ZMB Member Daniel Hoffmann

ZMB Member
Daniel Hoffmann

Next ZMB-Member
portrait photo of ZMB member Daniel Hoffmann
© D. Hoffmann

Prof. Dr. Daniel Hoffmann

Faculty of Biology
University of Duisburg-Essen
Universitätsstr. 2
45141 Essen

Research Overview

Quantitative Biology
Biology is a messy science. Its subjects - biomolecules, cells, tissues, organisms, ecosystems, etc. - are highly complex and variable. This makes it difficult to pin down laws as reliably as, say, in physics. It is therefore not surprising that biologists are fully occupied with taming their complex subjects, and with obtaining (using a minimum of mathematics) simple, qualitative results from experiments. However, we know that living systems are essentially quantitative; e.g. it matters a lot whether you have too little or too much of a substance in an organism. If we want to account for this, we have to use quantitative mathematical and computational models of biological systems or biological data. This is exactly what we do.

In our research we are developing mathematical or computational models for biological systems. Often these models are probabilistic because biological systems are variable and not completely characterized, and probabilities are an effective way of dealing with variability. We can then infer quantitative relationships by computational methods such as Bayesian analyses. This is a Swiss knife approach that is basically applicable to all kinds of biology. Accordingly, we have fruitful collaborations with researchers from many areas, e.g. developmental biologists, virologists, immunologists, cancer researchers, or ecologists.
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Selected Publications

    Journal articles

  • Kitanovski, Simo; Hoffmann, Daniel
    IgGeneUsage : differential gene usage in immune repertoires
    In: Bioinformatics Vol. 36 (2020) Nr. 11, pp. 3590 - 3591
    ISSN: 1367-4811; 1367-4803
  • Kitanovski, Simo; Hoffmann, Daniel
    IgGeneUsage : differential gene usage in immune repertoires
    In: Bioinformatics (2020)
    ISSN: 1367-4803; 1460-2059
  • Grüneboom, Anika; Hawwari, Ibrahim; Weidner, Daniela; Culemann, Stephan; Müller, Sylvia; Henneberg, Sophie; Brenzel, Alexandra; Merz, Simon; Bornemann, Lea; Zec, Kristina; Wülling, Manuela; Kling, Lasse; Hasenberg, Mike; Voortmann, Sylvia; Lang, Stefanie; Baum, Wolfgang; Ohs, Alexandra; Kraff, Oliver; Quick, Harald H.; Jäger, Marcus; Landgraeber, Stefan; Dudda, Marcel; Danuser, Renzo; Stein, Jens V.; Rohde, Manfred; Gelse, Kolja; Garbe, Annette I.; Adamczyk, Alexandra; Westendorf, Astrid; Hoffmann, Daniel; Christiansen, Silke; Engel, Daniel Robert; Vortkamp, Andrea; Krönke, Gerhard; Herrmann, Martin; Kamradt, Thomas; Schett, Georg; Hasenberg, Anja; Gunzer, Matthias
    A network of trans-cortical capillaries as mainstay for blood circulation in long bones
    In: Nature Metabolism Vol. 1 (2019) Nr. 2, pp. 236 - 250
    ISSN: 2522-5812
  • Karimzadeh, Hadi; Kiraithe, Muthamia M.; Oberhardt, Valerie; Salimi Alizei, Elahe; Bockmann, Jan; Schulze zur Wiesch, Julian; Budeus, Bettina; Hoffmann, Daniel; Wedemeyer, Heiner; Cornberg, Markus; Krawczyk, Adalbert; Rashidi-Alavijeh, Jassin; Rodríguez-Frías, Francisco; Casillas, Rosario; Buti, Maria; Smedile, Antonina; Alavian, Seyed Moayed; Heinold, Andreas; Emmerich, Florian; Panning, Marcus; Gostick, Emma; Price, David A.; Timm, Jörg; Hofmann, Maike; Raziorrouh, Bijan; Thimme, Robert; Protzer, Ulrike; Roggendorf, Michael; Neumann-Haefelin, Christoph
    Mutations in Hepatitis D Virus Allow It to Escape Detection by CD8⁺ T Cells and Evolve at the Population Level
    In: Gastroenterology Vol. 156 (2019) Nr. 6, pp. 1820 - 1833
    ISSN: 0016-5085; 1528-0012
  • Alavian, Seyed Moayed; Price, David A.; Panning, Marcus; Neumann-Haefelin, Christoph; Bockmann, Jan; Wiesch, Julian Schulze zur; Wedemeyer, Heiner; Heinold, Andreas; Alizei, Elahe Salimi; Timm, Jörg; Casillas, Rosario; Protzer, Ulrike; Raziorrouh, Bijan; Smedile, Antonina; Rodríguez-Frías, Francisco; Hoffmann, Daniel; Oberhardt, Valerie; Buti, Maria; Thimme, Robert; Roggendorf, Michael; Hofmann, Maike; Gostick, Emma; Budeus, Bettina; Emmerich, Florian; Kiraithe, Muthamia M.; Karimzadeh, Hadi
    Viral escape contributes to the failure of hepatitis D virus-specific CD8+ T-cells and drives evolution of HDV
    In: Journal of Hepatology Vol. 70 (2019) Nr. Suppl. 1, pp. e21
    ISSN: 0168-8278
  • Tucci, Felicia A.; Kitanovski, Simo; Johansson, Patricia; Klein-Hitpaß, Ludger; Kahraman, Alisan; Dürig, Jan; Hoffmann, Daniel; Küppers, Ralf
    Biased IGH VDJ gene repertoire and clonal expansions in B cells of chronically hepatitis C virus–infected individuals
    In: Blood Vol. 131 (2018) Nr. 5, pp. 546 - 557
    ISSN: 1528-0020; 0006-4971
  • Kefalakes, Helenie; Budeus, Bettina; Walker, Andreas; Jochum, Christoph; Hilgard, Gudrun; Heinold, Andreas; Heinemann, Falko M.; Gerken, Guido; Hoffmann, Daniel; Timm, Jörg
    Adaptation of the Hepatitis B Virus Core Protein to CD8+ T-Cell Selection Pressure
    In: Hepatology Vol. 62 (2015) Nr. 1, pp. 47 - 56
    ISSN: 0270-9139
  • Budeus, Bettina; De Reynoso, Stefanie Schweigle; Przekopowitz, Martina; Hoffmann, Daniel; Seifert, Marc; Küppers, Ralf
    Complexity of the human memory B-cell compartment is determined by the versatility of clonal diversification in germinal centers
    In: Proceedings of the National Academy of Sciences of the United States of America Vol. 112 (2015) Nr. 38, pp. E5281 - E5289
    ISSN: 1091-6490; 0027-8424
  • Skibbe, K.; Budeus, Bettina; Heinemann, Falko M.; Timmer, L.; Horn, Peter; van Esch, W.; Hoffmann, Daniel; Siemann, H.; Scherbaum, Norbert; Timm, Jörg
    HLA-B*27 is protective against HCV genotype 1 and 3 and associated with targeting of distinct genotype-specific CD8(+) cell epitopes
    In: Journal of Hepatology Vol. 60 (2014) Nr. Suppl. 1, pp. 140
    ISSN: 0168-8278
  • Lättig-Tünnemann, Gisela; Prinz, Manuel; Hoffmann, Daniel; Behlke, Joachim; Palm-Apergi, Caroline; Morano, Ingo; Herce, Henry D.; Cardoso, M. Cristina
    Backbone rigidity and static presentation of guanidinium groups increases cellular uptake of arginine-rich cell-penetrating peptides
    In: Nature Communications Vol. 2 (2011) pp. 453
    ISSN: 2041-1723
  • Ruhl, Marianne; Knuschke, Torben; Schewior, Kevin; Glavinic, Lejla; Neumann-Haefelin, Christoph; Chang, Dae-In; Klein, Marina; Heinemann, Falko M.; Tenckhoff, Hannelore; Wiese, Manfred; Horn, Peter A.; Viazov, Sergey; Spengler, Ulrich; Roggendorf, Michael; Scherbaum, Norbert; Nattermann, Jacob; Hoffmann, Daniel; Timm, Jörg; East German HCV Study Group
    CD8+ T-Cell Response Promotes Evolution of Hepatitis C Virus Nonstructural Proteins
    In: Gastroenterology Vol. 140 (2011) Nr. 7, pp. 2064 - 2073
    ISSN: 0016-5085
  • Ehrentraut, Stefan; Weber, Jan; Dybowski, Jan Nikolaj; Hoffmann, Daniel; Ehrenhofer-Murray, Ann
    Rpd3-dependent boundary formation at telomeres by removal of Sir2 substrate
    In: Proceedings of the National Academy of Sciences of the United States of America Vol. 107 (2010) Nr. 12, pp. 5522 - 5527
    ISSN: 1091-6490; 0027-8424
  • Beerenwinkel, Niko; Sing, Tobias; Lengauer, Thomas; Rahnenführer, Jörg; Roomp, Kirsten; Savenkov, Igor; Fischer, Roman; Hoffmann, Daniel; Selbig, Joachim; Korn, Klaus; Walter, Hauke; Berg, Thomas; Braun, Patrick; Fätkenheuer, Gerd; Oette, Mark; Rockstroh, Jürgen; Kupfer, Bernd; Kaiser, Rolf; Däumer, Martin
    Computational methods for the design of effective therapies against drug resistant HIV strains
    In: Bioinformatics Vol. 21 (2005) Nr. 21, pp. 3943 - 3950
    ISSN: 1460-2059
  • Beerenwinkel, Niko; Rahnenführer, Jörg; Kaiser, Rolf; Hoffmann, Daniel; Selbig, Joachim; Lengauer, Thomas
    Mtreemix : A software package for learning and using mixture models of mutagenetic trees
    In: Bioinformatics Vol. 21 (2005) Nr. 9, pp. 2106 - 2107
    ISSN: 1460-2059
  • Beerenwinkel, Niko; Lengauer, Thomas; Däumer, Martin; Kaiser, Rolf; Walter, Hauke; Korn, Klaus; Hoffmann, Daniel; Selbig, Joachim
    Methods for optimizing antiviral combination therapies
    In: Bioinformatics Vol. 19 (2003) Nr. Suppl 1,
    ISSN: 1460-2059
  • Beerenwinkel, Niko; Schmidt, Barbara; Walter, Hauke; Kaiser, Rolf; Lengauer, Thomas; Hoffmann, Daniel; Korn, Klaus; Selbig, Joachim
    Diversity and complexity of HIV-1 drug resistance: A bioinformatics approach to predicting phenotype from genotype
    In: Proceedings of the National Academy of Sciences of the United States of America Vol. 99 (2002) Nr. 12, pp. 8271 - 8276
    ISSN: 1091-6490; 0027-8424
  • Hoffmann, Daniel
    Web Site: The Protein Information Resource
    In: Angewandte Chemie International Edition (2002)
    ISSN: 1521-3773
  • Jacob, Joël; Geßler, Katrin; Hoffmann, Daniel; Sanbe, Haruyo; Koizumi, Kyoko; Smith, Steven M.; Takaha, Takeshi; Saenger, Wolfram
    Strain-Induced “Band Flips” in Cyclodecaamylose and Higher Homologues
    In: Angewandte Chemie International Edition Vol. 37 (1998) Nr. 5,
    ISSN: 1521-3773; 0570-0833; 1433-7851
  • Saenger, W.; Jacob, J.; Gessler, K.; Steiner, T.; Hoffmann, Daniel; Sanbe, H.; Koizumi, K.; Smith, S.M.; Takaha, T.
    Structures of the Common Cyclodextrins and Their Larger Analogues -- Beyond the Doughnu
    In: Chemical Reviews Vol. 98 (1998) pp. 1787 - 1802
    ISSN: 1520-6890; 0009-2665
  • Saenger, Wolfram; Jacob, Joël; Gessler, Katrin; Steiner, Thomas; Hoffmann, Daniel; Sanbe, Haruyo; Koizumi, Kyoko; Smith, Steven M.; Takaha, Takeshi
    Structures of the common cyclodextrins and their larger analogues : beyond the doughnut
    In: Chemical Reviews Vol. 98 (1998) Nr. 5, pp. 1787 - 1802
    ISSN: 0009-2665