Publications

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2017
Fuller ZL, Haynes GD, Richards S, Schaeffer SW. Genomics of natural populations: Evolutionary forces that establish and maintain gene arrangements in Drosophila pseudoobscura. Mol Ecol. 2017 ;26(23):6539-6562.
Prall TM, Graham ME, Karl JA, Wiseman RW, Ericsen AJ, Raveendran M, R Harris A, Muzny DM, Gibbs RA, Rogers J, O'Connor DH. Improved full-length killer cell immunoglobulin-like receptor transcript discovery in Mauritian cynomolgus macaques. Immunogenetics. 2017 ;69(5):325-339.
Posey JE, Harel T, Liu P, Rosenfeld JA, James RA, Akdemir ZHCoban, Walkiewicz M, Bi W, Xiao R, Ding Y, Xia F, Beaudet AL, Muzny DM, Gibbs RA, Boerwinkle E, Eng CM, V Sutton R, Shaw CA, Plon SE, Yang Y, Lupski JR. Resolution of Disease Phenotypes Resulting from Multilocus Genomic Variation. N Engl J Med. 2017 ;376(1):21-31.
2016
Szafranski P, Gambin T, Dharmadhikari AV, Akdemir KCaner, Jhangiani SN, Schuette J, Godiwala N, Yatsenko SA, Sebastian J, Madan-Khetarpal S, Surti U, Abellar RG, Bateman DA, Wilson AL, Markham MH, Slamon J, Santos-Simarro F, Palomares M, Nevado J, Lapunzina P, Chung BHon-Yin, Wong W-L, Chu YWing Yiu, Mok GTsz Kin, Kerem E, Reiter J, Ambalavanan N, Anderson SA, Kelly DR, Shieh J, Rosenthal TC, Scheible K, Steiner L, M Iqbal A, McKinnon ML, Hamilton SJane, Schlade-Bartusiak K, English D, Hendson G, Roeder ER, DeNapoli TS, Littlejohn ROkashah, Wolff DJ, Wagner CL, Yeung A, Francis D, Fiorino EK, Edelman M, Fox J, Hayes DA, Janssens S, De Baere E, Menten B, Loccufier A, Vanwalleghem L, Moerman P, Sznajer Y, Lay AS, Kussmann JL, Chawla J, Payton DJ, Phillips GE, Brosens E, Tibboel D, de Klein A, Maystadt I, Fisher R, Sebire N, Male A, Chopra M, Pinner J, Malcolm G, Peters G, Arbuckle S, Lees M, Mead Z, Quarrell O, Sayers R, Owens M, Shaw-Smith C, Lioy J, McKay E, de Leeuw N, Feenstra I, Spruijt L, Elmslie F, Thiruchelvam T, Bacino CA, Langston C, Lupski JR, Sen P, Popek E, Stankiewicz P. Pathogenetics of alveolar capillary dysplasia with misalignment of pulmonary veins. Hum Genet. 2016 ;135(5):569-86.
2015
Chong JX, Burrage LC, Beck AE, Marvin CT, McMillin MJ, Shively KM, Harrell TM, Buckingham KJ, Bacino CA, Jain M, Alanay Y, Berry SA, Carey JC, Gibbs RA, Lee BH, Krakow D, Shendure J, Nickerson DA, Bamshad MJ. Autosomal-Dominant Multiple Pterygium Syndrome Is Caused by Mutations in MYH3. Am J Hum Genet. 2015 ;96(5):841-9.
Zaneveld J, Siddiqui S, Li H, Wang X, Wang H, Wang K, Li H, Ren H, Lopez I, Dorfman A, Khan A, Wang F, Salvo J, Gelowani V, Li Y, Sui R, Koenekoop R, Chen R. Comprehensive analysis of patients with Stargardt macular dystrophy reveals new genotype-phenotype correlations and unexpected diagnostic revisions. Genet Med. 2015 ;17(4):262-70.
Alioto TS, Buchhalter I, Derdak S, Hutter B, Eldridge MD, Hovig E, Heisler LE, Beck TA, Simpson JT, Tonon L, Sertier A-S, Patch A-M, Jäger N, Ginsbach P, Drews R, Paramasivam N, Kabbe R, Chotewutmontri S, Diessl N, Previti C, Schmidt S, Brors B, Feuerbach L, Heinold M, Gröbner S, Korshunov A, Tarpey PS, Butler AP, Hinton J, Jones D, Menzies A, Raine K, Shepherd R, Stebbings L, Teague JW, Ribeca P, Giner FCastro, Beltran S, Raineri E, Dabad M, Heath SC, Gut M, Denroche RE, Harding NJ, Yamaguchi TN, Fujimoto A, Nakagawa H, Quesada V, Valdés-Mas R, Nakken S, Vodák D, Bower L, Lynch AG, Anderson CL, Waddell N, Pearson JV, Grimmond SM, Peto M, Spellman P, He M, Kandoth C, Lee S, Zhang J, Létourneau L, Ma S, Seth S, Torrents D, Xi L, Wheeler DA, López-Otín C, Campo E, Campbell PJ, Boutros PC, Puente XS, Gerhard DS, Pfister SM, McPherson JD, Hudson TJ, Schlesner M, Lichter P, Eils R, Jones DTW, Gut IG. A comprehensive assessment of somatic mutation detection in cancer using whole-genome sequencing. Nat Commun. 2015 ;6:10001.
Burrage LC, Charng W-L, Eldomery MK, Willer JR, Davis EE, Lugtenberg D, Zhu W, Leduc MS, Akdemir ZC, Azamian M, Zapata G, Hernandez PP, Schoots J, de Munnik SA, Roepman R, Pearring JN, Jhangiani S, Katsanis N, Vissers LELM, Brunner HG, Beaudet AL, Rosenfeld JA, Muzny DM, Gibbs RA, Eng CM, Xia F, Lalani SR, Lupski JR, Bongers EMHF, Yang Y. De Novo GMNN Mutations Cause Autosomal-Dominant Primordial Dwarfism Associated with Meier-Gorlin Syndrome. Am J Hum Genet. 2015 ;97(6):904-13.
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 ;16:143.
Bailey AL, Lauck M, Mohns M, Peterson EJ, Beheler K, Brunner KG, Crosno K, Mejia A, Mutschler J, Gehrke M, Greene J, Ericsen AJ, Weiler A, Lehrer-Brey G, Friedrich TC, Sibley SD, Kallas EG, Capuano S, Rogers J, Goldberg TL, Simmons HA, O'Connor DH. Durable sequence stability and bone marrow tropism in a macaque model of human pegivirus infection. Sci Transl Med. 2015 ;7(305):305ra144.
Pehlivan D, Akdemir ZCoban, Karaca E, Bayram Y, Jhangiani S, Yildiz EPembegul, Muzny DM, Uluc K, Gibbs RA, Elcioglu N, Lupski JR, Harel T. Exome sequencing reveals homozygous TRIM2 mutation in a patient with early onset CMT and bilateral vocal cord paralysis. Hum Genet. 2015 ;134(6):671-3.
Wang L, Ni X, Covington KR, Yang BY, Shiu J, Zhang X, Xi L, Meng Q, Langridge T, Drummond J, Donehower LA, Doddapaneni HV, Muzny DM, Gibbs RA, Wheeler DA, Duvic M. Genomic profiling of Sézary syndrome identifies alterations of key T cell signaling and differentiation genes. Nat Genet. 2015 ;47(12):1426-34.
Dogruluk T, Tsang YHuen, Espitia M, Chen F, Chen T, Chong Z, Appadurai V, Dogruluk A, Eterovic AKarina, Bonnen PE, Creighton CJ, Chen K, Mills GB, Scott KL. Identification of Variant-Specific Functions of PIK3CA by Rapid Phenotyping of Rare Mutations. Cancer Res. 2015 ;75(24):5341-54.
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.
Richards S. It's more than stamp collecting: how genome sequencing can unify biological research. Trends Genet. 2015 ;31(7):411-21.
Salvo J, Lyubasyuk V, Xu M, Wang H, Wang F, Nguyen D, Wang K, Luo H, Wen C, Shi C, Lin D, Zhang K, Chen R. Next-generation sequencing and novel variant determination in a cohort of 92 familial exudative vitreoretinopathy patients. Invest Ophthalmol Vis Sci. 2015 ;56(3):1937-46.
Ge Z, Bowles K, Goetz K, Scholl HPN, Wang F, Wang X, Xu S, Wang K, Wang H, Chen R. NGS-based Molecular diagnosis of 105 eyeGENE(®) probands with Retinitis Pigmentosa. Sci Rep. 2015 ;5:18287.
Wang M, Beck CR, English AC, Meng Q, Buhay C, Han Y, Doddapaneni HV, Yu F, Boerwinkle E, Lupski JR, Muzny DM, Gibbs RA. PacBio-LITS: a large-insert targeted sequencing method for characterization of human disease-associated chromosomal structural variations. BMC Genomics. 2015 ;16:214.
Ming R, VanBuren R, Wai CMan, Tang H, Schatz MC, Bowers JE, Lyons E, Wang M-L, Chen J, Biggers E, Zhang J, Huang L, Zhang L, Miao W, Zhang J, Ye Z, Miao C, Lin Z, Wang H, Zhou H, Yim WC, Priest HD, Zheng C, Woodhouse M, Edger PP, Guyot R, Guo H-B, Guo H, Zheng G, Singh R, Sharma A, Min X, Zheng Y, Lee H, Gurtowski J, Sedlazeck FJ, Harkess A, McKain MR, Liao Z, Fang J, Liu J, Zhang X, Zhang Q, Hu W, Qin Y, Wang K, Chen L-Y, Shirley N, Lin Y-R, Liu L-Y, Hernandez AG, Wright CL, Bulone V, Tuskan GA, Heath K, Zee F, Moore PH, Sunkar R, Leebens-Mack JH, Mockler T, Bennetzen JL, Freeling M, Sankoff D, Paterson AH, Zhu X, Yang X, J Smith AC, Cushman JC, Paull RE, Yu Q. The pineapple genome and the evolution of CAM photosynthesis. Nat Genet. 2015 ;47(12):1435-42.
Yazdani A, Yazdani A, Boerwinkle E. Rare variants analysis using penalization methods for whole genome sequence data. BMC Bioinformatics. 2015 ;16:405.
Jonsson P, Coarfa C, Mesmar F, Raz T, Rajapakshe K, Thompson JF, Gunaratne PH, Williams C. Single-Molecule Sequencing Reveals Estrogen-Regulated Clinically Relevant lncRNAs in Breast Cancer. Mol Endocrinol. 2015 ;29(11):1634-45.
Smolka M, Rescheneder P, Schatz MC, von Haeseler A, Sedlazeck FJ. Teaser: Individualized benchmarking and optimization of read mapping results for NGS data. Genome Biol. 2015 ;16:235.
2014
Fuller ZL, Haynes GD, Zhu D, Batterton M, Chao H, Dugan S, Javaid M, Jayaseelan JC, Lee S, Li M, Ongeri F, Qi S, Han Y, Doddapaneni HV, Richards S, Schaeffer SW. Evidence for stabilizing selection on codon usage in chromosomal rearrangements of Drosophila pseudoobscura. G3 (Bethesda). 2014 ;4(12):2433-49.
Lu JT, Campeau PM, Lee BH. Genotype-phenotype correlation--promiscuity in the era of next-generation sequencing. N Engl J Med. 2014 ;371(7):593-6.
Reid JG, Carroll A, Veeraraghavan N, Dahdouli M, Sundquist A, English A, Bainbridge MN, White S, Salerno WJ, 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.