ZMB Member Daniel Hoffmann
ZMB Member
Daniel Hoffmann
Next ZMB-Member
Prof. Dr. Daniel Hoffmann
Faculty of Biology
University of Duisburg-Essen
Universitätsstr. 2
45141 Essen
- +49 201 183 4391
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- Selected Publications
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- ZMB Research Program
Molecular and Chemical Cell Biology
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
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IgGeneUsage : differential gene usage in immune repertoiresIn: Bioinformatics Vol. 36 (2020) Nr. 11, pp. 3590 - 3591
ISSN: 1367-4811; 1367-4803Online Full Text: dx.doi.org/ -
IgGeneUsage : differential gene usage in immune repertoiresIn: Bioinformatics (2020)
ISSN: 1367-4803; 1460-2059Online Full Text: dx.doi.org/ -
A network of trans-cortical capillaries as mainstay for blood circulation in long bonesIn: Nature Metabolism Vol. 1 (2019) Nr. 2, pp. 236 - 250
ISSN: 2522-5812Online Full Text: dx.doi.org/ Online Full Text (Open Access) -
Mutations in Hepatitis D Virus Allow It to Escape Detection by CD8⁺ T Cells and Evolve at the Population LevelIn: Gastroenterology Vol. 156 (2019) Nr. 6, pp. 1820 - 1833
ISSN: 0016-5085; 1528-0012Online Full Text: dx.doi.org/ (Open Access) -
Viral escape contributes to the failure of hepatitis D virus-specific CD8+ T-cells and drives evolution of HDVIn: Journal of Hepatology Vol. 70 (2019) Nr. Suppl. 1, pp. e21
ISSN: 0168-8278Online Full Text: dx.doi.org/ -
Biased IGH VDJ gene repertoire and clonal expansions in B cells of chronically hepatitis C virus–infected individualsIn: Blood Vol. 131 (2018) Nr. 5, pp. 546 - 557
ISSN: 1528-0020; 0006-4971Online Full Text: dx.doi.org/ (Open Access) -
Adaptation of the Hepatitis B Virus Core Protein to CD8+ T-Cell Selection PressureIn: Hepatology Vol. 62 (2015) Nr. 1, pp. 47 - 56
ISSN: 0270-9139Online Full Text: dx.doi.org/ (Open Access) -
Complexity of the human memory B-cell compartment is determined by the versatility of clonal diversification in germinal centersIn: Proceedings of the National Academy of Sciences of the United States of America Vol. 112 (2015) Nr. 38, pp. E5281 - E5289
ISSN: 1091-6490; 0027-8424Online Full Text: dx.doi.org/ (Open Access) -
HLA-B*27 is protective against HCV genotype 1 and 3 and associated with targeting of distinct genotype-specific CD8(+) cell epitopesIn: Journal of Hepatology Vol. 60 (2014) Nr. Suppl. 1, pp. 140
ISSN: 0168-8278Online Full Text: dx.doi.org/ -
Backbone rigidity and static presentation of guanidinium groups increases cellular uptake of arginine-rich cell-penetrating peptidesIn: Nature Communications Vol. 2 (2011) pp. 453
ISSN: 2041-1723Online Full Text: dx.doi.org/ (Open Access) -
CD8+ T-Cell Response Promotes Evolution of Hepatitis C Virus Nonstructural ProteinsIn: Gastroenterology Vol. 140 (2011) Nr. 7, pp. 2064 - 2073
ISSN: 0016-5085Online Full Text: dx.doi.org/ -
Rpd3-dependent boundary formation at telomeres by removal of Sir2 substrateIn: Proceedings of the National Academy of Sciences of the United States of America Vol. 107 (2010) Nr. 12, pp. 5522 - 5527
ISSN: 1091-6490; 0027-8424Online Full Text: dx.doi.org/ -
Computational methods for the design of effective therapies against drug resistant HIV strainsIn: Bioinformatics Vol. 21 (2005) Nr. 21, pp. 3943 - 3950
ISSN: 1460-2059Online Full Text: dx.doi.org/ (Open Access) -
Mtreemix : A software package for learning and using mixture models of mutagenetic treesIn: Bioinformatics Vol. 21 (2005) Nr. 9, pp. 2106 - 2107
ISSN: 1460-2059Online Full Text: dx.doi.org/ Online Full Text (Open Access) -
Methods for optimizing antiviral combination therapiesIn: Bioinformatics Vol. 19 (2003) Nr. Suppl 1,
ISSN: 1460-2059Online Full Text: dx.doi.org/ (Open Access) -
Diversity and complexity of HIV-1 drug resistance: A bioinformatics approach to predicting phenotype from genotypeIn: Proceedings of the National Academy of Sciences of the United States of America Vol. 99 (2002) Nr. 12, pp. 8271 - 8276
ISSN: 1091-6490; 0027-8424Online Full Text: dx.doi.org/ -
Web Site: The Protein Information ResourceIn: Angewandte Chemie International Edition (2002)
ISSN: 1521-3773Online Full Text: dx.doi.org/ -
Strain-Induced “Band Flips” in Cyclodecaamylose and Higher HomologuesIn: Angewandte Chemie International Edition Vol. 37 (1998) Nr. 5,
ISSN: 1521-3773; 0570-0833; 1433-7851Online Full Text: dx.doi.org/ -
Structures of the Common Cyclodextrins and Their Larger Analogues -- Beyond the DoughnuIn: Chemical Reviews Vol. 98 (1998) pp. 1787 - 1802
ISSN: 1520-6890; 0009-2665 -
Structures of the common cyclodextrins and their larger analogues : beyond the doughnutIn: Chemical Reviews Vol. 98 (1998) Nr. 5, pp. 1787 - 1802
ISSN: 0009-2665Online Full Text: dx.doi.org/