Sven Rahmann

According to our database1, Sven Rahmann authored at least 77 papers between 2000 and 2020.

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Bibliography

2020
Cost-optimal assignment of elements in genome-scale multi-way bucketed Cuckoo hash tables.
Proceedings of the Symposium on Algorithm Engineering and Experiments, 2020

2019
Protein Complex Similarity Based on Weisfeiler-Lehman Labeling.
Proceedings of the Similarity Search and Applications - 12th International Conference, 2019

2018
Snakemake - a scalable bioinformatics workflow engine.
Bioinformatics, 2018

Spalter: A Meta Machine Learning Approach to Distinguish True DNA Variants from Sequencing Artefacts.
Proceedings of the 18th International Workshop on Algorithms in Bioinformatics, 2018

2017
Variant tolerant read mapping using min-hashing.
CoRR, 2017

A hybrid parameter estimation algorithm for beta mixtures and applications to methylation state classification.
Algorithms for Molecular Biology, 2017

Analysis of Min-Hashing for Variant Tolerant DNA Read Mapping.
Proceedings of the 17th International Workshop on Algorithms in Bioinformatics, 2017

2016
SimLoRD: Simulation of Long Read Data.
Bioinformatics, 2016

2015
Efficient duplicate rate estimation from subsamples of sequencing libraries.
PeerJ PrePrints, 2015

Invited presentations, junior research groups and research highlights at GCB 2015.
PeerJ PrePrints, 2015

An optimization approach to detect differentially methylated regions from Whole Genome Bisulfite Sequencing data.
PeerJ PrePrints, 2015

Poster abstracts of GCB 2015.
PeerJ PrePrints, 2015

An online peak extraction algorithm for ion mobility spectrometry data.
Algorithms for Molecular Biology, 2015

2014
Massively parallel read mapping on GPUs with PEANUT.
CoRR, 2014

Using the Expectation Maximization Algorithm with Heterogeneous Mixture Components for the Analysis of Spectrometry Data.
CoRR, 2014

A modular computational framework for automated peak extraction from ion mobility spectra.
BMC Bioinformatics, 2014

2013
Discovering motifs that induce sequencing errors.
BMC Bioinformatics, 2013

Aligning Flowgrams to DNA Sequences.
Proceedings of the German Conference on Bioinformatics 2013, 2013

PanCake: A Data Structure for Pangenomes.
Proceedings of the German Conference on Bioinformatics 2013, 2013

2012
Probabilistic Arithmetic Automata and Their Applications.
IEEE/ACM Trans. Comput. Biology Bioinform., 2012

Building and Documenting Workflows with Python-Based Snakemake.
Proceedings of the German Conference on Bioinformatics 2012, 2012

Designing q-Unique DNA Sequences with Integer Linear Programs and Euler Tours in De Bruijn Graphs.
Proceedings of the German Conference on Bioinformatics 2012, 2012

Peak modeling for Ion mobility spectrometry measurements.
Proceedings of the 20th European Signal Processing Conference, 2012

Solving the Minimum String Cover Problem.
Proceedings of the 14th Meeting on Algorithm Engineering & Experiments, 2012

2011
Extension and Robustness of Transitivity Clustering for Protein-Protein Interaction Network Analysis.
Internet Mathematics, 2011

Accurate statistics for local sequence alignment with position-dependent scoring by rare-event sampling.
BMC Bioinformatics, 2011

An Algorithm to Compute the Character Access Count Distribution for Pattern Matching Algorithms.
Algorithms, 2011

2010
Efficient Online Transcription Factor Binding Site Adjustment by Integrating Transitive Graph Projection with MoRAine 2.0.
J. Integrative Bioinformatics, 2010

Exact Analysis of Pattern Matching Algorithms with Probabilistic Arithmetic Automata
CoRR, 2010

Structural Identifiability in Low-Rank Matrix Factorization.
Algorithmica, 2010

Speeding Up Exact Motif Discovery by Bounding the Expected Clump Size.
Proceedings of the Algorithms in Bioinformatics, 10th International Workshop, 2010

Exact Analysis of Horspool's and Sunday's Pattern Matching Algorithms with Probabilistic Arithmetic Automata.
Proceedings of the Language and Automata Theory and Applications, 2010

Exact ILP solutions for phylogenetic minimum flip problems.
Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology, 2010

2009
Reliable transfer of transcriptional gene regulatory networks between taxonomically related organisms.
BMC Systems Biology, 2009

Efficient exact motif discovery.
Bioinformatics, 2009

Towards the integrated analysis, visualization and reconstruction of microbial gene regulatory networks.
Briefings in Bioinformatics, 2009

Modeling evolutionary fitness for DNA motif discovery.
Proceedings of the Genetic and Evolutionary Computation Conference, 2009

2008
Algorithms for subsequence combinatorics.
Theor. Comput. Sci., 2008

MoRAine - A web server for fast computational transcription factor binding motif re-annotation.
J. Integrative Bioinformatics, 2008

Compound Poisson Approximation of the Number of Occurrences of a Position Frequency Matrix (PFM) on Both Strands.
Journal of Computational Biology, 2008

Better GeneChip microarray Layouts by Combining Probe Placement and Embedding.
J. Bioinformatics and Computational Biology, 2008

Natural similarity measures between position frequency matrices with an application to clustering.
Bioinformatics, 2008

Computing Alignment Seed Sensitivity with Probabilistic Arithmetic Automata.
Proceedings of the Algorithms in Bioinformatics, 8th International Workshop, 2008

Probabilistic Arithmetic Automata and Their Application to Pattern Matching Statistics.
Proceedings of the Combinatorial Pattern Matching, 19th Annual Symposium, 2008

Structural Identifiability in Low-Rank Matrix Factorization.
Proceedings of the Computing and Combinatorics, 14th Annual International Conference, 2008

2007
IMS2 - An integrated medical software system for early lung cancer detection using ion mobility spectrometry data of human breath.
J. Integrative Bioinformatics, 2007

Deep Metazoan Phylogeny.
In Silico Biology, 2007

Integer linear programming approaches for non-unique probe selection.
Discret. Appl. Math., 2007

CoryneCenter - An online resource for the integrated analysis of corynebacterial genome and transcriptome data.
BMC Systems Biology, 2007

Large scale clustering of protein sequences with FORCE -A layout based heuristic for weighted cluster editing.
BMC Bioinformatics, 2007

2006
CoryneRegNet 2: An Integrative Bioinformatics Approach for Reconstruction and Comparison of Transcriptional Regulatory Networks in Prokaryotes.
J. Integrative Bioinformatics, 2006

Integer Linear Programs for Discovering Approximate Gene Clusters.
Proceedings of the Algorithms in Bioinformatics, 6th International Workshop, 2006

Improving the Layout of Oligonucleotide Microarrays: Pivot Partitioning.
Proceedings of the Algorithms in Bioinformatics, 6th International Workshop, 2006

Markov Additive Chains and Applications to Fragment Statistics for Peptide Mass Fingerprinting.
Proceedings of the Systems Biology and Computational Proteomics, 2006

Decoding non-unique oligonucleotide hybridization experiments of targets related by a phylogenetic tree.
Proceedings of the Proceedings 14th International Conference on Intelligent Systems for Molecular Biology 2006, 2006

Discovering Biomarkers for Myocardial Infarction from SELDI-TOF Spectra.
Proceedings of the Advances in Data Analysis, 2006

Microarray Layout as Quadratic Assignment Problem.
Proceedings of the German Conference on Bioinformatics GCB 2006, 19.09. 2006, 2006

Subsequence Combinatorics and Applications to Microarray Production, DNA Sequencing and Chaining Algorithms.
Proceedings of the Combinatorial Pattern Matching, 17th Annual Symposium, 2006

2005
T-Reg Comparator: an analysis tool for the comparison of position weight matrices.
Nucleic Acids Research, 2005

Editorial message: special track on bioinformatics.
Proceedings of the 2005 ACM Symposium on Applied Computing (SAC), 2005

2004
HMM Logos for visualization of protein families.
BMC Bioinformatics, 2004

Mean and variance of the Gibbs free energy of oligonucleotides in the nearest neighbor model under varying conditions.
Bioinformatics, 2004

Optimal robust non-unique probe selection using Integer Linear Programming.
Proceedings of the Proceedings Twelfth International Conference on Intelligent Systems for Molecular Biology/Third European Conference on Computational Biology 2004, 2004

Functional inference from non-random distributions of conserved predicted transcription factor binding sites.
Proceedings of the Proceedings Twelfth International Conference on Intelligent Systems for Molecular Biology/Third European Conference on Computational Biology 2004, 2004

Algorithmen für das Design von DNA-Microarrays.
Proceedings of the Ausgezeichnete Informatikdissertationen 2004, 2004

Algorithms for probe selection and DNA microarray design.
PhD thesis, 2004

2003
Combinatorics of periods in strings.
J. Comb. Theory, Ser. A, 2003

Fast Large Scale Oligonucleotide Selection Using the Longest Common Factor Approach.
J. Bioinformatics and Computational Biology, 2003

On The Distribution Of The Number Of Missing Words In Random Texts.
Combinatorics, Probability & Computing, 2003

Dynamic Programming Algorithms for Two Statistical Problems in Computational Biology.
Proceedings of the Algorithms in Bioinformatics, Third International Workshop, 2003

Robust estimation of the phylogeny of Chlorophyceae(Chlorophyta)based on profile distances.
Proceedings of the German Conference on Bioinformatics, 2003

The shortest common supersequence problem in a microarray production setting.
Proceedings of the European Conference on Computational Biology (ECCB 2003), 2003

Group Testing With DNA Chips: Generating Designs and Decoding Experiments.
Proceedings of the 2nd IEEE Computer Society Bioinformatics Conference, 2003

Fast and Sensitive Probe Selection for DNA Chips Using Jumps in Matching Statistics.
Proceedings of the 2nd IEEE Computer Society Bioinformatics Conference, 2003

2002
Rapid Large-Scale Oligonucleotide Selection for Microarrays.
Proceedings of the 1st IEEE Computer Society Bioinformatics Conference, 2002

2001
Non-symmetric score matrices and the detection of homologous transmembrane proteins.
Proceedings of the Ninth International Conference on Intelligent Systems for Molecular Biology, 2001

2000
Exact and Efficient Computation of the Expected Number of Missing and Common Words in Random Texts.
Proceedings of the Combinatorial Pattern Matching, 11th Annual Symposium, 2000


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