Publications

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Journal Article
Li J, Choi J, Cheng X, Ma J, Pema S, Sanes JR, Mardon G, Frankfort BJ, Tran NM, Li Y, Chen R. Comprehensive single-cell atlas of the mouse retina. iScience. 2024 ;27(6):109916.
Toffoli M, Chen X, Sedlazeck FJ, Lee C-Y, Mullin S, Higgins A, Koletsi S, Garcia-Segura MEmili, Sammler E, Scholz SW, Schapira AHV, Eberle MA, Proukakis C. Comprehensive short and long read sequencing analysis for the Gaucher and Parkinson's disease-associated GBA gene. Commun Biol. 2022 ;5(1):670.
Zheng S, Cherniack AD, Dewal N, Moffitt RA, Danilova L, Murray BA, Lerario AM, Else T, Knijnenburg TA, Ciriello G, Kim S, Assie G, Morozova O, Akbani R, Shih J, Hoadley KA, Choueiri TK, Waldmann J, Mete O, A Robertson G, Wu H-T, Raphael BJ, Shao L, Meyerson M, Demeure MJ, Beuschlein F, Gill AJ, Sidhu SB, Almeida MQ, Fragoso MCBV, Cope LM, Kebebew E, Habra MA, Whitsett TG, Bussey KJ, Rainey WE, Asa SL, Bertherat J, Fassnacht M, Wheeler DA, Hammer GD, Giordano TJ, Verhaak RGW. Comprehensive Pan-Genomic Characterization of Adrenocortical Carcinoma. Cancer Cell. 2016 ;29(5):723-736.
Berger AC, Korkut A, Kanchi RS, Hegde AM, Lenoir W, Liu W, Liu Y, Fan H, Shen H, Ravikumar V, Rao A, Schultz A, Li X, Sumazin P, Williams C, Mestdagh P, Gunaratne PH, Yau C, Bowlby R, A Robertson G, Tiezzi DG, Wang C, Cherniack AD, Godwin AK, Kuderer NM, Rader JS, Zuna RE, Sood AK, Lazar AJ, Ojesina AI, Adebamowo C, Adebamowo SN, Baggerly KA, Chen T-W, Chiu H-S, Lefever S, Liu L, MacKenzie K, Orsulic S, Roszik J, Shelley CSimon, Song Q, Vellano CP, Wentzensen N, Weinstein JN, Mills GB, Levine DA, Akbani R. A Comprehensive Pan-Cancer Molecular Study of Gynecologic and Breast Cancers. Cancer Cell. 2018 ;33(4):690-705.e9.
Wang H, Wang X, Zou X, Xu S, Li H, Soens ZTore, Wang K, Li Y, Dong F, Chen R, Sui R. Comprehensive Molecular Diagnosis of a Large Chinese Leber Congenital Amaurosis Cohort. Invest Ophthalmol Vis Sci. 2015 ;56(6):3642-55.
Jiang L, Liang X, Li Y, Wang J, Zaneveld JEric, Wang H, Xu S, Wang K, Wang B, Chen R, Sui R. Comprehensive molecular diagnosis of 67 Chinese Usher syndrome probands: high rate of ethnicity specific mutations in Chinese USH patients. Orphanet J Rare Dis. 2015 ;10:110.
Wang X, Wang H, Sun V, Tuan H-F, Keser V, Wang K, Ren H, Lopez I, Zaneveld JE, Siddiqui S, Bowles S, Khan A, Salvo J, Jacobson SG, Iannaccone A, Wang F, Birch D, Heckenlively JR, Fishman GA, Traboulsi EI, Li Y, Wheaton D, Koenekoop RK, Chen R. Comprehensive molecular diagnosis of 179 Leber congenital amaurosis and juvenile retinitis pigmentosa patients by targeted next generation sequencing. J Med Genet. 2013 ;50(10):674-88.
Comprehensive molecular characterization of human colon and rectal cancer. Nature. 2012 ;487(7407):330-7.
Comprehensive molecular characterization of clear cell renal cell carcinoma. Nature. 2013 ;499(7456):43-9.
Moss TJ, Qi Y, Xi L, Peng B, Kim T-B, Ezzedine NE, Mosqueda ME, Guo CC, Czerniak BA, Ittmann M, Wheeler DA, Lerner SP, Matin SF. Comprehensive Genomic Characterization of Upper Tract Urothelial Carcinoma. Eur Urol. 2017 ;72(4):641-649.
Comprehensive genomic characterization of head and neck squamous cell carcinomas. Nature. 2015 ;517(7536):576-82.
Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature. 2008 ;455(7216):1061-8.
Wiszniewski W, Gawlinski P, Gambin T, Bekiesinska-Figatowska M, Obersztyn E, Antczak-Marach D, Akdemir ZHande Coba, Harel T, Karaca E, Jurek M, Sobecka K, Nowakowska B, Kruk M, Terczynska I, Goszczanska-Ciuchta A, Rudzka-Dybala M, Jamroz E, Pyrkosz A, Jakubiuk-Tomaszuk A, Iwanowski P, Gieruszczak-Bialek D, Piotrowicz M, Sasiadek M, Kochanowska I, Gurda B, Steinborn B, Dawidziuk M, Castaneda J, Wlasienko P, Bezniakow N, Jhangiani SN, Hoffman-Zacharska D, Bal J, Szczepanik E, Boerwinkle E, Gibbs RA, Lupski JR. Comprehensive genomic analysis of patients with disorders of cerebral cortical development. Eur J Hum Genet. 2018 ;26(8):1121-1131.
Leduc MS, Shimmin LC, Klos KLE, Hanis C, Boerwinkle E, Hixson JE. Comprehensive evaluation of apolipoprotein H gene (APOH) variation identifies novel associations with measures of lipid metabolism in GENOA. J Lipid Res. 2008 ;49(12):2648-56.
Lumaka A, Race V, Peeters H, Corveleyn A, Coban-Akdemir Z, Jhangiani SN, Song X, Mubungu G, Posey J, Lupski JR, Vermeesch JR, Lukusa P, Devriendt K. A comprehensive clinical and genetic study in 127 patients with ID in Kinshasa, DR Congo. Am J Med Genet A. 2018 ;176(9):1897-1909.
Bailey MH, Tokheim C, Porta-Pardo E, Sengupta S, Bertrand D, Weerasinghe A, Colaprico A, Wendl MC, Kim J, Reardon B, Ng PKwok-Shing, Jeong KJin, Cao S, Wang Z, Gao J, Gao Q, Wang F, Liu EMinwei, Mularoni L, Rubio-Perez C, Nagarajan N, Cortés-Ciriano I, Zhou DCui, Liang W-W, Hess JM, Yellapantula VD, Tamborero D, Gonzalez-Perez A, Suphavilai C, Ko JYu, Khurana E, Park PJ, Van Allen EM, Liang H, Lawrence MS, Godzik A, Lopez-Bigas N, Stuart J, Wheeler D, Getz G, Chen K, Lazar AJ, Mills GB, Karchin R, Ding L. Comprehensive Characterization of Cancer Driver Genes and Mutations. Cell. 2018 ;173(2):371-385.e18.
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 and Integrative Genomic Characterization of Hepatocellular Carcinoma. Cell. 2017 ;169(7):1327-1341.e23.
Behera S, Catreux S, Rossi M, Truong S, Huang Z, Ruehle M, Visvanath A, Parnaby G, Roddey C, Onuchic V, Cameron DL, English A, Mehtalia S, Han J, Mehio R, Sedlazeck FJ. Comprehensive and accurate genome analysis at scale using DRAGEN accelerated algorithms. bioRxiv. 2024 ;.
Aganezov S, Goodwin S, Sherman RM, Sedlazeck FJ, Arun G, Bhatia S, Lee I, Kirsche M, Wappel R, Kramer M, Kostroff K, Spector DL, Timp W, W McCombie R, Schatz MC. Comprehensive analysis of structural variants in breast cancer genomes using single-molecule sequencing. Genome Res. 2020 ;30(9):1258-1273.
Zaneveld J, Siddiqui S, Li H, Wang X, Wang H, Wang K, Li H, Ren H, Lopez I, Dorfman A, Khan A, Wang F, Salvo J, Gelowani V, Li Y, Sui R, Koenekoop R, Chen R. Comprehensive analysis of patients with Stargardt macular dystrophy reveals new genotype-phenotype correlations and unexpected diagnostic revisions. Genet Med. 2015 ;17(4):262-70.
Nikpay M, Goel A, Won H-H, Hall LM, Willenborg C, Kanoni S, Saleheen D, Kyriakou T, Nelson CP, Hopewell JC, Webb TR, Zeng L, Dehghan A, Alver M, Armasu SM, Auro K, Bjonnes A, Chasman DI, Chen S, Ford I, Franceschini N, Gieger C, Grace C, Gustafsson S, Huang J, Hwang S-J, Kim YKyoung, Kleber ME, Lau KWai, Lu X, Lu Y, Lyytikäinen L-P, Mihailov E, Morrison AC, Pervjakova N, Qu L, Rose LM, Salfati E, Saxena R, Scholz M, Smith AV, Tikkanen E, Uitterlinden A, Yang X, Zhang W, Zhao W, de Andrade M, de Vries PS, Van Zuydam NR, Anand SS, Bertram L, Beutner F, Dedoussis G, Frossard P, Gauguier D, Goodall AH, Gottesman O, Haber M, Han B-G, Huang J, Jalilzadeh S, Kessler T, König IR, Lannfelt L, Lieb W, Lind L, Lindgren CM, Lokki M-L, Magnusson PK, Mallick NH, Mehra N, Meitinger T, Memon F-U-R, Morris AP, Nieminen MS, Pedersen NL, Peters A, Rallidis LS, Rasheed A, Samuel M, Shah SH, Sinisalo J, Stirrups KE, Trompet S, Wang L, Zaman KS, Ardissino D, Boerwinkle E, Borecki IB, Bottinger EP, Buring JE, Chambers JC, Collins R, L Cupples A, Danesh J, Demuth I, Elosua R, Epstein SE, Esko T, Feitosa MF, Franco OH, Franzosi MGrazia, Granger CB, Gu D, Gudnason V, Hall AS, Hamsten A, Harris TB, Hazen SL, Hengstenberg C, Hofman A, Ingelsson E, Iribarren C, J Jukema W, Karhunen PJ, Kim B-J, Kooner JS, Kullo IJ, Lehtimäki T, Loos RJF, Melander O, Metspalu A, Marz W, Palmer CN, Perola M, Quertermous T, Rader DJ, Ridker PM, Ripatti S, Roberts R, Salomaa V, Sanghera DK, Schwartz SM, Seedorf U, Stewart AF, Stott DJ, Thiery J, Zalloua PA, O'Donnell CJ, Reilly MP, Assimes TL, Thompson JR, Erdmann J, Clarke R, Watkins H, Kathiresan S, McPherson R, Deloukas P, Schunkert H, Samani NJ, Farrall M. A comprehensive 1,000 Genomes-based genome-wide association meta-analysis of coronary artery disease. Nat Genet. 2015 ;47(10):1121-1130.
Wu CWah, Sasa G, Salih A, Nicholas S, Vogel TP, Cahill G, Kuehn HSun, Rosenzweig SD, Zhou Q, Chinn IK, Yuan B. Complicated Diagnosis and Treatment of HA20 due to Contiguous Gene Deletions involving 6q23.3. J Clin Immunol. 2021 ;41(6):1420-1423.
Li JN, Carrero IG, Dong JF, Yu FL. Complexity and diversity of F8 genetic variations in the 1000 genomes. J Thromb Haemost. 2015 ;13(11):2031-40.
Nattestad M, Goodwin S, Ng K, Baslan T, Sedlazeck FJ, Rescheneder P, Garvin T, Fang H, Gurtowski J, Hutton E, Tseng E, Chin C-S, Beck T, Sundaravadanam Y, Kramer M, Antoniou E, McPherson JD, Hicks J, W McCombie R, Schatz MC. Complex rearrangements and oncogene amplifications revealed by long-read DNA and RNA sequencing of a breast cancer cell line. Genome Res. 2018 ;28(8):1126-1135.