Publications by authors named "Tobias Marschall"

41Publications

GraphAligner: rapid and versatile sequence-to-graph alignment.

Genome Biol 2020 Sep 24;21(1):253. Epub 2020 Sep 24.

Heinrich Heine University Düsseldorf, Medical Faculty, Institute for Medical Biometry and Bioinformatics, Moorenstraße 5, Düsseldorf, 40225, Germany.

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http://dx.doi.org/10.1186/s13059-020-02157-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7513500PMC
September 2020

Haplotype threading: accurate polyploid phasing from long reads.

Genome Biol 2020 Sep 21;21(1):252. Epub 2020 Sep 21.

Algorithmic Bioinformatics, Heinrich Heine University Düsseldorf, Universitätsstr. 1, Düsseldorf, 40225, Germany.

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http://dx.doi.org/10.1186/s13059-020-02158-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7504856PMC
September 2020

Pangenome Graphs.

Annu Rev Genomics Hum Genet 2020 Aug 26;21:139-162. Epub 2020 May 26.

Genomics Institute, University of California, Santa Cruz, California 95064, USA; email:

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http://dx.doi.org/10.1146/annurev-genom-120219-080406DOI Listing
August 2020

Chromatyping: Reconstructing Nucleosome Profiles from NOMe Sequencing Data.

J Comput Biol 2020 03;27(3):330-341

Cluster of Excellence for Multimodal Computing and Interaction, Saarland University, Saarland Informatics Campus E1.7, Saarbrücken, Germany.

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http://dx.doi.org/10.1089/cmb.2019.0457DOI Listing
March 2020

Fully-sensitive seed finding in sequence graphs using a hybrid index.

Bioinformatics 2019 07;35(14):i81-i89

Center for Bioinformatics, Saarland University, Saarbrücken, Germany.

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http://dx.doi.org/10.1093/bioinformatics/btz341DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6612829PMC
July 2019

Haplotype-aware diplotyping from noisy long reads.

Genome Biol 2019 06 3;20(1):116. Epub 2019 Jun 3.

UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, 95064, CA, USA.

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http://dx.doi.org/10.1186/s13059-019-1709-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6547545PMC
June 2019

Multi-platform discovery of haplotype-resolved structural variation in human genomes.

Nat Commun 2019 04 16;10(1):1784. Epub 2019 Apr 16.

The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA.

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http://www.nature.com/articles/s41467-018-08148-z
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http://dx.doi.org/10.1038/s41467-018-08148-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6467913PMC
April 2019

Bit-parallel sequence-to-graph alignment.

Bioinformatics 2019 10;35(19):3599-3607

Center for Bioinformatics, Saarland University, Saarland Informatics Campus E2.1, 66123 Saarbrücken, Germany.

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http://dx.doi.org/10.1093/bioinformatics/btz162DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6761980PMC
October 2019

A graph-based approach to diploid genome assembly.

Bioinformatics 2018 07;34(13):i105-i114

Center for Bioinformatics, Saarland University, Saarland Informatics Campus E2.1, Saarbrücken, Germany.

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https://academic.oup.com/bioinformatics/article/34/13/i105/5
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http://dx.doi.org/10.1093/bioinformatics/bty279DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6022571PMC
July 2018

Dense and accurate whole-chromosome haplotyping of individual genomes.

Nat Commun 2017 11 3;8(1):1293. Epub 2017 Nov 3.

Center for Bioinformatics, Saarland University, Saarland Informatics Campus E2.1, 66123, Saarbrücken, Germany.

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http://dx.doi.org/10.1038/s41467-017-01389-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5670131PMC
November 2017

PWHATSHAP: efficient haplotyping for future generation sequencing.

BMC Bioinformatics 2016 Sep 22;17(Suppl 11):342. Epub 2016 Sep 22.

Department of Computer Science, University of Pisa, Pisa, Italy.

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http://dx.doi.org/10.1186/s12859-016-1170-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5046197PMC
September 2016

Genotyping inversions and tandem duplications.

Bioinformatics 2017 Dec;33(24):4015-4023

Center for Bioinformatics, Saarland University, Saarbrücken, Germany.

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http://dx.doi.org/10.1093/bioinformatics/btx020DOI Listing
December 2017

Detecting horizontal gene transfer by mapping sequencing reads across species boundaries.

Bioinformatics 2016 09;32(17):i595-i604

Robert Koch Institute, Research Group Bioinformatics (NG4), 13353 Berlin, Germany.

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http://dx.doi.org/10.1093/bioinformatics/btw423DOI Listing
September 2016

Read-based phasing of related individuals.

Bioinformatics 2016 06;32(12):i234-i242

Center for Bioinformatics, Saarland University, Saarbrücken, Germany Max Planck Institute for Informatics, Saarbrücken, Germany.

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http://dx.doi.org/10.1093/bioinformatics/btw276DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4908360PMC
June 2016

Repeat- and error-aware comparison of deletions.

Bioinformatics 2015 Sep 15;31(18):2947-54. Epub 2015 May 15.

Genome Informatics, Faculty of Technology and Center for Biotechnology (CeBiTec), Bielefeld University, Germany, Center for Bioinformatics, Saarland University and Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarbrücken, Germany, Centrum Wiskunde & Informatica (CWI), Life Sciences Group, Amsterdam, The Netherlands and Helsinki Institute for Information Technology (HIIT), Department of Computer Science, University of Helsinki, Finland.

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http://dx.doi.org/10.1093/bioinformatics/btv304DOI Listing
September 2015

WhatsHap: Weighted Haplotype Assembly for Future-Generation Sequencing Reads.

J Comput Biol 2015 Jun 6;22(6):498-509. Epub 2015 Feb 6.

6VU University, Amsterdam, The Netherlands.

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http://dx.doi.org/10.1089/cmb.2014.0157DOI Listing
June 2015

Viral quasispecies assembly via maximal clique enumeration.

PLoS Comput Biol 2014 Mar 27;10(3):e1003515. Epub 2014 Mar 27.

Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland; SIB Swiss Institute of Bioinformatics, Basel, Switzerland.

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http://dx.doi.org/10.1371/journal.pcbi.1003515DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3967922PMC
March 2014

MATE-CLEVER: Mendelian-inheritance-aware discovery and genotyping of midsize and long indels.

Bioinformatics 2013 Dec 25;29(24):3143-50. Epub 2013 Sep 25.

Centrum Wiskunde & Informatica (CWI), Life Sciences Group, Science Park 123, Amsterdam 1098 XG, The Netherlands and Department of Computer Science and Brown University, Providence, Rhode Island 02906, USA.

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http://dx.doi.org/10.1093/bioinformatics/btt556DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3842759PMC
December 2013

Discovering motifs that induce sequencing errors.

BMC Bioinformatics 2013 10;14 Suppl 5:S1. Epub 2013 Apr 10.

Life Sciences Group, Centrum Wiskunde & Informatica, Amsterdam, Netherlands.

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http://dx.doi.org/10.1186/1471-2105-14-S5-S1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3622629PMC
December 2013

Identifying transcriptional miRNA biomarkers by integrating high-throughput sequencing and real-time PCR data.

Methods 2013 Jan 23;59(1):154-63. Epub 2012 Oct 23.

Bioinformatics, Computer Science XI, TU Dortmund, Germany; Collaborative Research Center (SFB) 876, TU Dortmund, Germany.

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http://dx.doi.org/10.1016/j.ymeth.2012.10.005DOI Listing
January 2013

CLEVER: clique-enumerating variant finder.

Bioinformatics 2012 Nov 11;28(22):2875-82. Epub 2012 Oct 11.

Centrum Wiskunde & Informatica, Life Sciences Group, Amsterdam, The Netherlands.

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http://bioinformatics.oxfordjournals.org/content/early/2012/
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http://bioinformatics.oxfordjournals.org/cgi/doi/10.1093/bio
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http://dx.doi.org/10.1093/bioinformatics/bts566DOI Listing
November 2012

Probabilistic arithmetic automata and their applications.

IEEE/ACM Trans Comput Biol Bioinform 2012 Nov-Dec;9(6):1737-50

Life Sciences Group, Centrum Wiskunde & Informatica (CWI), Science Park 123, 1098 XG Amsterdam, TheNetherlands.

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http://ieeexplore.ieee.org/document/6257364/
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http://dx.doi.org/10.1109/TCBB.2012.109DOI Listing
July 2013

Efficient exact motif discovery.

Bioinformatics 2009 Jun;25(12):i356-64

Computer Science Department, Bioinformatics for High-Throughput Technologies at the Chair of Algorithm Engineering, TU Dortmund, Dortmund, Germany.

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https://academic.oup.com/bioinformatics/article-lookup/doi/1
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http://dx.doi.org/10.1093/bioinformatics/btp188DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2687942PMC
June 2009