haeseler A, Williams JM, Willis JH, Wu Y, Zou X, Lawson D, Muzny DM, Worley KC, Gibbs RA, Akam M, Richards S. The first myriapod genome sequence reveals conservative arthropod gene content and genome organisation in the centipede Strigamia maritima. PLoS Biol. 2014 ;12(11):e1002005.
Carbone L, Harris RA, Gnerre S, Veeramah KR, Lorente-Galdos B, Huddleston J, Meyer TJ, Herrero J, Roos C, Aken B, Anaclerio F, Archidiacono N, Baker C, Barrell D, Batzer MA, Beal K, Blancher A, Bohrson CL, Brameier M, Campbell MS, Capozzi O, Casola C, Chiatante G, Cree A, Damert A, De Jong PJ, Dumas L, Fernandez-Callejo M, Flicek P, Fuchs NV, Gut I, Gut M, Hahn MW, Hernandez-Rodriguez J, Hillier LDW, Hubley R, Ianc B, Izsvák Z, Jablonski NG, Johnstone LM, Karimpour-Fard A, Konkel MK, Kostka D, Lazar NH, Lee SL, Lewis LR, Liu Y, Locke DP, Mallick S, Mendez FL, Muffato M, Nazareth LV, Nevonen KA, O'Bleness M, Ochis C, Odom DT, Pollard KS, Quilez J, Reich D, Rocchi M, Schumann GG, Searle S, Sikela JM, Skollar G, Smit A, Sonmez K, Hallers Bten, Terhune E, Thomas GWC, Ullmer B, Ventura M, Walker JA, Wall JD, Walter L, Ward MC, Wheelan SJ, Whelan CW, White S, Wilhelm LJ, Woerner AE, Yandell M, Zhu B, Hammer MF, Marques-Bonet T, Eichler EE, Fulton L, Fronick C, Muzny DM, Warren WC, Worley KC, Rogers J, Wilson RK, Gibbs RA. Gibbon genome and the fast karyotype evolution of small apes. Nature. 2014 ;513(7517):195-201.
Wangler MF, Gonzaga-Jauregui C, Gambin T, Penney S, Moss T, Chopra A, Probst FJ, Xia F, Yang Y, Werlin S, Eglite I, Kornejeva L, Bacino CA, Baldridge D, Neul J, Lehman ELev, Larson A, Beuten J, Muzny DM, Jhangiani S, Gibbs RA, Lupski JR, Beaudet A. Heterozygous de novo and inherited mutations in the smooth muscle actin (ACTG2) gene underlie megacystis-microcolon-intestinal hypoperistalsis syndrome. PLoS Genet. 2014 ;10(3):e1004258.
Karaca E, Weitzer S, Pehlivan D, Shiraishi H, Gogakos T, Hanada T, Jhangiani SN, Wiszniewski W, Withers M, Campbell IM, Erdin S, Isikay S, Franco LM, Gonzaga-Jauregui C, Gambin T, Gelowani V, Hunter JV, Yesil G, Koparir E, Yilmaz S, Brown M, Briskin D, Hafner M, Morozov P, Farazi TA, Bernreuther C, Glatzel M, Trattnig S, Friske J, Kronnerwetter C, Bainbridge MN, Gezdirici A, Seven M, Muzny DM, Boerwinkle E, Ozen M, Clausen T, Tuschl T, Yuksel A, Hess A, Gibbs RA, Martinez J, Penninger JM, Lupski JR. Human CLP1 mutations alter tRNA biogenesis, affecting both peripheral and central nervous system function. Cell. 2014 ;157(3):636-50.
Reid JG, Carroll A, Veeraraghavan N, Dahdouli M, Sundquist A, English A, Bainbridge M, White S, Salerno W, Buhay C, Yu F, Muzny DM, Daly R, Duyk G, Gibbs RA, Boerwinkle E. Launching genomics into the cloud: deployment of Mercury, a next generation sequence analysis pipeline. BMC Bioinformatics. 2014 ;15:30.
Bellott DW, Hughes JF, Skaletsky H, Brown LG, Pyntikova T, Cho T-J, Koutseva N, Zaghlul S, Graves T, Rock S, Kremitzki C, Fulton RS, Dugan S, Ding Y, Morton D, Khan Z, Lewis L, Buhay C, Wang Q, Watt J, Holder M, Lee S, Nazareth L, Alföldi J, Rozen S, Muzny DM, Warren WC, Gibbs RA, Wilson RK, Page DC. Mammalian Y chromosomes retain widely expressed dosage-sensitive regulators. Nature. 2014 ;508(7497):494-9.
Yang Y, Muzny DM, Xia F, Niu Z, Person R, Ding Y, Ward P, Braxton A, Wang M, Buhay C, Veeraraghavan N, Hawes A, Chiang T, Leduc M, Beuten J, Zhang J, He W, Scull J, Willis A, Landsverk M, Craigen WJ, Bekheirnia MReza, Stray-Pedersen A, Liu P, Wen S, Alcaraz W, Cui H, Walkiewicz M, Reid J, Bainbridge M, Patel A, Boerwinkle E, Beaudet AL, Lupski JR, Plon SE, Gibbs RA, Eng CM. Molecular findings among patients referred for clinical whole-exome sequencing. JAMA. 2014 ;312(18):1870-9.
Rainger J, Pehlivan D, Johansson S, Bengani H, Sanchez-Pulido L, Williamson KA, Ture M, Barker H, Rosendahl K, Spranger J, Horn D, Meynert A, Floyd JAB, Prescott T, Anderson CA, Rainger JK, Karaca E, Gonzaga-Jauregui C, Jhangiani S, Muzny DM, Seawright A, Soares DC, Kharbanda M, Murday V, Finch A, Gibbs RA, van Heyningen V, Taylor MS, Yakut T, Knappskog PM, Hurles ME, Ponting CP, Lupski JR, Houge G, FitzPatrick DR. Monoallelic and biallelic mutations in MAB21L2 cause a spectrum of major eye malformations. Am J Hum Genet. 2014 ;94(6):915-23.
Pickering CR, Zhou JH, J Lee J, Drummond JA, S Peng A, Saade RE, Tsai KY, Curry JL, Tetzlaff MT, Lai SY, Yu J, Muzny DM, Doddapaneni H, Shinbrot E, Covington KR, Zhang J, Seth S, Caulin C, Clayman GL, El-Naggar AK, Gibbs RA, Weber RS, Myers JN, Wheeler DA, Frederick MJ. Mutational landscape of aggressive cutaneous squamous cell carcinoma. Clin Cancer Res. 2014 ;20(24):6582-92.
Lalani SR, Zhang J, Schaaf CP, Brown CW, Magoulas P, Tsai AChun-Hui, El-Gharbawy A, Wierenga KJ, Bartholomew D, Fong C-T, Barbaro-Dieber T, Kukolich MK, Burrage LC, Austin E, Keller K, Pastore M, Fernandez F, Lotze T, Wilfong A, Purcarin G, Zhu W, Craigen WJ, McGuire M, Jain M, Cooney E, Azamian M, Bainbridge MN, Muzny DM, Boerwinkle E, Person RE, Niu Z, Eng CM, Lupski JR, Gibbs RA, Beaudet AL, Yang Y, Wang MC, Xia F. Mutations in PURA cause profound neonatal hypotonia, seizures, and encephalopathy in 5q31.3 microdeletion syndrome. Am J Hum Genet. 2014 ;95(5):579-83.
Chakraborty R, Hampton OA, Shen X, Simko SJ, Shih A, Abhyankar H, Lim KPhaik Har, Covington KR, Treviño L, Dewal N, Muzny DM, Doddapaneni H, Hu J, Wang L, Lupo PJ, M Hicks J, Bonilla DL, Dwyer KC, Berres M-L, Poulikakos PI, Merad M, McClain KL, Wheeler DA, Allen CE, D Parsons W. Mutually exclusive recurrent somatic mutations in MAP2K1 and BRAF support a central role for ERK activation in LCH pathogenesis. Blood. 2014 ;124(19):3007-15.
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.
Xie YAngela, Lee W, Cai C, Gambin T, Nõupuu K, Sujirakul T, Ayuso C, Jhangiani S, Muzny DM, Boerwinkle E, Gibbs RA, Greenstein VC, Lupski JR, Tsang SH, Allikmets R. New syndrome with retinitis pigmentosa is caused by nonsense mutations in retinol dehydrogenase RDH11. Hum Mol Genet. 2014 ;23(21):5774-80.
Chen P-C, Yin J, Yu H-W, Yuan T, Fernandez M, Yung CK, Trinh QM, Peltekova VD, Reid JG, Tworog-Dube E, Morgan MB, Muzny DM, Stein L, McPherson JD, Roberts AE, Gibbs RA, Neel BG, Kucherlapati R. Next-generation sequencing identifies rare variants associated with Noonan syndrome. Proc Natl Acad Sci U S A. 2014 ;111(31):11473-8.
Wang L, Yamaguchi S, Burstein MD, Terashima K, Chang K, Ng H-K, Nakamura H, He Z, Doddapaneni H, Lewis L, Wang M, Suzuki T, Nishikawa R, Natsume A, Terasaka S, Dauser R, Whitehead W, Adekunle A, Sun J, Qiao Y, Marth G, Muzny DM, Gibbs RA, Leal SM, Wheeler DA, Lau CC. Novel somatic and germline mutations in intracranial germ cell tumours. Nature. 2014 ;511(7508):241-5.
Bosch DGM, F Boonstra N, Gonzaga-Jauregui C, Xu M, de Ligt J, Jhangiani S, Wiszniewski W, Muzny DM, Yntema HG, Pfundt R, Vissers LELM, Spruijt L, Blokland EAW, Chen C-A, Lewis RA, Tsai SY, Gibbs RA, Tsai M-J, Lupski JR, Zoghbi HY, Cremers FPM, de Vries BBA, Schaaf CP. NR2F1 mutations cause optic atrophy with intellectual disability. Am J Hum Genet. 2014 ;94(2):303-9.
Stray-Pedersen A, Backe PH, Sorte HS, Mørkrid L, Chokshi NY, Erichsen HChristian, Gambin T, Elgstøen KBP, Bjørås M, Wlodarski MW, Krüger M, Jhangiani SN, Muzny DM, Patel A, Raymond KM, Sasa GS, Krance RA, Martinez CA, Abraham SM, Speckmann C, Ehl S, Hall P, Forbes LR, Merckoll E, Westvik J, Nishimura G, Rustad CF, Abrahamsen TG, Rønnestad A, Osnes LT, Egeland T, Rødningen OK, Beck CR, Boerwinkle E, Gibbs RA, Lupski JR, Orange JS, Lausch E, I Hanson C. PGM3 mutations cause a congenital disorder of glycosylation with severe immunodeficiency and skeletal dysplasia. Am J Hum Genet. 2014 ;95(1):96-107.
Lindstrand A, Davis EE, Carvalho CMB, Pehlivan D, Willer JR, Tsai I-C, Ramanathan S, Zuppan C, Sabo A, Muzny DM, Gibbs RA, Liu P, Lewis RA, Banin E, Lupski JR, Clark R, Katsanis N. Recurrent CNVs and SNVs at the NPHP1 locus contribute pathogenic alleles to Bardet-Biedl syndrome. Am J Hum Genet. 2014 ;94(5):745-54.
Wang L, Swierczek SI, Lanikova L, Kim SJ, Hickman K, Walker K, Wang K, Drummond J, Doddapaneni H, Reid JG, Muzny DM, Gibbs RA, Wheeler DA, Prchal JT. The relationship of JAK2(V617F) and acquired UPD at chromosome 9p in polycythemia vera. Leukemia. 2014 ;28(4):938-41.
Morrison AC, Bis JC, Hwang S-J, Ehret GB, Lumley T, Rice K, Muzny DM, Gibbs RA, Boerwinkle E, Psaty BM, Chakravarti A, Levy D. Sequence analysis of six blood pressure candidate regions in 4,178 individuals: the Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) targeted sequencing study. PLoS One. 2014 ;9(10):e109155.