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Bailey MH, Meyerson WU, Dursi LJonathan, Wang L-B, Dong G, Liang W-W, Weerasinghe A, Li S, Li Y, Kelso S, Saksena G, Ellrott K, Wendl MC, Wheeler DA, Getz G, Simpson JT, Gerstein MB, Ding L. Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples. Nat Commun. 2020 ;11(1):4748.
Kullo IJ, Olson J, Fan X, Jose M, Safarova M, Breitkopf CRadecki, Winkler E, Kochan DC, Snipes S, Pacyna JE, Carney M, Chute CG, Gupta J, Jose S, Venner E, Murugan M, Jiang Y, Zordok M, Farwati M, Philogene M, Smith E, Shaibi GQ, Caraballo P, Freimuth R, Lindor NM, Sharp R, Thibodeau SN. The Return of Actionable Variants Empirical (RAVE) Study, a Mayo Clinic Genomic Medicine Implementation Study: Design and Initial Results. Mayo Clin Proc. 2018 ;93(11):1600-1610.
Marafi D, Kozar N, Duan R, Bradley S, Yokochi K, Mutairi FAl, Saadi NWaill, Whalen S, Brunet T, Kotzaeridou U, Choukair D, Keren B, Nava C, Kato M, Arai H, Froukh T, Faqeih EAli, AlAsmari AM, Saleh MM, Vairo FPinto E, Pichurin PN, Klee EW, Schmitz CT, Grochowski CM, Mitani T, Herman I, Calame DG, Fatih JM, Du H, Coban-Akdemir Z, Pehlivan D, Jhangiani SN, Gibbs RA, Miyatake S, Matsumoto N, Wagstaff LJ, Posey JE, Lupski JR, Meijer D, Wagner M. A reverse genetics and genomics approach to gene paralog function and disease: Myokymia and the juxtaparanode. Am J Hum Genet. 2022 ;109(9):1713-1723.
Rossetti LZ, Glinton K, Yuan B, Liu P, Pillai N, Mizerik E, Magoulas P, Rosenfeld JA, Karaviti L, Sutton VR, Lalani SR, Scott DA. Review of the phenotypic spectrum associated with haploinsufficiency of MYRF. Am J Med Genet A. 2019 ;179(7):1376-1382.
Yang X, Li J, Fang Y, Zhang Z, Jin D, Chen X, Zhao Y, Li M, Huan L, Kent TA, Dong J-fei, Jiang R, Yang S, Jin L, Zhang J, Zhong TP, Yu F. Rho Guanine Nucleotide Exchange Factor Is a Risk Gene for Intracranial Aneurysms. Circ Genom Precis Med. 2018 ;11(7):e002099.
Thoresen LH, Jiao G-S, Haaland WC, Metzker ML, Burgess K. Rigid, conjugated, fluoresceinated thymidine triphosphates: syntheses and polymerase mediated incorporation into DNA analogues. Chemistry. 2003 ;9(19):4603-10.
Ma X, Edmonson M, Yergeau D, Muzny DM, Hampton OA, Rusch M, Song G, Easton J, Harvey RC, Wheeler DA, Ma J, Doddapaneni H, Vadodaria B, Wu G, Nagahawatte P, Carroll WL, Chen I-M, Gastier-Foster JM, Relling MV, Smith MA, Devidas M, Auvil JMGuidry, Downing JR, Loh ML, Willman CL, Gerhard DS, Mullighan CG, Hunger SP, Zhang J. Rise and fall of subclones from diagnosis to relapse in pediatric B-acute lymphoblastic leukaemia. Nat Commun. 2015 ;6:6604.
Calame DG, Herman I, Fatih JM, Du H, Akay G, Jhangiani SN, Coban-Akdemir Z, Milewicz DM, Gibbs RA, Posey JE, Marafi D, Hunter JV, Fan Y, Lupski JR, Miyake CY. Risk of sudden cardiac death in EXOSC5-related disease. Am J Med Genet A. 2021 ;185(8):2532-2540.
Bressler J, Kao WHLinda, Pankow JS, Boerwinkle E. Risk of type 2 diabetes and obesity is differentially associated with variation in FTO in whites and African-Americans in the ARIC study. PLoS One. 2010 ;5(5):e10521.
Li-Byarlay H, Li Y, Stroud H, Feng S, Newman TC, Kaneda M, Hou KK, Worley KC, Elsik CG, Wickline SA, Jacobsen SE, Ma J, Robinson GE. RNA interference knockdown of DNA methyl-transferase 3 affects gene alternative splicing in the honey bee. Proc Natl Acad Sci U S A. 2013 ;110(31):12750-5.
Wei P, Cao Y, Zhang Y, Xu Z, Kwak I-Y, Boerwinkle E, Pan W. On Robust Association Testing for Quantitative Traits and Rare Variants. G3 (Bethesda). 2016 ;6(12):3941-3950.
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.
Kwong AM, Blackwell TW, LeFaive J, de Andrade M, Barnard J, Barnes KC, Blangero J, Boerwinkle E, Burchard EG, Cade BE, Chasman DI, Chen H, Conomos MP, L Cupples A, Ellinor PT, Eng C, Gao Y, Guo X, Irvin MRyan, Kelly TN, Kim W, Kooperberg C, Lubitz SA, C Y Mak A, Manichaikul AW, Mathias RA, Montasser ME, Montgomery CG, Musani S, Palmer ND, Peloso GM, Qiao D, Reiner AP, Roden DM, M Shoemaker B, Smith JA, Smith NL, Su JLasky, Tiwari HK, Weeks DE, Weiss ST, Scott LJ, Smith AV, Abecasis GR, Boehnke M, Kang HMin. Robust, flexible, and scalable tests for Hardy-Weinberg equilibrium across diverse ancestries. Genetics. 2021 ;218(1).
Roger VL, Boerwinkle E, Crapo JD, Douglas PS, Epstein JA, Granger CB, Greenland P, Kohane I, Psaty BM. Roger et al. respond to "future of population studies". Am J Epidemiol. 2015 ;181(6):372-3.
Qian X, Srinivasan T, He J, Chen R. The Role of Ceramide in Inherited Retinal Disease Pathology. Adv Exp Med Biol. 2023 ;1415:303-307.
Pehlivan D, Beck CR, Okamoto Y, Harel T, Akdemir ZHC, Jhangiani SN, Withers MA, Goksungur MTuba, Carvalho CMB, Czesnik D, Gonzaga-Jauregui C, Wiszniewski W, Muzny DM, Gibbs RA, Rautenstrauss B, Sereda MW, Lupski JR. The role of combined SNV and CNV burden in patients with distal symmetric polyneuropathy. Genet Med. 2016 ;18(5):443-51.
Rahbar MH, Samms-Vaughan M, Ardjomand-Hessabi M, Loveland KA, Dickerson AS, Chen Z, Bressler J, Shakespeare-Pellington S, Grove ML, Bloom K, Wirth J, Pearson DA, Boerwinkle E. The role of drinking water sources, consumption of vegetables and seafood in relation to blood arsenic concentrations of Jamaican children with and without Autism Spectrum Disorders. Sci Total Environ. 2012 ;433:362-70.
Jordan VK, Beck TF, Hernandez-Garcia A, Kundert PN, Kim B-J, Jhangiani SN, Gambin T, Starkovich M, Punetha J, Paine IS, Posey JE, Li AH, Muzny DM, Hsu C-W, Lashua AJ, Sun X, Fernandes CJ, Dickinson ME, Lally KP, Gibbs RA, Boerwinkle E, Lupski JR, Scott DA. The role of FREM2 and FRAS1 in the development of congenital diaphragmatic hernia. Hum Mol Genet. 2018 ;27(12):2064-2075.
Wang Z, Chen H, Bartz TM, Bielak LF, Chasman DI, Feitosa MF, Franceschini N, Guo X, Lim E, Noordam R, Richard MA, Wang H, Cade B, L Cupples A, de Vries PS, Giulanini F, Lee J, Lemaitre RN, Martin LW, Reiner AP, Rich SS, Schreiner PJ, Sidney S, Sitlani CM, Smith JA, van Dijk KWillems, Yao J, Zhao W, Fornage M, Kardia SLR, Kooperberg C, Liu C-T, Mook-Kanamori DO, Province MA, Psaty BM, Redline S, Ridker PM, Rotter JI, Boerwinkle E, Morrison AC. Role of Rare and Low-Frequency Variants in Gene-Alcohol Interactions on Plasma Lipid Levels. Circ Genom Precis Med. 2020 ;13(4):e002772.
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Sapoval N, Mahmoud M, Jochum MD, Liu Y, Elworth RALeo, Wang Q, Albin D, Ogilvie HA, Lee MD, Villapol S, Hernandez KM, Berry IMaljkovic, Foox J, Beheshti A, Ternus K, Aagaard KM, Posada D, Mason CE, Sedlazeck FJ, Treangen TJ. SARS-CoV-2 genomic diversity and the implications for qRT-PCR diagnostics and transmission. Genome Res. 2021 ;31(4):635-644.
Oeyen JPhilip, Baa-Puyoulet P, Benoit JB, Beukeboom LW, Bornberg-Bauer E, Buttstedt A, Calevro F, Cash EI, Chao H, Charles H, Chen M-JMay, Childers C, Cridge AG, Dearden P, Dinh H, Doddapaneni H, Dolan A, Donath A, Dowling D, Dugan S, Duncan E, Elpidina EN, Friedrich M, Geuverink E, Gibson JD, Grath S, Grimmelikhuijzen CJP, Große-Wilde E, Gudobba C, Han Y, Hansson BS, Hauser F, Hughes DST, Ioannidis P, Jacquin-Joly E, Jennings EC, Jones JW, Klasberg S, Lee SL, Lesný P, Lovegrove M, Martin S, Martynov AG, Mayer C, Montagné N, Moris VC, Munoz-Torres M, Murali SCanchi, Muzny DM, Oppert B, Parisot N, Pauli T, Peters RS, Petersen M, Pick C, Persyn E, Podsiadlowski L, Poelchau MF, Provataris P, Qu J, Reijnders MJMF, von Reumont BMarcus, Rosendale AJ, Simão FA, Skelly J, Sotiropoulos AG, Stahl AL, Sumitani M, Szuter EM, Tidswell O, Tsitlakidis E, Vedder L, Waterhouse RM, Werren JH, Wilbrandt J, Worley KC, Yamamoto DS, van de Zande L, Zdobnov EM, Ziesmann T, Gibbs RA, Richards S, Hatakeyama M, Misof B, Niehuis O. Sawfly Genomes Reveal Evolutionary Acquisitions That Fostered the Mega-Radiation of Parasitoid and Eusocial Hymenoptera. Genome Biol Evol. 2020 ;12(7):1099-1188.
Kolmogorov M, Billingsley KJ, Mastoras M, Meredith M, Monlong J, Lorig-Roach R, Asri M, Jerez PAlvarez, Malik L, Dewan R, Reed X, Genner RM, Daida K, Behera S, Shafin K, Pesout T, Prabakaran J, Carnevali P, Yang J, Rhie A, Scholz SW, Traynor BJ, Miga KH, Jain M, Timp W, Phillippy AM, Chaisson M, Sedlazeck FJ, Blauwendraat C, Paten B. Scalable Nanopore sequencing of human genomes provides a comprehensive view of haplotype-resolved variation and methylation. Nat Methods. 2023 ;20(10):1483-1492.
Kolmogorov M, Billingsley KJ, Mastoras M, Meredith M, Monlong J, Lorig-Roach R, Asri M, Jerez PAlvarez, Malik L, Dewan R, Reed X, Genner RM, Daida K, Behera S, Shafin K, Pesout T, Prabakaran J, Carnevali P, Yang J, Rhie A, Scholz SW, Traynor BJ, Miga KH, Jain M, Timp W, Phillippy AM, Chaisson M, Sedlazeck FJ, Blauwendraat C, Paten B. Scalable Nanopore sequencing of human genomes provides a comprehensive view of haplotype-resolved variation and methylation. bioRxiv. 2023 ;.
Ellrott K, Bailey MH, Saksena G, Covington KR, Kandoth C, Stewart C, Hess J, Ma S, Chiotti KE, McLellan M, Sofia HJ, Hutter C, Getz G, Wheeler D, Ding L. Scalable Open Science Approach for Mutation Calling of Tumor Exomes Using Multiple Genomic Pipelines. Cell Syst. 2018 ;6(3):271-281.e7.
Salerno W, Havlak P, Miller J. Scale-invariant structure of strongly conserved sequence in genomic intersections and alignments. Proc Natl Acad Sci U S A. 2006 ;103(35):13121-5.