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ORCIDTobias Marschall
Person information
- affiliation: Heinrich Heine University Düsseldorf, Germany
- affiliation: Saarland University, Center for Bioinformatics, Saarbrücken, Germany
- affiliation: Max Planck Institute for Informatics, Saarbrücken, Germany
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Books and Theses
- 2011
[b1]Tobias Marschall:
Algorithms and statistical methods for exact motif discovery. Dortmund University of Technology, 2011
Journal Articles
- 2023
- [j26]Konstantinn Bonnet, Tobias Marschall, Daniel Doerr:
Constructing founder sets under allelic and non-allelic homologous recombination. Algorithms Mol. Biol. 18(1): 15 (2023) - [j25]Konstantinn Bonnet, Tobias Marschall, Daniel Doerr:
Correction: Constructing founder sets under allelic and non-allelic homologous recombination. Algorithms Mol. Biol. 18(1): 20 (2023) - 2022
- [j24]Fawaz Dabbaghie
, Jana Ebler, Tobias Marschall:
BubbleGun: enumerating bubbles and superbubbles in genome graphs. Bioinform. 38(17): 4217-4219 (2022) - 2021
- [j23]Mikko Rautiainen, Tobias Marschall:
MBG: Minimizer-based sparse de Bruijn Graph construction. Bioinform. 37(16): 2476-2478 (2021) - [j22]Christina Gros, Ashley D. Sanders, Jan O. Korbel, Tobias Marschall, Peter Ebert:
ASHLEYS: automated quality control for single-cell Strand-seq data. Bioinform. 37(19): 3356-3357 (2021) - 2020
- [j21]Shounak Chakraborty, Stefan Canzar, Tobias Marschall, Marcel H. Schulz:
Chromatyping: Reconstructing Nucleosome Profiles from NOMe Sequencing Data. J. Comput. Biol. 27(3): 330-341 (2020) - 2019
- [j20]Ali Ghaffaari, Tobias Marschall:
Fully-sensitive seed finding in sequence graphs using a hybrid index. Bioinform. 35(14): i81-i89 (2019) - [j19]Mikko Rautiainen, Veli Mäkinen, Tobias Marschall:
Bit-parallel sequence-to-graph alignment. Bioinform. 35(19): 3599-3607 (2019) - 2018
- [j18]Shilpa Garg, Mikko Rautiainen, Adam M. Novak, Erik Garrison, Richard Durbin, Tobias Marschall:
A graph-based approach to diploid genome assembly. Bioinform. 34(13): i105-i114 (2018) - [j17]Maryam Ghareghani, David Porubsky, Ashley D. Sanders, Sascha Meiers, Evan E. Eichler, Jan O. Korbel, Tobias Marschall:
Strand-seq enables reliable separation of long reads by chromosome via expectation maximization. Bioinform. 34(13): i115-i123 (2018) - 2017
- [j16]Jana Ebler, Alexander Schönhuth, Tobias Marschall:
Genotyping inversions and tandem duplications. Bioinform. 33(24): 4015-4023 (2017) - 2016
- [j15]Shilpa Garg, Marcel Martin, Tobias Marschall:
Read-based phasing of related individuals. Bioinform. 32(12): 234-242 (2016) - [j14]Kathrin Trappe, Tobias Marschall, Bernhard Y. Renard:
Detecting horizontal gene transfer by mapping sequencing reads across species boundaries. Bioinform. 32(17): 595-604 (2016) - [j13]Andrea Bracciali, Marco Aldinucci, Murray Patterson, Tobias Marschall, Nadia Pisanti, Ivan Merelli, Massimo Torquati:
PWHATSHAP: efficient haplotyping for future generation sequencing. BMC Bioinform. 17(S-11): 342 (2016) - 2015
- [j12]Roland Wittler, Tobias Marschall, Alexander Schönhuth, Veli Mäkinen:
Repeat- and error-aware comparison of deletions. Bioinform. 31(18): 2947-2954 (2015) - [j11]Robin Cijvat, Stefan Manegold, Martin L. Kersten, Gunnar W. Klau, Alexander Schönhuth, Tobias Marschall, Ying Zhang:
Genome sequence analysis with MonetDB - A case study on Ebola virus diversity. Datenbank-Spektrum 15(3): 185-191 (2015) - [j10]Murray Patterson, Tobias Marschall, Nadia Pisanti, Leo van Iersel, Leen Stougie, Gunnar W. Klau, Alexander Schönhuth:
WhatsHap: Weighted Haplotype Assembly for Future-Generation Sequencing Reads. J. Comput. Biol. 22(6): 498-509 (2015) - 2014
- [j9]Armin Töpfer, Tobias Marschall, Rowena A. Bull, Fabio Luciani, Alexander Schönhuth, Niko Beerenwinkel:
Viral Quasispecies Assembly via Maximal Clique Enumeration. PLoS Comput. Biol. 10(3) (2014) - 2013
- [j8]Tobias Marschall, Iman Hajirasouliha, Alexander Schönhuth:
MATE-CLEVER: Mendelian-inheritance-aware discovery and genotyping of midsize and long indels. Bioinform. 29(24): 3143-3150 (2013) - [j7]Mohammed El-Kebir, Tobias Marschall, Inken Wohlers, Murray Patterson, Jaap Heringa, Alexander Schönhuth, Gunnar W. Klau:
Mapping proteins in the presence of paralogs using units of coevolution. BMC Bioinform. 14(S-15): S18 (2013) - [j6]Manuel Allhoff, Alexander Schönhuth, Marcel Martin, Ivan G. Costa, Sven Rahmann, Tobias Marschall:
Discovering motifs that induce sequencing errors. BMC Bioinform. 14(S-5): S1 (2013) - 2012
- [j5]Tobias Marschall, Ivan G. Costa, Stefan Canzar, Markus Bauer, Gunnar W. Klau, Alexander Schliep, Alexander Schönhuth:
CLEVER: clique-enumerating variant finder. Bioinform. 28(22): 2875-2882 (2012) - [j4]Tobias Marschall, Inke Herms, Hans-Michael Kaltenbach, Sven Rahmann:
Probabilistic Arithmetic Automata and Their Applications. IEEE ACM Trans. Comput. Biol. Bioinform. 9(6): 1737-1750 (2012) - 2011
- [j3]Tobias Marschall, Sven Rahmann:
An Algorithm to Compute the Character Access Count Distribution for Pattern Matching Algorithms. Algorithms 4(4): 285-306 (2011) - [j2]Tobias Marschall:
Construction of minimal deterministic finite automata from biological motifs. Theor. Comput. Sci. 412(8-10): 922-930 (2011) - 2009
- [j1]Tobias Marschall, Sven Rahmann:
Efficient exact motif discovery. Bioinform. 25(12) (2009)
Conference and Workshop Papers
- 2022
- [c13]Konstantinn Bonnet, Tobias Marschall, Daniel Doerr:
Constructing Founder Sets Under Allelic and Non-Allelic Homologous Recombination. WABI 2022: 6:1-6:23 - 2018
- [c12]Shounak Chakraborty, Stefan Canzar, Tobias Marschall, Marcel H. Schulz:
Chromatyping: Reconstructing Nucleosome Profiles from NOMe Sequencing Data. RECOMB 2018: 21-36 - 2017
- [c11]Gunnar W. Klau, Tobias Marschall:
A Guided Tour to Computational Haplotyping. CiE 2017: 50-63 - 2015
- [c10]Robin Cijvat, Stefan Manegold, Martin L. Kersten, Gunnar W. Klau, Alexander Schönhuth, Tobias Marschall, Ying Zhang:
Genome sequence analysis with monetdb: a case study on ebola virus diversity. BTW Workshops 2015: 143-150 - 2014
- [c9]Marco Aldinucci, Andrea Bracciali, Tobias Marschall, Murray Patterson, Nadia Pisanti, Massimo Torquati:
High-Performance Haplotype Assembly. CIBB 2014: 245-258 - [c8]Murray Patterson, Tobias Marschall, Nadia Pisanti, Leo van Iersel, Leen Stougie, Gunnar W. Klau, Alexander Schönhuth:
WhatsHap: Haplotype Assembly for Future-Generation Sequencing Reads. RECOMB 2014: 237-249 - [c7]Armin Töpfer, Tobias Marschall, Rowena A. Bull, Fabio Luciani, Alexander Schönhuth, Niko Beerenwinkel:
Viral Quasispecies Assembly via Maximal Clique Enumeration. RECOMB 2014: 309-310 - 2012
- [c6]Stefan Canzar, Tobias Marschall, Sven Rahmann, Chris Schwiegelshohn:
Solving the Minimum String Cover Problem. ALENEX 2012: 75-83 - 2010
- [c5]Tobias Marschall, Sven Rahmann:
Exact Analysis of Horspool's and Sunday's Pattern Matching Algorithms with Probabilistic Arithmetic Automata. LATA 2010: 439-450 - [c4]Tobias Marschall, Sven Rahmann:
Speeding Up Exact Motif Discovery by Bounding the Expected Clump Size. WABI 2010: 337-349 - 2009
- [c3]Sven Rahmann, Tobias Marschall, Frank Behler, Oliver Kramer:
Modeling evolutionary fitness for DNA motif discovery. GECCO 2009: 225-232 - 2008
- [c2]Tobias Marschall, Sven Rahmann:
Probabilistic Arithmetic Automata and Their Application to Pattern Matching Statistics. CPM 2008: 95-106 - 2006
- [c1]Thomas Plötz, Gernot A. Fink, Peter Husemann, Sven Kanies, Kai Lienemann, Tobias Marschall, Marcel Martin, Lars Schillingmann, Matthias Steinrücken, Henner Sudek:
Automatic Detection of Song Changes in Music Mixes Using Stochastic Models. ICPR (3) 2006: 665-668
Informal and Other Publications
- 2019
- [i8]David Laehnemann, Johannes Köster, Ewa Szczurek, Davis J. McCarthy, Stephanie C. Hicks, Mark D. Robinson, Catalina A. Vallejos, Niko Beerenwinkel, Kieran R. Campbell, Ahmed Mahfouz, Luca Pinello, Pavel Skums, Alexandros Stamatakis, Camille Stephan-Otto Attolini, Samuel Aparicio, Jasmijn A. Baaijens, Marleen Balvert, Buys de Barbanson, Antonio Cappuccio, Giacomo Corleone, Bas E. Dutilh, Maria Florescu, Victor Guryev, Rens Holmer, Katharina Jahn, Thamar Jessurun Lobo, Emma M. Keizer, Indu Khatri, Szymon M. Kielbasa, Jan O. Korbel, Alexey M. Kozlov, Tzu-Hao Kuo, Boudewijn P. F. Lelieveldt, Ion I. Mandoiu, John C. Marioni, Tobias Marschall, Felix Mölder, Amir Niknejad, Lukasz Raczkowski, Marcel J. T. Reinders, Jeroen de Ridder, Antoine-Emmanuel Saliba, Antonios Somarakis, Oliver Stegle, Fabian J. Theis, Huan Yang, Alex Zelikovsky, Alice C. McHardy, Benjamin J. Raphael, Sohrab P. Shah, Alexander Schönhuth:
12 Grand Challenges in Single-Cell Data Science. PeerJ Prepr. 7: e27885 (2019) - 2016
- [i7]Tobias Marschall, Noemi E. Passing:
Representing Pattern Matching Algorithms by Polynomial-Size Automata. CoRR abs/1607.00138 (2016) - [i6]Alexander Schönhuth, Tobias Marschall:
Eliminating Blind Spots in Genetic Variant Discovery. ERCIM News 2016(104) (2016) - 2015
- [i5]Thomas Bellitto, Tobias Marschall, Alexander Schönhuth, Gunnar W. Klau:
Next generation cluster editing. PeerJ Prepr. 3: e1301 (2015) - 2013
- [i4]Thomas Bellitto, Tobias Marschall, Alexander Schönhuth, Gunnar W. Klau:
Next Generation Cluster Editing. CoRR abs/1310.3353 (2013) - 2010
- [i3]Tobias Marschall:
Construction of minimal DFAs from biological motifs. CoRR abs/1004.1298 (2010) - [i2]Tobias Marschall, Sven Rahmann:
Exact Analysis of Pattern Matching Algorithms with Probabilistic Arithmetic Automata. CoRR abs/1009.6114 (2010) - [i1]Tobias Marschall, Inke Herms, Hans-Michael Kaltenbach, Sven Rahmann:
Probabilistic Arithmetic Automata and their Applications. CoRR abs/1011.5778 (2010)
Coauthor Index
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