Publications by authors named "Thomas Manke"

60Publications

pyGenomeTracks: reproducible plots for multivariate genomic data sets.

Bioinformatics 2020 Aug 3. Epub 2020 Aug 3.

Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108 Freiburg im Breisgau, Germany.

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http://dx.doi.org/10.1093/bioinformatics/btaa692DOI Listing
August 2020

Galaxy HiCExplorer 3: a web server for reproducible Hi-C, capture Hi-C and single-cell Hi-C data analysis, quality control and visualization.

Nucleic Acids Res 2020 07;48(W1):W177-W184

Bioinformatics Group, Department of Computer Science, University of Freiburg, Georges-Köhler-Allee 106, 79110 Freiburg, Germany.

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http://dx.doi.org/10.1093/nar/gkaa220DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7319437PMC
July 2020

MAPCap allows high-resolution detection and differential expression analysis of transcription start sites.

Nat Commun 2019 07 30;10(1):3219. Epub 2019 Jul 30.

Max Planck Institute for Immunobiology and Epigenetics, 79108, Freiburg, Germany.

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http://dx.doi.org/10.1038/s41467-019-11115-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6667505PMC
July 2019

CAPRI enables comparison of evolutionarily conserved RNA interacting regions.

Nat Commun 2019 06 18;10(1):2682. Epub 2019 Jun 18.

Max Planck Institute of Immunobiology and Epigenetics, 79108, Freiburg im Breisgau, Germany.

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http://dx.doi.org/10.1038/s41467-019-10585-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6581911PMC
June 2019

DOT1L promotes progenitor proliferation and primes neuronal layer identity in the developing cerebral cortex.

Nucleic Acids Res 2019 01;47(1):168-183

Institute of Anatomy and Cell Biology, Department of Molecular Embryology, Medical Faculty, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany.

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http://dx.doi.org/10.1093/nar/gky953DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6326801PMC
January 2019

Differential Methylation of H3K79 Reveals DOT1L Target Genes and Function in the Cerebellum In Vivo.

Mol Neurobiol 2019 Jun 10;56(6):4273-4287. Epub 2018 Oct 10.

Institute for Anatomy and Cell Biology, Department of Molecular Embryology, Medical Faculty, University of Freiburg, 79104, Freiburg, Germany.

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http://link.springer.com/10.1007/s12035-018-1377-1
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http://dx.doi.org/10.1007/s12035-018-1377-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6505521PMC
June 2019

High-resolution TADs reveal DNA sequences underlying genome organization in flies.

Nat Commun 2018 01 15;9(1):189. Epub 2018 Jan 15.

Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108, Freiburg, Germany.

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http://dx.doi.org/10.1038/s41467-017-02525-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5768762PMC
January 2018

The histone code reader Spin1 controls skeletal muscle development.

Cell Death Dis 2017 11 23;8(11):e3173. Epub 2017 Nov 23.

Urologische Klinik und Zentrale Klinische Forschung, Klinikum der Universität Freiburg, Breisacher Str. 66, Freiburg, Germany.

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http://dx.doi.org/10.1038/cddis.2017.468DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5775400PMC
November 2017

DHX9 suppresses RNA processing defects originating from the Alu invasion of the human genome.

Nature 2017 04 29;544(7648):115-119. Epub 2017 Mar 29.

Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany.

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http://dx.doi.org/10.1038/nature21715DOI Listing
April 2017

Inactivation of Lsd1 triggers senescence in trophoblast stem cells by induction of Sirt4.

Cell Death Dis 2017 02 23;8(2):e2631. Epub 2017 Feb 23.

Urologische Klinik und Zentrale Klinische Forschung, Universitätsklinikum Freiburg, Medizinische Fakultät, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany.

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http://www.nature.com/articles/cddis201748
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http://dx.doi.org/10.1038/cddis.2017.48DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5386490PMC
February 2017

Lsd1 Ablation Triggers Metabolic Reprogramming of Brown Adipose Tissue.

Cell Rep 2016 10;17(4):1008-1021

Urologische Klinik und Zentrale Klinische Forschung, Klinikum der Universität Freiburg, Breisacherstrasse 66, 79106 Freiburg, Germany; BIOSS Centre of Biological Signalling Studies, Albert Ludwigs University, 79106 Freiburg, Germany; Deutsches Konsortium für Translationale Krebsforschung (DKTK), Standort Freiburg, 79108 Freiburg, Germany. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2016.09.053DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5081406PMC
October 2016

deepTools2: a next generation web server for deep-sequencing data analysis.

Nucleic Acids Res 2016 07 13;44(W1):W160-5. Epub 2016 Apr 13.

Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany

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http://dx.doi.org/10.1093/nar/gkw257DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4987876PMC
July 2016

Standardizing chromatin research: a simple and universal method for ChIP-seq.

Nucleic Acids Res 2016 Apr 23;44(7):e67. Epub 2015 Dec 23.

Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, Freiburg, 79108, Germany

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http://dx.doi.org/10.1093/nar/gkv1495DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4838356PMC
April 2016

deepTools: a flexible platform for exploring deep-sequencing data.

Nucleic Acids Res 2014 Jul 5;42(Web Server issue):W187-91. Epub 2014 May 5.

Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108 Freiburg, Germany

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http://dx.doi.org/10.1093/nar/gku365DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4086134PMC
July 2014

ChroMoS: an integrated web tool for SNP classification, prioritization and functional interpretation.

Bioinformatics 2013 Sep 19;29(17):2197-8. Epub 2013 Jun 19.

Bioinformatics and Deep-Sequencing Unit, Max-Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany.

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http://dx.doi.org/10.1093/bioinformatics/btt356DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3740627PMC
September 2013

The genomic landscape of the somatic linker histone subtypes H1.1 to H1.5 in human cells.

Cell Rep 2013 Jun 6;3(6):2142-54. Epub 2013 Jun 6.

Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS UMR 7104, INSERM U 964, Université de Strasbourg, 67404 Illkirch, France.

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http://dx.doi.org/10.1016/j.celrep.2013.05.003DOI Listing
June 2013

The NSL complex regulates housekeeping genes in Drosophila.

PLoS Genet 2012 14;8(6):e1002736. Epub 2012 Jun 14.

Max-Planck Institute of Immunobiology and Epigenetics, Freiburg im Breisgau, Germany.

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http://dx.doi.org/10.1371/journal.pgen.1002736DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3375229PMC
September 2012

Transcription factor binding predictions using TRAP for the analysis of ChIP-seq data and regulatory SNPs.

Nat Protoc 2011 Nov 3;6(12):1860-9. Epub 2011 Nov 3.

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

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http://dx.doi.org/10.1038/nprot.2011.409DOI Listing
November 2011

Heterochromatin boundaries are hotspots for de novo kinetochore formation.

Nat Cell Biol 2011 Jun 19;13(7):799-808. Epub 2011 Jun 19.

Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108 Freiburg, Germany.

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http://dx.doi.org/10.1038/ncb2272DOI Listing
June 2011

Functional analysis and identification of cis-regulatory elements of human chromosome 21 gene promoters.

Nucleic Acids Res 2010 Oct 21;38(18):6112-23. Epub 2010 May 21.

Department for Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, 14195 Berlin, Germany.

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http://dx.doi.org/10.1093/nar/gkq402DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2952857PMC
October 2010

Quantifying the effect of sequence variation on regulatory interactions.

Hum Mutat 2010 Apr;31(4):477-83

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

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http://dx.doi.org/10.1002/humu.21209DOI Listing
April 2010

A genome-wide association study identifies GLT6D1 as a susceptibility locus for periodontitis.

Hum Mol Genet 2010 Feb 6;19(3):553-62. Epub 2009 Nov 6.

Institute for Clinical Molecular Biology, Christian-Albrechts-University Kiel, Schittenhelmstrasse 12, Kiel, Germany.

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https://academic.oup.com/hmg/article-lookup/doi/10.1093/hmg/
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http://dx.doi.org/10.1093/hmg/ddp508DOI Listing
February 2010

Short ultraconserved promoter regions delineate a class of preferentially expressed alternatively spliced transcripts.

Genomics 2009 Nov 4;94(5):308-16. Epub 2009 Aug 4.

Institute for Medical Genetics, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany.

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http://linkinghub.elsevier.com/retrieve/pii/S088875430900161
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http://dx.doi.org/10.1016/j.ygeno.2009.07.005DOI Listing
November 2009

Paracrine control of oligodendrocyte differentiation by SRF-directed neuronal gene expression.

Nat Neurosci 2009 Apr 8;12(4):418-27. Epub 2009 Mar 8.

Neuronal Gene Expression Laboratory, Eberhard Karls University Tübingen, Interfaculty Institute for Cell Biology, Department of Molecular Biology, Tübingen, Germany.

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http://dx.doi.org/10.1038/nn.2280DOI Listing
April 2009

Integrating sequence, evolution and functional genomics in regulatory genomics.

Genome Biol 2009 30;10(1):202. Epub 2009 Jan 30.

Computational Molecular Biology, Max-Planck-Institut für molekulare Genetik, Berlin, Germany.

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http://dx.doi.org/10.1186/gb-2009-10-1-202DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2687781PMC
September 2009

PASTAA: identifying transcription factors associated with sets of co-regulated genes.

Bioinformatics 2009 Feb 9;25(4):435-42. Epub 2008 Dec 9.

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

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https://academic.oup.com/bioinformatics/article-lookup/doi/1
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http://dx.doi.org/10.1093/bioinformatics/btn627DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2642637PMC
February 2009

Statistical modeling of transcription factor binding affinities predicts regulatory interactions.

PLoS Comput Biol 2008 Mar 21;4(3):e1000039. Epub 2008 Mar 21.

Max Planck Institute for Molecular Genetics, Berlin, Germany.

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http://dx.doi.org/10.1371/journal.pcbi.1000039DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2266803PMC
March 2008

Prioritization of gene regulatory interactions from large-scale modules in yeast.

BMC Bioinformatics 2008 Jan 22;9:32. Epub 2008 Jan 22.

Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany.

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http://dx.doi.org/10.1186/1471-2105-9-32DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2244593PMC
January 2008

Predicting transcription factor affinities to DNA from a biophysical model.

Bioinformatics 2007 Jan 10;23(2):134-41. Epub 2006 Nov 10.

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

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http://dx.doi.org/10.1093/bioinformatics/btl565DOI Listing
January 2007

An entropic characterization of protein interaction networks and cellular robustness.

J R Soc Interface 2006 Dec;3(11):843-50

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

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http://dx.doi.org/10.1098/rsif.2006.0140DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1885358PMC
December 2006

Lethality and entropy of protein interaction networks.

Genome Inform 2005 ;16(1):159-63

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

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January 2006

Control of replication initiation and heterochromatin formation in Saccharomyces cerevisiae by a regulator of meiotic gene expression.

Genes Dev 2005 Aug;19(15):1811-22

Otto-Warburg-Laboratorium and Department for Computational Molecular Biology, Max-Planck-Institut für Molekulare Genetik, D-14195 Berlin, Germany.

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http://dx.doi.org/10.1101/gad.334805DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1182343PMC
August 2005

Correlating protein-DNA and protein-protein interaction networks.

J Mol Biol 2003 Oct;333(1):75-85

Max-Planck-Institute for Molecular Genetics, Abt Bioinformatik, Ihnestr. 73, 14195 Berlin, Germany.

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https://linkinghub.elsevier.com/retrieve/pii/S00222836030101
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http://dx.doi.org/10.1016/j.jmb.2003.08.004DOI Listing
October 2003