Steve Hoffmann

Steve Hoffmann

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Steve Hoffmann

Steve Hoffmann

Publications by authors named "Steve Hoffmann"

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DREAM and RB cooperate to induce gene repression and cell-cycle arrest in response to p53 activation.

Nucleic Acids Res 2019 Sep;47(17):9087-9103

Molecular Oncology, Department of Gynaecology, Medical School, Leipzig University, 04103 Leipzig, Germany.

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http://dx.doi.org/10.1093/nar/gkz635DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6753476PMC
September 2019

RBFOX2 and alternative splicing in B-cell lymphoma.

Blood Cancer J 2018 08 10;8(8):77. Epub 2018 Aug 10.

Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.

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http://dx.doi.org/10.1038/s41408-018-0114-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6086906PMC
August 2018

DIEGO: detection of differential alternative splicing using Aitchison's geometry.

Bioinformatics 2018 03;34(6):1066-1068

Transcriptome Bioinformatics Group, Interdisciplinary Center for Bioinformatics, Leipzig University, 04107 Leipzig.

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http://dx.doi.org/10.1093/bioinformatics/btx690DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5860559PMC
March 2018

Generalized enhanced suffix array construction in external memory.

Algorithms Mol Biol 2017 7;12:26. Epub 2017 Dec 7.

Institute of Mathematics and Computer Science, University of São Paulo, Av. Trabalhador São-carlense, 400, São Carlos, 13560-970 Brazil.

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http://dx.doi.org/10.1186/s13015-017-0117-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5719966PMC
December 2017

Customized workflow development and data modularization concepts for RNA-Sequencing and metatranscriptome experiments.

J Biotechnol 2017 Nov 1;261:85-96. Epub 2017 Jul 1.

Genetics and Experimental Bioinformatics, Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S01681656173149
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http://dx.doi.org/10.1016/j.jbiotec.2017.06.1203DOI Listing
November 2017

Keeping it complicated: Mitochondrial genome plasticity across diplonemids.

Sci Rep 2017 10 26;7(1):14166. Epub 2017 Oct 26.

Department of biochemistry and Robert-Cedergren Centre for Bioinformatics and Genomics, Université de Montréal, 2900 Edouard-Montpetit, Montreal, H3T 1J4, QC, Canada.

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http://dx.doi.org/10.1038/s41598-017-14286-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5658414PMC
October 2017

metilene: fast and sensitive calling of differentially methylated regions from bisulfite sequencing data.

Genome Res 2016 Feb 2;26(2):256-62. Epub 2015 Dec 2.

Transcriptome Bioinformatics Group, LIFE - Leipzig Research Center for Civilization Diseases, University of Leipzig, 04107 Leipzig, Germany; Interdisciplinary Center for Bioinformatics and Bioinformatics Group, Faculty of Computer Science, University of Leipzig, 04107 Leipzig, Germany;

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http://dx.doi.org/10.1101/gr.196394.115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4728377PMC
February 2016

Reply to Hart et al.: MINCR and MYC: More than expression correlation.

Proc Natl Acad Sci U S A 2016 Feb 25;113(5):E498. Epub 2016 Jan 25.

Institute of Human Genetics, University Hospital Schleswig-Holstein, Christian-Albrechts-University, D-24105 Kiel, Germany; Institute of Genetics and Biophysics "A.Buzzati-Traverso", Consiglio Nazionale delle Ricerche, I-80131 Naples, Italy

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http://dx.doi.org/10.1073/pnas.1520413113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4747763PMC
February 2016

A simple data-adaptive probabilistic variant calling model.

Algorithms Mol Biol 2015 4;10:10. Epub 2015 Mar 4.

Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Härtelstraße 16-18, Leipzig, D-04107 Germany ; Department of Epidemiology and Biostatistics, Imperial College London, Norfolk Place, London W2 1PG, UK.

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http://dx.doi.org/10.1186/s13015-015-0037-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4363181PMC
March 2015

Atypical RNAs in the coelacanth transcriptome.

J Exp Zool B Mol Dev Evol 2014 Sep 30;322(6):342-51. Epub 2013 Oct 30.

Department of Computer Science, Bioinformatics Group, University of Leipzig, Leipzig, Germany; Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany.

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http://dx.doi.org/10.1002/jez.b.22542DOI Listing
September 2014

Lacking alignments? The next-generation sequencing mapper segemehl revisited.

Bioinformatics 2014 Jul 13;30(13):1837-43. Epub 2014 Mar 13.

Transcriptome Bioinformatics Junior Research Group, LIFE-Leipzig Research Center for Civilization Diseases, Interdisciplinary Center for Bioinformatics, Bioinformatics Group, Department of Computer Science, University Leipzig, RNomics Group, Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany, Santa Fe Institute, Santa Fe, New Mexico, USA, Department of Theoretical Chemistry, University of Vienna, Austria, Max-Planck-Institute for Mathematics in Sciences, Leipzig, Germany and Center for non-coding RNA in Technology and Health, University of Copenhagen, DenmarkTranscriptome Bioinformatics Junior Research Group, LIFE-Leipzig Research Center for Civilization Diseases, Interdisciplinary Center for Bioinformatics, Bioinformatics Group, Department of Computer Science, University Leipzig, RNomics Group, Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany, Santa Fe Institute, Santa Fe, New Mexico, USA, Department of Theoretical Chemistry, University of Vienna, Austria, Max-Planck-Institute for Mathematics in Sciences, Leipzig, Germany and Center for non-coding RNA in Technology and Health, University of Copenhagen, Denmark.

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http://dx.doi.org/10.1093/bioinformatics/btu146DOI Listing
July 2014

A first glimpse at the genome of the Baikalian amphipod Eulimnogammarus verrucosus.

J Exp Zool B Mol Dev Evol 2014 May 12;322(3):177-89. Epub 2014 Feb 12.

Department of Bioanalytical Ecotoxicology, UFZ-Helmholtz Centre for Environmental Research, Leipzig, Germany; Interdisciplinary Center for Bioinformatics, University Leipzig, Leipzig, Germany.

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http://dx.doi.org/10.1002/jez.b.22560DOI Listing
May 2014

Mapping the RNA-Seq trash bin: unusual transcripts in prokaryotic transcriptome sequencing data.

RNA Biol 2013 Jul 13;10(7):1204-10. Epub 2013 May 13.

Bioinformatics Group; Department of Computer Science, and Interdisciplinary Center for Bioinformatics; University of Leipzig; Leipzig, Germany; Transcriptome Bioinformatics; LIFE - Leipzig Research Center for Civilization Diseases; University of Leipzig; Leipzig, Germany.

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http://dx.doi.org/10.4161/rna.24972DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3849169PMC
July 2013

Identification of purple sea urchin telomerase RNA using a next-generation sequencing based approach.

RNA 2013 Jun 12;19(6):852-60. Epub 2013 Apr 12.

Department of Chemistry & Biochemistry, Arizona State University, Tempe, Arizona 85287, USA.

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http://dx.doi.org/10.1261/rna.039131.113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3683918PMC
June 2013

The African coelacanth genome provides insights into tetrapod evolution.

Nature 2013 Apr;496(7445):311-6

Molecular Genetics Program, Benaroya Research Institute, Seattle, Washington 98101, USA.

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http://dx.doi.org/10.1038/nature12027DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3633110PMC
April 2013

Dicer-processed small RNAs: rules and exceptions.

J Exp Zool B Mol Dev Evol 2013 Jan 16;320(1):35-46. Epub 2012 Nov 16.

LIFE, Leipzig Research Center for Civilization Diseases, University Leipzig, Leipzig, Germany.

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http://dx.doi.org/10.1002/jez.b.22481DOI Listing
January 2013

Fast and sensitive mapping of bisulfite-treated sequencing data.

Bioinformatics 2012 Jul 10;28(13):1698-704. Epub 2012 May 10.

Interdisciplinary Center for Bioinformatics and Bioinformatics Group, Department of Computer Science, University Leipzig, 04107 Leipzig, Germany.

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http://dx.doi.org/10.1093/bioinformatics/bts254DOI Listing
July 2012

Genome-wide transcriptome analysis of the plant pathogen Xanthomonas identifies sRNAs with putative virulence functions.

Nucleic Acids Res 2012 Mar 12;40(5):2020-31. Epub 2011 Nov 12.

Department of Genetics, Martin-Luther-Universität Halle-Wittenberg, Institute for Biology, D-06099 Halle, Germany.

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http://dx.doi.org/10.1093/nar/gkr904DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3300014PMC
March 2012

deepBlockAlign: a tool for aligning RNA-seq profiles of read block patterns.

Bioinformatics 2012 Jan 3;28(1):17-24. Epub 2011 Nov 3.

Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, Universität Leipzig, Philipp-Rosenthal-Strasse 27, D-04107 Leipzig, Germany.

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http://dx.doi.org/10.1093/bioinformatics/btr598DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3244762PMC
January 2012

DARIO: a ncRNA detection and analysis tool for next-generation sequencing experiments.

Nucleic Acids Res 2011 Jul 27;39(Web Server issue):W112-7. Epub 2011 May 27.

Interdisciplinary Center for Bioinformatics and Bioinformatics Group, Department of Computer Science, University Leipzig, Germany.

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https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/
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http://dx.doi.org/10.1093/nar/gkr357DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3125765PMC
July 2011

Computational analysis of high throughput sequencing data.

Authors:
Steve Hoffmann

Methods Mol Biol 2011 ;719:199-217

Interdisciplinary Center for Bioinformatics and The Junior Research Group for Transcriptome Bioinformatics in the LIFE Research Cluster, University Leipzig, Leipzig, Germany.

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http://dx.doi.org/10.1007/978-1-61779-027-0_9DOI Listing
June 2011

Traces of post-transcriptional RNA modifications in deep sequencing data.

Biol Chem 2011 Apr 24;392(4):305-13. Epub 2011 Feb 24.

Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelsrtrasse 16-18, Leipzig, Germany.

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http://dx.doi.org/10.1515/BC.2011.043DOI Listing
April 2011

Fast local fragment chaining using sum-of-pair gap costs.

Algorithms Mol Biol 2011 Mar 18;6. Epub 2011 Mar 18.

Bioinformatics Group, Dept, of Computer Science, University of Leipzig, Germany.

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http://dx.doi.org/10.1186/1748-7188-6-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3072320PMC
March 2011

Multi-platform next-generation sequencing of the domestic turkey (Meleagris gallopavo): genome assembly and analysis.

PLoS Biol 2010 Sep 7;8(9). Epub 2010 Sep 7.

Avian Immunobiology Laboratory, Department of Animal and Poultry Sciences, Virginia Tech, Blacksburg, Virginia, United States of America.

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http://dx.doi.org/10.1371/journal.pbio.1000475DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2935454PMC
September 2010

The primary transcriptome of the major human pathogen Helicobacter pylori.

Nature 2010 Mar 17;464(7286):250-5. Epub 2010 Feb 17.

Max Planck Institute for Infection Biology, RNA Biology Group, D-10117 Berlin, Germany.

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http://dx.doi.org/10.1038/nature08756DOI Listing
March 2010

Evolution of vault RNAs.

Mol Biol Evol 2009 Sep 2;26(9):1975-91. Epub 2009 Jun 2.

Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany.

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http://dx.doi.org/10.1093/molbev/msp112DOI Listing
September 2009

Evidence for human microRNA-offset RNAs in small RNA sequencing data.

Bioinformatics 2009 Sep 6;25(18):2298-301. Epub 2009 Jul 6.

Department of Computer Science, University of Leipzig, Leipzig, Germany.

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http://dx.doi.org/10.1093/bioinformatics/btp419DOI Listing
September 2009

Fast mapping of short sequences with mismatches, insertions and deletions using index structures.

PLoS Comput Biol 2009 Sep 11;5(9):e1000502. Epub 2009 Sep 11.

Bioinformatics Group, Department of Computer Science, University of Leipzig, Leipzig, Germany.

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http://dx.doi.org/10.1371/journal.pcbi.1000502DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2730575PMC
September 2009

The role of the polio virus receptor and the herpesvirus entry mediator B genes for the development of MS.

J Neuroimmunol 2004 Nov;156(1-2):171-7

Clinical Neuroimmunology Group, Department of Neurology, Philipps-University, Marburg, Germany; Department of Neurology, Heinrich-Heine-University, Duesseldorf, Germany.

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http://linkinghub.elsevier.com/retrieve/pii/S016557280400226
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http://dx.doi.org/10.1016/j.jneuroim.2004.07.001DOI Listing
November 2004

ORFer--retrieval of protein sequences and open reading frames from GenBank and storage into relational databases or text files.

BMC Bioinformatics 2002 Dec 19;3:40. Epub 2002 Dec 19.

Protein Structure Factory, Max Planck Institute of Molecular Genetics, Heubnerweg 6, 14059 Berlin, Germany.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC139979PMC
December 2002

A novel mutation in PTPRC interferes with splicing and alters the structure of the human CD45 molecule.

Immunogenetics 2002 Jun 27;54(3):158-63. Epub 2002 Apr 27.

Department of Neurology, Philipps University, Rudolf-Bultmann Strasse 8, 35033 Marburg, Germany.

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http://dx.doi.org/10.1007/s00251-002-0455-7DOI Listing
June 2002