Sven Rahmann

Publication Activity (10 Years)

Years Active: 2000-2024
Publications (10 Years): 20

Top Topics

Computational Framework

Approximate Pattern Matching

Automated Design

Top Venues

FU Berlin (PHD)

Education History

FU Berlin

PHD

Publications

Jens Zentgraf, Sven Rahmann
Swiftly Identifying Strongly Unique k-Mers. WABI (2024)
Luca Renders, Lore Depuydt, Sven Rahmann, Jan Fostier
Automated Design of Efficient Search Schemes for Lossless Approximate Pattern Matching. RECOMB (2024)
Jens Zentgraf, Sven Rahmann
Fast Gapped k-mer Counting with Subdivided Multi-Way Bucketed Cuckoo Hash Tables. WABI (2022)
Jens Zentgraf, Sven Rahmann
Fast lightweight accurate xenograft sorting. Algorithms Mol. Biol. 16 (1) (2021)
Tizian Schulz, Roland Wittler, Sven Rahmann, Faraz Hach, Jens Stoye
Detecting high-scoring local alignments in pangenome graphs. Bioinform. 37 (16) (2021)
Felix Mölder, Ulrik Stervbo, Lucie Loyal, Petra Bacher, Nina Babel, Sven Rahmann
Rapid T-cell receptor interaction grouping with ting. Bioinform. 37 (20) (2021)
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. Bioinform. 37 (19) (2021)
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. F1000Research 10 (2021)
Jens Zentgraf, Henning Timm, Sven Rahmann
Cost-optimal assignment of elements in genome-scale multi-way bucketed Cuckoo hash tables. ALENEX (2020)
Marius Wöste, Elsa Leitão, Sandra Laurentino, Bernhard Horsthemke, Sven Rahmann, Christopher Schröder
wg-blimp: an end-to-end analysis pipeline for whole genome bisulfite sequencing data. BMC Bioinform. 21 (1) (2020)
Jens Zentgraf, Sven Rahmann
Fast Lightweight Accurate Xenograft Sorting. WABI (2020)
Elias Kuthe, Sven Rahmann
Engineering Fused Lasso Solvers on Trees. SEA (2020)
Bianca K. Stöcker, Till Schäfer, Petra Mutzel, Johannes Köster, Nils M. Kriege, Sven Rahmann
Protein Complex Similarity Based on Weisfeiler-Lehman Labeling. SISAP (2019)
Johannes Köster, Sven Rahmann
Snakemake - a scalable bioinformatics workflow engine. Bioinform. 34 (20) (2018)
Till Hartmann, Sven Rahmann
Spalter: A Meta Machine Learning Approach to Distinguish True DNA Variants from Sequencing Artefacts. WABI (2018)
Jens Quedenfeld, Sven Rahmann
Variant tolerant read mapping using min-hashing. CoRR (2017)
Jens Quedenfeld, Sven Rahmann
Analysis of Min-Hashing for Variant Tolerant DNA Read Mapping. WABI (2017)
Christopher Schröder, Sven Rahmann
A hybrid parameter estimation algorithm for beta mixtures and applications to methylation state classification. Algorithms Mol. Biol. 12 (1) (2017)
Christopher Schröder, Sven Rahmann
A Hybrid Parameter Estimation Algorithm for Beta Mixtures and Applications to Methylation State Classification. WABI (2016)
Bianca K. Stöcker, Johannes Köster, Sven Rahmann
SimLoRD: Simulation of Long Read Data. Bioinform. 32 (17) (2016)
Christopher Schröder, Sven Rahmann
Efficient duplicate rate estimation from subsamples of sequencing libraries. PeerJ Prepr. 3 (2015)
Martin Eisenacher, Jörg Rahnenführer, Axel Mosig, Sven Rahmann
Poster abstracts of GCB 2015. PeerJ Prepr. 3 (2015)
Nina Hesse, Christopher Schröder, Sven Rahmann
An optimization approach to detect differentially methylated regions from Whole Genome Bisulfite Sequencing data. PeerJ Prepr. 3 (2015)
Dominik Kopczynski, Sven Rahmann
An online peak extraction algorithm for ion mobility spectrometry data. Algorithms Mol. Biol. 10 (2015)
Axel Mosig, Jörg Rahnenführer, Martin Eisenacher, Sven Rahmann
Invited presentations, junior research groups and research highlights at GCB 2015. PeerJ Prepr. 3 (2015)
Dominik Kopczynski, Sven Rahmann
Using the Expectation Maximization Algorithm with Heterogeneous Mixture Components for the Analysis of Spectrometry Data. CoRR (2014)
Johannes Köster, Sven Rahmann
Massively parallel read mapping on GPUs with PEANUT. CoRR (2014)
Marianna D'Addario, Dominik Kopczynski, Jörg Ingo Baumbach, Sven Rahmann
A modular computational framework for automated peak extraction from ion mobility spectra. BMC Bioinform. 15 (2014)
Dominik Kopczynski, Sven Rahmann
An Online Peak Extraction Algorithm for Ion Mobility Spectrometry Data. WABI (2014)
Manuel Allhoff, Alexander Schönhuth, Marcel Martin, Ivan G. Costa, Sven Rahmann, Tobias Marschall
Discovering motifs that induce sequencing errors. BMC Bioinform. 14 (S-5) (2013)
Corinna Ernst, Sven Rahmann
PanCake: A Data Structure for Pangenomes. GCB (2013)
Marcel Martin, Sven Rahmann
Aligning Flowgrams to DNA Sequences. GCB (2013)
Marianna D'Addario, Nils M. Kriege, Sven Rahmann
Designing q-Unique DNA Sequences with Integer Linear Programs and Euler Tours in De Bruijn Graphs. GCB (2012)
Stefan Canzar, Tobias Marschall, Sven Rahmann, Chris Schwiegelshohn
Solving the Minimum String Cover Problem. ALENEX (2012)
Tobias Marschall, Inke Herms, Hans-Michael Kaltenbach, Sven Rahmann
Probabilistic Arithmetic Automata and Their Applications. IEEE ACM Trans. Comput. Biol. Bioinform. 9 (6) (2012)
Johannes Köster, Sven Rahmann
Snakemake - a scalable bioinformatics workflow engine. Bioinform. 28 (19) (2012)
Johannes Köster, Sven Rahmann
Building and Documenting Workflows with Python-Based Snakemake. GCB (2012)
Dominik Kopczynski, Jörg Ingo Baumbach, Sven Rahmann
Peak modeling for Ion mobility spectrometry measurements. EUSIPCO (2012)
Tobias Marschall, Sven Rahmann
An Algorithm to Compute the Character Access Count Distribution for Pattern Matching Algorithms. Algorithms 4 (4) (2011)
Tobias Wittkop, Sven Rahmann, Richard Röttger, Sebastian Böcker, Jan Baumbach
Extension and Robustness of Transitivity Clustering for Protein-Protein Interaction Network Analysis. Internet Math. 7 (4) (2011)
Stefan Wolfsheimer, Inke Herms, Sven Rahmann, Alexander K. Hartmann
Accurate statistics for local sequence alignment with position-dependent scoring by rare-event sampling. BMC Bioinform. 12 (2011)
Epameinondas Fritzilas, Martin Milanic, Sven Rahmann, Yasmín Á. Ríos-Solís
Structural Identifiability in Low-Rank Matrix Factorization. Algorithmica 56 (3) (2010)
Tobias Marschall, Sven Rahmann
Exact Analysis of Pattern Matching Algorithms with Probabilistic Arithmetic Automata CoRR (2010)
Tobias Marschall, Sven Rahmann
Exact Analysis of Horspool's and Sunday's Pattern Matching Algorithms with Probabilistic Arithmetic Automata. LATA (2010)
Tobias Wittkop, Sven Rahmann, Jan Baumbach
Efficient Online Transcription Factor Binding Site Adjustment by Integrating Transitive Graph Projection with MoRAine 2.0. J. Integr. Bioinform. 7 (3) (2010)
Tobias Marschall, Inke Herms, Hans-Michael Kaltenbach, Sven Rahmann
Probabilistic Arithmetic Automata and their Applications CoRR (2010)
Tobias Marschall, Sven Rahmann
Speeding Up Exact Motif Discovery by Bounding the Expected Clump Size. WABI (2010)
Markus Chimani, Sven Rahmann, Sebastian Böcker
Exact ILP solutions for phylogenetic minimum flip problems. BCB (2010)
Jan Baumbach, Sven Rahmann, Andreas Tauch
Reliable transfer of transcriptional gene regulatory networks between taxonomically related organisms. BMC Syst. Biol. 3 (2009)
Jan Baumbach, Andreas Tauch, Sven Rahmann
Towards the integrated analysis, visualization and reconstruction of microbial gene regulatory networks. Briefings Bioinform. 10 (1) (2009)
Tobias Marschall, Sven Rahmann
Efficient exact motif discovery. Bioinform. 25 (12) (2009)
Sven Rahmann, Tobias Marschall, Frank Behler, Oliver Kramer
Modeling evolutionary fitness for DNA motif discovery. GECCO (2009)
Inke Herms, Sven Rahmann
Computing Alignment Seed Sensitivity with Probabilistic Arithmetic Automata. WABI (2008)
Jan Baumbach, Tobias Wittkop, Jochen Weile, Thomas Kohl, Sven Rahmann
MoRAine - A web server for fast computational transcription factor binding motif re-annotation. J. Integr. Bioinform. 5 (2) (2008)
Tobias Marschall, Sven Rahmann
Probabilistic Arithmetic Automata and Their Application to Pattern Matching Statistics. CPM (2008)
Sérgio A. de Carvalho, Sven Rahmann
Better GeneChip microarray Layouts by Combining Probe Placement and Embedding. J. Bioinform. Comput. Biol. 6 (3) (2008)
Utz J. Pape, Sven Rahmann, Martin Vingron
Natural similarity measures between position frequency matrices with an application to clustering. Bioinform. 24 (3) (2008)
Cees H. Elzinga, Sven Rahmann, Hui Wang
Algorithms for subsequence combinatorics. Theor. Comput. Sci. 409 (3) (2008)
Epameinondas Fritzilas, Yasmín Á. Ríos-Solís, Sven Rahmann
Structural Identifiability in Low-Rank Matrix Factorization. COCOON (2008)
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. J. Comput. Biol. 15 (6) (2008)
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. J. Integr. Bioinform. 4 (3) (2007)
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. BMC Bioinform. 8 (2007)
Daniel Gerlach, Matthias Wolf, Thomas Dandekar, Tobias Müller, Andreas Pokorny, Sven Rahmann
Deep Metazoan Phylogeny. Silico Biol. 7 (2) (2007)
Gunnar W. Klau, Sven Rahmann, Alexander Schliep, Martin Vingron, Knut Reinert
Integer linear programming approaches for non-unique probe selection. Discret. Appl. Math. 155 (6-7) (2007)
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. BMC Syst. Biol. 1 (2007)
Sven Rahmann
Subsequence Combinatorics and Applications to Microarray Production, DNA Sequencing and Chaining Algorithms. CPM (2006)
Sérgio A. de Carvalho, Sven Rahmann
Improving the Layout of Oligonucleotide Microarrays: Pivot Partitioning. WABI (2006)
Hans-Michael Kaltenbach, Sebastian Böcker, Sven Rahmann
Markov Additive Chains and Applications to Fragment Statistics for Peptide Mass Fingerprinting. Systems Biology and Computational Proteomics (2006)
Alexander Schliep, Sven Rahmann
Decoding non-unique oligonucleotide hybridization experiments of targets related by a phylogenetic tree. ISMB (Supplement of Bioinformatics) (2006)
Sérgio A. de Carvalho, Sven Rahmann
Microarray Layout as Quadratic Assignment Problem. German Conference on Bioinformatics (2006)
Christian Höner zu Siederdissen, Susanne Ragg, Sven Rahmann
Discovering Biomarkers for Myocardial Infarction from SELDI-TOF Spectra. GfKl (2006)
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. J. Integr. Bioinform. 3 (2) (2006)
Sven Rahmann, Gunnar W. Klau
Integer Linear Programs for Discovering Approximate Gene Clusters. WABI (2006)
Stefan Roepcke, Steffen Grossmann, Sven Rahmann, Martin Vingron
T-Reg Comparator: an analysis tool for the comparison of position weight matrices. Nucleic Acids Res. 33 (Web-Server-Issue) (2005)
Mathew J. Palakal, Sven Rahmann, Birong Liao
Editorial message: special track on bioinformatics. SAC (2005)
Benjamin Schuster-Böckler, Jörg Schultz, Sven Rahmann
HMM Logos for visualization of protein families. BMC Bioinform. 5 (2004)
Gunnar W. Klau, Sven Rahmann, Alexander Schliep, Martin Vingron, Knut Reinert
Optimal robust non-unique probe selection using Integer Linear Programming. ISMB/ECCB (Supplement of Bioinformatics) (2004)
Sven Rahmann, Christine Gräfe
Mean and variance of the Gibbs free energy of oligonucleotides in the nearest neighbor model under varying conditions. Bioinform. 20 (17) (2004)
Sven Rahmann
Algorithmen für das Design von DNA-Microarrays. Ausgezeichnete Informatikdissertationen (2004)
Christoph Dieterich, Sven Rahmann, Martin Vingron
Functional inference from non-random distributions of conserved predicted transcription factor binding sites. ISMB/ECCB (Supplement of Bioinformatics) (2004)
Tobias Müller, Sven Rahmann, Thomas Dandekar, Matthias Wolf
Robust estimation of the phylogeny of Chlorophyceae(Chlorophyta)based on profile distances. German Conference on Bioinformatics (2003)
Sven Rahmann
The shortest common supersequence problem in a microarray production setting. ECCB (2003)
Sven Rahmann
Fast Large Scale Oligonucleotide Selection Using the Longest Common Factor Approach. J. Bioinform. Comput. Biol. 1 (2) (2003)
Alexander Schliep, David C. Torney, Sven Rahmann
Group Testing With DNA Chips: Generating Designs and Decoding Experiments. CSB (2003)
Sven Rahmann, Eric Rivals
On The Distribution Of The Number Of Missing Words In Random Texts. Comb. Probab. Comput. 12 (1) (2003)
Sven Rahmann
Dynamic Programming Algorithms for Two Statistical Problems in Computational Biology. WABI (2003)
Sven Rahmann
Fast and Sensitive Probe Selection for DNA Chips Using Jumps in Matching Statistics. CSB (2003)
Eric Rivals, Sven Rahmann
Combinatorics of periods in strings. J. Comb. Theory, Ser. A 104 (1) (2003)
Sven Rahmann
Rapid Large-Scale Oligonucleotide Selection for Microarrays. WABI (2002)
Sven Rahmann
Rapid Large-Scale Oligonucleotide Selection for Microarrays. CSB (2002)
Eric Rivals, Sven Rahmann
Combinatorics of Periods in Strings. ICALP (2001)
Tobias Müller, Sven Rahmann, Marc Rehmsmeier
Non-symmetric score matrices and the detection of homologous transmembrane proteins. ISMB (Supplement of Bioinformatics) (2001)
Sven Rahmann, Eric Rivals
Exact and Efficient Computation of the Expected Number of Missing and Common Words in Random Texts. CPM (2000)