Publications

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2024
Brock DC, Wang M, Hussain HMuhammad J, Rauch DE, Marra M, Pennesi ME, Yang P, Everett L, Ajlan RS, Colbert J, Porto FBelga Otto, Matynia A, Gorin MB, Koenekoop RK, Lopez I, Sui R, Zou G, Li Y, Chen R. Comparative analysis of in-silico tools in identifying pathogenic variants in dominant inherited retinal diseases. Hum Mol Genet. 2024 ;.
2020
Byrd DA, Sinha R, Hoffman KL, Chen J, Hua X, Shi J, Chia N, Petrosino J, Vogtmann E. Comparison of Methods To Collect Fecal Samples for Microbiome Studies Using Whole-Genome Shotgun Metagenomic Sequencing. mSphere. 2020 ;5(1).
2001
Cai WW, Chen R, Gibbs RA, Bradley A. A clone-array pooled shotgun strategy for sequencing large genomes. Genome Res. 2001 ;11(10):1619-23.
2023
Calame DG, Vadillo CMoreno, Berger S, Lotze T, Shinawi M, Poupak J, Heller C, Cohen J, Person R, Telegrafi A, Phitsanuwong C, Fiala K, Thiffault I, Del Viso F, Zhou D, Fleming EA, Pastinen T, Fatemi A, Thomas S, Pascual SI, Torres RJ, Prior C, Gómez-González C, Biskup S, Lupski JR, Maric D, Holmgren M, Regier D, Yano ST. Cation leak through the ATP1A3 pump causes spasticity and intellectual disability. Brain. 2023 ;146(8):3162-3171.
2015
Comprehensive genomic characterization of head and neck squamous cell carcinomas. Nature. 2015 ;517(7536):576-82.
2012
Comprehensive molecular characterization of human colon and rectal cancer. Nature. 2012 ;487(7407):330-7.
2013
Weinstein JN, Collisson EA, Mills GB, Shaw KRMills, Ozenberger BA, Ellrott K, Shmulevich I, Sander C, Stuart JM. The Cancer Genome Atlas Pan-Cancer analysis project. Nat Genet. 2013 ;45(10):1113-20.
Comprehensive molecular characterization of clear cell renal cell carcinoma. Nature. 2013 ;499(7456):43-9.
2008
Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature. 2008 ;455(7216):1061-8.
2017
Comprehensive and Integrative Genomic Characterization of Hepatocellular Carcinoma. Cell. 2017 ;169(7):1327-1341.e23.
2023
Caron V, Chassaing N, Ragge N, Boschann F, Ngu AMy-Hoa, Meloche E, Chorfi S, Lakhani SA, Ji W, Steiner L, Marcadier J, Jansen PR, van de Pol LA, van Hagen JM, Russi ASerrano, Le Guyader G, Nordenskjöld M, Nordgren A, Anderlid B-M, Plaisancié J, Stoltenburg C, Horn D, Drenckhahn A, Hamdan FF, Lefebvre M, Attié-Bitach T, Forey P, Smirnov V, Ernould F, Jacquemont M-L, Grotto S, Alcantud A, Coret A, Ferrer-Avargues R, Srivastava S, Vincent-Delorme C, Romoser S, Safina N, Saade D, Lupski JR, Calame DG, Geneviève D, Chatron N, Schluth-Bolard C, Myers KA, Dobyns WB, Calvas P, Salmon C, Holt R, Elmslie F, Allaire M, Prigozhin DM, Tremblay A, Michaud JL. Clinical and functional heterogeneity associated with the disruption of retinoic acid receptor beta. Genet Med. 2023 ;25(8):100856.
2022
M Casanova I, Chen R, Garzel LM, Olstad KJ, Kim S, Harris RA, Li Y, Raveendran M, Liang Q, Wang J, Yiu G, Stout JTimothy, Roberts JA, Rogers J, Moshiri A, Thomasy SM. Clinical presentation, treatment, and genetic and histopathological analysis of juvenile cataracts and secondary glaucoma in a rhesus macaque (Macaca mulatta). J Med Primatol. 2022 ;51(2):119-123.
2014
Chen Z-X, Sturgill D, Qu J, Jiang H, Park S, Boley N, Suzuki AMaria, Fletcher AR, Plachetzki DC, FitzGerald PC, Artieri CG, Atallah J, Barmina O, Brown JB, Blankenburg KP, Clough E, Dasgupta A, Gubbala S, Han Y, Jayaseelan JC, Kalra D, Kim Y-A, Kovar CL, Lee SL, Li M, Malley JD, Malone JH, Mathew T, Mattiuzzo NR, Munidasa M, Muzny DM, Ongeri F, Perales L, Przytycka TM, Pu L-L, Robinson G, Thornton RL, Saada N, Scherer SE, Smith HE, Vinson C, Warner CB, Worley KC, Wu Y-Q, Zou X, Cherbas P, Kellis M, Eisen MB, Piano F, Kionte K, Fitch DH, Sternberg PW, Cutter AD, Duff MO, Hoskins RA, Graveley BR, Gibbs RA, Bickel PJ, Kopp A, Carninci P, Celniker SE, Oliver B, Richards S. Comparative validation of the D. melanogaster modENCODE transcriptome annotation. Genome Res. 2014 ;24(7):1209-23.
2001
Chen R, Bouck JB, Weinstock GM, Gibbs RA. Comparing vertebrate whole-genome shotgun reads to the human genome. Genome Res. 2001 ;11(11):1807-16.
2017
Chen Y, Bartanus J, Liang D, Zhu H, Breman AM, Smith JL, Wang H, Ren Z, Patel A, Stankiewicz P, Cram DS, Cheung SWai, Wu L, Yu F. Characterization of chromosomal abnormalities in pregnancy losses reveals critical genes and loci for human early development. Hum Mutat. 2017 ;38(6):669-677.
2020
Chen C-A, Pal R, Yin J, Tao H, Amawi A, Sabo A, Bainbridge MN, Gibbs RA, Zoghbi HY, Schaaf CP. Combination of whole exome sequencing and animal modeling identifies TMPRSS9 as a candidate gene for autism spectrum disorder. Hum Mol Genet. 2020 ;29(3):459-470.
Chen N, Caruso C, Alonso A, Derebail VK, Kshirsagar AV, A Sharrett R, Key NS, Gottesman RF, Grove ML, Bressler J, Boerwinkle E, B Windham G, Mosley TH, Hyacinth HI. Corrigendum to 'Association of sickle cell trait with measures of cognitive function and dementia in African Americans' Vol. 16 (2019), 100,201. eNeurologicalSci. 2020 ;21:100281.
2010
Cheverud JM, Fawcett GL, Jarvis JP, Norgard EA, Pavlicev M, L Pletscher S, Polonsky KS, Ye H, Bell GI, Semenkovich CF. Calpain-10 is a component of the obesity-related quantitative trait locus Adip1. J Lipid Res. 2010 ;51(5):907-13.
2001
Chew LJ, Yuan X, Scherer SE, Qie L, Huang F, Hayes WP, Gallo V. Characterization of the rat GRIK5 kainate receptor subunit gene promoter and its intragenic regions involved in neural cell specificity. J Biol Chem. 2001 ;276(45):42162-71.
2006
Childers CP, Newkirk HL, Honeycutt DA, Ramlachan N, Muzny DM, Sodergren E, Gibbs RA, Weinstock GM, Womack JE, Skow LC. Comparative analysis of the bovine MHC class IIb sequence identifies inversion breakpoints and three unexpected genes. Anim Genet. 2006 ;37(2):121-9.
2016
Chitsazzadeh V, Coarfa C, Drummond JA, Nguyen T, Joseph A, Chilukuri S, Charpiot E, Adelmann CH, Ching G, Nguyen TN, Nicholas C, Thomas VD, Migden M, MacFarlane D, Thompson E, Shen J, Takata Y, McNiece K, Polansky MA, Abbas HA, Rajapakshe K, Gower A, Spira A, Covington KR, Xiao W, Gunaratne P, Pickering C, Frederick M, Myers JN, Shen L, Yao H, Su X, Rapini RP, Wheeler DA, Hawk ET, Flores ER, Tsai KY. Cross-species identification of genomic drivers of squamous cell carcinoma development across preneoplastic intermediates. Nat Commun. 2016 ;7:12601.
1991
Clemens PR, Fenwick RG, Chamberlain JS, Gibbs RA, de Andrade M, Chakraborty R, Caskey CT. Carrier detection and prenatal diagnosis in Duchenne and Becker muscular dystrophy families, using dinucleotide repeat polymorphisms. Am J Hum Genet. 1991 ;49(5):951-60.
2018
Creighton CJ. The clinical applications of The Cancer Genome Atlas project for bladder cancer. Expert Rev Anticancer Ther. 2018 ;18(10):973-980.
2022
Creighton CJ. Clinical proteomics towards multiomics in cancer. Mass Spectrom Rev. 2022 ;:e21827.
2003
Csuros M, Li B, Milosavljevic A. Clone-array pooled shotgun mapping and sequencing: design and analysis of experiments. Genome Inform. 2003 ;14:186-95.