Publications

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2016
Deiros DRio, Gibbs RA, Rogers J. DNAism: exploring genomic datasets on the web with Horizon Charts. BMC Bioinformatics. 2016 ;17:49.
Bailey P, Chang DK, Nones K, Johns AL, Patch A-M, Gingras M-C, Miller DK, Christ AN, Bruxner TJC, Quinn MC, Nourse C, L Murtaugh C, Harliwong I, Idrisoglu S, Manning S, Nourbakhsh E, Wani S, Fink L, Holmes O, Chin V, Anderson MJ, Kazakoff S, Leonard C, Newell F, Waddell N, Wood S, Xu Q, Wilson PJ, Cloonan N, Kassahn KS, Taylor D, Quek K, Robertson A, Pantano L, Mincarelli L, Sanchez LN, Evers L, Wu J, Pinese M, Cowley MJ, Jones MD, Colvin EK, Nagrial AM, Humphrey ES, Chantrill LA, Mawson A, Humphris J, Chou A, Pajic M, Scarlett CJ, Pinho AV, Giry-Laterriere M, Rooman I, Samra JS, Kench JG, Lovell JA, Merrett ND, Toon CW, Epari K, Nguyen NQ, Barbour A, Zeps N, Moran-Jones K, Jamieson NB, Graham JS, Duthie F, Oien K, Hair J, Grützmann R, Maitra A, Iacobuzio-Donahue CA, Wolfgang CL, Morgan RA, Lawlor RT, Corbo V, Bassi C, Rusev B, Capelli P, Salvia R, Tortora G, Mukhopadhyay D, Petersen GM, Munzy DM, Fisher WE, Karim SA, Eshleman JR, Hruban RH, Pilarsky C, Morton JP, Sansom OJ, Scarpa A, Musgrove EA, Bailey U-MHagbo, Hofmann O, Sutherland RL, Wheeler DA, Gill AJ, Gibbs RA, Pearson JV, Waddell N, Biankin AV, Grimmond SM. Genomic analyses identify molecular subtypes of pancreatic cancer. Nature. 2016 ;531(7592):47-52.
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.
Becnel LB, Pereira S, Drummond JA, Gingras M-C, Covington KR, Kovar CL, Doddapaneni HV, Hu J, Muzny DM, McGuire AL, Wheeler DA, Gibbs RA. An open access pilot freely sharing cancer genomic data from participants in Texas. Sci Data. 2016 ;3:160010.
Szafranski P, Gambin T, Dharmadhikari AV, Akdemir KCaner, Jhangiani SN, Schuette J, Godiwala N, Yatsenko SA, Sebastian J, Madan-Khetarpal S, Surti U, Abellar RG, Bateman DA, Wilson AL, Markham MH, Slamon J, Santos-Simarro F, Palomares M, Nevado J, Lapunzina P, Chung BHon-Yin, Wong W-L, Chu YWing Yiu, Mok GTsz Kin, Kerem E, Reiter J, Ambalavanan N, Anderson SA, Kelly DR, Shieh J, Rosenthal TC, Scheible K, Steiner L, M Iqbal A, McKinnon ML, Hamilton SJane, Schlade-Bartusiak K, English D, Hendson G, Roeder ER, DeNapoli TS, Littlejohn ROkashah, Wolff DJ, Wagner CL, Yeung A, Francis D, Fiorino EK, Edelman M, Fox J, Hayes DA, Janssens S, De Baere E, Menten B, Loccufier A, Vanwalleghem L, Moerman P, Sznajer Y, Lay AS, Kussmann JL, Chawla J, Payton DJ, Phillips GE, Brosens E, Tibboel D, de Klein A, Maystadt I, Fisher R, Sebire N, Male A, Chopra M, Pinner J, Malcolm G, Peters G, Arbuckle S, Lees M, Mead Z, Quarrell O, Sayers R, Owens M, Shaw-Smith C, Lioy J, McKay E, de Leeuw N, Feenstra I, Spruijt L, Elmslie F, Thiruchelvam T, Bacino CA, Langston C, Lupski JR, Sen P, Popek E, Stankiewicz P. Pathogenetics of alveolar capillary dysplasia with misalignment of pulmonary veins. Hum Genet. 2016 ;135(5):569-86.
Liu X, White S, Peng B, Johnson AD, Brody JA, Li AH, Huang Z, Carroll A, Wei P, Gibbs RA, Klein RJ, Boerwinkle E. WGSA: an annotation pipeline for human genome sequencing studies. J Med Genet. 2016 ;53(2):111-2.
2015
Gu S, Yuan B, Campbell IM, Beck CR, Carvalho CMB, Nagamani SCS, Erez A, Patel A, Bacino CA, Shaw CA, Stankiewicz P, Cheung SWai, Bi W, Lupski JR. Alu-mediated diverse and complex pathogenic copy-number variants within human chromosome 17 at p13.3. Hum Mol Genet. 2015 ;24(14):4061-77.
Li AH, Morrison AC, Kovar C, L Cupples A, Brody JA, Polfus LM, Yu B, Metcalf G, Muzny DM, Veeraraghavan N, Liu X, Lumley T, Mosley TH, Gibbs RA, Boerwinkle E. Analysis of loss-of-function variants and 20 risk factor phenotypes in 8,554 individuals identifies loci influencing chronic disease. Nat Genet. 2015 ;47(6):640-2.
English AC, Salerno W, Hampton OA, Gonzaga-Jauregui C, Ambreth S, Ritter DI, Beck CR, Davis CF, Dahdouli M, Ma S, Carroll A, Veeraraghavan N, Bruestle J, Drees B, Hastie A, Lam ET, White S, Mishra P, Wang M, Han Y, Zhang F, Stankiewicz P, Wheeler DA, Reid JG, Muzny DM, Rogers J, Sabo A, Worley KC, Lupski JR, Boerwinkle E, Gibbs RA. Assessing structural variation in a personal genome-towards a human reference diploid genome. BMC Genomics. 2015 ;16:286.
Allen CE, D Parsons W. Biological and clinical significance of somatic mutations in Langerhans cell histiocytosis and related histiocytic neoplastic disorders. Hematology Am Soc Hematol Educ Program. 2015 ;2015:559-64.
Yuan B, Liu P, Gupta A, Beck CR, Tejomurtula A, Campbell IM, Gambin T, Simmons AD, Withers MA, R Harris A, Rogers J, Schwartz DC, Lupski JR. Comparative Genomic Analyses of the Human NPHP1 Locus Reveal Complex Genomic Architecture and Its Regional Evolution in Primates. PLoS Genet. 2015 ;11(12):e1005686.
Dong C, Wei P, Jian X, Gibbs RA, Boerwinkle E, Wang K, Liu X. Comparison and integration of deleteriousness prediction methods for nonsynonymous SNVs in whole exome sequencing studies. Hum Mol Genet. 2015 ;24(8):2125-37.
Alioto TS, Buchhalter I, Derdak S, Hutter B, Eldridge MD, Hovig E, Heisler LE, Beck TA, Simpson JT, Tonon L, Sertier A-S, Patch A-M, Jäger N, Ginsbach P, Drews R, Paramasivam N, Kabbe R, Chotewutmontri S, Diessl N, Previti C, Schmidt S, Brors B, Feuerbach L, Heinold M, Gröbner S, Korshunov A, Tarpey PS, Butler AP, Hinton J, Jones D, Menzies A, Raine K, Shepherd R, Stebbings L, Teague JW, Ribeca P, Giner FCastro, Beltran S, Raineri E, Dabad M, Heath SC, Gut M, Denroche RE, Harding NJ, Yamaguchi TN, Fujimoto A, Nakagawa H, Quesada V, Valdés-Mas R, Nakken S, Vodák D, Bower L, Lynch AG, Anderson CL, Waddell N, Pearson JV, Grimmond SM, Peto M, Spellman P, He M, Kandoth C, Lee S, Zhang J, Létourneau L, Ma S, Seth S, Torrents D, Xi L, Wheeler DA, López-Otín C, Campo E, Campbell PJ, Boutros PC, Puente XS, Gerhard DS, Pfister SM, McPherson JD, Hudson TJ, Schlesner M, Lichter P, Eils R, Jones DTW, Gut IG. A comprehensive assessment of somatic mutation detection in cancer using whole-genome sequencing. Nat Commun. 2015 ;6:10001.
Comprehensive genomic characterization of head and neck squamous cell carcinomas. Nature. 2015 ;517(7536):576-82.
Challis D, Antunes L, Garrison E, Banks E, Evani US, Muzny DM, Poplin R, Gibbs RA, Marth G, Yu F. The distribution and mutagenesis of short coding INDELs from 1,128 whole exomes. BMC Genomics. 2015 ;16:143.
Vasquez YM, Mazur EC, Li X, Kommagani R, Jiang L, Chen R, Lanz RB, Kovanci E, Gibbons WE, DeMayo FJ. FOXO1 is required for binding of PR on IRF4, novel transcriptional regulator of endometrial stromal decidualization. Mol Endocrinol. 2015 ;29(3):421-33.
Ritter DI, Haines K, Cheung H, Davis CF, Lau CC, Berg JS, Brown CW, Thompson PA, Gibbs RA, Wheeler DA, Plon SE. Identifying gene disruptions in novel balanced de novo constitutional translocations in childhood cancer patients by whole-genome sequencing. Genet Med. 2015 ;17(10):831-5.
Yuan B, Harel T, Gu S, Liu P, Burglen L, Chantot-Bastaraud S, Gelowani V, Beck CR, Carvalho CMB, Cheung SWai, Coe A, Malan V, Munnich A, Magoulas PL, Potocki L, Lupski JR. Nonrecurrent 17p11.2p12 Rearrangement Events that Result in Two Concomitant Genomic Disorders: The PMP22-RAI1 Contiguous Gene Duplication Syndrome. Am J Hum Genet. 2015 ;97(5):691-707.
Yazdani A, Yazdani A, Boerwinkle E. Rare variants analysis using penalization methods for whole genome sequence data. BMC Bioinformatics. 2015 ;16:405.
Campbell IM, Shaw CA, Stankiewicz P, Lupski JR. Somatic mosaicism: implications for disease and transmission genetics. Trends Genet. 2015 ;31(7):382-92.