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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. Wenger AM, et al. Among authors: marschall t. Nat Biotechnol. 2019 Oct;37(10):1155-1162. doi: 10.1038/s41587-019-0217-9. Epub 2019 Aug 12. Nat Biotechnol. 2019. PMID: 31406327 Free PMC article.
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.
Viral quasispecies assembly via maximal clique enumeration.
Töpfer A, Marschall T, Bull RA, Luciani F, Schönhuth A, Beerenwinkel N. Töpfer A, et al. Among authors: marschall t. PLoS Comput Biol. 2014 Mar 27;10(3):e1003515. doi: 10.1371/journal.pcbi.1003515. eCollection 2014 Mar. PLoS Comput Biol. 2014. PMID: 24675810 Free PMC article.
Read-based phasing of related individuals.
Garg S, Martin M, Marschall T. Garg S, et al. Among authors: marschall t. Bioinformatics. 2016 Jun 15;32(12):i234-i242. doi: 10.1093/bioinformatics/btw276. Bioinformatics. 2016. PMID: 27307622 Free PMC article.
AVAILABILITY AND IMPLEMENTATION: https://bitbucket.org/whatshap/whatshap CONTACT: t.marschall@mpi-inf.mpg.de....
AVAILABILITY AND IMPLEMENTATION: https://bitbucket.org/whatshap/whatshap CONTACT: t.marschall@mpi-inf.mpg.de....
A high-quality human reference panel reveals the complexity and distribution of genomic structural variants.
Hehir-Kwa JY, Marschall T, Kloosterman WP, Francioli LC, Baaijens JA, Dijkstra LJ, Abdellaoui A, Koval V, Thung DT, Wardenaar R, Renkens I, Coe BP, Deelen P, de Ligt J, Lameijer EW, van Dijk F, Hormozdiari F; Genome of the Netherlands Consortium; Uitterlinden AG, van Duijn CM, Eichler EE, de Bakker PI, Swertz MA, Wijmenga C, van Ommen GB, Slagboom PE, Boomsma DI, Schönhuth A, Ye K, Guryev V. Hehir-Kwa JY, et al. Among authors: marschall t. Nat Commun. 2016 Oct 6;7:12989. doi: 10.1038/ncomms12989. Nat Commun. 2016. PMID: 27708267 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.
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 …
Mapping and phasing of structural variation in patient genomes using nanopore sequencing.
Cretu Stancu M, van Roosmalen MJ, Renkens I, Nieboer MM, Middelkamp S, de Ligt J, Pregno G, Giachino D, Mandrile G, Espejo Valle-Inclan J, Korzelius J, de Bruijn E, Cuppen E, Talkowski ME, Marschall T, de Ridder J, Kloosterman WP. Cretu Stancu M, et al. Among authors: marschall t. Nat Commun. 2017 Nov 6;8(1):1326. doi: 10.1038/s41467-017-01343-4. Nat Commun. 2017. PMID: 29109544 Free PMC article.
131 results