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ASHLEYS: automated quality control for single-cell Strand-seq data.
Gros C, Sanders AD, Korbel JO, Marschall T, Ebert P. Gros C, et al. Among authors: marschall t. Bioinformatics. 2021 Oct 11;37(19):3356-3357. doi: 10.1093/bioinformatics/btab221. Bioinformatics. 2021. PMID: 33792647 Free PMC article.
A framework for the detection of de novo mutations in family-based sequencing data.
Francioli LC, Cretu-Stancu M, Garimella KV, Fromer M, Kloosterman WP; Genome of the Netherlands consortium; Samocha KE, Neale BM, Daly MJ, Banks E, DePristo MA, de Bakker PI. Francioli LC, et al. Eur J Hum Genet. 2017 Feb;25(2):227-233. doi: 10.1038/ejhg.2016.147. Epub 2016 Nov 23. Eur J Hum Genet. 2017. PMID: 27876817 Free PMC article.
Repeat- and error-aware comparison of deletions.
Wittler R, Marschall T, Schönhuth A, Mäkinen V. Wittler R, et al. Among authors: marschall t. Bioinformatics. 2015 Sep 15;31(18):2947-54. doi: 10.1093/bioinformatics/btv304. Epub 2015 May 15. Bioinformatics. 2015. PMID: 25979471
AVAILABILITY AND IMPLEMENTATION: Implementation is open source and available from https://bitbucket.org/readdi/readdi CONTACT: roland.wittler@uni-bielefeld.de or t.marschall@mpi-inf.mpg.de SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics …
AVAILABILITY AND IMPLEMENTATION: Implementation is open source and available from https://bitbucket.org/readdi/readdi CONTACT: roland.wittle …
Computational pan-genomics: status, promises and challenges.
Computational Pan-Genomics Consortium. Computational Pan-Genomics Consortium. Brief Bioinform. 2018 Jan 1;19(1):118-135. doi: 10.1093/bib/bbw089. Brief Bioinform. 2018. PMID: 27769991 Free PMC article. Review.
Genotyping inversions and tandem duplications.
Ebler J, Schönhuth A, Marschall T. Ebler J, et al. Among authors: marschall t. Bioinformatics. 2017 Dec 15;33(24):4015-4023. doi: 10.1093/bioinformatics/btx020. Bioinformatics. 2017. PMID: 28169394
AVAILABILITY AND IMPLEMENTATION: https://bitbucket.org/jana_ebler/digtyper.git. CONTACT: t.marschall@mpi-inf.mpg.de. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online....
AVAILABILITY AND IMPLEMENTATION: https://bitbucket.org/jana_ebler/digtyper.git. CONTACT: t.marschall@mpi-inf.mpg.de. SUPPLEMEN …
Bit-parallel sequence-to-graph alignment.
Rautiainen M, Mäkinen V, Marschall T. Rautiainen M, et al. Among authors: marschall t. Bioinformatics. 2019 Oct 1;35(19):3599-3607. doi: 10.1093/bioinformatics/btz162. Bioinformatics. 2019. PMID: 30851095 Free PMC article.
Multi-platform discovery of haplotype-resolved structural variation in human genomes.
Chaisson MJP, Sanders AD, Zhao X, Malhotra A, Porubsky D, Rausch T, Gardner EJ, Rodriguez OL, Guo L, Collins RL, Fan X, Wen J, Handsaker RE, Fairley S, Kronenberg ZN, Kong X, Hormozdiari F, Lee D, Wenger AM, Hastie AR, Antaki D, Anantharaman T, Audano PA, Brand H, Cantsilieris S, Cao H, Cerveira E, Chen C, Chen X, Chin CS, Chong Z, Chuang NT, Lambert CC, Church DM, Clarke L, Farrell A, Flores J, Galeev T, Gorkin DU, Gujral M, Guryev V, Heaton WH, Korlach J, Kumar S, Kwon JY, Lam ET, Lee JE, Lee J, Lee WP, Lee SP, Li S, Marks P, Viaud-Martinez K, Meiers S, Munson KM, Navarro FCP, Nelson BJ, Nodzak C, Noor A, Kyriazopoulou-Panagiotopoulou S, Pang AWC, Qiu Y, Rosanio G, Ryan M, Stütz A, Spierings DCJ, Ward A, Welch AE, Xiao M, Xu W, Zhang C, Zhu Q, Zheng-Bradley X, Lowy E, Yakneen S, McCarroll S, Jun G, Ding L, Koh CL, Ren B, Flicek P, Chen K, Gerstein MB, Kwok PY, Lansdorp PM, Marth GT, Sebat J, Shi X, Bashir A, Ye K, Devine SE, Talkowski ME, Mills RE, Marschall T, Korbel JO, Eichler EE, Lee C. Chaisson MJP, et al. Among authors: marschall t. Nat Commun. 2019 Apr 16;10(1):1784. doi: 10.1038/s41467-018-08148-z. Nat Commun. 2019. PMID: 30992455 Free PMC article.
131 results