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Pangenome Graphs.
Eizenga JM, Novak AM, Sibbesen JA, Heumos S, Ghaffaari A, Hickey G, Chang X, Seaman JD, Rounthwaite R, Ebler J, Rautiainen M, Garg S, Paten B, Marschall T, Sirén J, Garrison E. Eizenga JM, et al. Among authors: marschall t. Annu Rev Genomics Hum Genet. 2020 Aug 31;21:139-162. doi: 10.1146/annurev-genom-120219-080406. Epub 2020 May 26. Annu Rev Genomics Hum Genet. 2020. PMID: 32453966 Free PMC article. Review.
Assembly of 43 human Y chromosomes reveals extensive complexity and variation.
Hallast P, Ebert P, Loftus M, Yilmaz F, Audano PA, Logsdon GA, Bonder MJ, Zhou W, Höps W, Kim K, Li C, Hoyt SJ, Dishuck PC, Porubsky D, Tsetsos F, Kwon JY, Zhu Q, Munson KM, Hasenfeld P, Harvey WT, Lewis AP, Kordosky J, Hoekzema K; Human Genome Structural Variation Consortium (HGSVC); O'Neill RJ, Korbel JO, Tyler-Smith C, Eichler EE, Shi X, Beck CR, Marschall T, Konkel MK, Lee C. Hallast P, et al. Among authors: marschall t. Nature. 2023 Sep;621(7978):355-364. doi: 10.1038/s41586-023-06425-6. Epub 2023 Aug 23. Nature. 2023. PMID: 37612510 Free PMC article.
Functional analysis of structural variants in single cells using Strand-seq.
Jeong H, Grimes K, Rauwolf KK, Bruch PM, Rausch T, Hasenfeld P, Benito E, Roider T, Sabarinathan R, Porubsky D, Herbst SA, Erarslan-Uysal B, Jann JC, Marschall T, Nowak D, Bourquin JP, Kulozik AE, Dietrich S, Bornhauser B, Sanders AD, Korbel JO. Jeong H, et al. Among authors: marschall t. Nat Biotechnol. 2023 Jun;41(6):832-844. doi: 10.1038/s41587-022-01551-4. Epub 2022 Nov 24. Nat Biotechnol. 2023. PMID: 36424487 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....
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 …
A graph-based approach to diploid genome assembly.
Garg S, Rautiainen M, Novak AM, Garrison E, Durbin R, Marschall T. Garg S, et al. Among authors: marschall t. Bioinformatics. 2018 Jul 1;34(13):i105-i114. doi: 10.1093/bioinformatics/bty279. Bioinformatics. 2018. PMID: 29949989 Free PMC article.
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.
Haplotype-aware diplotyping from noisy long reads.
Ebler J, Haukness M, Pesout T, Marschall T, Paten B. Ebler J, et al. Among authors: marschall t. Genome Biol. 2019 Jun 3;20(1):116. doi: 10.1186/s13059-019-1709-0. Genome Biol. 2019. PMID: 31159868 Free PMC article.
131 results