Cleanifier: contamination removal from microbial sequences using spaced seeds of a human pangenome index.

Sven Rahmann Saarland University, Germany Technical University of Dortmund, Germany http://www.rahmannlab.de/ https://scholar.google.com/citations?user=zKHCVfoAAAAJ https://dl.acm.org/profile/81100603971 https://zbmath.org/authors/?q=ai:rahmann.sven https://mathscinet.ams.org/mathscinet/MRAuthorID/669584 https://mathgenealogy.org/id.php?id=56414 https://orcid.org/0000-0002-8536-6065 https://www.wikidata.org/entity/Q51354033 https://www.wikidata.org/entity/Q30303501 https://d-nb.info/gnd/1075470188

Jens Zentgraf Johanna Elena Schmitz Sven Rahmann Cleanifier: contamination removal from microbial sequences using spaced seeds of a human pangenome index. 2026 42 Bioinform. 1 https://doi.org/10.1093/bioinformatics/btaf632 db/journals/bioinformatics/bioinformatics42.html#ZentgrafSR26 streams/journals/bioinformatics

Johanna Elena Schmitz Jens Zentgraf Sven Rahmann Smaller and More Flexible Cuckoo Filters. 44-56 2026 ALENEX https://doi.org/10.1137/1.9781611978957.4 conf/alenex/2026 db/conf/alenex/alenex2026.html#SchmitzZR26

Jens Zentgraf Sven Rahmann Swiftly identifying strongly unique k-mers. 13 2025 December 20 Algorithms Mol. Biol. 1 https://doi.org/10.1186/s13015-025-00286-6 db/journals/almob/almob20.html#ZentgrafR25 streams/journals/almob

Johanna Elena Schmitz Sven Rahmann A comprehensive review and evaluation of species richness estimation. 2025 March 26 Briefings Bioinform. 2 https://doi.org/10.1093/bib/bbaf158 db/journals/bib/bib26.html#SchmitzR24 streams/journals/bib

Jens Zentgraf Sven Rahmann Design of Worst-Case-Optimal Spaced Seeds. 22:1-22:17 2025 WABI https://doi.org/10.4230/LIPIcs.WABI.2025.22 conf/wabi/2025 db/conf/wabi/wabi2025.html#ZentgrafR25 Johanna Elena Schmitz Jens Zentgraf Sven Rahmann Blocked Bloom Filters with Choices. 25:1-25:20 2025 SEA https://doi.org/10.4230/LIPIcs.SEA.2025.25 conf/wea/2025 db/conf/wea/sea2025.html#SchmitzZR25 Sven Rahmann Jens Zentgraf Worst-case-optimal Spaced Seeds. 2025 August https://doi.org/10.4230/artifacts.23732 DROPS Artifacts streams/repo/drops Johanna Elena Schmitz Jens Zentgraf Sven Rahmann BlowChoc filters. 2025 July https://doi.org/10.4230/artifacts.23082 DROPS Artifacts streams/repo/drops

Johanna Elena Schmitz Jens Zentgraf Sven Rahmann Blocked Bloom Filters with Choices. 2025 January abs/2501.18977 CoRR https://doi.org/10.48550/arXiv.2501.18977 db/journals/corr/corr2501.html#abs-2501-18977 streams/journals/corr

Johanna Elena Schmitz Jens Zentgraf Sven Rahmann Smaller and More Flexible Cuckoo Filters. 2025 May abs/2505.05847 CoRR https://doi.org/10.48550/arXiv.2505.05847 db/journals/corr/corr2505.html#abs-2505-05847 streams/journals/corr

Johanna Elena Schmitz Nihit Aggarwal Lukas Laufer Jörn Walter Abdulrahman Salhab Sven Rahmann EpiSegMix: a flexible distribution hidden Markov model with duration modeling for chromatin state discovery. 2024 40 Bioinform. 4 https://doi.org/10.1093/bioinformatics/btae178 db/journals/bioinformatics/bioinformatics40.html#SchmitzALWSR24

Luca Renders Lore Depuydt Sven Rahmann Jan Fostier Lossless Approximate Pattern Matching: Automated Design of Efficient Search Schemes. 975-989 2024 31 J. Comput. Biol. 10 https://doi.org/10.1089/cmb.2024.0664 db/journals/jcb/jcb31.html#RendersDRF24 streams/journals/jcb

Luca Renders Lore Depuydt Sven Rahmann Jan Fostier Automated Design of Efficient Search Schemes for Lossless Approximate Pattern Matching. 164-184 2024 RECOMB https://doi.org/10.1007/978-1-0716-3989-4_11 conf/recomb/2024 db/conf/recomb/recomb2024.html#RendersDRF24 Jens Zentgraf Sven Rahmann Swiftly Identifying Strongly Unique k-Mers. 15:1-15:15 2024 WABI https://doi.org/10.4230/LIPIcs.WABI.2024.15 conf/wabi/2024 db/conf/wabi/wabi2024.html#ZentgrafR24 Jens Zentgraf Sven Rahmann Fast Gapped k-mer Counting with Subdivided Multi-Way Bucketed Cuckoo Hash Tables. 12:1-12:20 2022 WABI https://doi.org/10.4230/LIPIcs.WABI.2022.12 conf/wabi/2022 db/conf/wabi/wabi2022.html#ZentgrafR22 Sven Rahmann Alexander Schramm Johannes Köster Cancer Diagnostics and Therapy from Molecular Data. 43-57 2022 Mach. Learn. under Resour. Constraints Vol. 3 (3) https://doi.org/10.1515/9783110785982-011 books/degruyter/22/MM2022-3 db/books/collections/MM2022-3.html#RahmannSK22 Bianca K. Stöcker Till Schäfer Petra Mutzel Johannes Köster Nils M. Kriege Sven Rahmann Protein Complex Similarity. 85-102 2022 Mach. Learn. under Resour. Constraints Vol. 3 (3) https://doi.org/10.1515/9783110785982-014 books/degruyter/22/MM2022-3 db/books/collections/MM2022-3.html#StockerSMKKR22 Christina Boucher 0001 Sven Rahmann 22nd International Workshop on Algorithms in Bioinformatics, WABI 2022, Potsdam, Germany, September 5-7, 2022 WABI Schloss Dagstuhl - Leibniz-Zentrum für Informatik 2022 LIPIcs 242 978-3-95977-243-3 https://www.dagstuhl.de/dagpub/978-3-95977-243-3 db/conf/wabi/wabi2022.html

Jens Zentgraf Sven Rahmann Fast lightweight accurate xenograft sorting. 2 2021 16 Algorithms Mol. Biol. 1 https://doi.org/10.1186/s13015-021-00181-w db/journals/almob/almob16.html#ZentgrafR21

Tizian Schulz Roland Wittler Sven Rahmann Faraz Hach Jens Stoye Detecting high-scoring local alignments in pangenome graphs. 2266-2274 2021 37 Bioinform. 16 https://doi.org/10.1093/bioinformatics/btab077 db/journals/bioinformatics/bioinformatics37.html#SchulzWRHS21

Julia Markowski Rieke Kempfer Alexander Kukalev Ibai Irastorza-Azcarate Gesa Loof Birte Kehr Ana Pombo Sven Rahmann Roland F. Schwarz GAMIBHEAR: whole-genome haplotype reconstruction from Genome Architecture Mapping data. 3128-3135 2021 37 Bioinform. 19 https://doi.org/10.1093/bioinformatics/btab238 db/journals/bioinformatics/bioinformatics37.html#MarkowskiKKILKP21

Felix Mölder Ulrik Stervbo Lucie Loyal Petra Bacher Nina Babel Sven Rahmann Rapid T-cell receptor interaction grouping with ting. 3444-3448 2021 37 Bioinform. 20 https://doi.org/10.1093/bioinformatics/btab361 db/journals/bioinformatics/bioinformatics37.html#MolderSLBBR21

Felix Mölder Kim Philipp Jablonski Brice Letcher Michael B. Hall Christopher Tomkins-Tinch Vanessa V. Sochat Jan Forster Soohyun Lee Sven Twardziok Alexander Kanitz Andreas Wilm Manuel Holtgrewe Sven Rahmann Sven Nahnsen Johannes Köster Sustainable data analysis with Snakemake. 33 2021 10 F1000Research https://doi.org/10.12688/f1000research.29032.1 db/journals/f1000research/f1000research10.html#MolderJLHTSFLTKWHRNK21

Marius Wöste Elsa Leitão Sandra Laurentino Bernhard Horsthemke Sven Rahmann Christopher Schröder 0002 wg-blimp: an end-to-end analysis pipeline for whole genome bisulfite sequencing data. 169 2020 21 BMC Bioinform. 1 https://doi.org/10.1186/s12859-020-3470-5 https://www.wikidata.org/entity/Q94481771 db/journals/bmcbi/bmcbi21.html#WosteLLHRS20

Jens Zentgraf Henning Timm Sven Rahmann Cost-optimal assignment of elements in genome-scale multi-way bucketed Cuckoo hash tables. 186-198 2020 ALENEX https://doi.org/10.1137/1.9781611976007.15 conf/alenex/2020 db/conf/alenex/alenex2020.html#ZentgrafTR20 Jens Zentgraf Sven Rahmann Fast Lightweight Accurate Xenograft Sorting. 4:1-4:16 2020 WABI https://doi.org/10.4230/LIPIcs.WABI.2020.4 conf/wabi/2020 db/conf/wabi/wabi2020.html#ZentgrafR20 Elias Kuthe Sven Rahmann Engineering Fused Lasso Solvers on Trees. 23:1-23:14 2020 SEA https://doi.org/10.4230/LIPIcs.SEA.2020.23 conf/wea/2020 db/conf/wea/sea2020.html#KutheR20 Bianca K. Stöcker Till Schäfer Petra Mutzel Johannes Köster Nils M. Kriege Sven Rahmann Protein Complex Similarity Based on Weisfeiler-Lehman Labeling. 308-322 2019 SISAP https://doi.org/10.1007/978-3-030-32047-8_27 conf/sisap/2019 db/conf/sisap/sisap2019.html#StockerSMKKR19

Johannes Köster Sven Rahmann Snakemake - a scalable bioinformatics workflow engine. 3600 2018 34 Bioinform. 20 https://doi.org/10.1093/bioinformatics/bty350 https://www.wikidata.org/entity/Q57461484 db/journals/bioinformatics/bioinformatics34.html#KosterR18

Till Hartmann Sven Rahmann Spalter: A Meta Machine Learning Approach to Distinguish True DNA Variants from Sequencing Artefacts. 13:1-13:8 2018 WABI https://doi.org/10.4230/LIPIcs.WABI.2018.13 conf/wabi/2018 db/conf/wabi/wabi2018.html#HartmannR18

Christopher Schröder 0002 Sven Rahmann A hybrid parameter estimation algorithm for beta mixtures and applications to methylation state classification. 21:1-21:12 2017 12 Algorithms Mol. Biol. 1 https://doi.org/10.1186/s13015-017-0112-1 https://www.wikidata.org/entity/Q38615062 db/journals/almob/almob12.html#SchroderR17

Jens Quedenfeld Sven Rahmann Analysis of Min-Hashing for Variant Tolerant DNA Read Mapping. 21:1-21:13 2017 WABI https://doi.org/10.4230/LIPIcs.WABI.2017.21 conf/wabi/2017 db/conf/wabi/wabi2017.html#QuedenfeldR17

Jens Quedenfeld Sven Rahmann Variant tolerant read mapping using min-hashing. 2017 abs/1702.01703 CoRR http://arxiv.org/abs/1702.01703 db/journals/corr/corr1702.html#QuedenfeldR17

Bianca K. Stöcker Johannes Köster Sven Rahmann SimLoRD: Simulation of Long Read Data. 2704-2706 2016 32 Bioinform. 17 https://doi.org/10.1093/bioinformatics/btw286 https://www.wikidata.org/entity/Q31095248 db/journals/bioinformatics/bioinformatics32.html#StockerKR16

Christopher Schröder 0002 Sven Rahmann A Hybrid Parameter Estimation Algorithm for Beta Mixtures and Applications to Methylation State Classification. 307-319 2016 WABI https://doi.org/10.1007/978-3-319-43681-4_25 conf/wabi/2016 db/conf/wabi/wabi2016.html#SchroderR16

Dominik Kopczynski Sven Rahmann An online peak extraction algorithm for ion mobility spectrometry data. 17 2015 10 Algorithms Mol. Biol. https://doi.org/10.1186/s13015-015-0045-5 https://www.wikidata.org/entity/Q30979396 db/journals/almob/almob10.html#KopczynskiR15

Nina Hesse Christopher Schröder 0002 Sven Rahmann An optimization approach to detect differentially methylated regions from Whole Genome Bisulfite Sequencing data. e1287 2015 3 PeerJ Prepr. https://doi.org/10.7287/peerj.preprints.1287v2 db/journals/peerjpre/peerjpre3.html#HesseSR15

Christopher Schröder 0002 Sven Rahmann Efficient duplicate rate estimation from subsamples of sequencing libraries. e1298 2015 3 PeerJ Prepr. https://doi.org/10.7287/peerj.preprints.1298v1 db/journals/peerjpre/peerjpre3.html#SchroderR15

Martin Eisenacher Jörg Rahnenführer Axel Mosig Sven Rahmann Poster abstracts of GCB 2015. e1350 2015 3 PeerJ Prepr. https://doi.org/10.7287/peerj.preprints.1350v2 db/journals/peerjpre/peerjpre3.html#EisenacherRMR15

Axel Mosig Jörg Rahnenführer Martin Eisenacher Sven Rahmann Invited presentations, junior research groups and research highlights at GCB 2015. e1352 2015 3 PeerJ Prepr. https://doi.org/10.7287/peerj.preprints.1352v1 db/journals/peerjpre/peerjpre3.html#MosigRER15

Marianna D'Addario Dominik Kopczynski Jörg Ingo Baumbach Sven Rahmann A modular computational framework for automated peak extraction from ion mobility spectra. 25 2014 15 BMC Bioinform. https://doi.org/10.1186/1471-2105-15-25 https://www.wikidata.org/entity/Q35085941 db/journals/bmcbi/bmcbi15.html#DAddarioKBR14

Dominik Kopczynski Sven Rahmann An Online Peak Extraction Algorithm for Ion Mobility Spectrometry Data. 232-246 2014 WABI https://doi.org/10.1007/978-3-662-44753-6_18 https://www.wikidata.org/entity/Q62846305 conf/wabi/2014 db/conf/wabi/wabi2014.html#KopczynskiR14

Johannes Köster Sven Rahmann Massively parallel read mapping on GPUs with PEANUT. 2014 abs/1403.1706 CoRR http://arxiv.org/abs/1403.1706 db/journals/corr/corr1403.html#KosterR14

Dominik Kopczynski Sven Rahmann Using the Expectation Maximization Algorithm with Heterogeneous Mixture Components for the Analysis of Spectrometry Data. 2014 abs/1405.5501 CoRR http://arxiv.org/abs/1405.5501 db/journals/corr/corr1405.html#KopczynskiR14

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

Corinna Ernst Sven Rahmann PanCake: A Data Structure for Pangenomes. 35-45 2013 GCB https://doi.org/10.4230/OASIcs.GCB.2013.35 conf/gcb/2013 db/conf/gcb/gcb2013.html#ErnstR13 Marcel Martin Sven Rahmann Aligning Flowgrams to DNA Sequences. 125-135 2013 GCB https://doi.org/10.4230/OASIcs.GCB.2013.125 conf/gcb/2013 db/conf/gcb/gcb2013.html#MartinR13

Johannes Köster Sven Rahmann Snakemake - a scalable bioinformatics workflow engine. 2520-2522 2012 28 Bioinform. 19 https://doi.org/10.1093/bioinformatics/bts480 https://www.wikidata.org/entity/Q34386337 db/journals/bioinformatics/bioinformatics28.html#KosterR12

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 Dominik Kopczynski Jörg Ingo Baumbach Sven Rahmann Peak modeling for Ion mobility spectrometry measurements. 1801-1805 2012 EUSIPCO https://ieeexplore.ieee.org/document/6333986/ conf/eusipco/2012 db/conf/eusipco/eusipco2012.html#KopczynskiBR12 Johannes Köster Sven Rahmann Building and Documenting Workflows with Python-Based Snakemake. 49-56 2012 GCB https://doi.org/10.4230/OASIcs.GCB.2012.49 conf/gcb/2012 db/conf/gcb/gcb2012.html#KosterR12 Marianna D'Addario Nils M. Kriege Sven Rahmann Designing q-Unique DNA Sequences with Integer Linear Programs and Euler Tours in De Bruijn Graphs. 82-92 2012 GCB https://doi.org/10.4230/OASIcs.GCB.2012.82 conf/gcb/2012 db/conf/gcb/gcb2012.html#DAddarioKR12

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

Stefan Wolfsheimer Inke Herms Sven Rahmann Alexander K. Hartmann Accurate statistics for local sequence alignment with position-dependent scoring by rare-event sampling. 47 2011 12 BMC Bioinform. https://doi.org/10.1186/1471-2105-12-47 https://www.wikidata.org/entity/Q33811380 db/journals/bmcbi/bmcbi12.html#WolfsheimerHRH11

Tobias Wittkop Sven Rahmann Richard Röttger Sebastian Böcker Jan Baumbach Extension and Robustness of Transitivity Clustering for Protein-Protein Interaction Network Analysis. 255-273 2011 7 Internet Math. 4 https://doi.org/10.1080/15427951.2011.604559 https://www.wikidata.org/entity/Q62780060 db/journals/im/im7.html#WittkopRRBB11

Epameinondas Fritzilas Martin Milanic Sven Rahmann Yasmín Á. Ríos-Solís Structural Identifiability in Low-Rank Matrix Factorization. 313-332 2010 56 Algorithmica 3 https://doi.org/10.1007/s00453-009-9331-2 https://www.wikidata.org/entity/Q61704601 db/journals/algorithmica/algorithmica56.html#FritzilasMRR10

Tobias Wittkop Sven Rahmann Jan Baumbach Efficient Online Transcription Factor Binding Site Adjustment by Integrating Transitive Graph Projection with MoRAine 2.0. 2010 7 J. Integr. Bioinform. 3 https://doi.org/10.2390/biecoll-jib-2010-117 https://www.wikidata.org/entity/Q84019542 db/journals/jib/jib7.html#WittkopRB10

Markus Chimani Sven Rahmann Sebastian Böcker Exact ILP solutions for phylogenetic minimum flip problems. 147-153 2010 BCB https://doi.org/10.1145/1854776.1854800 https://www.wikidata.org/entity/Q61704590 conf/bcb/2010 db/conf/bcb/bcb2010.html#ChimaniRB10 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 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

Jan Baumbach Andreas Tauch Sven Rahmann Towards the integrated analysis, visualization and reconstruction of microbial gene regulatory networks. 75-83 2009 10 Briefings Bioinform. 1 https://doi.org/10.1093/bib/bbn055 https://www.wikidata.org/entity/Q37089719 db/journals/bib/bib10.html#BaumbachTR09

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

Jan Baumbach Sven Rahmann Andreas Tauch Reliable transfer of transcriptional gene regulatory networks between taxonomically related organisms. 8 2009 3 BMC Syst. Biol. https://doi.org/10.1186/1752-0509-3-8 https://www.wikidata.org/entity/Q30486383 db/journals/bmcsb/bmcsb3.html#BaumbachRT09

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

Utz J. Pape Sven Rahmann Martin Vingron Natural similarity measures between position frequency matrices with an application to clustering. 350-357 2008 24 Bioinform. 3 https://doi.org/10.1093/bioinformatics/btm610 https://www.wikidata.org/entity/Q48367238 db/journals/bioinformatics/bioinformatics24.html#PapeRV08

Sérgio A. de Carvalho Sven Rahmann Better GeneChip microarray Layouts by Combining Probe Placement and Embedding. 623-641 2008 6 J. Bioinform. Comput. Biol. 3 https://doi.org/10.1142/S0219720008003576 https://www.wikidata.org/entity/Q44324443 db/journals/jbcb/jbcb6.html#CarvalhoCR08

Utz J. Pape Sven Rahmann Fengzhu Sun Martin Vingron Compound Poisson Approximation of the Number of Occurrences of a Position Frequency Matrix (PFM) on Both Strands. 547-564 2008 15 J. Comput. Biol. 6 https://doi.org/10.1089/cmb.2007.0084 https://www.wikidata.org/entity/Q41835048 db/journals/jcb/jcb15.html#PapeRSV08

Jan Baumbach Tobias Wittkop Jochen Weile Thomas Kohl Sven Rahmann MoRAine - A web server for fast computational transcription factor binding motif re-annotation. 2008 5 J. Integr. Bioinform. 2 https://doi.org/10.2390/biecoll-jib-2008-91 https://www.wikidata.org/entity/Q51897640 db/journals/jib/jib5.html#BaumbachWWKR08

Cees H. Elzinga Sven Rahmann Hui Wang 0001 Algorithms for subsequence combinatorics. 394-404 2008 409 Theor. Comput. Sci. 3 https://doi.org/10.1016/j.tcs.2008.08.035 https://www.wikidata.org/entity/Q61704582 db/journals/tcs/tcs409.html#ElzingaRW08

Epameinondas Fritzilas Yasmín Á. Ríos-Solís Sven Rahmann Structural Identifiability in Low-Rank Matrix Factorization. 140-148 2008 COCOON https://doi.org/10.1007/978-3-540-69733-6_15 conf/cocoon/2008 db/conf/cocoon/cocoon2008.html#FritzilasRR08 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 Inke Herms Sven Rahmann Computing Alignment Seed Sensitivity with Probabilistic Arithmetic Automata. 318-329 2008 WABI https://doi.org/10.1007/978-3-540-87361-7_27 conf/wabi/2008 db/conf/wabi/wabi2008.html#HermsR08

Tobias Wittkop Jan Baumbach Francisco Pereira Lobo Sven Rahmann Large scale clustering of protein sequences with FORCE -A layout based heuristic for weighted cluster editing. 2007 8 BMC Bioinform. https://doi.org/10.1186/1471-2105-8-396 https://www.wikidata.org/entity/Q30480876 db/journals/bmcbi/bmcbi8.html#WittkopBLR07

Heiko Neuweger Jan Baumbach Stefan P. Albaum Thomas Bekel Michael Dondrup Andrea T. Hüser Jörn Kalinowski Sebastian Oehm Alfred Pühler Sven Rahmann Jochen Weile Alexander Goesmann CoryneCenter - An online resource for the integrated analysis of corynebacterial genome and transcriptome data. 55 2007 1 BMC Syst. Biol. https://doi.org/10.1186/1752-0509-1-55 https://www.wikidata.org/entity/Q31137521 db/journals/bmcsb/bmcsb1.html#NeuwegerBABDHKOPRWG07

Gunnar W. Klau Sven Rahmann Alexander Schliep Martin Vingron Knut Reinert Integer linear programming approaches for non-unique probe selection. 840-856 2007 155 Discret. Appl. Math. 6-7 https://doi.org/10.1016/j.dam.2005.09.021 https://www.wikidata.org/entity/Q57710067 db/journals/dam/dam155.html#KlauRSVR07

Daniel Gerlach Matthias Wolf 0002 Thomas Dandekar Tobias Müller 0001 Andreas Pokorny Sven Rahmann Deep Metazoan Phylogeny. 151-154 2007 7 Silico Biol. 2 http://content.iospress.com/articles/in-silico-biology/isb00285 db/journals/isb/isb7.html#GerlachWDMPR07

Jan Baumbach Alexander Bunkowski Sita Lange Timm Oberwahrenbrock Nils Kleinbölting Sven Rahmann Jörg Ingo Baumbach IMS2 - An integrated medical software system for early lung cancer detection using ion mobility spectrometry data of human breath. 2007 4 J. Integr. Bioinform. 3 https://doi.org/10.2390/biecoll-jib-2007-75 db/journals/jib/jib4.html#BaumbachBLOKRB07

Jan Baumbach Karina Brinkrolf Tobias Wittkop Andreas Tauch Sven Rahmann CoryneRegNet 2: An Integrative Bioinformatics Approach for Reconstruction and Comparison of Transcriptional Regulatory Networks in Prokaryotes. 2006 3 J. Integr. Bioinform. 2 https://doi.org/10.2390/biecoll-jib-2006-24 db/journals/jib/jib3.html#BaumbachBWTR06

Sven Rahmann Subsequence Combinatorics and Applications to Microarray Production, DNA Sequencing and Chaining Algorithms. 153-164 2006 conf/cpm/2006 CPM https://doi.org/10.1007/11780441_15 db/conf/cpm/cpm2006.html#Rahmann06 Sérgio A. de Carvalho Sven Rahmann Microarray Layout as Quadratic Assignment Problem. 11-20 2006 German Conference on Bioinformatics conf/gcb/2006 db/conf/gcb/gcb2006.html#CarvalhoR06 https://dl.gi.de/handle/20.500.12116/24211 http://subs.emis.de/LNI/Proceedings/Proceedings83/article5489.html Christian Höner zu Siederdissen Susanne Ragg Sven Rahmann Discovering Biomarkers for Myocardial Infarction from SELDI-TOF Spectra. 569-576 2006 GfKl https://doi.org/10.1007/978-3-540-70981-7_65 https://www.wikidata.org/entity/Q57591731 conf/gfkl/2006 db/conf/gfkl/gfkl2006.html#SiederdissenRR06 Alexander Schliep Sven Rahmann Decoding non-unique oligonucleotide hybridization experiments of targets related by a phylogenetic tree. 424-430 2006 conf/ismb/2006 ISMB (Supplement of Bioinformatics) https://doi.org/10.1093/bioinformatics/btl254 https://www.wikidata.org/entity/Q33252086 db/conf/ismb/ismb2006.html#SchliepR06 Hans-Michael Kaltenbach Sebastian Böcker Sven Rahmann Markov Additive Chains and Applications to Fragment Statistics for Peptide Mass Fingerprinting. 29-41 2006 conf/recomb/2006sbcp Systems Biology and Computational Proteomics https://doi.org/10.1007/978-3-540-73060-6_3 db/conf/recomb/sbcp2006.html#KaltenbachBR06 Sven Rahmann Gunnar W. Klau Integer Linear Programs for Discovering Approximate Gene Clusters. 298-309 2006 conf/wabi/2006 WABI https://doi.org/10.1007/11851561_28 db/conf/wabi/wabi2006.html#RahmannK06 Sérgio A. de Carvalho Sven Rahmann Improving the Layout of Oligonucleotide Microarrays: Pivot Partitioning. 321-332 2006 conf/wabi/2006 WABI https://doi.org/10.1007/11851561_30 db/conf/wabi/wabi2006.html#CarvalhoR06

Stefan Roepcke Steffen Grossmann Sven Rahmann Martin Vingron T-Reg Comparator: an analysis tool for the comparison of position weight matrices. 438-441 2005 33 Nucleic Acids Res. Web-Server-Issue https://doi.org/10.1093/nar/gki590 https://www.wikidata.org/entity/Q24813630 db/journals/nar/nar33.html#RoepckeGRV05

Mathew J. Palakal Sven Rahmann Birong Liao Editorial message: special track on bioinformatics. 99 2005 conf/sac/2005 SAC https://doi.org/10.1145/1066677.1066705 db/conf/sac/sac2005.html#PalakalRL05 Sven Rahmann Algorithms for probe selection and DNA microarray design. I-XVIII, 1-188 FU Berlin 2004

Sven Rahmann Christine Gräfe Mean and variance of the Gibbs free energy of oligonucleotides in the nearest neighbor model under varying conditions. 2928-2933 2004 20 Bioinform. 17 https://doi.org/10.1093/bioinformatics/bth334 https://www.wikidata.org/entity/Q48540320 db/journals/bioinformatics/bioinformatics20.html#RahmannG04

Benjamin Schuster-Böckler Jörg Schultz Sven Rahmann HMM Logos for visualization of protein families. 7 2004 5 BMC Bioinform. https://doi.org/10.1186/1471-2105-5-7 https://www.wikidata.org/entity/Q24796508 db/journals/bmcbi/bmcbi5.html#Schuster-BocklerSR04

Christoph Dieterich Sven Rahmann Martin Vingron Functional inference from non-random distributions of conserved predicted transcription factor binding sites. 109-115 2004 conf/ismb/2004 ISMB/ECCB (Supplement of Bioinformatics) https://doi.org/10.1093/bioinformatics/bth908 https://www.wikidata.org/entity/Q48533979 db/conf/ismb/ismb2004.html#DieterichRV04 Gunnar W. Klau Sven Rahmann Alexander Schliep Martin Vingron Knut Reinert Optimal robust non-unique probe selection using Integer Linear Programming. 186-193 2004 conf/ismb/2004 ISMB/ECCB (Supplement of Bioinformatics) https://doi.org/10.1093/bioinformatics/bth936 https://www.wikidata.org/entity/Q48533869 db/conf/ismb/ismb2004.html#KlauRSVR04 Sven Rahmann Algorithmen für das Design von DNA-Microarrays. 145-154 2004 Ausgezeichnete Informatikdissertationen https://dl.gi.de/handle/20.500.12116/4499 https://subs.emis.de/LNI/Dissertation/Dissertation5/article41.html conf/gi/2004diss db/conf/gi/diss2004.html#Rahmann04

Sven Rahmann Eric Rivals On The Distribution Of The Number Of Missing Words In Random Texts. 2003 12 Comb. Probab. Comput. 1 db/journals/cpc/cpc12.html#RahmannR03 https://doi.org/10.1017/S0963548302005473 https://www.wikidata.org/entity/Q61704596 73-87

Sven Rahmann Fast Large Scale Oligonucleotide Selection Using the Longest Common Factor Approach. 343-362 2003 1 J. Bioinform. Comput. Biol. 2 https://doi.org/10.1142/S0219720003000125 https://www.wikidata.org/entity/Q51595908 db/journals/jbcb/jbcb1.html#Rahmann03

Eric Rivals Sven Rahmann Combinatorics of periods in strings. 95-113 2003 104 J. Comb. Theory A 1 https://doi.org/10.1016/S0097-3165(03)00123-7 https://www.wikidata.org/entity/Q61704585 db/journals/jct/jcta104.html#RivalsR03

Sven Rahmann Fast and Sensitive Probe Selection for DNA Chips Using Jumps in Matching Statistics. 57-64 2003 conf/csb/2003 CSB https://doi.org/10.1109/CSB.2003.1227304 https://doi.ieeecomputersociety.org/10.1109/CSB.2003.1227304 db/conf/csb/csb2003.html#Rahmann03 Alexander Schliep David C. Torney Sven Rahmann Group Testing With DNA Chips: Generating Designs and Decoding Experiments. 84-93 2003 conf/csb/2003 CSB https://doi.org/10.1109/CSB.2003.1227307 https://doi.ieeecomputersociety.org/10.1109/CSB.2003.1227307 db/conf/csb/csb2003.html#SchliepTR03 Sven Rahmann The shortest common supersequence problem in a microarray production setting. 156-161 2003 conf/eccb/2003 ECCB db/conf/eccb/eccb2003.html#Rahmann03 https://doi.org/10.1093/bioinformatics/btg1073 Tobias Müller 0001 Sven Rahmann Thomas Dandekar Matthias Wolf 0002 Robust estimation of the phylogeny of Chlorophyceae(Chlorophyta)based on profile distances. 97-101 2003 conf/gcb/2003 German Conference on Bioinformatics db/conf/gcb/gcb2003.html#MullerRDW03 Sven Rahmann Dynamic Programming Algorithms for Two Statistical Problems in Computational Biology. 151-164 https://doi.org/10.1007/978-3-540-39763-2_12 2003 conf/wabi/2003 WABI db/conf/wabi/wabi2003.html#Rahmann03 Sven Rahmann Rapid Large-Scale Oligonucleotide Selection for Microarrays. 54-63 2002 conf/csb/2002 CSB https://doi.org/10.1109/CSB.2002.1039329 https://doi.ieeecomputersociety.org/10.1109/CSB.2002.1039329 db/conf/csb/csb2002.html#Rahman02 Sven Rahmann Rapid Large-Scale Oligonucleotide Selection for Microarrays. 434 2002 conf/wabi/2002 WABI https://doi.org/10.1007/3-540-45784-4_33 db/conf/wabi/wabi2002.html#Rahmann02 Eric Rivals Sven Rahmann Combinatorics of Periods in Strings. 615-626 2001 conf/icalp/2001 ICALP https://doi.org/10.1007/3-540-48224-5_51 db/conf/icalp/icalp2001.html#RivalsR01 Tobias Müller 0001 Sven Rahmann Marc Rehmsmeier Non-symmetric score matrices and the detection of homologous transmembrane proteins. 182-189 2001 conf/ismb/2001 ISMB (Supplement of Bioinformatics) db/conf/ismb/ismb2001.html#MullerRR01 https://doi.org/10.1093/bioinformatics/17.suppl_1.s182 Sven Rahmann Eric Rivals Exact and Efficient Computation of the Expected Number of Missing and Common Words in Random Texts. 375-387 https://doi.org/10.1007/3-540-45123-4_31 2000 conf/cpm/2000 CPM db/conf/cpm/cpm2000.html#RahmannR00 Nihit Aggarwal Stefan P. Albaum Manuel Allhoff Nina Babel Petra Bacher Jan Baumbach Jörg Ingo Baumbach Frank Behler Thomas Bekel Sebastian Böcker Christina Boucher 0001 Karina Brinkrolf Alexander Bunkowski Stefan Canzar Sérgio A. de Carvalho Markus Chimani Ivan G. Costa Marianna D'Addario Thomas Dandekar Lore Depuydt Christoph Dieterich Michael Dondrup Martin Eisenacher Cees H. Elzinga Corinna Ernst Jan Forster Jan Fostier Epameinondas Fritzilas Daniel Gerlach Alexander Goesmann Christine Gräfe Steffen Grossmann Faraz Hach Michael B. Hall Alexander K. Hartmann Till Hartmann Inke Herms Nina Hesse Manuel Holtgrewe Bernhard Horsthemke Andrea T. Hüser Ibai Irastorza-Azcarate Kim Philipp Jablonski Jörn Kalinowski Hans-Michael Kaltenbach Alexander Kanitz Birte Kehr Rieke Kempfer Gunnar W. Klau Nils Kleinbölting Thomas Kohl Dominik Kopczynski Johannes Köster Oliver Kramer 0001 Nils M. Kriege Alexander Kukalev Elias Kuthe Sita Lange Lukas Laufer Sandra Laurentino Soohyun Lee Elsa Leitão Brice Letcher Birong Liao Francisco Pereira Lobo Gesa Loof Lucie Loyal Julia Markowski Tobias Marschall Marcel Martin Martin Milanic Felix Mölder Axel Mosig Tobias Müller 0001 Petra Mutzel Sven Nahnsen Heiko Neuweger Timm Oberwahrenbrock Sebastian Oehm Mathew J. Palakal Utz J. Pape Andreas Pokorny Ana Pombo Alfred Pühler Jens Quedenfeld Susanne Ragg Jörg Rahnenführer Marc Rehmsmeier Knut Reinert Luca Renders Yasmín Á. Ríos-Solís Eric Rivals Stefan Roepcke Richard Röttger Abdulrahman Salhab Till Schäfer Alexander Schliep Johanna Elena Schmitz Alexander Schönhuth Alexander Schramm Christopher Schröder 0002 Jörg Schultz Tizian Schulz Benjamin Schuster-Böckler Roland F. Schwarz Chris Schwiegelshohn Christian Höner zu Siederdissen Vanessa V. Sochat Ulrik Stervbo Bianca K. Stöcker Jens Stoye Fengzhu Sun Andreas Tauch Henning Timm Christopher Tomkins-Tinch David C. Torney Sven Twardziok Martin Vingron Jörn Walter Hui Wang 0001 Jochen Weile Andreas Wilm Tobias Wittkop Roland Wittler Matthias Wolf 0002 Stefan Wolfsheimer Marius Wöste Jens Zentgraf