Publications

2014

Bailey AL, Lauck M, Sibley SD, Pecotte J, Rice K, Weny G, Tumukunde A, Hyeroba D, Greene J, Correll M, Gleicher M, Friedrich TC, Jahrling PB, Kuhn JH, Goldberg TL, Rogers J, O'Connor DH. Two novel simian arteriviruses in captive and wild baboons (Papio spp.). J Virol. 2014 ;88(22):13231-9.

2015

Jalali A, E Amirian S, Bainbridge MN, Armstrong GN, Liu Y, Tsavachidis S, Jhangiani SN, Plon SE, Lau CC, Claus EB, Barnholtz-Sloan JS, Il'yasova D, Schildkraut J, Ali-Osman F, Sadetzki S, Johansen C, Houlston RS, Jenkins RB, Lachance D, Olson SH, Bernstein JL, Merrell RT, Wrensch MR, Davis FG, Lai R, Shete S, Aldape K, Amos CI, Muzny DM, Gibbs RA, Melin BS, Bondy ML. Targeted sequencing in chromosome 17q linkage region identifies familial glioma candidates in the Gliogene Consortium. Sci Rep. 2015 ;5:8278.

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.

Chittani M, Zaninello R, Lanzani C, Frau F, Ortu MF, Salvi E, Fresu G, Citterio L, Braga D, Piras DA, Carpini SDelli, Velayutham D, Simonini M, Argiolas G, Pozzoli S, Troffa C, Glorioso V, Kontula KK, Hiltunen TP, Donner KM, Turner ST, Boerwinkle E, Chapman AB, Padmanabhan S, Dominiczak AF, Melander O, Johnson JA, Cooper-Dehoff RM, Gong Y, Rivera NV, Condorelli G, Trimarco B, Manunta P, Cusi D, Glorioso N, Barlassina C. TET2 and CSMD1 genes affect SBP response to hydrochlorothiazide in never-treated essential hypertensives. J Hypertens. 2015 ;33(6):1301-9.

Peng X, Thierry-Mieg J, Thierry-Mieg D, Nishida A, Pipes L, Bozinoski M, Thomas MJ, Kelly S, Weiss JM, Raveendran M, Muzny D, Gibbs RA, Rogers J, Schroth GP, Katze MG, Mason CE. Tissue-specific transcriptome sequencing analysis expands the non-human primate reference transcriptome resource (NHPRTR). Nucleic Acids Res. 2015 ;43(Database issue):D737-42.

Del-Aguila JL, Cooper-Dehoff RM, Chapman AB, Gums JG, Beitelshees AL, Bailey K, Turner ST, Johnson JA, Boerwinkle E. Transethnic meta-analysis suggests genetic variation in the HEME pathway influences potassium response in patients treated with hydrochlorothiazide. Pharmacogenomics J. 2015 ;15(2):153-7.

2016

Ozantürk A, Davis EE, Sabo A, Weiss MM, Muzny D, Dugan-Perez S, Sistermans EA, Gibbs RA, Özgül KR, Yalnızoglu D, Serdaroglu E, Dursun A, Katsanis N. A t(5;16) translocation is the likely driver of a syndrome with ambiguous genitalia, facial dysmorphism, intellectual disability, and speech delay. Cold Spring Harb Mol Case Stud. 2016 ;2(2):a000703.

Hsu Y-H, Li G, Liu C-T, Brody JA, Karasik D, Chou W-C, Demissie S, Nandakumar K, Zhou Y, Cheng C-H, Gill R, Gibbs RA, Muzny D, Santibanez J, Estrada K, Rivadeneira F, Harris T, Gudnason V, Uitterlinden A, Psaty BM, Robbins JA, L Cupples A, Kiel DP. Targeted sequencing of genome wide significant loci associated with bone mineral density (BMD) reveals significant novel and rare variants: the Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) targeted sequencing study. Hum Mol Genet. 2016 ;25(23):5234-5243.

Zhdanova IV, Rogers J, González-Martínez J, Farrer LA. The ticking clock of Cayo Santiago macaques and its implications for understanding human circadian rhythm disorders. Am J Primatol. 2016 ;78(1):117-26.

Chan CK, Pan Y, Nyberg K, Marra MA, Lim EL, Jones SJM, Maar D, Gibb EA, Gunaratne PH, A Robertson G, Rowat AC. Tumour-suppressor microRNAs regulate ovarian cancer cell physical properties and invasive behaviour. Open Biol. 2016 ;6(11).

Prescott TE, Kulseth MAnn, Heimdal KR, Stadheim B, Hopp E, Gambin T, Akdemir ZHCoban, Jhangiani SN, Muzny DM, Gibbs RA, Lupski JR, Stray-Pedersen A. Two male sibs with severe micrognathia and a missense variant in MED12. Eur J Med Genet. 2016 ;59(8):367-72.

2017

Allen CE, Laetsch TW, Mody R, Irwin MS, Lim MS, Adamson PC, Seibel NL, D Parsons W, Y Cho J, Janeway K. Target and Agent Prioritization for the Children's Oncology Group-National Cancer Institute Pediatric MATCH Trial. J Natl Cancer Inst. 2017 ;109(5).

Whittle SB, Punia JN, López-Terrada D, Gaikwad A, Hampton OA, Heczey A. Therapy-related Acute Leukemia With Mixed Phenotype and Novel t(1: 6)(q25;p23) After Treatment for High-risk Neuroblastoma. J Pediatr Hematol Oncol. 2017 ;39(8):e486-e488.

Sedlazeck FJ, Dhroso A, Bodian DL, Paschall J, Hermes F, Zook JM. Tools for annotation and comparison of structural variation. F1000Res. 2017 ;6:1795.

Chhibber A, French CE, Yee SW, Gamazon ER, Theusch E, Qin X, Webb A, Papp AC, Wang A, Simmons CQ, Konkashbaev A, Chaudhry AS, Mitchel K, Stryke D, Ferrin TE, Weiss ST, Kroetz DL, Sadee W, Nickerson DA, Krauss RM, George AL, Schuetz EG, Medina MW, Cox NJ, Scherer SE, Giacomini KM, Brenner SE. Transcriptomic variation of pharmacogenes in multiple human tissues and lymphoblastoid cell lines. Pharmacogenomics J. 2017 ;17(2):137-145.

Jeffares DC, Jolly C, Hoti M, Speed D, Shaw L, Rallis C, Balloux F, Dessimoz C, Bähler J, Sedlazeck FJ. Transient structural variations have strong effects on quantitative traits and reproductive isolation in fission yeast. Nat Commun. 2017 ;8:14061.

2018

Singh S, Wang Z, Shahin MH, Langaee TY, Gong Y, Turner ST, Chapman AB, Gums JG, McDonough CW, Bailey KR, Beitelshees AL, Cooper-Dehoff RM, Scherer SE, Boerwinkle E, Johnson JA. Targeted sequencing identifies a missense variant in the BEST3 gene associated with antihypertensive response to hydrochlorothiazide. Pharmacogenet Genomics. 2018 ;28(11):251-255.

Stewart CJ, Ajami NJ, O'Brien JL, Hutchinson DS, Smith DP, Wong MC, Ross MC, Lloyd RE, Doddapaneni H, Metcalf GA, Muzny DM, Gibbs RA, Vatanen T, Huttenhower C, Xavier RJ, Rewers M, Hagopian W, Toppari J, Ziegler A-G, She J-X, Akolkar B, Lernmark A, Hyoty H, Vehik K, Krischer JP, Petrosino JF. Temporal development of the gut microbiome in early childhood from the TEDDY study. Nature. 2018 ;562(7728):583-588.

Poynton HC, Hasenbein S, Benoit JB, Sepulveda MS, Poelchau MF, Hughes DST, Murali SC, Chen S, Glastad KM, Goodisman MAD, Werren JH, Vineis JH, Bowen JL, Friedrich M, Jones J, Robertson HM, Feyereisen R, Mechler-Hickson A, Mathers N, Lee CEunmi, Colbourne JK, Biales A, J Johnston S, Wellborn GA, Rosendale AJ, Cridge AG, Munoz-Torres MC, Bain PA, Manny AR, Major KM, Lambert FN, Vulpe CD, Tuck P, Blalock BJ, Lin Y-Y, Smith ME, Ochoa-Acuña H, Chen M-JMay, Childers CP, Qu J, Dugan S, Lee SL, Chao H, Dinh H, Han Y, Doddapaneni H, Worley KC, Muzny DM, Gibbs RA, Richards S. The Toxicogenome of Hyalella azteca: A Model for Sediment Ecotoxicology and Evolutionary Toxicology. Environ Sci Technol. 2018 ;52(10):6009-6022.

Chen C, Meng Q, Xia Y, Ding C, Wang L, Dai R, Cheng L, Gunaratne P, Gibbs RA, Min S, Coarfa C, Reid JG, Zhang C, Jiao C, Jiang Y, Giase G, Thomas A, Fitzgerald D, Brunetti T, Shieh A, Xia C, Wang Y, Wang Y, Badner JA, Gershon ES, White KP, Liu C. The transcription factor POU3F2 regulates a gene coexpression network in brain tissue from patients with psychiatric disorders. Sci Transl Med. 2018 ;10(472).

Cheng H, Dharmadhikari AV, Varland S, Ma N, Domingo D, Kleyner R, Rope AF, Yoon M, Stray-Pedersen A, Posey JE, Crews SR, Eldomery MK, Akdemir ZCoban, Lewis AM, Sutton VR, Rosenfeld JA, Conboy E, Agre K, Xia F, Walkiewicz M, Longoni M, High FA, van Slegtenhorst MA, Mancini GMS, Finnila CR, van Haeringen A, Hollander Nden, Ruivenkamp C, Naidu S, Mahida S, Palmer EE, Murray L, Lim D, Jayakar P, Parker MJ, Giusto S, Stracuzzi E, Romano C, Beighley JS, Bernier RA, Küry S, Nizon M, Corbett MA, Shaw M, Gardner A, Barnett C, Armstrong R, Kassahn KS, Van Dijck A, Vandeweyer G, Kleefstra T, Schieving J, Jongmans MJ, de Vries BBA, Pfundt R, Kerr B, Rojas SK, Boycott KM, Person R, Willaert R, Eichler EE, R Kooy F, Yang Y, Wu JC, Lupski JR, Arnesen T, Cooper GM, Chung WK, Gecz J, Stessman HAF, Meng L, Lyon GJ. Truncating Variants in NAA15 Are Associated with Variable Levels of Intellectual Disability, Autism Spectrum Disorder, and Congenital Anomalies. Am J Hum Genet. 2018 ;102(5):985-994.

2019

Liu J, Wu N, Yang N, Takeda K, Chen W, Li W, Du R, Liu S, Zhou Y, Zhang L, Liu Z, Zuo Y, Zhao S, Blank R, Pehlivan D, Dong S, Zhang J, Shen J, Si N, Wang Y, Liu G, Li S, Zhao Y, Zhao H, Chen Y, Zhao Y, Song X, Hu J, Lin M, Tian Y, Yuan B, Yu K, Niu Y, Yu B, Li X, Chen J, Yan Z, Zhu Q, Meng X, Chen X, Su J, Zhao X, Wang X, Ming Y, Li X, Raggio CL, Zhang B, Weng X, Zhang S, Zhang X, Watanabe K, Matsumoto M, Jin L, Shen Y, Sobreira NL, Posey JE, Giampietro PF, Valle D, Liu P, Wu Z, Ikegawa S, Lupski JR, Zhang F, Qiu G. TBX6-associated congenital scoliosis (TACS) as a clinically distinguishable subtype of congenital scoliosis: further evidence supporting the compound inheritance and TBX6 gene dosage model. Genet Med. 2019 ;21(7):1548-1558.

Park YH, Snook JD, Ostrin EJ, Kim S, Chen R, Frankfort BJ. Transcriptomic profiles of retinal ganglion cells are defined by the magnitude of intraocular pressure elevation in adult mice. Sci Rep. 2019 ;9(1):2594.

2020

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.

Chen W, Lin J, Wang L, Li X, Zhao S, Liu J, Akdemir ZC, Zhao Y, Du R, Ye Y, Song X, Zhang Y, Yan Z, Yang X, Lin M, Shen J, Wang S, Gao N, Yang Y, Liu Y, Li W, Liu J, Zhang N, Yang X, Xu Y, Zhang J, Delgado MR, Posey JE, Qiu G, Rios JJ, Liu P, Wise CA, Zhang F, Wu Z, Lupski JR, Wu N. TBX6 missense variants expand the mutational spectrum in a non-Mendelian inheritance disease. Hum Mutat. 2020 ;41(1):182-195.