Publications

Santi CM, Yuan A, Fawcett G, Wang Z-W, Butler A, Nonet ML, Wei A, Rojas P, Salkoff L. Dissection of K+ currents in Caenorhabditis elegans muscle cells by genetics and RNA interference. Proc Natl Acad Sci U S A. 2003 ;100(24):14391-6.

Bahrambeigi V, Song X, Sperle K, Beck CR, Hijazi H, Grochowski CM, Gu S, Seeman P, Woodward KJ, Carvalho CMB, Hobson GM, Lupski JR. Distinct patterns of complex rearrangements and a mutational signature of microhomeology are frequently observed in PLP1 copy number gain structural variants. Genome Med. 2019 ;11(1):80.

Garcia A, Desrosiers L, Scollon S, Gruner S, Reuther J, Gandhi I, Patil N, Fuller MY, Dai H, Muzny DM, Gibbs RA, Bercaw-Pratt JL, Rao SL, Rainusso N, Fisher KE, Lin FY, Plon SE, D Parsons W, Roy A. Distinct somatic DICER1 hotspot mutations in three metachronous ovarian Sertoli-Leydig cell tumors in a patient with DICER1 syndrome. Cancer Genet. 2022 ;262-263:53-56.

Kang Y, Ji Z, Li H, Tsao H. Divergent BRAF Inhibitor Resistance Mechanisms Revealed through Epigenetic Mapping. J Invest Dermatol. 2023 ;143(5):842-853.e6.

Mamun AAmar MAl, Marians KJ, M Humayun Z. DNA polymerase III from Escherichia coli cells expressing mutA mistranslator tRNA is error-prone. J Biol Chem. 2002 ;277(48):46319-27.

Pappu KS, Ostrin EJ, Middlebrooks BW, Sili BTavsanli, Chen R, Atkins MR, Gibbs RA, Mardon G. Dual regulation and redundant function of two eye-specific enhancers of the Drosophila retinal determination gene dachshund. Development. 2005 ;132(12):2895-905.

Qin X, Singh KV, Xu Y, Weinstock GM, Murray BE. Effect of disruption of a gene encoding an autolysin of Enterococcus faecalis OG1RF. Antimicrob Agents Chemother. 1998 ;42(11):2883-8.

Parikh N, Hilsenbeck S, Creighton CJ, Dayaram T, Shuck R, Shinbrot E, Xi L, Gibbs RA, Wheeler DA, Donehower LA. Effects of TP53 mutational status on gene expression patterns across 10 human cancer types. J Pathol. 2014 ;232(5):522-33.

Mamun AAmar MAl. Elevated expression of DNA polymerase II increases spontaneous mutagenesis in Escherichia coli. Mutat Res. 2007 ;625(1-2):29-39.

Sajan SA, Jhangiani SN, Muzny DM, Gibbs RA, Lupski JR, Glaze DG, Kaufmann WE, Skinner SA, Annese F, Friez MJ, Lane J, Percy AK, Neul JL. Enrichment of mutations in chromatin regulators in people with Rett syndrome lacking mutations in MECP2. Genet Med. 2017 ;19(1):13-19.

Parvandeh S, Donehower LA, Panagiotis K, Hsu T-K, Asmussen JK, Lee K, Lichtarge O. EPIMUTESTR: a nearest neighbor machine learning approach to predict cancer driver genes from the evolutionary action of coding variants. Nucleic Acids Res. 2022 ;50(12):e70.

Mamun AA al, Rahman MS, Humayun MZ. Escherichia coli cells bearing mutA, a mutant glyV tRNA gene, express a recA-dependent error-prone DNA replication activity. Mol Microbiol. 1999 ;33(4):732-40.

Liu X, Fu Y-X, Maxwell TJ, Boerwinkle E. Estimating population genetic parameters and comparing model goodness-of-fit using DNA sequences with error. Genome Res. 2010 ;20(1):101-9.

Vatta M, Niu Z, Lupski JR, Putnam P, Spoonamore KG, Fang P, Eng CM, Willis AS. Evidence for replicative mechanism in a CHD7 rearrangement in a patient with CHARGE syndrome. Am J Med Genet A. 2013 ;161A(12):3182-6.

Gibbs RA, Rogers J, Katze MG, Bumgarner R, Weinstock GM, Mardis ER, Remington KA, Strausberg RL, J Venter C, Wilson RK, Batzer MA, Bustamante CD, Eichler EE, Hahn MW, Hardison RC, Makova KD, Miller W, Milosavljevic A, Palermo RE, Siepel A, Sikela JM, Attaway T, Bell S, Bernard KE, Buhay CJ, Chandrabose MN, Dao M, Davis C, Delehaunty KD, Ding Y, Dinh HH, Dugan-Rocha S, Fulton LA, Gabisi RAyiesha, Garner TT, Godfrey J, Hawes AC, Hernandez J, Hines S, Holder M, Hume J, Jhangiani SN, Joshi V, Khan Z, Kirkness EF, Cree A, R Fowler G, Lee S, Lewis LR, Li Z, Liu Y-S, Moore SM, Muzny DM, Nazareth LV, Ngo DNgoc, Okwuonu GO, Pai G, Parker D, Paul HA, Pfannkoch C, Pohl CS, Rogers Y-H, Ruiz SJuana, Sabo A, Santibanez J, Schneider BW, Smith SM, Sodergren E, Svatek AF, Utterback TR, Vattathil S, Warren W, White CSherell, Chinwalla AT, Feng Y, Halpern AL, Hillier LDW, Huang X, Minx P, Nelson JO, Pepin KH, Qin X, Sutton GG, Venter E, Walenz BP, Wallis JW, Worley KC, Yang S-P, Jones SM, Marra MA, Rocchi M, Schein JE, Baertsch R, Clarke L, Csuros M, Glasscock J, Harris RA, Havlak P, Jackson AR, Jiang H, Liu Y, Messina DN, Shen Y, Song HXing-Zhi, Wylie T, Zhang L, Birney E, Han K, Konkel MK, Lee J, Smit AFA, Ullmer B, Wang H, Xing J, Burhans R, Cheng Z, Karro JE, Ma J, Raney B, She X, Cox MJ, Demuth JP, Dumas LJ, Han S-G, Hopkins J, Karimpour-Fard A, Kim YH, Pollack JR, Vinar T, Addo-Quaye C, Degenhardt J, Denby A, Hubisz MJ, Indap A, Kosiol C, Lahn BT, Lawson HA, Marklein A, Nielsen R, Vallender EJ, Clark AG, Ferguson B, Hernandez RD, Hirani K, Kehrer-Sawatzki H, Kolb J, Patil S, Pu L-L, Ren Y, Smith DGlenn, Wheeler DA, Schenck I, Ball EV, Chen R, Cooper DN, Giardine B, Hsu F, W Kent J, Lesk A, Nelson DL, O'brien WE, Prüfer K, Stenson PD, Wallace JC, Ke H, Liu X-M, Wang P, Xiang APeng, Yang F, Barber GP, Haussler D, Karolchik D, Kern AD, Kuhn RM, Smith KE, Zwieg AS. Evolutionary and biomedical insights from the rhesus macaque genome. Science. 2007 ;316(5822):222-34.

Conley BA, Staudt L, Takebe N, Wheeler DA, Wang L, Cardenas MF, Korchina V, Zenklusen JClaude, McShane LM, Tricoli JV, Williams PM, Lubensky I, O'Sullivan-Coyne G, Kohn E, Little RF, White J, Malik S, Harris LN, Mann B, Weil C, Tarnuzzer R, Karlovich C, Rodgers B, Shankar L, Jacobs PM, Nolan T, Berryman SM, Gastier-Foster J, Bowen J, Leraas K, Shen H, Laird PW, Esteller M, Miller V, Johnson A, Edmondson EF, Giordano TJ, Kim B, S Ivy P. The Exceptional Responders Initiative: Feasibility of a National Cancer Institute Pilot Study. J Natl Cancer Inst. 2021 ;113(1):27-37.

Gonzaga-Jauregui C, Harel T, Gambin T, Kousi M, Griffin LB, Francescatto L, Ozes B, Karaca E, Jhangiani SN, Bainbridge MN, Lawson KS, Pehlivan D, Okamoto Y, Withers M, Mancias P, Slavotinek A, Reitnauer PJ, Goksungur MT, Shy M, Crawford TO, Koenig M, Willer J, Flores BN, Pediaditrakis I, Us O, Wiszniewski W, Parman Y, Antonellis A, Muzny DM, Katsanis N, Battaloglu E, Boerwinkle E, Gibbs RA, Lupski JR. Exome Sequence Analysis Suggests that Genetic Burden Contributes to Phenotypic Variability and Complex Neuropathy. Cell Rep. 2015 ;12(7):1169-83.

Bayram Y, Aydin H, Gambin T, Akdemir ZCoban, Atik MM, Karaca E, Karaman A, Pehlivan D, Jhangiani SN, Gibbs RA, Lupski JR. Exome sequencing identifies a homozygous C5orf42 variant in a Turkish kindred with oral-facial-digital syndrome type VI. Am J Med Genet A. 2015 ;167A(9):2132-7.

Rajagopal A, Braslavsky D, Lu JT, Kleppe S, Clément F, Cassinelli H, Liu DS, Liern JMiguel, Vallejo G, Bergadá I, Gibbs RA, Campeau PM, Lee BH. Exome sequencing identifies a novel homozygous mutation in the phosphate transporter SLC34A1 in hypophosphatemia and nephrocalcinosis. J Clin Endocrinol Metab. 2014 ;99(11):E2451-6.

Do R, Stitziel NO, Won H-H, Jørgensen ABerg, Duga S, Merlini PAngelica, Kiezun A, Farrall M, Goel A, Zuk O, Guella I, Asselta R, Lange LA, Peloso GM, Auer PL, Girelli D, Martinelli N, Farlow DN, DePristo MA, Roberts R, Stewart AFR, Saleheen D, Danesh J, Epstein SE, Sivapalaratnam S, G Hovingh K, Kastelein JJ, Samani NJ, Schunkert H, Erdmann J, Shah SH, Kraus WE, Davies R, Nikpay M, Johansen CT, Wang J, Hegele RA, Hechter E, Marz W, Kleber ME, Huang J, Johnson AD, Li M, Burke GL, Gross M, Liu Y, Assimes TL, Heiss G, Lange EM, Folsom AR, Taylor HA, Olivieri O, Hamsten A, Clarke R, Reilly DF, Yin W, Rivas MA, Donnelly P, Rossouw JE, Psaty BM, Herrington DM, Wilson JG, Rich SS, Bamshad MJ, Tracy RP, L Cupples A, Rader DJ, Reilly MP, Spertus JA, Cresci S, Hartiala J, Tang WHWilson, Hazen SL, Allayee H, Reiner AP, Carlson CS, Kooperberg C, Jackson RD, Boerwinkle E, Lander ES, Schwartz SM, Siscovick DS, McPherson R, Tybjaerg-Hansen A, Abecasis GR, Watkins H, Nickerson DA, Ardissino D, Sunyaev SR, O'Donnell CJ, Altshuler D, Gabriel S, Kathiresan S. Exome sequencing identifies rare LDLR and APOA5 alleles conferring risk for myocardial infarction. Nature. 2015 ;518(7537):102-6.

Agrawal N, Frederick MJ, Pickering CR, Bettegowda C, Chang K, Li RJ, Fakhry C, Xie T-X, Zhang J, Wang J, Zhang N, El-Naggar AK, Jasser SA, Weinstein JN, Treviño L, Drummond JA, Muzny DM, Wu Y, Wood LD, Hruban RH, Westra WH, Koch WM, Califano JA, Gibbs RA, Sidransky D, Vogelstein B, Velculescu VE, Papadopoulos N, Wheeler DA, Kinzler KW, Myers JN. Exome sequencing of head and neck squamous cell carcinoma reveals inactivating mutations in NOTCH1. Science. 2011 ;333(6046):1154-7.

Fan X, Zhao S, Yu C, Wu D, Yan Z, Fan L, Song Y, Wang Y, Li C, Ming Y, Gui B, Niu Y, Li X, Yang X, Luo S, Zhang Q, Zhao X, Pan H, Li M, Xia W, Qiu G, Liu P, Zhang S, Zhang J, Wu Z, Lupski JR, Posey JE, Chen S, Gong C, Wu N. Exome sequencing reveals genetic architecture in patients with isolated or syndromic short stature. J Genet Genomics. 2021 ;48(5):396-402.

Patel RM, Liu D, Gonzaga-Jauregui C, Jhangiani S, Lu JT, V Sutton R, Fernbach SD, Azamian M, White L, Edmond JC, Paysse EA, Belmont JW, Muzny D, Lupski JR, Gibbs RA, Lewis RAlan, Lee BH, Lalani SR, Campeau PM. An exome sequencing study of Moebius syndrome including atypical cases reveals an individual with CFEOM3A and a mutation. Cold Spring Harb Mol Case Stud. 2017 ;3(2):a000984.

Okamoto Y, Goksungur MTuba, Pehlivan D, Beck CR, Gonzaga-Jauregui C, Muzny DM, Atik MM, Carvalho CMB, Matur Z, Bayraktar S, Boone PM, Akyuz K, Gibbs RA, Battaloglu E, Parman Y, Lupski JR. Exonic duplication CNV of NDRG1 associated with autosomal-recessive HMSN-Lom/CMT4D. Genet Med. 2014 ;16(5):386-394.

Hanchard NA, Murdock DR, Magoulas PL, Bainbridge MN, Muzny DM, Wu Y, Wang M, Lupski JR, Gibbs RA, Brown CW. Exploring the utility of whole-exome sequencing as a diagnostic tool in a child with atypical episodic muscle weakness. Clin Genet. 2013 ;83(5):457-461.