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Bradnam KR, Fass JN, Alexandrov A, Baranay P, Bechner M, Birol I, Boisvert S, Chapman JA, Chapuis G, Chikhi R, Chitsaz H, Chou W-C, Corbeil J, Del Fabbro C, T Docking R, Durbin R, Earl D, Emrich S, Fedotov P, Fonseca NA, Ganapathy G, Gibbs RA, Gnerre S, Godzaridis E, Goldstein S, Haimel M, Hall G, Haussler D, Hiatt JB, Ho IY, Howard J, Hunt M, Jackman SD, Jaffe DB, Jarvis ED, Jiang H, Kazakov S, Kersey PJ, Kitzman JO, Knight JR, Koren S, Lam T-W, Lavenier D, Laviolette F, Li Y, Li Z, Liu B, Liu Y, Luo R, Maccallum I, Macmanes MD, Maillet N, Melnikov S, Naquin D, Ning Z, Otto TD, Paten B, Paulo OS, Phillippy AM, Pina-Martins F, Place M, Przybylski D, Qin X, Qu C, Ribeiro FJ, Richards S, Rokhsar DS, J Ruby G, Scalabrin S, Schatz MC, Schwartz DC, Sergushichev A, Sharpe T, Shaw TI, Shendure J, Shi Y, Simpson JT, Song H, Tsarev F, Vezzi F, Vicedomini R, Vieira BM, Wang J, Worley KC, Yin S, Yiu S-M, Yuan J, Zhang G, Zhang H, Zhou S, Korf IF. Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species. Gigascience. 2013 ;2(1):10.

Matynia A, Wang J, Kim S, Li Y, Dimashkie A, Jiang Z, Hu J, Strom SP, Radu RA, Chen R, Gorin MB. Assessing Variant Causality and Severity Using Retinal Pigment Epithelial Cells Derived from Stargardt Disease Patients. Transl Vis Sci Technol. 2022 ;11(3):33.

Bertrand RElaine, Wang J, Xiong KH, Thangavel C, Qian X, Ba-Abbad R, Liang Q, Simões RT, Sampaio SAM, Carss KJ, F Raymond L, Robson AG, Webster AR, Arno G, Porto FBelga Otto, Chen R. Ceramide synthase TLCD3B is a novel gene associated with human recessive retinal dystrophy. Genet Med. 2021 ;23(3):488-497.

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.

Bertrand RElaine, Wang J, Li Y, Cheng X, Wang K, Stoilov P, Chen R. Cwc27, associated with retinal degeneration, functions as a splicing factor in vivo. Hum Mol Genet. 2022 ;31(8):1278-1292.

Muzny DM, Scherer SE, Kaul R, Wang J, Yu J, Sudbrak R, Buhay CJ, Chen R, Cree A, Ding Y, Dugan-Rocha S, Gill R, Gunaratne P, Harris RA, Hawes AC, Hernandez J, Hodgson AV, Hume J, Jackson A, Khan ZMohid, Kovar-Smith C, Lewis LR, Lozado RJ, Metzker ML, Milosavljevic A, Miner GR, Morgan MB, Nazareth LV, Scott G, Sodergren E, Song X-Z, Steffen D, Wei S, Wheeler DA, Wright MW, Worley KC, Yuan Y, Zhang Z, Adams CQ, M Ansari-Lari A, Ayele M, Brown MJ, Chen G, Chen Z, Clendenning J, Clerc-Blankenburg KP, Chen R, Chen Z, Davis C, Delgado O, Dinh HH, Dong W, Draper H, Ernst S, Fu G, Gonzalez-Garay ML, Garcia DK, Gillett W, Gu J, Hao B, Haugen E, Havlak P, He X, Hennig S, Hu S, Huang W, Jackson LR, Jacob LS, Kelly SH, Kube M, Levy R, Li Z, Liu B, Liu J, Liu W, Lu J, Maheshwari M, Nguyen B-V, Okwuonu GO, Palmeiri A, Pasternak S, Perez LM, Phelps KA, Plopper FJH, Qiang B, Raymond C, Rodriguez R, Saenphimmachak C, Santibanez J, Shen H, Shen Y, Subramanian S, Tabor PE, Verduzco D, Waldron L, Wang J, Wang J, Wang Q, Williams GA, Wong GK-S, Yao Z, Zhang J, Zhang X, Zhao G, Zhou J, Zhou Y, Nelson D, Lehrach H, Reinhardt R, Naylor SL, Yang H, Olson M, Weinstock G, Gibbs RA. The DNA sequence, annotation and analysis of human chromosome 3. Nature. 2006 ;440(7088):1194-8.

Rozowsky J, Gao J, Borsari B, Yang YT, Galeev T, Gürsoy G, Epstein CB, Xiong K, Xu J, Li T, Liu J, Yu K, Berthel A, Chen Z, Navarro F, Sun MS, Wright J, Chang J, Cameron CJF, Shoresh N, Gaskell E, Drenkow J, Adrian J, Aganezov S, Aguet F, Balderrama-Gutierrez G, Banskota S, Corona GBarreto, Chee S, Chhetri SB, Martins GConte Cort, Danyko C, Davis CA, Farid D, Farrell NP, Gabdank I, Gofin Y, Gorkin DU, Gu M, Hecht V, Hitz BC, Issner R, Jiang Y, Kirsche M, Kong X, Lam BR, Li S, Li B, Li X, Lin KZin, Luo R, Mackiewicz M, Meng R, Moore JE, Mudge J, Nelson N, Nusbaum C, Popov I, Pratt HE, Qiu Y, Ramakrishnan S, Raymond J, Salichos L, Scavelli A, Schreiber JM, Sedlazeck FJ, See LHoon, Sherman RM, Shi X, Shi M, Sloan CAlicia, J Strattan S, Tan Z, Tanaka FY, Vlasova A, Wang J, Werner J, Williams B, Xu M, Yan C, Yu L, Zaleski C, Zhang J, Ardlie K, J Cherry M, Mendenhall EM, Noble WS, Weng Z, Levine ME, Dobin A, Wold B, Mortazavi A, Ren B, Gillis J, Myers RM, Snyder MP, Choudhary J, Milosavljevic A, Schatz MC, Bernstein BE, Guigó R, Gingeras TR, Gerstein M. The EN-TEx resource of multi-tissue personal epigenomes & variant-impact models. Cell. 2023 ;186(7):1493-1511.e40.

Strausberg RL, Feingold EA, Grouse LH, Derge JG, Klausner RD, Collins FS, Wagner L, Shenmen CM, Schuler GD, Altschul SF, Zeeberg B, Buetow KH, Schaefer CF, Bhat NK, Hopkins RF, Jordan H, Moore T, Max SI, Wang J, Hsieh F, Diatchenko L, Marusina K, Farmer AA, Rubin GM, Hong L, Stapleton M, M Soares B, Bonaldo MF, Casavant TL, Scheetz TE, Brownstein MJ, Usdin TB, Toshiyuki S, Carninci P, Prange C, Raha SS, Loquellano NA, Peters GJ, Abramson RD, Mullahy SJ, Bosak SA, McEwan PJ, McKernan KJ, Malek JA, Gunaratne PH, Richards S, Worley KC, Hale S, Garcia AM, Gay LJ, Hulyk SW, Villalon DK, Muzny DM, Sodergren EJ, Lu X, Gibbs RA, Fahey J, Helton E, Ketteman M, Madan A, Rodrigues S, Sanchez A, Whiting M, Madan A, Young AC, Shevchenko Y, Bouffard GG, Blakesley RW, Touchman JW, Green ED, Dickson MC, Rodriguez AC, Grimwood J, Schmutz J, Myers RM, Butterfield YSN, Krzywinski MI, Skalska U, Smailus DE, Schnerch A, Schein JE, Jones SJM, Marra MA. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Proc Natl Acad Sci U S A. 2002 ;99(26):16899-903.

Kim S, Lowe A, Dharmat R, Lee S, Owen LA, Wang J, Shakoor A, Li Y, Morgan DJ, Hejazi AA, Cvekl A, DeAngelis MM, Z Zhou J, Chen R, Liu W. Generation, transcriptome profiling, and functional validation of cone-rich human retinal organoids. Proc Natl Acad Sci U S A. 2019 ;116(22):10824-10833.

Kyrpides NC, Hugenholtz P, Eisen JA, Woyke T, Göker M, Parker CT, Amann R, Beck BJ, Chain PSG, Chun J, Colwell RR, Danchin A, Dawyndt P, Dedeurwaerdere T, DeLong EF, Detter JC, De Vos P, Donohue TJ, Dong X-Z, Ehrlich DS, Fraser C, Gibbs RA, Gilbert J, Gilna P, Glöckner FOliver, Jansson JK, Keasling JD, Knight R, Labeda D, Lapidus A, Lee J-S, Li W-J, Ma J, Markowitz V, Moore ERB, Morrison M, Meyer F, Nelson KE, Ohkuma M, Ouzounis CA, Pace N, Parkhill J, Qin N, Rossello-Mora R, Sikorski J, Smith D, Sogin M, Stevens R, Stingl U, Suzuki K-I, Taylor D, Tiedje JM, Tindall B, Wagner M, Weinstock G, Weissenbach J, White O, Wang J, Zhang L, Zhou Y-G, Field D, Whitman WB, Garrity GM, Klenk H-P. Genomic encyclopedia of bacteria and archaea: sequencing a myriad of type strains. PLoS Biol. 2014 ;12(8):e1001920.

Wang J, Zhao L, Wang X, Chen Y, Xu M, Soens ZT, Ge Z, Wang PRonghan, Wang F, Chen R. GRIPT: a novel case-control analysis method for Mendelian disease gene discovery. Genome Biol. 2018 ;19(1):203.

Qian X, Wang J, Wang M, Igelman AD, Jones KD, Li Y, Wang K, Goetz KE, Birch DG, Yang P, Pennesi ME, Chen R. Identification of Deep-Intronic Splice Mutations in a Large Cohort of Patients With Inherited Retinal Diseases. Front Genet. 2021 ;12:647400.

Zou G, Zhang T, Cheng X, Igelman AD, Wang J, Qian X, Fu S, Wang K, Koenekoop RK, Fishman GA, Yang P, Li Y, Pennesi ME, Chen R. Noncoding mutation in contributes to inherited retinal degenerations. Mol Vis. 2021 ;27:95-106.

Moshiri A, Chen R, Kim S, Harris RA, Li Y, Raveendran M, Davis S, Liang Q, Pomerantz O, Wang J, Garzel L, Cameron A, Yiu G, J Stout T, Huang Y, Murphy CJ, Roberts J, Gopalakrishna KN, Boyd K, Artemyev NO, Rogers J, Thomasy SM. A nonhuman primate model of inherited retinal disease. J Clin Invest. 2019 ;129(2):863-874.

Wang J, Liu H, Bertrand RElaine, Sarrion-Perdigones A, Gonzalez Y, Venken KJT, Chen R. A novel statistical method for interpreting the pathogenicity of rare variants. Genet Med. 2021 ;23(1):59-68.

Jiang Y, Xie M, Chen W, Talbot R, Maddox JF, Faraut T, Wu C, Muzny DM, Li Y, Zhang W, Stanton J-A, Brauning R, Barris WC, Hourlier T, Aken BL, Searle SMJ, Adelson DL, Bian C, Cam GR, Chen Y, Cheng S, DeSilva U, Dixen K, Dong Y, Fan G, Franklin IR, Fu S, Fuentes-Utrilla P, Guan R, Highland MA, Holder ME, Huang G, Ingham AB, Jhangiani SN, Kalra D, Kovar CL, Lee SL, Liu W, Liu X, Lu C, Lv T, Mathew T, McWilliam S, Menzies M, Pan S, Robelin D, Servin B, Townley D, Wang W, Wei B, White SN, Yang X, Ye C, Yue Y, Zeng P, Zhou Q, Hansen JB, Kristiansen K, Gibbs RA, Flicek P, Warkup CC, Jones HE, V Oddy H, Nicholas FW, McEwan JC, Kijas JW, Wang J, Worley KC, Archibald AL, Cockett N, Xu X, Wang W, Dalrymple BP. The sheep genome illuminates biology of the rumen and lipid metabolism. Science. 2014 ;344(6188):1168-73.

MacArthur DG, Balasubramanian S, Frankish A, Huang N, Morris J, Walter K, Jostins L, Habegger L, Pickrell JK, Montgomery SB, Albers CA, Zhang ZD, Conrad DF, Lunter G, Zheng H, Ayub Q, DePristo MA, Banks E, Hu M, Handsaker RE, Rosenfeld JA, Fromer M, Jin M, Mu XJasmine, Khurana E, Ye K, Kay M, Saunders GIan, Suner M-M, Hunt T, Barnes IHA, Amid C, Carvalho-Silva DR, Bignell AH, Snow C, Yngvadottir B, Bumpstead S, Cooper DN, Xue Y, Romero IGallego, Wang J, Li Y, Gibbs RA, McCarroll SA, Dermitzakis ET, Pritchard JK, Barrett JC, Harrow J, Hurles ME, Gerstein MB, Tyler-Smith C. A systematic survey of loss-of-function variants in human protein-coding genes. Science. 2012 ;335(6070):823-8.

Liang Q, Wu N, Zaneveld S, Liu H, Fu S, Wang K, Bertrand R, Wang J, Li Y, Chen R. Transcript isoforms of Reep6 have distinct functions in the retina. Hum Mol Genet. 2021 ;30(21):1907-1918.