Publications

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Integrating ethics and science in the International HapMap Project. Nat Rev Genet. 2004 ;5(6):467-75.
Khurana E, Fu Y, Colonna V, Mu XJasmine, Kang HMin, Lappalainen T, Sboner A, Lochovsky L, Chen J, Harmanci A, Das J, Abyzov A, Balasubramanian S, Beal K, Chakravarty D, Challis D, Chen Y, Clarke D, Clarke L, Cunningham F, Evani US, Flicek P, Fragoza R, Garrison E, Gibbs R, Gümüş ZH, Herrero J, Kitabayashi N, Kong Y, Lage K, Liluashvili V, Lipkin SM, MacArthur DG, Marth G, Muzny D, Pers TH, Ritchie GRS, Rosenfeld JA, Sisu C, Wei X, Wilson M, Xue Y, Yu F, Dermitzakis ET, Yu H, Rubin MA, Tyler-Smith C, Gerstein M. Integrative annotation of variants from 1092 humans: application to cancer genomics. Science. 2013 ;342(6154):1235587.
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.
The International HapMap Project. Nature. 2003 ;426(6968):789-96.
Grochowski CM, Bengtsson JD, Du H, Gandhi M, Lun MYin, Mehaffey MG, Park KH, Höps W, Benito E, Hasenfeld P, Korbel JO, Mahmoud M, Paulin LF, Jhangiani SN, Hwang JPaul, Bhamidipati SV, Muzny DM, Fatih JM, Gibbs RA, Pendleton M, Harrington E, Juul S, Lindstrand A, Sedlazeck FJ, Pehlivan D, Lupski JR, Carvalho CMB. Inverted triplications formed by iterative template switches generate structural variant diversity at genomic disorder loci. Cell Genom. 2024 ;4(7):100590.
Zhao Z, Fu Y-X, Hewett-Emmett D, Boerwinkle E. Investigating single nucleotide polymorphism (SNP) density in the human genome and its implications for molecular evolution. Gene. 2003 ;312:207-13.
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Lee E, Iskow R, Yang L, Gokcumen O, Haseley P, Luquette LJ, Lohr JG, Harris CC, Ding L, Wilson RK, Wheeler DA, Gibbs RA, Kucherlapati R, Lee C, Kharchenko PV, Park PJ. Landscape of somatic retrotransposition in human cancers. Science. 2012 ;337(6097):967-71.
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.
Hampton OA, Koriabine M, Miller CA, Coarfa C, Li J, Hollander PDen, Schoenherr C, Carbone L, Nefedov M, Hallers BFHTen, Lee AV, De Jong PJ, Milosavljevic A. Long-range massively parallel mate pair sequencing detects distinct mutations and similar patterns of structural mutability in two breast cancer cell lines. Cancer Genet. 2011 ;204(8):447-57.
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Abecasis GR, Altshuler D, Auton A, Brooks LD, Durbin RM, Gibbs RA, Hurles ME, McVean GA. A map of human genome variation from population-scale sequencing. Nature. 2010 ;467(7319):1061-73.
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.
Gu S, Szafranski P, Akdemir ZCoban, Yuan B, Cooper ML, Magriñá MA, Bacino CA, Lalani SR, Breman AM, Smith JL, Patel A, Song RH, Bi W, Cheung SWai, Carvalho CMB, Stankiewicz P, Lupski JR. Mechanisms for Complex Chromosomal Insertions. PLoS Genet. 2016 ;12(11):e1006446.
Gu S, Posey JE, Yuan B, Carvalho CMB, Luk HM, Erikson K, Lo IFM, Leung GKC, Pickering CR, H Y Chung B, Lupski JR. Mechanisms for the Generation of Two Quadruplications Associated with Split-Hand Malformation. Hum Mutat. 2016 ;37(2):160-4.
Carvalho CMB, Lupski JR. Mechanisms underlying structural variant formation in genomic disorders. Nat Rev Genet. 2016 ;17(4):224-38.
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.
van Leeuwen EM, Sabo A, Bis JC, Huffman JE, Manichaikul A, Smith AV, Feitosa MF, Demissie S, Joshi PK, Duan Q, Marten J, van Klinken JB, Surakka I, Nolte IM, Zhang W, Mbarek H, Li-Gao R, Trompet S, Verweij N, Evangelou E, Lyytikäinen L-P, Tayo BO, Deelen J, van der Most PJ, van der Laan SW, Arking DE, Morrison A, Dehghan A, Franco OH, Hofman A, Rivadeneira F, Sijbrands EJ, Uitterlinden AG, Mychaleckyj JC, Campbell A, Hocking LJ, Padmanabhan S, Brody JA, Rice KM, White CC, Harris T, Isaacs A, Campbell H, Lange LA, Rudan I, Kolcic I, Navarro P, Zemunik T, Salomaa V, Kooner AS, Kooner JS, Lehne B, Scott WR, Tan S-T, de Geus EJ, Milaneschi Y, Penninx BWJH, Willemsen G, de Mutsert R, Ford I, Gansevoort RT, Segura-Lepe MP, Raitakari OT, Viikari JS, Nikus K, Forrester T, McKenzie CA, de Craen AJM, de Ruijter HM, Pasterkamp G, Snieder H, Oldehinkel AJ, P Slagboom E, Cooper RS, Kähönen M, Lehtimäki T, Elliott P, van der Harst P, J Jukema W, Mook-Kanamori DO, Boomsma DI, Chambers JC, Swertz M, Ripatti S, van Dijk KWillems, Vitart V, Polasek O, Hayward C, Wilson JG, Wilson JF, Gudnason V, Rich SS, Psaty BM, Borecki IB, Boerwinkle E, Rotter JI, L Cupples A, van Duijn CM. Meta-analysis of 49 549 individuals imputed with the 1000 Genomes Project reveals an exonic damaging variant in ANGPTL4 determining fasting TG levels. J Med Genet. 2016 ;53(7):441-9.
Fu Y, Aganezov S, Mahmoud M, Beaulaurier J, Juul S, Treangen TJ, Sedlazeck FJ. MethPhaser: methylation-based long-read haplotype phasing of human genomes. Nat Commun. 2024 ;15(1):5327.
Posey JE, Rosenfeld JA, James RA, Bainbridge M, Niu Z, Wang X, Dhar S, Wiszniewski W, Akdemir ZHC, Gambin T, Xia F, Person RE, Walkiewicz M, Shaw CA, V Sutton R, Beaudet AL, Muzny DM, Eng CM, Yang Y, Gibbs RA, Lupski JR, Boerwinkle E, Plon SE. Molecular diagnostic experience of whole-exome sequencing in adult patients. Genet Med. 2016 ;18(7):678-85.
Campbell IM, Gambin T, Jhangiani S, Grove ML, Veeraraghavan N, Muzny DM, Shaw CA, Gibbs RA, Boerwinkle E, Yu F, Lupski JR. Multiallelic Positions in the Human Genome: Challenges for Genetic Analyses. Hum Mutat. 2016 ;37(3):231-234.
Bozkurt-Yozgatli T, Pehlivan D, Gibbs RA, Sezerman U, Posey JE, Lupski JR, Coban-Akdemir Z. Multilocus pathogenic variants contribute to intrafamilial clinical heterogeneity: a retrospective study of sibling pairs with neurodevelopmental disorders. BMC Med Genomics. 2024 ;17(1):85.
Kille B, Balaji A, Sedlazeck FJ, Nute M, Treangen TJ. Multiple genome alignment in the telomere-to-telomere assembly era. Genome Biol. 2022 ;23(1):182.
Chin C-S, Behera S, Khalak A, Sedlazeck FJ, Sudmant PH, Wagner J, Zook JM. Multiscale analysis of pangenomes enables improved representation of genomic diversity for repetitive and clinically relevant genes. Nat Methods. 2023 ;20(8):1213-1221.
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.
Fu Q, Xu M, Chen X, Sheng X, Yuan Z, Liu Y, Li H, Sun Z, Li H, Yang L, Wang K, Zhang F, Li Y, Zhao C, Sui R, Chen R. is mutated in a distinct type of Usher syndrome. J Med Genet. 2017 ;54(3):190-195.
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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.