Sven Rahmann

108 papers A* 1A 4B 7C 17Misc 2Journal 56Unranked 17
YearRankTypeTitle / Venue / Authors
2026 J jnl
Cleanifier: contamination removal from microbial sequences using spaced seeds of a human pangenome index.
Bioinform.
Jens Zentgraf, Johanna Elena Schmitz, Sven Rahmann
2026 J jnl
Hecate: A Modular Genomic Compressor.
CoRR
Kamila Szewczyk, Sven Rahmann
2026 A conf
Smaller and More Flexible Cuckoo Filters.
ALENEX
Johanna Elena Schmitz, Jens Zentgraf, Sven Rahmann
2025 J jnl
A comprehensive review and evaluation of species richness estimation.
Briefings Bioinform.
Johanna Elena Schmitz, Sven Rahmann
2025 B conf
Blocked Bloom Filters with Choices.
SEA
Johanna Elena Schmitz, Jens Zentgraf, Sven Rahmann
2025 J jnl
Blocked Bloom Filters with Choices.
CoRR
Johanna Elena Schmitz, Jens Zentgraf, Sven Rahmann
2025 C conf
Design of Worst-Case-Optimal Spaced Seeds.
WABI
Jens Zentgraf, Sven Rahmann
2025 J jnl
Smaller and More Flexible Cuckoo Filters.
CoRR
Johanna Elena Schmitz, Jens Zentgraf, Sven Rahmann
2025 J jnl
Swiftly identifying strongly unique k-mers.
Algorithms Mol. Biol.
Jens Zentgraf, Sven Rahmann
2024 B conf
Automated Design of Efficient Search Schemes for Lossless Approximate Pattern Matching.
RECOMB
Luca Renders, Lore Depuydt, Sven Rahmann, Jan Fostier
2024 J jnl
EpiSegMix: a flexible distribution hidden Markov model with duration modeling for chromatin state discovery.
Bioinform.
Johanna Elena Schmitz, Nihit Aggarwal, Lukas Laufer, Jörn Walter, Abdulrahman Salhab, Sven Rahmann
2024 J jnl
Lossless Approximate Pattern Matching: Automated Design of Efficient Search Schemes.
J. Comput. Biol.
Luca Renders, Lore Depuydt, Sven Rahmann, Jan Fostier
2024 C conf
Swiftly Identifying Strongly Unique k-Mers.
WABI
Jens Zentgraf, Sven Rahmann
2022 C ed.
22nd International Workshop on Algorithms in Bioinformatics, WABI 2022, Potsdam, Germany, September 5-7, 2022
WABI
Christina Boucher, Sven Rahmann
2022 — ch.
Cancer Diagnostics and Therapy from Molecular Data.
Mach. Learn. under Resour. Constraints Vol. 3 (3)
Sven Rahmann, Alexander Schramm, Johannes Köster
2022 C conf
Fast Gapped k-mer Counting with Subdivided Multi-Way Bucketed Cuckoo Hash Tables.
WABI
Jens Zentgraf, Sven Rahmann
2022 — ch.
Protein Complex Similarity.
Mach. Learn. under Resour. Constraints Vol. 3 (3)
Bianca K. Stöcker, Till Schäfer, Petra Mutzel, Johannes Köster, Nils M. Kriege, Sven Rahmann
2021 J jnl
Detecting high-scoring local alignments in pangenome graphs.
Bioinform.
Tizian Schulz, Roland Wittler, Sven Rahmann, Faraz Hach, Jens Stoye
2021 J jnl
Fast lightweight accurate xenograft sorting.
Algorithms Mol. Biol.
Jens Zentgraf, Sven Rahmann
2021 J jnl
GAMIBHEAR: whole-genome haplotype reconstruction from Genome Architecture Mapping data.
Bioinform.
Julia Markowski, Rieke Kempfer, Alexander Kukalev, Ibai Irastorza-Azcarate, Gesa Loof, Birte Kehr, Ana Pombo, Sven Rahmann, Roland F. Schwarz
2021 J jnl
Rapid T-cell receptor interaction grouping with ting.
Bioinform.
Felix Mölder, Ulrik Stervbo, Lucie Loyal, Petra Bacher, Nina Babel, Sven Rahmann
2021 J jnl
Sustainable data analysis with Snakemake.
F1000Research
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
2020 A conf
Cost-optimal assignment of elements in genome-scale multi-way bucketed Cuckoo hash tables.
ALENEX
Jens Zentgraf, Henning Timm, Sven Rahmann
2020 B conf
Engineering Fused Lasso Solvers on Trees.
SEA
Elias Kuthe, Sven Rahmann
2020 C conf
Fast Lightweight Accurate Xenograft Sorting.
WABI
Jens Zentgraf, Sven Rahmann
2020 J jnl
wg-blimp: an end-to-end analysis pipeline for whole genome bisulfite sequencing data.
BMC Bioinform.
Marius Wöste, Elsa Leitão, Sandra Laurentino, Bernhard Horsthemke, Sven Rahmann, Christopher Schröder
2019 B conf
Protein Complex Similarity Based on Weisfeiler-Lehman Labeling.
SISAP
Bianca K. Stöcker, Till Schäfer, Petra Mutzel, Johannes Köster, Nils M. Kriege, Sven Rahmann
2018 J jnl
Snakemake - a scalable bioinformatics workflow engine.
Bioinform.
Johannes Köster, Sven Rahmann
2018 C conf
Spalter: A Meta Machine Learning Approach to Distinguish True DNA Variants from Sequencing Artefacts.
WABI
Till Hartmann, Sven Rahmann
2017 J jnl
A hybrid parameter estimation algorithm for beta mixtures and applications to methylation state classification.
Algorithms Mol. Biol.
Christopher Schröder, Sven Rahmann
2017 C conf
Analysis of Min-Hashing for Variant Tolerant DNA Read Mapping.
WABI
Jens Quedenfeld, Sven Rahmann
2017 J jnl
Variant tolerant read mapping using min-hashing.
CoRR
Jens Quedenfeld, Sven Rahmann
2016 C conf
A Hybrid Parameter Estimation Algorithm for Beta Mixtures and Applications to Methylation State Classification.
WABI
Christopher Schröder, Sven Rahmann
2016 J jnl
SimLoRD: Simulation of Long Read Data.
Bioinform.
Bianca K. Stöcker, Johannes Köster, Sven Rahmann
2015 J jnl
An online peak extraction algorithm for ion mobility spectrometry data.
Algorithms Mol. Biol.
Dominik Kopczynski, Sven Rahmann
2015 J jnl
An optimization approach to detect differentially methylated regions from Whole Genome Bisulfite Sequencing data.
PeerJ Prepr.
Nina Hesse, Christopher Schröder, Sven Rahmann
2015 J jnl
Efficient duplicate rate estimation from subsamples of sequencing libraries.
PeerJ Prepr.
Christopher Schröder, Sven Rahmann
2015 J jnl
Invited presentations, junior research groups and research highlights at GCB 2015.
PeerJ Prepr.
Axel Mosig, Jörg Rahnenführer, Martin Eisenacher, Sven Rahmann
2015 J jnl
Poster abstracts of GCB 2015.
PeerJ Prepr.
Martin Eisenacher, Jörg Rahnenführer, Axel Mosig, Sven Rahmann
2014 J jnl
A modular computational framework for automated peak extraction from ion mobility spectra.
BMC Bioinform.
Marianna D'Addario, Dominik Kopczynski, Jörg Ingo Baumbach, Sven Rahmann
2014 C conf
An Online Peak Extraction Algorithm for Ion Mobility Spectrometry Data.
WABI
Dominik Kopczynski, Sven Rahmann
2014 J jnl
Massively parallel read mapping on GPUs with PEANUT.
CoRR
Johannes Köster, Sven Rahmann
2014 J jnl
Using the Expectation Maximization Algorithm with Heterogeneous Mixture Components for the Analysis of Spectrometry Data.
CoRR
Dominik Kopczynski, Sven Rahmann
2013 — conf
Aligning Flowgrams to DNA Sequences.
GCB
Marcel Martin, Sven Rahmann
2013 J jnl
Discovering motifs that induce sequencing errors.
BMC Bioinform.
Manuel Allhoff, Alexander Schönhuth, Marcel Martin, Ivan G. Costa, Sven Rahmann, Tobias Marschall
2013 — conf
PanCake: A Data Structure for Pangenomes.
GCB
Corinna Ernst, Sven Rahmann
2012 — conf
Building and Documenting Workflows with Python-Based Snakemake.
GCB
Johannes Köster, Sven Rahmann
2012 — conf
Designing q-Unique DNA Sequences with Integer Linear Programs and Euler Tours in De Bruijn Graphs.
GCB
Marianna D'Addario, Nils M. Kriege, Sven Rahmann
2012 — conf
Peak modeling for Ion mobility spectrometry measurements.
EUSIPCO
Dominik Kopczynski, Jörg Ingo Baumbach, Sven Rahmann
2012 J jnl
Probabilistic Arithmetic Automata and Their Applications.
IEEE ACM Trans. Comput. Biol. Bioinform.
Tobias Marschall, Inke Herms, Hans-Michael Kaltenbach, Sven Rahmann
2012 J jnl
Snakemake - a scalable bioinformatics workflow engine.
Bioinform.
Johannes Köster, Sven Rahmann
2012 A conf
Solving the Minimum String Cover Problem.
ALENEX
Stefan Canzar, Tobias Marschall, Sven Rahmann, Chris Schwiegelshohn
2011 J jnl
Accurate statistics for local sequence alignment with position-dependent scoring by rare-event sampling.
BMC Bioinform.
Stefan Wolfsheimer, Inke Herms, Sven Rahmann, Alexander K. Hartmann
2011 J jnl
An Algorithm to Compute the Character Access Count Distribution for Pattern Matching Algorithms.
Algorithms
Tobias Marschall, Sven Rahmann
2011 J jnl
Extension and Robustness of Transitivity Clustering for Protein-Protein Interaction Network Analysis.
Internet Math.
Tobias Wittkop, Sven Rahmann, Richard Röttger, Sebastian Böcker, Jan Baumbach
2010 J jnl
Efficient Online Transcription Factor Binding Site Adjustment by Integrating Transitive Graph Projection with MoRAine 2.0.
J. Integr. Bioinform.
Tobias Wittkop, Sven Rahmann, Jan Baumbach
2010 C conf
Exact Analysis of Horspool's and Sunday's Pattern Matching Algorithms with Probabilistic Arithmetic Automata.
LATA
Tobias Marschall, Sven Rahmann
2010 J jnl
Exact Analysis of Pattern Matching Algorithms with Probabilistic Arithmetic Automata
CoRR
Tobias Marschall, Sven Rahmann
2010 — conf
Exact ILP solutions for phylogenetic minimum flip problems.
BCB
Markus Chimani, Sven Rahmann, Sebastian Böcker
2010 J jnl
Probabilistic Arithmetic Automata and their Applications
CoRR
Tobias Marschall, Inke Herms, Hans-Michael Kaltenbach, Sven Rahmann
2010 C conf
Speeding Up Exact Motif Discovery by Bounding the Expected Clump Size.
WABI
Tobias Marschall, Sven Rahmann
2010 J jnl
Structural Identifiability in Low-Rank Matrix Factorization.
Algorithmica
Epameinondas Fritzilas, Martin Milanic, Sven Rahmann, Yasmín Á. Ríos-Solís
2009 J jnl
Efficient exact motif discovery.
Bioinform.
Tobias Marschall, Sven Rahmann
2009 A conf
Modeling evolutionary fitness for DNA motif discovery.
GECCO
Sven Rahmann, Tobias Marschall, Frank Behler, Oliver Kramer
2009 J jnl
Reliable transfer of transcriptional gene regulatory networks between taxonomically related organisms.
BMC Syst. Biol.
Jan Baumbach, Sven Rahmann, Andreas Tauch
2009 J jnl
Towards the integrated analysis, visualization and reconstruction of microbial gene regulatory networks.
Briefings Bioinform.
Jan Baumbach, Andreas Tauch, Sven Rahmann
2008 J jnl
Algorithms for subsequence combinatorics.
Theor. Comput. Sci.
Cees H. Elzinga, Sven Rahmann, Hui Wang
2008 J jnl
Better GeneChip microarray Layouts by Combining Probe Placement and Embedding.
J. Bioinform. Comput. Biol.
Sérgio A. de Carvalho, Sven Rahmann
2008 J jnl
Compound Poisson Approximation of the Number of Occurrences of a Position Frequency Matrix (PFM) on Both Strands.
J. Comput. Biol.
Utz J. Pape, Sven Rahmann, Fengzhu Sun, Martin Vingron
2008 C conf
Computing Alignment Seed Sensitivity with Probabilistic Arithmetic Automata.
WABI
Inke Herms, Sven Rahmann
2008 J jnl
MoRAine - A web server for fast computational transcription factor binding motif re-annotation.
J. Integr. Bioinform.
Jan Baumbach, Tobias Wittkop, Jochen Weile, Thomas Kohl, Sven Rahmann
2008 J jnl
Natural similarity measures between position frequency matrices with an application to clustering.
Bioinform.
Utz J. Pape, Sven Rahmann, Martin Vingron
2008 B conf
Probabilistic Arithmetic Automata and Their Application to Pattern Matching Statistics.
CPM
Tobias Marschall, Sven Rahmann
2008 Misc conf
Structural Identifiability in Low-Rank Matrix Factorization.
COCOON
Epameinondas Fritzilas, Yasmín Á. Ríos-Solís, Sven Rahmann
2007 J jnl
CoryneCenter - An online resource for the integrated analysis of corynebacterial genome and transcriptome data.
BMC Syst. Biol.
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
2007 J jnl
Deep Metazoan Phylogeny.
Silico Biol.
Daniel Gerlach, Matthias Wolf, Thomas Dandekar, Tobias Müller, Andreas Pokorny, Sven Rahmann
2007 J jnl
IMS2 - An integrated medical software system for early lung cancer detection using ion mobility spectrometry data of human breath.
J. Integr. Bioinform.
Jan Baumbach, Alexander Bunkowski, Sita Lange, Timm Oberwahrenbrock, Nils Kleinbölting, Sven Rahmann, Jörg Ingo Baumbach
2007 J jnl
Integer linear programming approaches for non-unique probe selection.
Discret. Appl. Math.
Gunnar W. Klau, Sven Rahmann, Alexander Schliep, Martin Vingron, Knut Reinert
2007 J jnl
Large scale clustering of protein sequences with FORCE -A layout based heuristic for weighted cluster editing.
BMC Bioinform.
Tobias Wittkop, Jan Baumbach, Francisco Pereira Lobo, Sven Rahmann
2006 J jnl
CoryneRegNet 2: An Integrative Bioinformatics Approach for Reconstruction and Comparison of Transcriptional Regulatory Networks in Prokaryotes.
J. Integr. Bioinform.
Jan Baumbach, Karina Brinkrolf, Tobias Wittkop, Andreas Tauch, Sven Rahmann
2006 — conf
Decoding non-unique oligonucleotide hybridization experiments of targets related by a phylogenetic tree.
ISMB (Supplement of Bioinformatics)
Alexander Schliep, Sven Rahmann
2006 — conf
Discovering Biomarkers for Myocardial Infarction from SELDI-TOF Spectra.
GfKl
Christian Höner zu Siederdissen, Susanne Ragg, Sven Rahmann
2006 C conf
Improving the Layout of Oligonucleotide Microarrays: Pivot Partitioning.
WABI
Sérgio A. de Carvalho, Sven Rahmann
2006 C conf
Integer Linear Programs for Discovering Approximate Gene Clusters.
WABI
Sven Rahmann, Gunnar W. Klau
2006 — conf
Markov Additive Chains and Applications to Fragment Statistics for Peptide Mass Fingerprinting.
Systems Biology and Computational Proteomics
Hans-Michael Kaltenbach, Sebastian Böcker, Sven Rahmann
2006 — conf
Microarray Layout as Quadratic Assignment Problem.
German Conference on Bioinformatics
Sérgio A. de Carvalho, Sven Rahmann
2006 B conf
Subsequence Combinatorics and Applications to Microarray Production, DNA Sequencing and Chaining Algorithms.
CPM
Sven Rahmann
2005 Misc conf
Editorial message: special track on bioinformatics.
SAC
Mathew J. Palakal, Sven Rahmann, Birong Liao
2005 J jnl
T-Reg Comparator: an analysis tool for the comparison of position weight matrices.
Nucleic Acids Res.
Stefan Roepcke, Steffen Grossmann, Sven Rahmann, Martin Vingron
2004 — ch.
Algorithmen für das Design von DNA-Microarrays.
Ausgezeichnete Informatikdissertationen
Sven Rahmann
2004 — —
Algorithms for probe selection and DNA microarray design.
Sven Rahmann
2004 — conf
Functional inference from non-random distributions of conserved predicted transcription factor binding sites.
ISMB/ECCB (Supplement of Bioinformatics)
Christoph Dieterich, Sven Rahmann, Martin Vingron
2004 J jnl
HMM Logos for visualization of protein families.
BMC Bioinform.
Benjamin Schuster-Böckler, Jörg Schultz, Sven Rahmann
2004 J jnl
Mean and variance of the Gibbs free energy of oligonucleotides in the nearest neighbor model under varying conditions.
Bioinform.
Sven Rahmann, Christine Gräfe
2004 — conf
Optimal robust non-unique probe selection using Integer Linear Programming.
ISMB/ECCB (Supplement of Bioinformatics)
Gunnar W. Klau, Sven Rahmann, Alexander Schliep, Martin Vingron, Knut Reinert
2003 J jnl
Combinatorics of periods in strings.
J. Comb. Theory A
Eric Rivals, Sven Rahmann
2003 C conf
Dynamic Programming Algorithms for Two Statistical Problems in Computational Biology.
WABI
Sven Rahmann
2003 J jnl
Fast Large Scale Oligonucleotide Selection Using the Longest Common Factor Approach.
J. Bioinform. Comput. Biol.
Sven Rahmann
2003 — conf
Fast and Sensitive Probe Selection for DNA Chips Using Jumps in Matching Statistics.
CSB
Sven Rahmann
2003 — conf
Group Testing With DNA Chips: Generating Designs and Decoding Experiments.
CSB
Alexander Schliep, David C. Torney, Sven Rahmann
2003 J jnl
On The Distribution Of The Number Of Missing Words In Random Texts.
Comb. Probab. Comput.
Sven Rahmann, Eric Rivals
2003 — conf
Robust estimation of the phylogeny of Chlorophyceae(Chlorophyta)based on profile distances.
German Conference on Bioinformatics
Tobias Müller, Sven Rahmann, Thomas Dandekar, Matthias Wolf
2003 C conf
The shortest common supersequence problem in a microarray production setting.
ECCB
Sven Rahmann
2002 — conf
Rapid Large-Scale Oligonucleotide Selection for Microarrays.
CSB
Sven Rahmann
2002 C conf
Rapid Large-Scale Oligonucleotide Selection for Microarrays.
WABI
Sven Rahmann
2001 A* conf
Combinatorics of Periods in Strings.
ICALP
Eric Rivals, Sven Rahmann
2001 — conf
Non-symmetric score matrices and the detection of homologous transmembrane proteins.
ISMB (Supplement of Bioinformatics)
Tobias Müller, Sven Rahmann, Marc Rehmsmeier
2000 B conf
Exact and Efficient Computation of the Expected Number of Missing and Common Words in Random Texts.
CPM
Sven Rahmann, Eric Rivals