Publications by authors named "Sven Rahmann"

82Publications

Machine learning reveals a PD-L1-independent prediction of response to immunotherapy of non-small cell lung cancer by gene expression context.

Eur J Cancer 2020 Oct 12;140:76-85. Epub 2020 Oct 12.

Department of Medical Oncology, West German Cancer Center, University Hospital Essen, University Duisburg-Essen, Hufelandstrasse 55, 45122 Essen, Germany; Division of Thoracic Oncology, University Medicine Essen - Ruhrlandklinik, University Duisburg-Essen, Tüschener Weg 40, 45239 Essen, Germany; German Cancer Consortium (DKTK), Partner Site University Hospital Essen, Hufelandstrasse 55, 45122 Essen, Germany. Electronic address:

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http://dx.doi.org/10.1016/j.ejca.2020.09.015DOI Listing
October 2020

A germ cell-specific ageing pattern in otherwise healthy men.

Aging Cell 2020 Oct 20;19(10):e13242. Epub 2020 Sep 20.

Centre of Reproductive Medicine and Andrology, University of Münster, Münster, Germany.

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http://dx.doi.org/10.1111/acel.13242DOI Listing
October 2020

Meiotic recombination in the offspring of Microbotryum hybrids and its impact on pathogenicity.

BMC Evol Biol 2020 Sep 17;20(1):123. Epub 2020 Sep 17.

AG Geobotanik, Ruhr-Universität Bochum, Universitätsstraße 150, 44780, Bochum, Germany.

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http://dx.doi.org/10.1186/s12862-020-01689-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7499883PMC
September 2020

wg-blimp: an end-to-end analysis pipeline for whole genome bisulfite sequencing data.

BMC Bioinformatics 2020 May 1;21(1):169. Epub 2020 May 1.

Institute of Human Genetics, University of Duisburg-Essen, University Hospital Essen, Hufelandstraße 55, Essen, 45147, Germany.

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http://dx.doi.org/10.1186/s12859-020-3470-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7195798PMC
May 2020

Silver stress differentially affects growth of phototrophic and heterotrophic chrysomonad flagellate populations.

Environ Pollut 2019 Jan 11;244:314-322. Epub 2018 Oct 11.

Aquatic Ecology, University of Duisburg-Essen, Universitätsstr. 5, 45141 Essen, Germany; Centre for Water and Environmental Research (ZWU), University of Duisburg-Essen, Universitätsstr. 5, 45141 Essen, Germany.

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http://dx.doi.org/10.1016/j.envpol.2018.09.146DOI Listing
January 2019

Snakemake-a scalable bioinformatics workflow engine.

Bioinformatics 2018 10;34(20):3600

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http://dx.doi.org/10.1093/bioinformatics/bty350DOI Listing
October 2018

Modeling and simulating networks of interdependent protein interactions.

Integr Biol (Camb) 2018 05;10(5):290-305

Genome Informatics, Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany.

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http://dx.doi.org/10.1039/c8ib00012cDOI Listing
May 2018

Locus-Specific DNA Methylation Analysis by Targeted Deep Bisulfite Sequencing.

Methods Mol Biol 2018 ;1767:351-366

Institute of Human Genetics, University of Duisburg-Essen, University Hospital Essen, Essen, Germany.

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http://dx.doi.org/10.1007/978-1-4939-7774-1_19DOI Listing
February 2019

Evolution of heterotrophy in chrysophytes as reflected by comparative transcriptomics.

FEMS Microbiol Ecol 2018 04;94(4)

Biodiversity, Faculty of Biology, University of Duisburg-Essen, Universitätsstr. 5, D-45141 Essen, Germany.

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http://dx.doi.org/10.1093/femsec/fiy039DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6019013PMC
April 2018

Cancer evolution, mutations, and clonal selection in relapse neuroblastoma.

Cell Tissue Res 2018 May 24;372(2):263-268. Epub 2018 Feb 24.

Molecular Oncology, Internal Medicine/Cancer Research Unit, University Hospital Essen, University of Duisburg-Essen, Hufelandstraße 55, 45147, Essen, Germany.

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http://dx.doi.org/10.1007/s00441-018-2810-5DOI Listing
May 2018

ddrage: A data set generator to evaluate ddRADseq analysis software.

Mol Ecol Resour 2018 May 27;18(3):681-690. Epub 2017 Dec 27.

Genome Informatics, Institute of Human Genetics, University of Duisburg-Essen, University Hospital Essen, Essen, Germany.

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http://doi.wiley.com/10.1111/1755-0998.12743
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http://dx.doi.org/10.1111/1755-0998.12743DOI Listing
May 2018

TaxMapper: an analysis tool, reference database and workflow for metatranscriptome analysis of eukaryotic microorganisms.

BMC Genomics 2017 Oct 16;18(1):787. Epub 2017 Oct 16.

Genome Informatics, University of Duisburg-Essen, University Hospital Essen, Hufelandstr. 55, Essen, 45147, Germany.

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http://dx.doi.org/10.1186/s12864-017-4168-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5644092PMC
October 2017

A hybrid parameter estimation algorithm for beta mixtures and applications to methylation state classification.

Algorithms Mol Biol 2017 18;12:21. Epub 2017 Aug 18.

Genome Informatics, Institute of Human Genetics, University of Duisburg-Essen, University Hospital Essen, Hufelandstr. 55, 45147 Essen, Germany.

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http://dx.doi.org/10.1186/s13015-017-0112-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5563068PMC
August 2017

Trade-off between taxon diversity and functional diversity in European lake ecosystems.

Mol Ecol 2016 Dec 14;25(23):5876-5888. Epub 2016 Nov 14.

Biodiversity Department and Centre for Water and Environmental Research, University of Duisburg-Essen, 45141, Essen, Germany.

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http://dx.doi.org/10.1111/mec.13878DOI Listing
December 2016

SimLoRD: Simulation of Long Read Data.

Bioinformatics 2016 09 10;32(17):2704-6. Epub 2016 May 10.

Genome Informatics, Institute of Human Genetics, University of Duisburg-Essen, Essen, 45147, Germany.

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https://academic.oup.com/bioinformatics/article-lookup/doi/1
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http://dx.doi.org/10.1093/bioinformatics/btw286DOI Listing
September 2016

Recurrent alterations of TNFAIP3 (A20) in T-cell large granular lymphocytic leukemia.

Int J Cancer 2016 Jan 30;138(1):121-4. Epub 2015 Jul 30.

Institute of Cell Biology (Cancer Research), Medical Faculty, University of Duisburg-Essen, Essen, Germany.

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http://dx.doi.org/10.1002/ijc.29697DOI Listing
January 2016

An online peak extraction algorithm for ion mobility spectrometry data.

Algorithms Mol Biol 2015 13;10:17. Epub 2015 May 13.

Bioinformatics for High-Throughput Technologies, Computer Science XI, and Collaborative Research Center SFB 876, TU Dortmund, Dortmund, Germany ; Genome Informatics, Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Essen, Germany.

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http://dx.doi.org/10.1186/s13015-015-0045-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4495807PMC
July 2015

Mutational dynamics between primary and relapse neuroblastomas.

Nat Genet 2015 Aug 29;47(8):872-7. Epub 2015 Jun 29.

1] Pediatric Oncology and Hematology, University Children's Hospital Essen, University of Duisburg-Essen, Essen, Germany. [2] Pediatric Oncology and Hematology, Charité University Medicine, Berlin, Germany. [3] German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany.

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http://search.proquest.com/openview/bef3fe020af3cd6708016aba
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http://dx.doi.org/10.1038/ng.3349DOI Listing
August 2015

N6-adenosine methylation in MiRNAs.

PLoS One 2015 27;10(2):e0118438. Epub 2015 Feb 27.

Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Essen, Germany.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0118438PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4344304PMC
November 2015

Massively parallel read mapping on GPUs with the q-group index and PEANUT.

PeerJ 2014 30;2:e606. Epub 2014 Sep 30.

Genome Informatics, Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen , Germany.

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http://dx.doi.org/10.7717/peerj.606DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4184027PMC
October 2014

Supratentorial ependymomas of childhood carry C11orf95-RELA fusions leading to pathological activation of the NF-κB signaling pathway.

Acta Neuropathol 2014 Apr 22;127(4):609-11. Epub 2014 Feb 22.

Department of Neuropathology, University of Bonn, Sigmund-Freud-St. 25, 53105, Bonn, Germany,

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http://dx.doi.org/10.1007/s00401-014-1264-4DOI Listing
April 2014

A modular computational framework for automated peak extraction from ion mobility spectra.

BMC Bioinformatics 2014 Jan 22;15:25. Epub 2014 Jan 22.

Collaborative Research Center SFB 876, TU Dortmund University, Dortmund, Germany.

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http://dx.doi.org/10.1186/1471-2105-15-25DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3930762PMC
January 2014

Discovering motifs that induce sequencing errors.

BMC Bioinformatics 2013 10;14 Suppl 5:S1. Epub 2013 Apr 10.

Life Sciences Group, Centrum Wiskunde & Informatica, Amsterdam, Netherlands.

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http://dx.doi.org/10.1186/1471-2105-14-S5-S1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3622629PMC
December 2013

Peak detection method evaluation for ion mobility spectrometry by using machine learning approaches.

Metabolites 2013 Apr 16;3(2):277-93. Epub 2013 Apr 16.

Computational Systems Biology Group, Max Planck Institute for Informatics, Saarbrücken, Germany.

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http://dx.doi.org/10.3390/metabo3020277DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3901270PMC
April 2013

Identifying transcriptional miRNA biomarkers by integrating high-throughput sequencing and real-time PCR data.

Methods 2013 Jan 23;59(1):154-63. Epub 2012 Oct 23.

Bioinformatics, Computer Science XI, TU Dortmund, Germany; Collaborative Research Center (SFB) 876, TU Dortmund, Germany.

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http://dx.doi.org/10.1016/j.ymeth.2012.10.005DOI Listing
January 2013

Snakemake--a scalable bioinformatics workflow engine.

Bioinformatics 2012 Oct 20;28(19):2520-2. Epub 2012 Aug 20.

Genome Informatics, Institute of Human Genetics, University of Duisburg-Essen and Paediatric Oncology, University Childrens Hospital, 45147 Essen, Germany.

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http://dx.doi.org/10.1093/bioinformatics/bts480DOI Listing
October 2012

Probabilistic arithmetic automata and their applications.

IEEE/ACM Trans Comput Biol Bioinform 2012 Nov-Dec;9(6):1737-50

Life Sciences Group, Centrum Wiskunde & Informatica (CWI), Science Park 123, 1098 XG Amsterdam, TheNetherlands.

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http://ieeexplore.ieee.org/document/6257364/
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http://dx.doi.org/10.1109/TCBB.2012.109DOI Listing
July 2013

Efficiently mining protein interaction dependencies from large text corpora.

Integr Biol (Camb) 2012 Jul 15;4(7):805-12. Epub 2012 Jun 15.

Genome Informatics, Institute of Human Genetics, Faculty of Medicine, University of Duisburg-Essen, Essen, Germany.

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http://dx.doi.org/10.1039/c2ib00126hDOI Listing
July 2012

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

BMC Bioinformatics 2011 Feb 3;12:47. Epub 2011 Feb 3.

Laboratoire MAP5 (UMR CNRS 8145), Université Paris Descartes, Paris, France.

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http://bmcbioinformatics.biomedcentral.com/articles/10.1186/
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http://dx.doi.org/10.1186/1471-2105-12-47DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3042914PMC
February 2011

Efficient online transcription factor binding site adjustment by integrating transitive graph projection with MoRAine 2.0.

J Integr Bioinform 2010 Mar 25;7(3). Epub 2010 Mar 25.

Genome Informatics, Bielefeld University, Bielefeld, Germany.

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http://dx.doi.org/10.2390/biecoll-jib-2010-117DOI Listing
March 2010

Detecting species-site dependencies in large multiple sequence alignments.

Nucleic Acids Res 2009 Oct 6;37(18):5959-68. Epub 2009 Aug 6.

Institute of Hygiene and Microbiology, Josef-Schneider-Strasse 2/E1, 97080, Germany.

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http://dx.doi.org/10.1093/nar/gkp634DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2764451PMC
October 2009

Efficient exact motif discovery.

Bioinformatics 2009 Jun;25(12):i356-64

Computer Science Department, Bioinformatics for High-Throughput Technologies at the Chair of Algorithm Engineering, TU Dortmund, Dortmund, Germany.

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https://academic.oup.com/bioinformatics/article-lookup/doi/1
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http://dx.doi.org/10.1093/bioinformatics/btp188DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2687942PMC
June 2009

Modelling cross-hybridization on phylogenetic DNA microarrays increases the detection power of closely related species.

Mol Ecol Resour 2009 Jan 6;9(1):83-93. Epub 2008 Oct 6.

Department of Bioinformatics, Biocentre, University of Würzburg, Am Hubland, D-97074 Würzburg, Germany.

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http://dx.doi.org/10.1111/j.1755-0998.2008.02199.xDOI Listing
January 2009

Towards the integrated analysis, visualization and reconstruction of microbial gene regulatory networks.

Brief Bioinform 2009 Jan 12;10(1):75-83. Epub 2008 Dec 12.

International Computer Science Institute, Berkeley, USA.

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https://academic.oup.com/bib/article-lookup/doi/10.1093/bib/
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http://dx.doi.org/10.1093/bib/bbn055DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2638629PMC
January 2009

Compound poisson approximation of the number of occurrences of a position frequency matrix (PFM) on both strands.

J Comput Biol 2008 Jul-Aug;15(6):547-64

Computational Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany.

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http://dx.doi.org/10.1089/cmb.2007.0084DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2607244PMC
October 2008

Better genechip microarray layouts by combining probe placement and embedding.

J Bioinform Comput Biol 2008 Jun;6(3):623-41

Computational Methods for Emerging Technologies, Genome Informatics, Technische Fakultät, Bielefeld University, D-33594 Bielefeld, Germany.

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http://dx.doi.org/10.1142/s0219720008003576DOI Listing
June 2008

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

Bioinformatics 2008 Feb 2;24(3):350-7. Epub 2008 Jan 2.

Computational Biology, Max Planck Institute f. Molecular Genetics, Ihnestr. 73, 14195 Berlin, Germany.

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http://dx.doi.org/10.1093/bioinformatics/btm610DOI Listing
February 2008

MoRAine--a web server for fast computational transcription factor binding motif re-annotation.

J Integr Bioinform 2008 Aug 25;5(2). Epub 2008 Aug 25.

Genome Informatics, Faculty of Technology, Bielefeld University, D-33594 Bielefeld, Germany.

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http://dx.doi.org/10.2390/biecoll-jib-2008-91DOI Listing
August 2008

Improving the design of genechip arrays by combining placement and embedding.

Comput Syst Bioinformatics Conf 2007 ;6:417-27

Computational Methods for Emerging Technologies, Genome Informatics, Technische Fakultät, Bielefeld University, D-33594 Bielefeld, Germany.

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December 2007

Exact and heuristic algorithms for weighted cluster editing.

Comput Syst Bioinformatics Conf 2007 ;6:391-401

Computational Methods for Emerging Technologies group, Genome Informatics, Technische Fakultät, Bielefeld University, D-33594 Bielefeld, Germany.

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December 2007

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

BMC Bioinformatics 2007 Oct 17;8:396. Epub 2007 Oct 17.

Computational Methods for Emerging Technologies, Bielefeld University, Bielefeld, Germany.

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http://bmcbioinformatics.biomedcentral.com/articles/10.1186/
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http://dx.doi.org/10.1186/1471-2105-8-396DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2147039PMC
October 2007

Deep metazoan phylogeny.

In Silico Biol 2007 ;7(2):151-4

Department of Bioinformatics, Biocenter, University of Würzburg, Am Hubland, D-97074 Würzburg, Germany.

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January 2008

CoryneRegNet 3.0--an interactive systems biology platform for the analysis of gene regulatory networks in corynebacteria and Escherichia coli.

J Biotechnol 2007 Apr 20;129(2):279-89. Epub 2006 Dec 20.

Algorithms and Statistics for Systems Biology Group, Genominformatik, Technische Fakultät, Universität Bielefeld, Universitätsstrasse 25, D-33615 Bielefeld, Germany.

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http://linkinghub.elsevier.com/retrieve/pii/S016816560601033
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http://dx.doi.org/10.1016/j.jbiotec.2006.12.012DOI Listing
April 2007

Decoding non-unique oligonucleotide hybridization experiments of targets related by a phylogenetic tree.

Bioinformatics 2006 Jul;22(14):e424-30

Dept. Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, D-14195 Berlin, Germany.

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https://academic.oup.com/bioinformatics/article-lookup/doi/1
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http://dx.doi.org/10.1093/bioinformatics/btl254DOI Listing
July 2006

On the power of profiles for transcription factor binding site detection.

Stat Appl Genet Mol Biol 2003 29;2:Article7. Epub 2003 Nov 29.

Computational Molecular Biology, Max Planck Institute for Molecular Genetics, and Department of Mathematics and Computer Science, Freie Universität Berlin.

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http://dx.doi.org/10.2202/1544-6115.1032DOI Listing
May 2006

CoryneRegNet: an ontology-based data warehouse of corynebacterial transcription factors and regulatory networks.

BMC Genomics 2006 Feb 14;7:24. Epub 2006 Feb 14.

International NRW Graduate School in Bioinformatics and Genome Research, Centrum für Biotechnologie, Universität Bielefeld, Universitätsstrasse 25, D-33615 Bielefeld, Germany.

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http://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2
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http://dx.doi.org/10.1186/1471-2164-7-24DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1382212PMC
February 2006

Group testing with DNA chips: generating designs and decoding experiments.

Proc IEEE Comput Soc Bioinform Conf 2003 ;2:84-91

Department of Computational Molecular Biology, Max-Planck-Institute for Molecular Genetics, Inestrasse 63-73, D-14195 Berlin , Germany.

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August 2006

Fast and sensitive probe selection for DNA chips using jumps in matching statistics.

Authors:
Sven Rahmann

Proc IEEE Comput Soc Bioinform Conf 2003 ;2:57-64

Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Inestrasse 73, D-14195 Berlin, Germany.

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August 2006

T-Reg Comparator: an analysis tool for the comparison of position weight matrices.

Nucleic Acids Res 2005 Jul;33(Web Server issue):W438-41

Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195 Berlin, Germany.

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http://dx.doi.org/10.1093/nar/gki590DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1160266PMC
July 2005

Rapid large-scale oligonucleotide selection for microarrays.

Authors:
Sven Rahmann

Proc IEEE Comput Soc Bioinform Conf 2002 ;1:54-63

Computational Molecular Biology, MPI for Molecular Genetics, Dept. of Mathematics and Computer Science, Free University of Berlin, Berlin, Germany.

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May 2005

Fast large scale oligonucleotide selection using the longest common factor approach.

Authors:
Sven Rahmann

J Bioinform Comput Biol 2003 Jul;1(2):343-61

Max-Planck-Institute for Molecular Genetics, Ihnestrasse 63-73, D-14195 Berlin, Germany.

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http://dx.doi.org/10.1142/s0219720003000125DOI Listing
July 2003

Optimal robust non-unique probe selection using Integer Linear Programming.

Bioinformatics 2004 Aug;20 Suppl 1:i186-93

Institute of Computer Graphics and Algorithms, Vienna University of Technology, Vienna, Austria.

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http://dx.doi.org/10.1093/bioinformatics/bth936DOI Listing
August 2004

Functional inference from non-random distributions of conserved predicted transcription factor binding sites.

Bioinformatics 2004 Aug;20 Suppl 1:i109-15

Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany.

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http://dx.doi.org/10.1093/bioinformatics/bth908DOI Listing
August 2004

Accurate and robust phylogeny estimation based on profile distances: a study of the Chlorophyceae (Chlorophyta).

BMC Evol Biol 2004 Jun 28;4:20. Epub 2004 Jun 28.

Department of Bioinformatics, Biocenter, University of Würzburg, Am Hubland, D-97074 Würzburg, Germany.

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http://bmcevolbiol.biomedcentral.com/articles/10.1186/1471-2
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http://dx.doi.org/10.1186/1471-2148-4-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC449703PMC
June 2004

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

Bioinformatics 2004 Nov 16;20(17):2928-33. Epub 2004 Jun 16.

Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Ihnestrasse 73, D-14195 Berlin, Germany.

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http://dx.doi.org/10.1093/bioinformatics/bth334DOI Listing
November 2004

HMM Logos for visualization of protein families.

BMC Bioinformatics 2004 Jan 21;5. Epub 2004 Jan 21.

Department of Mathematics and Computer Science, Freie Universität Berlin, Germany.

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http://dx.doi.org/10.1186/1471-2105-5-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC341448PMC
January 2004

The shortest common supersequence problem in a microarray production setting.

Authors:
Sven Rahmann

Bioinformatics 2003 Oct;19 Suppl 2:ii156-61

Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany.

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http://dx.doi.org/10.1093/bioinformatics/btg1073DOI Listing
October 2003