DiVerG: Scalable Distance Index for Validation of Paired-End Alignments in Sequence Graphs.

Tobias Marschall http://mpi-inf.mpg.de/~marschal https://scholar.google.com/citations?user=erp_AUwAAAAJ https://orcid.org/0000-0002-9376-1030 https://www.wikidata.org/entity/Q47133848 Heinrich Heine University Düsseldorf, Germany Saarland University, Center for Bioinformatics, Saarbrücken, Germany Max Planck Institute for Informatics, Saarbrücken, Germany Ali Ghaffaari Alexander Schönhuth Tobias Marschall DiVerG: Scalable Distance Index for Validation of Paired-End Alignments in Sequence Graphs. 10:1-10:24 2025 WABI https://doi.org/10.4230/LIPIcs.WABI.2025.10 conf/wabi/2025 db/conf/wabi/wabi2025.html#GhaffaariSM25

Luca Parmigiani Erik Garrison Jens Stoye Tobias Marschall Daniel Doerr Panacus: fast and exact pangenome growth and core size estimation. 2024 40 Bioinform. 12 https://doi.org/10.1093/bioinformatics/btae720 db/journals/bioinformatics/bioinformatics40.html#ParmigianiGSMD24

Konstantinn Bonnet Tobias Marschall Daniel Doerr Constructing founder sets under allelic and non-allelic homologous recombination. 15 2023 December 18 Algorithms Mol. Biol. 1 https://doi.org/10.1186/s13015-023-00241-3 db/journals/almob/almob18.html#BonnetMD23

Konstantinn Bonnet Tobias Marschall Daniel Doerr Correction: Constructing founder sets under allelic and non-allelic homologous recombination. 20 2023 December 18 Algorithms Mol. Biol. 1 https://doi.org/10.1186/s13015-023-00244-0 db/journals/almob/almob18.html#BonnetMD23a

Fawaz Dabbaghie Jana Ebler Tobias Marschall BubbleGun: enumerating bubbles and superbubbles in genome graphs. 4217-4219 2022 38 Bioinform. 17 https://doi.org/10.1093/bioinformatics/btac448 db/journals/bioinformatics/bioinformatics38.html#DabbaghieEM22

Konstantinn Bonnet Tobias Marschall Daniel Doerr Constructing Founder Sets Under Allelic and Non-Allelic Homologous Recombination. 6:1-6:23 2022 WABI https://doi.org/10.4230/LIPIcs.WABI.2022.6 conf/wabi/2022 db/conf/wabi/wabi2022.html#BonnetMD22

Mikko Rautiainen Tobias Marschall MBG: Minimizer-based sparse de Bruijn Graph construction. 2476-2478 2021 37 Bioinform. 16 https://doi.org/10.1093/bioinformatics/btab004 db/journals/bioinformatics/bioinformatics37.html#RautiainenM21

Christina Gros Ashley D. Sanders Jan O. Korbel Tobias Marschall Peter Ebert ASHLEYS: automated quality control for single-cell Strand-seq data. 3356-3357 2021 37 Bioinform. 19 https://doi.org/10.1093/bioinformatics/btab221 db/journals/bioinformatics/bioinformatics37.html#GrosSKME21

Shounak Chakraborty 0003 Stefan Canzar Tobias Marschall Marcel H. Schulz Chromatyping: Reconstructing Nucleosome Profiles from NOMe Sequencing Data. 330-341 2020 27 J. Comput. Biol. 3 https://doi.org/10.1089/cmb.2019.0457 https://www.wikidata.org/entity/Q90234919 db/journals/jcb/jcb27.html#0003CMS20

Ali Ghaffaari Tobias Marschall Fully-sensitive seed finding in sequence graphs using a hybrid index. i81-i89 2019 35 Bioinform. 14 https://doi.org/10.1093/bioinformatics/btz341 https://www.wikidata.org/entity/Q90064820 db/journals/bioinformatics/bioinformatics35.html#GhaffaariM19

Mikko Rautiainen Veli Mäkinen Tobias Marschall Bit-parallel sequence-to-graph alignment. 3599-3607 2019 35 Bioinform. 19 https://doi.org/10.1093/bioinformatics/btz162 https://www.wikidata.org/entity/Q92239384 db/journals/bioinformatics/bioinformatics35.html#RautiainenMM19

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 0001 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. e27885 2019 7 PeerJ Prepr. https://doi.org/10.7287/peerj.preprints.27885v3 db/journals/peerjpre/peerjpre7.html#LaehnemannKSMHR19

Shilpa Garg Mikko Rautiainen Adam M. Novak Erik Garrison Richard Durbin Tobias Marschall A graph-based approach to diploid genome assembly. i105-i114 2018 34 Bioinform. 13 https://doi.org/10.1093/bioinformatics/bty279 https://www.wikidata.org/entity/Q55514124 db/journals/bioinformatics/bioinformatics34.html#GargRNGDM18

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. i115-i123 2018 34 Bioinform. 13 https://doi.org/10.1093/bioinformatics/bty290 https://www.wikidata.org/entity/Q55514097 db/journals/bioinformatics/bioinformatics34.html#GhareghaniPSMEK18

Shounak Chakraborty 0003 Stefan Canzar Tobias Marschall Marcel H. Schulz Chromatyping: Reconstructing Nucleosome Profiles from NOMe Sequencing Data. 21-36 2018 RECOMB https://doi.org/10.1007/978-3-319-89929-9_2 conf/recomb/2018 db/conf/recomb/recomb2018.html#ChakrabortyCMS18

Jana Ebler Alexander Schönhuth Tobias Marschall Genotyping inversions and tandem duplications. 4015-4023 2017 33 Bioinform. 24 https://doi.org/10.1093/bioinformatics/btx020 https://www.wikidata.org/entity/Q38974550 db/journals/bioinformatics/bioinformatics33.html#EblerSM17

Gunnar W. Klau Tobias Marschall A Guided Tour to Computational Haplotyping. 50-63 2017 CiE https://doi.org/10.1007/978-3-319-58741-7_6 conf/cie/2017 db/conf/cie/cie2017.html#KlauM17

Shilpa Garg Marcel Martin Tobias Marschall Read-based phasing of related individuals. 234-242 2016 32 Bioinform. 12 https://doi.org/10.1093/bioinformatics/btw276 https://www.wikidata.org/entity/Q39679905 db/journals/bioinformatics/bioinformatics32.html#GargMM16

Kathrin Trappe Tobias Marschall Bernhard Y. Renard Detecting horizontal gene transfer by mapping sequencing reads across species boundaries. 595-604 2016 32 Bioinform. 17 https://doi.org/10.1093/bioinformatics/btw423 https://www.wikidata.org/entity/Q39429363 db/journals/bioinformatics/bioinformatics32.html#TrappeMR16

Andrea Bracciali Marco Aldinucci Murray Patterson Tobias Marschall Nadia Pisanti Ivan Merelli Massimo Torquati PWHATSHAP: efficient haplotyping for future generation sequencing. 342 2016 17 BMC Bioinform. S-11 https://doi.org/10.1186/s12859-016-1170-y https://www.wikidata.org/entity/Q37303784 db/journals/bmcbi/bmcbi17S.html#BraccialiAPMPMT16

Tobias Marschall Noemi E. Passing Representing Pattern Matching Algorithms by Polynomial-Size Automata. 2016 abs/1607.00138 CoRR http://arxiv.org/abs/1607.00138 db/journals/corr/corr1607.html#MarschallP16

Alexander Schönhuth Tobias Marschall Eliminating Blind Spots in Genetic Variant Discovery. 2016 2016 ERCIM News 104 http://ercim-news.ercim.eu/en104/special/eliminating-blind-spots-in-genetic-variant-discovery db/journals/ercim/ercim2016.html#SchonhuthM16

Roland Wittler Tobias Marschall Alexander Schönhuth Veli Mäkinen Repeat- and error-aware comparison of deletions. 2947-2954 2015 31 Bioinform. 18 https://doi.org/10.1093/bioinformatics/btv304 https://www.wikidata.org/entity/Q40934428 db/journals/bioinformatics/bioinformatics31.html#WittlerMSM15

Robin Cijvat Stefan Manegold Martin L. Kersten Gunnar W. Klau Alexander Schönhuth Tobias Marschall Ying Zhang 0027 Genome sequence analysis with MonetDB - A case study on Ebola virus diversity. 185-191 2015 15 Datenbank-Spektrum 3 https://doi.org/10.1007/s13222-015-0198-x db/journals/dbsk/dbsk15.html#CijvatMKKSMZ15

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. 498-509 2015 22 J. Comput. Biol. 6 https://doi.org/10.1089/cmb.2014.0157 https://www.wikidata.org/entity/Q39042392 db/journals/jcb/jcb22.html#PattersonMPISKS15

Robin Cijvat Stefan Manegold Martin L. Kersten Gunnar W. Klau Alexander Schönhuth Tobias Marschall Ying Zhang 0027 Genome sequence analysis with monetdb: a case study on ebola virus diversity. 143-150 2015 BTW Workshops https://dl.gi.de/handle/20.500.12116/2378 conf/btw/2015w db/conf/btw/btw2015w.html#CijvatMKKSMZ15

Thomas Bellitto Tobias Marschall Alexander Schönhuth Gunnar W. Klau Next generation cluster editing. e1301 2015 3 PeerJ Prepr. https://doi.org/10.7287/peerj.preprints.1301v1 db/journals/peerjpre/peerjpre3.html#BellittoMSK15

Armin Töpfer Tobias Marschall Rowena A. Bull Fabio Luciani Alexander Schönhuth Niko Beerenwinkel Viral Quasispecies Assembly via Maximal Clique Enumeration. 2014 10 PLoS Comput. Biol. 3 https://doi.org/10.1371/journal.pcbi.1003515 https://www.wikidata.org/entity/Q28541589 db/journals/ploscb/ploscb10.html#TopferMBLSB14

Marco Aldinucci Andrea Bracciali Tobias Marschall Murray Patterson Nadia Pisanti Massimo Torquati High-Performance Haplotype Assembly. 245-258 2014 CIBB https://doi.org/10.1007/978-3-319-24462-4_21 https://www.wikidata.org/entity/Q62046283 conf/cibb/2014 db/conf/cibb/cibb2014.html#AldinucciBMPPT14 Murray Patterson Tobias Marschall Nadia Pisanti Leo van Iersel Leen Stougie Gunnar W. Klau Alexander Schönhuth WhatsHap: Haplotype Assembly for Future-Generation Sequencing Reads. 237-249 2014 RECOMB https://doi.org/10.1007/978-3-319-05269-4_19 conf/recomb/2014 db/conf/recomb/recomb2014.html#PattersonMPISKS14 Armin Töpfer Tobias Marschall Rowena A. Bull Fabio Luciani Alexander Schönhuth Niko Beerenwinkel Viral Quasispecies Assembly via Maximal Clique Enumeration. 309-310 2014 RECOMB https://doi.org/10.1007/978-3-319-05269-4_25 conf/recomb/2014 db/conf/recomb/recomb2014.html#TopferMBLSB14

Tobias Marschall Iman Hajirasouliha Alexander Schönhuth MATE-CLEVER: Mendelian-inheritance-aware discovery and genotyping of midsize and long indels. 3143-3150 2013 29 Bioinform. 24 https://doi.org/10.1093/bioinformatics/btt556 https://www.wikidata.org/entity/Q30558007 db/journals/bioinformatics/bioinformatics29.html#MarschallHS13

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. S18 2013 14 BMC Bioinform. S-15 https://doi.org/10.1186/1471-2105-14-S15-S18 https://www.wikidata.org/entity/Q35101729 db/journals/bmcbi/bmcbi14S.html#El-KebirMWPHSK13

Manuel Allhoff Alexander Schönhuth Marcel Martin Ivan G. Costa Sven Rahmann Tobias Marschall Discovering motifs that induce sequencing errors. S1 2013 14 BMC Bioinform. S-5 https://doi.org/10.1186/1471-2105-14-S5-S1 https://www.wikidata.org/entity/Q34756561 db/journals/bmcbi/bmcbi14S.html#AllhoffSMCRM13

Thomas Bellitto Tobias Marschall Alexander Schönhuth Gunnar W. Klau Next Generation Cluster Editing. 2013 CoRR http://arxiv.org/abs/1310.3353 abs/1310.3353 db/journals/corr/corr1310.html#BellittoMSK13

Tobias Marschall Ivan G. Costa Stefan Canzar Markus Bauer 0001 Gunnar W. Klau Alexander Schliep Alexander Schönhuth CLEVER: clique-enumerating variant finder. 2875-2882 2012 28 Bioinform. 22 https://doi.org/10.1093/bioinformatics/bts566 https://www.wikidata.org/entity/Q42672459 db/journals/bioinformatics/bioinformatics28.html#MarschallCCBKSS12

Tobias Marschall Inke Herms Hans-Michael Kaltenbach Sven Rahmann Probabilistic Arithmetic Automata and Their Applications. 1737-1750 2012 9 IEEE ACM Trans. Comput. Biol. Bioinform. 6 https://doi.org/10.1109/TCBB.2012.109 https://doi.ieeecomputersociety.org/10.1109/TCBB.2012.109 https://dl.acm.org/doi/10.1109/TCBB.2012.109 https://www.wikidata.org/entity/Q38032460 db/journals/tcbb/tcbb9.html#MarschallHKR12

Stefan Canzar Tobias Marschall Sven Rahmann Chris Schwiegelshohn Solving the Minimum String Cover Problem. 75-83 2012 ALENEX https://doi.org/10.1137/1.9781611972924.8 conf/alenex/2012 db/conf/alenex/alenex2012.html#CanzarMRS12 Tobias Marschall Algorithms and statistical methods for exact motif discovery. 2011 Dortmund University of Technology https://hdl.handle.net/2003/27760 https://nbn-resolving.org/urn:nbn:de:101:1-201106083559 https://d-nb.info/1012572064

Tobias Marschall Sven Rahmann An Algorithm to Compute the Character Access Count Distribution for Pattern Matching Algorithms. 285-306 2011 4 Algorithms 4 https://doi.org/10.3390/a4040285 https://www.wikidata.org/entity/Q61704584 db/journals/algorithms/algorithms4.html#MarschallR11

Tobias Marschall Construction of minimal deterministic finite automata from biological motifs. 922-930 2011 412 Theor. Comput. Sci. 8-10 https://doi.org/10.1016/j.tcs.2010.12.003 db/journals/tcs/tcs412.html#Marschall11

Tobias Marschall Sven Rahmann Exact Analysis of Horspool's and Sunday's Pattern Matching Algorithms with Probabilistic Arithmetic Automata. 439-450 2010 LATA https://doi.org/10.1007/978-3-642-13089-2_37 conf/lata/2010 db/conf/lata/lata2010.html#MarschallR10 Tobias Marschall Sven Rahmann Speeding Up Exact Motif Discovery by Bounding the Expected Clump Size. 337-349 2010 WABI https://doi.org/10.1007/978-3-642-15294-8_28 conf/wabi/2010 db/conf/wabi/wabi2010.html#MarschallR10

Tobias Marschall Construction of minimal DFAs from biological motifs http://arxiv.org/abs/1004.1298 2010 CoRR abs/1004.1298 db/journals/corr/corr1004.html#abs-1004-1298

Tobias Marschall Sven Rahmann Exact Analysis of Pattern Matching Algorithms with Probabilistic Arithmetic Automata http://arxiv.org/abs/1009.6114 2010 CoRR abs/1009.6114 db/journals/corr/corr1009.html#abs-1009-6114

Tobias Marschall Inke Herms Hans-Michael Kaltenbach Sven Rahmann Probabilistic Arithmetic Automata and their Applications http://arxiv.org/abs/1011.5778 2010 CoRR abs/1011.5778 db/journals/corr/corr1011.html#abs-1011-5778

Tobias Marschall Sven Rahmann Efficient exact motif discovery. 2009 25 Bioinform. 12 https://doi.org/10.1093/bioinformatics/btp188 https://www.wikidata.org/entity/Q33455318 db/journals/bioinformatics/bioinformatics25.html#MarschallR09

Sven Rahmann Tobias Marschall Frank Behler Oliver Kramer 0001 Modeling evolutionary fitness for DNA motif discovery. 225-232 2009 GECCO https://doi.org/10.1145/1569901.1569933 https://www.wikidata.org/entity/Q61704594 conf/gecco/2009g db/conf/gecco/gecco2009.html#RahmannMBK09 Tobias Marschall Sven Rahmann Probabilistic Arithmetic Automata and Their Application to Pattern Matching Statistics. 95-106 2008 CPM https://doi.org/10.1007/978-3-540-69068-9_11 conf/cpm/2008 db/conf/cpm/cpm2008.html#MarschallR08 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. 665-668 2006 conf/icpr/2006 ICPR (3) https://doi.org/10.1109/ICPR.2006.297 https://doi.ieeecomputersociety.org/10.1109/ICPR.2006.297 https://www.wikidata.org/entity/Q61957110 db/conf/icpr/icpr2006-3.html#PlotzFHKLMMSSS06 Marco Aldinucci Manuel Allhoff Samuel Aparicio Camille Stephan-Otto Attolini Jasmijn A. Baaijens Marleen Balvert Buys de Barbanson Markus Bauer 0001 Niko Beerenwinkel Frank Behler Thomas Bellitto Konstantinn Bonnet Andrea Bracciali Rowena A. Bull Kieran R. Campbell Stefan Canzar Antonio Cappuccio Shounak Chakraborty 0003 Robin Cijvat Giacomo Corleone Ivan G. Costa Fawaz Dabbaghie Daniel Doerr Richard Durbin Bas E. Dutilh Peter Ebert Jana Ebler Evan E. Eichler Mohammed El-Kebir Gernot A. Fink Maria Florescu Shilpa Garg Erik Garrison Ali Ghaffaari Maryam Ghareghani Christina Gros Victor Guryev Iman Hajirasouliha Jaap Heringa Inke Herms Stephanie C. Hicks Rens Holmer Peter Husemann Leo van Iersel Katharina Jahn 0001 Hans-Michael Kaltenbach Sven Kanies Emma M. Keizer Martin L. Kersten Indu Khatri Szymon M. Kielbasa Gunnar W. Klau Jan O. Korbel Johannes Köster Alexey M. Kozlov Oliver Kramer 0001 Tzu-Hao Kuo David Laehnemann Boudewijn P. F. Lelieveldt Kai Lienemann Thamar Jessurun Lobo Fabio Luciani Ahmed Mahfouz Veli Mäkinen Ion I. Mandoiu Stefan Manegold John C. Marioni Marcel Martin Davis J. McCarthy Alice C. McHardy Sascha Meiers Ivan Merelli Felix Mölder Amir Niknejad Adam M. Novak Luca Parmigiani Noemi PassingNoemi E. Passing Murray Patterson Luca Pinello Nadia Pisanti Thomas Plötz David Porubsky Lukasz Raczkowski Sven Rahmann Benjamin J. Raphael Mikko Rautiainen Marcel J. T. Reinders Bernhard Y. Renard Jeroen de Ridder Mark D. Robinson Antoine-Emmanuel Saliba Ashley D. Sanders Lars Schillingmann Alexander Schliep Alexander Schönhuth Marcel H. Schulz Chris Schwiegelshohn Sohrab P. Shah Pavel Skums Antonios Somarakis Alexandros Stamatakis Oliver Stegle Matthias Steinrücken Leen Stougie Jens Stoye Henner Sudek Ewa Szczurek Fabian J. Theis Armin Töpfer Massimo Torquati Kathrin Trappe Catalina A. Vallejos Roland Wittler Inken Wohlers Huan Yang Alex Zelikovsky Ying Zhang 0027