Publications

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Filters: Keyword is Genomic Structural Variation  [Clear All Filters]
2020
Weissensteiner MH, Bunikis I, Catalán A, Francoijs K-J, Knief U, Heim W, Peona V, Pophaly SD, Sedlazeck FJ, Suh A, Warmuth VM, Wolf JBW. Discovery and population genomics of structural variation in a songbird genus. Nat Commun. 2020 ;11(1):3403.
Zhang Y, Chen F, Fonseca NA, He Y, Fujita M, Nakagawa H, Zhang Z, Brazma A, Creighton CJ. High-coverage whole-genome analysis of 1220 cancers reveals hundreds of genes deregulated by rearrangement-mediated cis-regulatory alterations. Nat Commun. 2020 ;11(1):736.
Alonge M, Wang X, Benoit M, Soyk S, Pereira L, Zhang L, Suresh H, Ramakrishnan S, Maumus F, Ciren D, Levy Y, Harel THai, Shalev-Schlosser G, Amsellem Z, Razifard H, Caicedo AL, Tieman DM, Klee H, Kirsche M, Aganezov S, T Ranallo-Benavidez R, Lemmon ZH, Kim J, Robitaille G, Kramer M, Goodwin S, W McCombie R, Hutton S, Van Eck J, Gillis J, Eshed Y, Sedlazeck FJ, van der Knaap E, Schatz MC, Lippman ZB. Major Impacts of Widespread Structural Variation on Gene Expression and Crop Improvement in Tomato. Cell. 2020 ;182(1):145-161.e23.
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. A robust benchmark for detection of germline large deletions and insertions. Nat Biotechnol. 2020 ;38(11):1347-1355.
2019
Tusso S, Nieuwenhuis BPS, Sedlazeck FJ, Davey JW, Jeffares DC, Wolf JBW. Ancestral Admixture Is the Main Determinant of Global Biodiversity in Fission Yeast. Mol Biol Evol. 2019 ;36(9):1975-1989.
Chander V, Gibbs RA, Sedlazeck FJ. Evaluation of computational genotyping of structural variation for clinical diagnoses. Gigascience. 2019 ;8(9).
Zhang Y, Yang L, Kucherlapati M, Hadjipanayis A, Pantazi A, Bristow CA, Lee EAlice, Mahadeshwar HS, Tang J, Zhang J, Seth S, Lee S, Ren X, Song X, Sun H, Seidman J, Luquette LJ, Xi R, Chin L, Protopopov A, Park PJ, Kucherlapati R, Creighton CJ. Global impact of somatic structural variation on the DNA methylome of human cancers. Genome Biol. 2019 ;20(1):209.
Beck CR, Carvalho CMB, Akdemir ZC, Sedlazeck FJ, Song X, Meng Q, Hu J, Doddapaneni H, Chong Z, Chen ES, Thornton PC, Liu P, Yuan B, Withers M, Jhangiani SN, Kalra D, Walker K, English AC, Han Y, Chen K, Muzny DM, Ira G, Shaw CA, Gibbs RA, Hastings PJ, Lupski JR. Megabase Length Hypermutation Accompanies Human Structural Variation at 17p11.2. Cell. 2019 ;176(6):1310-1324.e10.
Chen S, Krusche P, Dolzhenko E, Sherman RM, Petrovski R, Schlesinger F, Kirsche M, Bentley DR, Schatz MC, Sedlazeck FJ, Eberle MA. Paragraph: a graph-based structural variant genotyper for short-read sequence data. Genome Biol. 2019 ;20(1):291.
Alonge M, Soyk S, Ramakrishnan S, Wang X, Goodwin S, Sedlazeck FJ, Lippman ZB, Schatz MC. RaGOO: fast and accurate reference-guided scaffolding of draft genomes. Genome Biol. 2019 ;20(1):224.
Mahmoud M, Gobet N, Cruz-Dávalos DIvette, Mounier N, Dessimoz C, Sedlazeck FJ. Structural variant calling: the long and the short of it. Genome Biol. 2019 ;20(1):246.