Publications

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Vij S, Kuhl H, Kuznetsova IS, Komissarov A, Yurchenko AA, Van Heusden P, Singh S, Thevasagayam NM, Prakki SRama Srida, Purushothaman K, Saju JM, Jiang J, Mbandi SKimbung, Jonas M, Tong AHin Yan, Mwangi S, Lau D, Ngoh SYan, Liew WChang, Shen X, Hon LS, Drake JP, Boitano M, Hall R, Chin C-S, Lachumanan R, Korlach J, Trifonov V, Kabilov M, Tupikin A, Green D, Moxon S, Garvin T, Sedlazeck FJ, Vurture GW, Gopalapillai G, Katneni VKumar, Noble TH, Scaria V, Sivasubbu S, Jerry DR, O'Brien SJ, Schatz MC, Dalmay T, Turner SW, Lok S, Christoffels A, Orbán L. Chromosomal-Level Assembly of the Asian Seabass Genome Using Long Sequence Reads and Multi-layered Scaffolding. PLoS Genet. 2016 ;12(4):e1005954.
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Wagner J, Olson ND, Harris L, Khan Z, Farek J, Mahmoud M, Stankovic A, Kovacevic V, Yoo B, Miller N, Rosenfeld JA, Ni B, Zarate S, Kirsche M, Aganezov S, Schatz MC, Narzisi G, Byrska-Bishop M, Clarke W, Evani US, Markello C, Shafin K, Zhou X, Sidow A, Bansal V, Ebert P, Marschall T, Lansdorp P, Hanlon V, Mattsson C-A, Barrio AMartinez, Fiddes IT, Xiao C, Fungtammasan A, Chin C-S, Wenger AM, Rowell WJ, Sedlazeck FJ, Carroll A, Salit M, Zook JM. Benchmarking challenging small variants with linked and long reads. Cell Genom. 2022 ;2(5).
A
Soyk S, Lemmon ZH, Sedlazeck FJ, Jiménez-Gómez JM, Alonge M, Hutton SF, Van Eck J, Schatz MC, Lippman ZB. Author Correction: Duplication of a domestication locus neutralized a cryptic variant that caused a breeding barrier in tomato. Nat Plants. 2019 ;5(8):903.
Zook JM, Hansen NF, Olson ND, Chapman L, Mullikin JC, Xiao C, Sherry S, Koren S, Phillippy AM, Boutros PC, Sahraeian SMohammad E, Huang V, Rouette A, Alexander N, Mason CE, Hajirasouliha I, Ricketts C, Lee J, Tearle R, Fiddes IT, Barrio AMartinez, Wala J, Carroll A, Ghaffari N, Rodriguez OL, Bashir A, Jackman S, Farrell JJ, Wenger AM, Alkan C, Soylev A, Schatz MC, Garg S, Church G, Marschall T, Chen K, Fan X, English AC, Rosenfeld JA, Zhou W, Mills RE, Sage JM, Davis JR, Kaiser MD, Oliver JS, Catalano AP, Chaisson MJP, Spies N, Sedlazeck FJ, Salit M. Author Correction: A robust benchmark for detection of germline large deletions and insertions. Nat Biotechnol. 2020 ;38(11):1357.
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.
Krittanawong C, Johnson KW, Choi E, Kaplin S, Venner E, Murugan M, Wang Z, Glicksberg BS, Amos CI, Schatz MC, Tang WHWilson. Artificial Intelligence and Cardiovascular Genetics. Life (Basel). 2022 ;12(2).
Sedlazeck FJ, Rescheneder P, Smolka M, Fang H, Nattestad M, von Haeseler A, Schatz MC. Accurate detection of complex structural variations using single-molecule sequencing. Nat Methods. 2018 ;15(6):461-468.
Wenger AM, Peluso P, Rowell WJ, Chang P-C, Hall RJ, Concepcion GT, Ebler J, Fungtammasan A, Kolesnikov A, Olson ND, Töpfer A, Alonge M, Mahmoud M, Qian Y, Chin C-S, Phillippy AM, Schatz MC, Myers G, DePristo MA, Ruan J, Marschall T, Sedlazeck FJ, Zook JM, Li H, Koren S, Carroll A, Rank DR, Hunkapiller MW. Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome. Nat Biotechnol. 2019 ;37(10):1155-1162.