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Items: 33

1.

Evaluation of computational genotyping of structural variation for clinical diagnoses.

Chander V, Gibbs RA, Sedlazeck FJ.

Gigascience. 2019 Sep 1;8(9). pii: giz110. doi: 10.1093/gigascience/giz110.

2.

Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome.

Wenger AM, Peluso P, Rowell WJ, Chang PC, Hall RJ, Concepcion GT, Ebler J, Fungtammasan A, Kolesnikov A, Olson ND, Töpfer A, Alonge M, Mahmoud M, Qian Y, Chin CS, 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.

Nat Biotechnol. 2019 Aug 12. doi: 10.1038/s41587-019-0217-9. [Epub ahead of print]

PMID:
31406327
3.

Author Correction: Duplication of a domestication locus neutralized a cryptic variant that caused a breeding barrier in tomato.

Soyk S, Lemmon ZH, Sedlazeck FJ, Jiménez-Gómez JM, Alonge M, Hutton SF, Van Eck J, Schatz MC, Lippman ZB.

Nat Plants. 2019 Aug;5(8):903. doi: 10.1038/s41477-019-0488-7.

PMID:
31292536
4.

Ancestral Admixture Is the Main Determinant of Global Biodiversity in Fission Yeast.

Tusso S, Nieuwenhuis BPS, Sedlazeck FJ, Davey JW, Jeffares DC, Wolf JBW.

Mol Biol Evol. 2019 Sep 1;36(9):1975-1989. doi: 10.1093/molbev/msz126.

5.

Duplication of a domestication locus neutralized a cryptic variant that caused a breeding barrier in tomato.

Soyk S, Lemmon ZH, Sedlazeck FJ, Jiménez-Gómez JM, Alonge M, Hutton SF, Van Eck J, Schatz MC, Lippman ZB.

Nat Plants. 2019 May;5(5):471-479. doi: 10.1038/s41477-019-0422-z. Epub 2019 May 6. Erratum in: Nat Plants. 2019 Aug;5(8):903.

PMID:
31061537
6.

Atlas-CNV: a validated approach to call single-exon CNVs in the eMERGESeq gene panel.

Chiang T, Liu X, Wu TJ, Hu J, Sedlazeck FJ, White S, Schaid D, Andrade M, Jarvik GP, Crosslin D, Stanaway I, Carrell DS, Connolly JJ, Hakonarson H, Groopman EE, Gharavi AG, Fedotov A, Bi W, Leduc MS, Murdock DR, Jiang Y, Meng L, Eng CM, Wen S, Yang Y, Muzny DM, Boerwinkle E, Salerno W, Venner E, Gibbs RA.

Genet Med. 2019 Sep;21(9):2135-2144. doi: 10.1038/s41436-019-0475-4. Epub 2019 Mar 20.

PMID:
30890783
7.

Megabase Length Hypermutation Accompanies Human Structural Variation at 17p11.2.

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.

Cell. 2019 Mar 7;176(6):1310-1324.e10. doi: 10.1016/j.cell.2019.01.045. Epub 2019 Feb 28.

PMID:
30827684
8.

A multi-task convolutional deep neural network for variant calling in single molecule sequencing.

Luo R, Sedlazeck FJ, Lam TW, Schatz MC.

Nat Commun. 2019 Mar 1;10(1):998. doi: 10.1038/s41467-019-09025-z.

9.

Combined transcriptome and proteome profiling reveals specific molecular brain signatures for sex, maturation and circalunar clock phase.

Schenk S, Bannister SC, Sedlazeck FJ, Anrather D, Minh BQ, Bileck A, Hartl M, von Haeseler A, Gerner C, Raible F, Tessmar-Raible K.

Elife. 2019 Feb 15;8. pii: e41556. doi: 10.7554/eLife.41556.

10.

Evaluation of the detection of GBA missense mutations and other variants using the Oxford Nanopore MinION.

Leija-Salazar M, Sedlazeck FJ, Toffoli M, Mullin S, Mokretar K, Athanasopoulou M, Donald A, Sharma R, Hughes D, Schapira AHV, Proukakis C.

Mol Genet Genomic Med. 2019 Mar;7(3):e564. doi: 10.1002/mgg3.564. Epub 2019 Jan 13.

11.

Genome-wide patterns of transposon proliferation in an evolutionary young hybrid fish.

Dennenmoser S, Sedlazeck FJ, Schatz MC, Altmüller J, Zytnicki M, Nolte AW.

Mol Ecol. 2019 Mar;28(6):1491-1505. doi: 10.1111/mec.14969. Epub 2019 Feb 6.

PMID:
30520198
12.

Complex rearrangements and oncogene amplifications revealed by long-read DNA and RNA sequencing of a breast cancer cell line.

Nattestad M, Goodwin S, Ng K, Baslan T, Sedlazeck FJ, Rescheneder P, Garvin T, Fang H, Gurtowski J, Hutton E, Tseng E, Chin CS, Beck T, Sundaravadanam Y, Kramer M, Antoniou E, McPherson JD, Hicks J, McCombie WR, Schatz MC.

Genome Res. 2018 Aug;28(8):1126-1135. doi: 10.1101/gr.231100.117. Epub 2018 Jun 28.

13.

Accurate detection of complex structural variations using single-molecule sequencing.

Sedlazeck FJ, Rescheneder P, Smolka M, Fang H, Nattestad M, von Haeseler A, Schatz MC.

Nat Methods. 2018 Jun;15(6):461-468. doi: 10.1038/s41592-018-0001-7. Epub 2018 Apr 30.

14.

Piercing the dark matter: bioinformatics of long-range sequencing and mapping.

Sedlazeck FJ, Lee H, Darby CA, Schatz MC.

Nat Rev Genet. 2018 Jun;19(6):329-346. doi: 10.1038/s41576-018-0003-4. Review.

PMID:
29599501
15.

LRSim: A Linked-Reads Simulator Generating Insights for Better Genome Partitioning.

Luo R, Sedlazeck FJ, Darby CA, Kelly SM, Schatz MC.

Comput Struct Biotechnol J. 2017 Nov 9;15:478-484. doi: 10.1016/j.csbj.2017.10.002. eCollection 2017.

16.

Tools for annotation and comparison of structural variation.

Sedlazeck FJ, Dhroso A, Bodian DL, Paschall J, Hermes F, Zook JM.

F1000Res. 2017 Oct 3;6:1795. doi: 10.12688/f1000research.12516.1. eCollection 2017.

17.

Copy number increases of transposable elements and protein-coding genes in an invasive fish of hybrid origin.

Dennenmoser S, Sedlazeck FJ, Iwaszkiewicz E, Li XY, Altmüller J, Nolte AW.

Mol Ecol. 2017 Sep;26(18):4712-4724. doi: 10.1111/mec.14134. Epub 2017 Apr 28.

18.

GenomeScope: fast reference-free genome profiling from short reads.

Vurture GW, Sedlazeck FJ, Nattestad M, Underwood CJ, Fang H, Gurtowski J, Schatz MC.

Bioinformatics. 2017 Jul 15;33(14):2202-2204. doi: 10.1093/bioinformatics/btx153.

19.

Transient structural variations have strong effects on quantitative traits and reproductive isolation in fission yeast.

Jeffares DC, Jolly C, Hoti M, Speed D, Shaw L, Rallis C, Balloux F, Dessimoz C, Bähler J, Sedlazeck FJ.

Nat Commun. 2017 Jan 24;8:14061. doi: 10.1038/ncomms14061.

20.

Correction: Chromosomal-Level Assembly of the Asian Seabass Genome Using Long Sequence Reads and Multi-layered Scaffolding.

Vij S, Kuhl H, Kuznetsova IS, Komissarov A, Yurchenko AA, Van Heusden P, Singh S, Thevasagayam NM, Prakki SR, Purushothaman K, Saju JM, Jiang J, Mbandi SK, Jonas M, Hin Yan Tong A, Mwangi S, Lau D, Ngoh SY, Liew WC, Shen X, Hon LS, Drake JP, Boitano M, Hall R, Chin CS, Lachumanan R, Korlach J, Trifonov V, Kabilov M, Tupikin A, Green D, Moxon S, Garvin T, Sedlazeck FJ, Vurture GW, Gopalapillai G, Katneni VK, Noble TH, Scaria V, Sivasubbu S, Jerry DR, O'Brien SJ, Schatz MC, Dalmay T, Turner SW, Lok S, Christoffels A, Orbán L.

PLoS Genet. 2016 Dec 9;12(12):e1006500. doi: 10.1371/journal.pgen.1006500. eCollection 2016 Dec.

21.

The genomic basis of circadian and circalunar timing adaptations in a midge.

Kaiser TS, Poehn B, Szkiba D, Preussner M, Sedlazeck FJ, Zrim A, Neumann T, Nguyen LT, Betancourt AJ, Hummel T, Vogel H, Dorner S, Heyd F, von Haeseler A, Tessmar-Raible K.

Nature. 2016 Dec 1;540(7631):69-73. doi: 10.1038/nature20151. Epub 2016 Nov 21.

22.

Phased diploid genome assembly with single-molecule real-time sequencing.

Chin CS, Peluso P, Sedlazeck FJ, Nattestad M, Concepcion GT, Clum A, Dunn C, O'Malley R, Figueroa-Balderas R, Morales-Cruz A, Cramer GR, Delledonne M, Luo C, Ecker JR, Cantu D, Rank DR, Schatz MC.

Nat Methods. 2016 Dec;13(12):1050-1054. doi: 10.1038/nmeth.4035. Epub 2016 Oct 17.

23.

Chromosomal-Level Assembly of the Asian Seabass Genome Using Long Sequence Reads and Multi-layered Scaffolding.

Vij S, Kuhl H, Kuznetsova IS, Komissarov A, Yurchenko AA, Van Heusden P, Singh S, Thevasagayam NM, Prakki SR, Purushothaman K, Saju JM, Jiang J, Mbandi SK, Jonas M, Hin Yan Tong A, Mwangi S, Lau D, Ngoh SY, Liew WC, Shen X, Hon LS, Drake JP, Boitano M, Hall R, Chin CS, Lachumanan R, Korlach J, Trifonov V, Kabilov M, Tupikin A, Green D, Moxon S, Garvin T, Sedlazeck FJ, Vurture GW, Gopalapillai G, Kumar Katneni V, Noble TH, Scaria V, Sivasubbu S, Jerry DR, O'Brien SJ, Schatz MC, Dalmay T, Turner SW, Lok S, Christoffels A, Orbán L.

PLoS Genet. 2016 Apr 15;12(4):e1005954. doi: 10.1371/journal.pgen.1005954. eCollection 2016 Apr. Erratum in: PLoS Genet. 2016 Dec 9;12 (12 ):e1006500.

24.

The pineapple genome and the evolution of CAM photosynthesis.

Ming R, VanBuren R, Wai CM, Tang H, Schatz MC, Bowers JE, Lyons E, Wang ML, Chen J, Biggers E, Zhang J, Huang L, Zhang L, Miao W, Zhang J, Ye Z, Miao C, Lin Z, Wang H, Zhou H, Yim WC, Priest HD, Zheng C, Woodhouse M, Edger PP, Guyot R, Guo HB, Guo H, Zheng G, Singh R, Sharma A, Min X, Zheng Y, Lee H, Gurtowski J, Sedlazeck FJ, Harkess A, McKain MR, Liao Z, Fang J, Liu J, Zhang X, Zhang Q, Hu W, Qin Y, Wang K, Chen LY, Shirley N, Lin YR, Liu LY, Hernandez AG, Wright CL, Bulone V, Tuskan GA, Heath K, Zee F, Moore PH, Sunkar R, Leebens-Mack JH, Mockler T, Bennetzen JL, Freeling M, Sankoff D, Paterson AH, Zhu X, Yang X, Smith JA, Cushman JC, Paull RE, Yu Q.

Nat Genet. 2015 Dec;47(12):1435-42. doi: 10.1038/ng.3435. Epub 2015 Nov 2.

25.

Teaser: Individualized benchmarking and optimization of read mapping results for NGS data.

Smolka M, Rescheneder P, Schatz MC, von Haeseler A, Sedlazeck FJ.

Genome Biol. 2015 Oct 22;16:235. doi: 10.1186/s13059-015-0803-1.

26.

The Candida albicans Histone Acetyltransferase Hat1 Regulates Stress Resistance and Virulence via Distinct Chromatin Assembly Pathways.

Tscherner M, Zwolanek F, Jenull S, Sedlazeck FJ, Petryshyn A, Frohner IE, Mavrianos J, Chauhan N, von Haeseler A, Kuchler K.

PLoS Pathog. 2015 Oct 16;11(10):e1005218. doi: 10.1371/journal.ppat.1005218. eCollection 2015 Oct.

27.

Decreased expression of endogenous feline leukemia virus in cat lymphomas: a case control study.

Krunic M, Ertl R, Hagen B, Sedlazeck FJ, Hofmann-Lehmann R, von Haeseler A, Klein D.

BMC Vet Res. 2015 Apr 10;11:90. doi: 10.1186/s12917-015-0378-9.

28.

ADAR2 induces reproducible changes in sequence and abundance of mature microRNAs in the mouse brain.

Vesely C, Tauber S, Sedlazeck FJ, Tajaddod M, von Haeseler A, Jantsch MF.

Nucleic Acids Res. 2014 Oct 29;42(19):12155-68. doi: 10.1093/nar/gku844. Epub 2014 Sep 26.

29.

NextGenMap: fast and accurate read mapping in highly polymorphic genomes.

Sedlazeck FJ, Rescheneder P, von Haeseler A.

Bioinformatics. 2013 Nov 1;29(21):2790-1. doi: 10.1093/bioinformatics/btt468. Epub 2013 Aug 23.

PMID:
23975764
30.

Updating benchtop sequencing performance comparison.

Jünemann S, Sedlazeck FJ, Prior K, Albersmeier A, John U, Kalinowski J, Mellmann A, Goesmann A, von Haeseler A, Stoye J, Harmsen D.

Nat Biotechnol. 2013 Apr;31(4):294-6. doi: 10.1038/nbt.2522. No abstract available. Erratum in: Nat Biotechnol. 2013 Dec;31(12):1148.

PMID:
23563421
31.

Benefit-of-doubt (BOD) scoring: a sequencing-based method for SNP candidate assessment from high to medium read number data sets.

Sedlazeck FJ, Talloji P, von Haeseler A, Bachmair A.

Genomics. 2013 Mar;101(3):204-9. doi: 10.1016/j.ygeno.2012.12.001. Epub 2012 Dec 12.

32.

Advanced methylome analysis after bisulfite deep sequencing: an example in Arabidopsis.

Dinh HQ, Dubin M, Sedlazeck FJ, Lettner N, Mittelsten Scheid O, von Haeseler A.

PLoS One. 2012;7(7):e41528. doi: 10.1371/journal.pone.0041528. Epub 2012 Jul 20.

33.

Adenosine deaminases that act on RNA induce reproducible changes in abundance and sequence of embryonic miRNAs.

Vesely C, Tauber S, Sedlazeck FJ, von Haeseler A, Jantsch MF.

Genome Res. 2012 Aug;22(8):1468-76. doi: 10.1101/gr.133025.111. Epub 2012 Feb 6.

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