Publications by authors named "Carl Herrmann"

42Publications

Automated 3D light-sheet screening with high spatiotemporal resolution reveals mitotic phenotypes.

J Cell Sci 2020 Jun 1;133(11). Epub 2020 Jun 1.

Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany

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http://dx.doi.org/10.1242/jcs.245043DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7286290PMC
June 2020

Passenger Mutations in More Than 2,500 Cancer Genomes: Overall Molecular Functional Impact and Consequences.

Cell 2020 03 20;180(5):915-927.e16. Epub 2020 Feb 20.

Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA; Department of Computer Science, Yale University, New Haven, CT 06511, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2020.01.032DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7210002PMC
March 2020

Analyses of non-coding somatic drivers in 2,658 cancer whole genomes.

Nature 2020 02 5;578(7793):102-111. Epub 2020 Feb 5.

The Broad Institute of MIT and Harvard, Cambridge, MA, USA.

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http://dx.doi.org/10.1038/s41586-020-1965-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7054214PMC
February 2020

Single-nucleus chromatin accessibility reveals intratumoral epigenetic heterogeneity in IDH1 mutant gliomas.

Acta Neuropathol Commun 2019 12 5;7(1):201. Epub 2019 Dec 5.

Neurology Clinic and National Center for Tumor Diseases, University Hospital Heidelberg, INF 460, 69120, Heidelberg, Germany.

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http://dx.doi.org/10.1186/s40478-019-0851-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6896263PMC
December 2019

Impact of cancer mutational signatures on transcription factor motifs in the human genome.

BMC Med Genomics 2019 05 20;12(1):64. Epub 2019 May 20.

Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, 69120, Germany.

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http://dx.doi.org/10.1186/s12920-019-0525-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6528224PMC
May 2019

Identification of Embryonic Neural Plate Border Stem Cells and Their Generation by Direct Reprogramming from Adult Human Blood Cells.

Cell Stem Cell 2019 01 20;24(1):166-182.e13. Epub 2018 Dec 20.

Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany; Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ), and DKFZ-ZMBH Alliance, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany; German Cancer Consortium (DKTK), 69120 Heidelberg, Germany. Electronic address:

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http://dx.doi.org/10.1016/j.stem.2018.11.015DOI Listing
January 2019

A self-avoiding walk with neural delays as a model of fixational eye movements.

Sci Rep 2017 10 11;7(1):12958. Epub 2017 Oct 11.

Department of Psychology, University of Potsdam, Potsdam, D-14476, Germany.

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http://dx.doi.org/10.1038/s41598-017-13489-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5636902PMC
October 2017

LedPred: an R/bioconductor package to predict regulatory sequences using support vector machines.

Bioinformatics 2016 04 1;32(7):1091-3. Epub 2015 Dec 1.

INSERM, UMR1090 TAGC, Marseille, F-13288 France, Aix-Marseille Université, UMR1090 TAGC, Marseille, F-13288 France.

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http://dx.doi.org/10.1093/bioinformatics/btv705DOI Listing
April 2016

Evolutionary conserved gene co-expression drives generation of self-antigen diversity in medullary thymic epithelial cells.

J Autoimmun 2016 Feb 23;67:65-75. Epub 2015 Oct 23.

Division of Developmental Immunology, Tumor Immunology Program, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S08968411153004
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http://dx.doi.org/10.1016/j.jaut.2015.10.001DOI Listing
February 2016

PrOnto database : GO term functional dissimilarity inferred from biological data.

Front Genet 2015 3;6:200. Epub 2015 Jun 3.

Inserm, UMR_S1090 TAGC Marseille, France ; Aix-Marseille Université, UMR_S1090 TAGC Marseille, France ; Centre National de la Recherche Scientifique Marseille, France.

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http://dx.doi.org/10.3389/fgene.2015.00200DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4452890PMC
June 2015

MapMyFlu: visualizing spatio-temporal relationships between related influenza sequences.

Nucleic Acids Res 2015 Jul 4;43(W1):W547-51. Epub 2015 May 4.

Institute of Pharmacy and Molecular Biotechnology, and Bioquant Center, University of Heidelberg, Im Neuenheimer Feld 267, Heidelberg 69120, Germany Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, Heidelberg 69120, Germany

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http://dx.doi.org/10.1093/nar/gkv417DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4489300PMC
July 2015

RSAT 2015: Regulatory Sequence Analysis Tools.

Nucleic Acids Res 2015 Jul 22;43(W1):W50-6. Epub 2015 Apr 22.

European Genomic Institute for Diabetes (EGID), F-3508, 59000 Lille, France Laboratoire de Bioinformatique des Génomes et des Réseaux (BiGRe), Université Libre de Bruxelles, Campus Plaine, CP 263, Bld du Triomphe, B-1050 Bruxelles, Belgium

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http://dx.doi.org/10.1093/nar/gkv362DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4489296PMC
July 2015

Identification of regulatory networks in HSCs and their immediate progeny via integrated proteome, transcriptome, and DNA methylome analysis.

Cell Stem Cell 2014 Oct 21;15(4):507-522. Epub 2014 Aug 21.

Division of Stem Cells and Cancer, Deutsches Krebsforschungszentrum (DKFZ), 69120 Heidelberg, Germany; Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), 69120 Heidelberg, Germany; German Cancer Consortium (DKTK), 69120 Heidelberg, Germany. Electronic address:

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http://www.cell.com/cms/attachment/2035154136/2050496774/mmc
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http://www-huber.embl.de/pub/pdf/CabezasWallscheid2014.pdf
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http://linkinghub.elsevier.com/retrieve/pii/S193459091400301
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http://dx.doi.org/10.1016/j.stem.2014.07.005DOI Listing
October 2014

Transcriptional and epigenetic signatures of zygotic genome activation during early Drosophila embryogenesis.

BMC Genomics 2013 Apr 5;14:226. Epub 2013 Apr 5.

Technological Advances for Genomics and Clinics (TAGC), INSERM U1090, Université de la Méditerranée, Campus de Luminy, 13288 Marseille Cedex 9, France.

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http://dx.doi.org/10.1186/1471-2164-14-226DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3706223PMC
April 2013

A complete workflow for the analysis of full-size ChIP-seq (and similar) data sets using peak-motifs.

Nat Protoc 2012 Jul 26;7(8):1551-68. Epub 2012 Jul 26.

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

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http://dx.doi.org/10.1038/nprot.2012.088DOI Listing
July 2012

i-cisTarget: an integrative genomics method for the prediction of regulatory features and cis-regulatory modules.

Nucleic Acids Res 2012 Aug 20;40(15):e114. Epub 2012 Jun 20.

TAGC - Inserm U1090 and Aix-Marseille Université, Campus de Luminy, 13288 Marseille, France.

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http://dx.doi.org/10.1093/nar/gks543DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3424583PMC
August 2012

RSAT peak-motifs: motif analysis in full-size ChIP-seq datasets.

Nucleic Acids Res 2012 Feb 8;40(4):e31. Epub 2011 Dec 8.

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

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http://dx.doi.org/10.1093/nar/gkr1104DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3287167PMC
February 2012

Using cisTargetX to predict transcriptional targets and networks in Drosophila.

Methods Mol Biol 2012 ;786:291-314

TAGC Inserm U928 and Université de la Mediterranée, Marseille, France.

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http://dx.doi.org/10.1007/978-1-61779-292-2_18DOI Listing
February 2012

RSAT 2011: regulatory sequence analysis tools.

Nucleic Acids Res 2011 Jul;39(Web Server issue):W86-91

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

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http://dx.doi.org/10.1093/nar/gkr377DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3125777PMC
July 2011

SimCT: a generic tool to visualize ontology-based relationships for biological objects.

Bioinformatics 2009 Dec 23;25(23):3197-8. Epub 2009 Sep 23.

TAGC-U928 Inserm, Faculté des Sciences, Université de la Méditerranée, Campus de Luminy Case 928, Marseille, France.

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http://bioinformatics.oxfordjournals.org/content/early/2009/
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http://bioinformatics.oxfordjournals.org/cgi/doi/10.1093/bio
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http://dx.doi.org/10.1093/bioinformatics/btp553DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2778334PMC
December 2009

Metagenome annotation using a distributed grid of undergraduate students.

PLoS Biol 2008 Nov;6(11):e296

Département de Biologie, Faculté des Sciences de Luminy, Université de la Méditerranée, Information Génomiqueet Structurale, CNRS, UPR2589, Marseille, France.

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http://dx.doi.org/10.1371/journal.pbio.0060296DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2586363PMC
November 2008

Clustering proteins from interaction networks for the prediction of cellular functions.

BMC Bioinformatics 2004 Jul 13;5:95. Epub 2004 Jul 13.

Laboratoire de Génétique et Physiologie du Développement, IBDM, CNRS/INSERM/Université de la Méditerranée.

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http://dx.doi.org/10.1186/1471-2105-5-95DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC487898PMC
July 2004

Connectivity distribution of spatial networks.

Phys Rev E Stat Nonlin Soft Matter Phys 2003 Aug 26;68(2 Pt 2):026128. Epub 2003 Aug 26.

Dipartimento di Fisica Teorica dell'Università di Torino and INFN, Sezione di Torino, Via P. Giuria 1, 10125 Torino, Italy.

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http://dx.doi.org/10.1103/PhysRevE.68.026128DOI Listing
August 2003