Publications

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2020
Brasó-Vives M, Povolotskaya IS, Hartasánchez DA, Farré X, Fernandez-Callejo M, Raveendran M, Harris RA, Rosene DL, Lorente-Galdos B, Navarro A, Marques-Bonet T, Rogers J, Juan D. Copy number variants and fixed duplications among 198 rhesus macaques (Macaca mulatta). PLoS Genet. 2020 ;16(5):e1008742.
Gambin T, Liu Q, Karolak JA, Grochowski CM, Xie NG, Wu LR, Yan YHelen, Cao Y, Akdemir ZHCoban, Wilson TA, Jhangiani SN, Chen E, Eng CM, Muzny DM, Posey JE, Yang Y, Zhang DY, Shaw C, Liu P, Lupski JR, Stankiewicz P. Low-level parental somatic mosaic SNVs in exomes from a large cohort of trios with diverse suspected Mendelian conditions. Genet Med. 2020 ;22(11):1768-1776.
Abel HJ, Larson DE, Regier AA, Chiang C, Das I, Kanchi KL, Layer RM, Neale BM, Salerno WJ, Reeves C, Buyske S, Matise TC, Muzny DM, Zody MC, Lander ES, Dutcher SK, Stitziel NO, Hall IM. Mapping and characterization of structural variation in 17,795 human genomes. Nature. 2020 ;583(7814):83-89.
Shafin K, Pesout T, Lorig-Roach R, Haukness M, Olsen HE, Bosworth C, Armstrong J, Tigyi K, Maurer N, Koren S, Sedlazeck FJ, Marschall T, Mayes S, Costa V, Zook JM, Liu KJ, Kilburn D, Sorensen M, Munson KM, Vollger MR, Monlong J, Garrison E, Eichler EE, Salama S, Haussler D, Green RE, Akeson M, Phillippy A, Miga KH, Carnevali P, Jain M, Paten B. Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes. Nat Biotechnol. 2020 ;38(9):1044-1053.
Yin J, Chun C-A, Zavadenko NN, Pechatnikova NL, Naumova OYu, Doddapaneni H, Hu J, Muzny DM, Schaaf CP, Grigorenko EL. Next Generation Sequencing of 134 Children with Autism Spectrum Disorder and Regression. Genes (Basel). 2020 ;11(8).
Liu Q, Grochowski CM, Bi W, Lupski JR, Stankiewicz P. Quantitative Assessment of Parental Somatic Mosaicism for Copy-Number Variant (CNV) Deletions. Curr Protoc Hum Genet. 2020 ;106(1):e99.
Dharmat R, Kim S, Li Y, Chen R. Single-Cell Capture, RNA-seq, and Transcriptome Analysis from the Neural Retina. Methods Mol Biol. 2020 ;2092:159-186.
Gilpatrick T, Lee I, Graham JE, Raimondeau E, Bowen R, Heron A, Downs B, Sukumar S, Sedlazeck FJ, Timp W. Targeted nanopore sequencing with Cas9-guided adapter ligation. Nat Biotechnol. 2020 ;38(4):433-438.
Amendola LM, Muenzen K, Biesecker LG, Bowling KM, Cooper GM, Dorschner MO, Driscoll C, Foreman AKatherine, Golden-Grant K, Greally JM, Hindorff L, Kanavy D, Jobanputra V, Johnston JJ, Kenny EE, McNulty S, Murali P, Ou J, Powell BC, Rehm HL, Rolf B, Roman TS, Van Ziffle J, Guha S, Abhyankar A, Crosslin D, Venner E, Yuan B, Zouk H, Jarvik GP. Variant Classification Concordance using the ACMG-AMP Variant Interpretation Guidelines across Nine Genomic Implementation Research Studies. Am J Hum Genet. 2020 ;107(5):932-941.
2019
Wenger AM, Peluso P, Rowell WJ, Chang P-C, Hall RJ, Concepcion GT, Ebler J, Fungtammasan A, Kolesnikov A, Olson ND, Töpfer A, Alonge M, Mahmoud M, Qian Y, Chin C-S, Phillippy AM, Schatz MC, Myers G, DePristo MA, Ruan J, Marschall T, Sedlazeck FJ, Zook JM, Li H, Koren S, Carroll A, Rank DR, Hunkapiller MW. Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome. Nat Biotechnol. 2019 ;37(10):1155-1162.
Zascavage RR, Hall CL, Thorson K, Mahmoud M, Sedlazeck FJ, Planz JV. Approaches to Whole Mitochondrial Genome Sequencing on the Oxford Nanopore MinION. Curr Protoc Hum Genet. 2019 ;104(1):e94.
Richards S. Arthropod Genome Sequencing and Assembly Strategies. Methods Mol Biol. 2019 ;1858:1-14.
Chiang T, Liu X, Wu T-J, Hu J, Sedlazeck FJ, White S, Schaid D, de Andrade M, Jarvik GP, Crosslin D, Stanaway I, Carrell DS, Connolly JJ, Hakonarson H, Groopman EE, Gharavi AG, Fedotov A, Bi W, Leduc MS, Murdock DR, Jiang Y, Meng L, Eng CM, Wen S, Yang Y, Muzny DM, Boerwinkle E, Salerno WJ, Venner E, Gibbs RA. Atlas-CNV: a validated approach to call single-exon CNVs in the eMERGESeq gene panel. Genet Med. 2019 ;21(9):2135-2144.
Boycott KM, Hartley T, Biesecker LG, Gibbs RA, A Innes M, Riess O, Belmont J, Dunwoodie SL, Jojic N, Lassmann T, Mackay D, I Temple K, Visel A, Baynam G. A Diagnosis for All Rare Genetic Diseases: The Horizon and the Next Frontiers. Cell. 2019 ;177(1):32-37.
He KY, Li X, Kelly TN, Liang J, Cade BE, Assimes TL, Becker LC, Beitelshees AL, Bress AP, Chang Y-PChristy, Chen Y-DIda, de Vries PS, Fox ER, Franceschini N, Furniss A, Gao Y, Guo X, Haessler J, Hwang S-J, Irvin MRyan, Kalyani RR, Liu C-T, Liu C, Martin LWarsinger, Montasser ME, Muntner PM, Mwasongwe S, Palmas W, Reiner AP, Shimbo D, Smith JA, Snively BM, Yanek LR, Boerwinkle E, Correa A, L Cupples A, He J, Kardia SLR, Kooperberg C, Mathias RA, Mitchell BD, Psaty BM, Vasan RS, Rao DC, Rich SS, Rotter JI, Wilson JG, Chakravarti A, Morrison AC, Levy D, Arnett DK, Redline S, Zhu X. Leveraging linkage evidence to identify low-frequency and rare variants on 16p13 associated with blood pressure using TOPMed whole genome sequencing data. Hum Genet. 2019 ;138(2):199-210.
Floyd JS, Bloch KM, Brody JA, Maroteau C, Siddiqui MK, Gregory R, Carr DF, Molokhia M, Liu X, Bis JC, Ahmed A, Liu X, Hallberg P, Yue Q-Y, Magnusson PKE, Brisson D, Wiggins KL, Morrison AC, Khoury E, McKeigue P, Stricker BH, Lapeyre-Mestre M, Heckbert SR, Gallagher AM, Chinoy H, Gibbs RA, Bondon-Guitton E, Tracy R, Boerwinkle E, Gaudet D, Conforti A, van Staa T, Sitlani CM, Rice KM, van der Zee A-HMaitland-, Wadelius M, Morris AP, Pirmohamed M, Palmer CAN, Psaty BM, Alfirevic A. Pharmacogenomics of statin-related myopathy: Meta-analysis of rare variants from whole-exome sequencing. PLoS One. 2019 ;14(6):e0218115.
Leung YYee, Valladares O, Chou Y-F, Lin H-J, Kuzma AB, Cantwell L, Qu L, Gangadharan P, Salerno WJ, Schellenberg GD, San Wang L-. VCPA: genomic variant calling pipeline and data management tool for Alzheimer's Disease Sequencing Project. Bioinformatics. 2019 ;35(10):1768-1770.
2018
Sedlazeck FJ, Rescheneder P, Smolka M, Fang H, Nattestad M, von Haeseler A, Schatz MC. Accurate detection of complex structural variations using single-molecule sequencing. Nat Methods. 2018 ;15(6):461-468.
Numanagić I, Malikić S, Ford M, Qin X, Toji L, Radovich M, Skaar TC, Pratt VM, Berger B, Scherer SE, S Sahinalp C. Allelic decomposition and exact genotyping of highly polymorphic and structurally variant genes. Nat Commun. 2018 ;9(1):828.
Sanghvi RV, Buhay CJ, Powell BC, Tsai EA, Dorschner MO, Hong CS, Lebo MS, Sasson A, Hanna DS, McGee S, Bowling KM, Cooper GM, Gray DE, Lonigro RJ, Dunford A, Brennan CA, Cibulskis C, Walker K, Carneiro MO, Sailsbery J, Hindorff LA, Robinson DR, Santani A, Sarmady M, Rehm HL, Biesecker LG, Nickerson DA, Hutter CM, Garraway L, Muzny DM, Wagle N. Characterizing reduced coverage regions through comparison of exome and genome sequencing data across 10 centers. Genet Med. 2018 ;20(8):855-866.
Nattestad M, Goodwin S, Ng K, Baslan T, Sedlazeck FJ, Rescheneder P, Garvin T, Fang H, Gurtowski J, Hutton E, Tseng E, Chin C-S, Beck T, Sundaravadanam Y, Kramer M, Antoniou E, McPherson JD, Hicks J, W McCombie R, Schatz MC. Complex rearrangements and oncogene amplifications revealed by long-read DNA and RNA sequencing of a breast cancer cell line. Genome Res. 2018 ;28(8):1126-1135.
Lewin HA, Robinson GE, W Kress J, Baker WJ, Coddington J, Crandall KA, Durbin R, Edwards SV, Forest F, M Gilbert TP, Goldstein MM, Grigoriev IV, Hackett KJ, Haussler D, Jarvis ED, Johnson WE, Patrinos A, Richards S, Castilla-Rubio JCarlos, van Sluys M-A, Soltis PS, Xu X, Yang H, Zhang G. Earth BioGenome Project: Sequencing life for the future of life. Proc Natl Acad Sci U S A. 2018 ;115(17):4325-4333.
Chinn IK, Eckstein OS, Peckham-Gregory EC, Goldberg BR, Forbes LR, Nicholas SK, Mace EM, Vogel TP, Abhyankar HA, Diaz MI, Heslop HE, Krance RA, Martinez CA, Nguyen TC, Bashir DA, Goldman JR, Stray-Pedersen A, Pedroza LA, M Poli C, Aldave-Becerra JC, McGhee SA, Al-Herz W, Chamdin A, Coban-Akdemir ZH, Jhangiani SN, Muzny DM, Cao TN, Hong DN, Gibbs RA, Lupski JR, Orange JS, McClain KL, Allen CE. Genetic and mechanistic diversity in pediatric hemophagocytic lymphohistiocytosis. Blood. 2018 ;132(1):89-100.
Tanner J-A, Zhu AZ, Claw KG, Prasad B, Korchina V, Hu J, Doddapaneni H, Muzny DM, Schuetz EG, Lerman C, Thummel KE, Scherer SE, Tyndale RF. Novel CYP2A6 diplotypes identified through next-generation sequencing are associated with in-vitro and in-vivo nicotine metabolism. Pharmacogenet Genomics. 2018 ;28(1):7-16.
Gawliński P, Pelc M, Ciara E, Jhangiani S, Jurkiewicz E, Gambin T, Różdżyńska-Świątkowska A, Dawidziuk M, Coban-Akdemir ZH, Guilbride DL, Muzny DM, Lupski JR, Krajewska-Walasek M. Phenotype expansion and development in Kosaki overgrowth syndrome. Clin Genet. 2018 ;93(4):919-924.