ZMB Member Daniel Hoffmann

Prof. dr. Daniel Hoffmann

Prof. Dr. Daniel Hoffmann

+49 201 183 4391

Fakultät für Biologie
Room S03 S03 A26
Universität Duisburg-Essen
45117 Essen


Bioinformatics and Computational Biophysics

Research Overview

Computational molecular evolution

Evolution is one of the keys to understanding biology, including biomedicine. For instance, we work on seemingly disparate phenomena as the biodiversity in our environment, resistance of viruses to therapies, or development of cancer, all of which can be understood in the light of evolution in ecosystems and organisms. Another unifying viewpoint on biology is the molecular level, where all biology speaks the same language of genes, proteins, etc. In our research we bring together both unifying aspects of biology by discovering the mechanics of evolution at the molecular level.

An example to illustrate this mode of work is the discovery of specific genetic mutations of viruses. By statistical analysis of data collected from many patients, we identify mutations that allow a virus such as HIV-1 or HCV to evade the immune systems of patients. By computational modeling, we study physical effects of these mutations on the affected molecules to gain a quantitative, mechanistic understanding of this evolutionary process at the molecular level.

    Journal articles

  • Smolin, Daniel; Tötsch, Niklas; Grad, Jean-Noël; Linders, Jürgen; Kaschani, Farnusch; Kaiser, Markus; Kirsch, Michael; Hoffmann, Daniel; Schrader, Thomas
    Accelerated trypsin autolysis by affinity polymer templates
    In: RSC Advances Vol. 10 (2020) Nr. 48, pp. 28711 - 28719
    ISSN: 2046-2069
  • Smolin, Daniel; Tötsch, Niklas; Grad, Jean-Noël; Linders, Jürgen; Kaschani, Farnusch; Kaiser, Markus; Kirsch, Michael; Hoffmann, Daniel; Schrader, Thomas
    Accelerated trypsin autolysis by affinity polymer templates
    In: RSC Advances Vol. 10 (2020) Nr. 48, pp. 28711 - 28719
    ISSN: 2046-2069
  • Severmann, Ann-Christine; Jochmann, Katja; Feller, Konstantina; Bachvarova, Velina; Piombo, Virginia; Stange, Richard; Holzer, Tatjana; Brachvogel, Bent; Esko, Jeffrey; Pap, Thomas; Hoffmann, Daniel; Vortkamp, Andrea
    An altered heparan sulfate structure in the articular cartilage protects against osteoarthritis
    In: Osteoarthritis and Cartilage (2020)
    ISSN: 1063-4584; 1522-9653
  • Severmann, Ann-Christine; Jochmann, Katja; Feller, K.; Bachvarova, Velina; Piombo, Virginia; Stange, Richard; Holzer, Tatjana; Brachvogel, Bent; Esko, Jeffrey D.; Pap, Thomas; Hoffmann, Daniel; Vortkamp, Andrea
    An altered heparan sulfate structure in the articular cartilage protects against osteoarthritis
    In: Osteoarthritis and Cartilage Vol. 28 (2020) Nr. 7, pp. 977 - 987
    ISSN: 1522-9653; 1063-4584
  • Tötsch, Niklas; Hoffmann, Daniel
    Bayesian Data Integration Questions Classic Study on Protease Self-Digest Kinetics
    In: ACS Omega Vol. 5 (2020) Nr. 25, pp. 15162 - 15168
    ISSN: 2470-1343
  • Bachvarova, Velina; Dierker, Tabea; Esko, Jeffrey; Hoffmann, Daniel; Kjellen, Lena; Vortkamp, Andrea
    Chondrocytes respond to an altered heparan sulfate composition with distinct changes of heparan sulfate structure and increased levels of chondroitin sulfate
    In: Matrix Biology: Journal of the International Society for Matrix Biology (2020)
    ISSN: 1569-1802; 0945-053X
  • Wang, Jun; Li, Qian; Yin, Yongmei; Zhang, Yingying; Cao, Yingying; Lin, Xiaoming; Huang, Lihua; Hoffmann, Daniel; Lu, Mengji; Qiu, Yuanwang
    Excessive Neutrophils and Neutrophil Extracellular Traps in COVID-19
    In: Frontiers in Immunology Vol. 11 (2020)
    ISSN: 1664-3224
  • 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
  • Spassova, Ivelina; Ugurel, Selma; Terheyden, Patrick; Sucker, Antje; Hassel, Jessica C.; Ritter, Cathrin; Kubat, Linda; Habermann, Daniel; Farahpour, Farnoush; Saeedghalati, Mohammadkarim; Peiffer, Lukas; Kumar, Rajiv; Schrama, David; Hoffmann, Daniel; Schadendorf, Dirk; Becker, Jürgen
    Predominance of Central Memory T Cells with High T-Cell Receptor Repertoire Diversity is Associated with Response to PD-1/PD-L1 Inhibition in Merkel Cell Carcinoma
    In: Clinical Cancer Research Vol. 26 (2020) Nr. 9, pp. 2257 - 2267
    ISSN: 1078-0432; 1557-3265
  • Mysior, Patryk; Tenberken, Erik; Stecher, Melanie; Vehreschild, Jörg-Janne; Schafberger, Armin; Perea, Ines; Brillen, Anna-Lena; Bartmeyer, Barbara; Esser, Stefan; Bremer, Viviane; Marcus, Ulrich; Hoffmann, Daniel; Streeck, Hendrik
    Rapid uptake of pre-exposure prophylaxis (PrEP) after significant price reduction in Germany highlights importance of PrEP accessibility
    In: AIDS Research and Human Retroviruses (2020)
    ISSN: 0889-2229; 1931-8405
  • Wülling, Manuela; Schneider, Sabine; Schröther, Verena A.; Waterkamp, Christoph; Hoffmann, Daniel; Vortkamp, Andrea
    Wnt5a is a transcriptional target of Gli3 and Trps1 at the onset of chondrocyte hypertrophy
    In: Developmental Biology Vol. 457 (2020) Nr. 1, pp. 104 - 118
    ISSN: 0012-1606; 1095-564X
  • 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
  • Gigante, Alba; Grad, Jean-Noël; Briels, Jeroen; Bartel, Maria; Hoffmann, Daniel; Ottmann, Christian; Schmuck, Carsten
    A new class of supramolecular ligands stabilizes 14-3-3 protein-protein interactions by up to two orders of magnitude
    In: Chemical Communications Vol. 55 (2019) Nr. 1, pp. 111 - 114
    ISSN: 1364-548X; 0009-241X; 0022-4936; 1359-7345
  • Schröder, Nadine; Wülling, Manuela; Hoffmann, Daniel; Brand-Saberi, Beate; Vortkamp, Andrea;
    Wijnen, Andre van; (Eds.)
    Atoh8 acts as a regulator of chondrocyte proliferation and differentiation in endochondral bones
    In: PLoS ONE Vol. 14 (2019) Nr. 8, pp. e0218230
    ISSN: 1932-6203
  • Xia, Youchen; Pan, Wen; Ke, Xiaoyu; Skibbe, Kathrin; Walker, Andreas; Hoffmann, Daniel; Lu, Yinping; Yang, Xuecheng; Feng, Xuemei; Tong, Qiaoxia; Timm, Jörg; Yang, Dongliang
    Differential escape of HCV from CD8⁺ T cell selection pressure between China and Germany depends on the presenting HLA class I molecule
    In: Journal of Viral Hepatitis Vol. 26 (2019) Nr. 1, pp. 73 - 82
    ISSN: 1365-2893; 1352-0504
  • Kehrmann, Jan; Menzel, Jannis; Saeedghalati, Mohammadkarim; Obeid, Rima; Schulze, Christina; Holzendorf, Volker; Farahpour, Farnoush; Reinsch, Nico; Klein-Hitpaß, Ludger; Streeck, Hendrik; Hoffmann, Daniel; Buer, Jan; Esser, Stefan
    Gut Microbiota in Human Immunodeficiency Virus-Infected Individuals Linked to Coronary Heart Disease
    In: The Journal of Infectious Diseases Vol. 219 (2019) Nr. 3, pp. 497 - 508
    ISSN: 1537-6613; 0022-1899
  • 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
  • Yang, Li; Liu, Feifei; Tong, Xiankun; Hoffmann, Daniel; Zuo, Jianping; Lu, Mengji
    Treatment of Chronic Hepatitis B Virus Infection Using Small Molecule Modulators of Nucleocapsid Assembly : Recent Advances and Perspectives
    In: ACS Infectious Diseases Vol. 5 (2019) Nr. 5, pp. 713 - 724
    ISSN: 2373-8227
  • 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
  • Karimzadeh, Hadi; Kiraithe, Muthamia M.; Kosinska, Anna D.; Glaser, Manuel; Fiedler, Melanie; Oberhardt, Valerie; Alizei, Elahe Salimi; Hofmann, Maike; Mok, Juk Yee; Nguyen, Melanie; van Esch, Wim J.E.; Budeus, Bettina; Grabowski, Jan; Homs, Maria; Olivero, Antonella; Keyvani, Hossein; Rodríguez-Frías, Francisco; Tabernero, David; Buti, Maria; Heinold, Andreas; Alavian, Seyed Moayed; Bauer, Tanja; Wiesch, Julian Schulze zur; Raziorrouh, Bijan; Hoffmann, Daniel; Smedile, Antonina; Rizzetto, Mario; Wedemeyer, Heiner; Timm, Jörg; Antes, Iris; Neumann-Haefelin, Christoph; Protzer, Ulrike; Roggendorf, Michael
    Amino acid substitutions within HLA-B*27- restricted T cell epitopes prevent recognition by hepatitis delta virus-specific CD8⁺ T cells
    In: Journal of Virology Vol. 92 (2018) Nr. 13, pp. e01891 - 17
    ISSN: 1098-5514; 0022-538X
  • 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
  • Wang, Hongye; Yuan, Ting; Li, Tingting; Li, Yanpeng; Qian, Feng; Zhu, Chuanwu; Liang, Shujia; Hoffmann, Daniel; Dittmer, Ulf; Sun, Binlian; Yang, Rongge
    Evaluation of susceptibility of HIV-1 CRF01_AE variants to neutralization by a panel of broadly neutralizing antibodies
    In: Archives of Virology Vol. 163 (2018) Nr. 12, pp. 3303 - 3315
    ISSN: 0304-8608
  • Dunkel, Thiemo; Lizette de León Gallegos, Erika; Bock, Christina; Lange, Anja; Hoffmann, Daniel; Boenigk, Jens; Denecke, Martin
    Illumina sequencing for the identification of filamentous bulking and foaming bacteria in industrial activated sludge plants
    In: International Journal of Environmental Science and Technology Vol. 15 (2018) Nr. 6, pp. 1139 - 1158
    ISSN: 1735-2630; 1735-1472
  • Grad, Jean-Noël; Gigante, Alba; Wilms, Christoph; Dybowski, Jan Nikolaj; Ohl, Ludwig; Ottmann, Christian; Schmuck, Carsten; Hoffmann, Daniel
    Locating Large, Flexible Ligands on Proteins
    In: Journal of Chemical Information and Modeling Vol. 58 (2018) Nr. 2, pp. 315 - 327
    ISSN: 1549-9596; 1520-5142; 0021-9576; 0095-2338
  • Schürmann, Sabine; Steffes, Georg; Manikowski, Dominique; Kastl, Philipp; Malkus, Ursula; Bandari, Shyam; Ohlig, Stefanie; Ortmann, Corinna; Rebollido-Rios, Rocio; Otto, Mandy; Nüsse, Harald; Hoffmann, Daniel; Klämbt, Christian; Galic, Milos; Klingauf, Jürgen; Grobe, Kay
    Proteolytic processing of palmitoylated Hedgehog peptides specifies the 3-4 intervein region of the Drosophila wing
    In: eLife Vol. 7 (2018) pp. e33033
    ISSN: 2050-084X
  • Ehlers, Martin; Grad, Jean-Noël; Mittal, Sumit; Bier, David; Mertel, Marcel; Ohl, Ludwig; Bartel, Maria; Briels, Jeroen; Heimann, Marius; Ottmann, Christian; Sanchez-Garcia, Elsa; Hoffmann, Daniel; Schmuck, Carsten
    Rational Design, Binding Studies, and Crystal-Structure Evaluation of the First Ligand Targeting the Dimerization Interface of the 14-3-3ζ Adapter Protein
    In: ChemBioChem Vol. 19 (2018) Nr. 6, pp. 591 - 595
    ISSN: 1439-4227; 1439-7633
  • Piombo, Virginia; Jochmann, Katja; Hoffmann, Daniel; Wülling, Manuela; Vortkamp, Andrea
    Signaling systems affecting the severity of multiple osteochondromas
    In: Bone: Official Journal of the International Bone and Mineral Society (IBMS) Vol. 111 (2018) pp. 71 - 81
    ISSN: 1873-2763; 8756-3282
  • Farahpour, Farnoush; Saeedghalati, Mohammadkarim; Brauer, Verena S.; Hoffmann, Daniel
    Trade-off shapes diversity in eco-evolutionary dynamics
    In: eLife Vol. 7 (2018) pp. e36273
    ISSN: 2050-084X
  • Jakobs, Petra; Schulz, Philipp; Schürmann, Sabine; Niland, Stephan; Exner, Sebastian; Rebollido-Rios, Rocio; Manikowski, Dominique; Hoffmann, Daniel; Seidler, Daniela G.; Grobe, Kay
    Ca2+ coordination controls sonic hedgehog structure and its Scube2-regulated release
    In: Journal of Cell Science Vol. 130 (2017) Nr. 19, pp. 3261 - 3271
    ISSN: 0021-9533; 1477-9137; 0370-2952
  • Drabczyk-Pluta, Malgorzata; Werner, Tanja; Hoffmann, Daniel; Leng, Qibin; Chen, Lieping; Dittmer, Ulf; Zelinskyy, Gennadiy
    Granulocytic myeloid-derived suppressor cells suppress virus-specific CD8+ T cell responses during acute Friend retrovirus infection
    In: Retrovirology Vol. 14 (2017) pp. 42
    ISSN: 1742-4690
  • Nemec, Mike; Hoffmann, Daniel
    Quantitative Assessment of Molecular Dynamics Sampling for Flexible Systems
    In: Jounal of Chemical Theory and Computation Vol. 13 (2017) Nr. 2, pp. 400 - 414
    ISSN: 1549-9618; 1549-9626
  • Saeedghalati, Mohammadkarim; Farahpour, Farnoush; Budeus, Bettina; Lange, Anja; Westendorf, Astrid; Seifert, Marc; Küppers, Ralf; Hoffmann, Daniel
    Quantitative Comparison of Abundance Structures of Generalized Communities : from B-Cell Receptor Repertoires to Microbiomes
    In: PLoS Computational Biology Vol. 13 (2017) Nr. 1, pp. e1005362
    ISSN: 1553-734X; 1553-7358
  • Kletenkov, K.; Hoffmann, Daniel; Böni, Jürg; Yerly, Sabine; Aubert, Vincent; Schöni-Affolter, Franziska; Struck, Daniel; Verheyen, Jens; Klimkait, Thomas H.
    Role of Gag mutations in PI resistance in the Swiss HIV cohort study : bystanders or contributors?
    In: Journal of Antimicrobial Chemotherapy Vol. 72 (2017) Nr. 3, pp. 866 - 875
    ISSN: 1460-2091; 0305-7453
  • Großmann, Lars; Jensen, Manfred; Heider, Dominik; Jost, Steffen; Glücksmann, Edvard; Hartikainen, Hanna; Mahamdallie, Shazia S.; Gardner, Michelle; Hoffmann, Daniel; Bass, David; Boenigk, Jens
    Protistan community analysis : key findings of a large scale molecular sampling
    In: ISME Journal Vol. 10 (2016) pp. 2269 - 2279
    ISSN: 1751-7370; 1751-7362
  • Budeus, Bettina; Timm, Jörg; Hoffmann, Daniel
    SeqFeatR for the Discovery of Feature-Sequence Associations
    In: PLoS ONE Vol. 11 (2016) Nr. 1, pp. e0146409
    ISSN: 1932-6203
  • 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
  • Lange, Anja; Jost, Steffen Oliver; Heider, Dominik; Bock, Christina; Budeus, Bettina; Schilling, Elmar; Strittmatter, Axel; Boenigk, Jens; Hoffmann, Daniel
    AmpliconDuo : a split-sample filtering protocol for high-throughput amplicon sequencing of microbial communities
    In: PLoS ONE Vol. 10 (2015) Nr. 11, pp. e0141590
    ISSN: 1932-6203
  • 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
  • Sierra, Saleta; Dybowski, J. Nikolai; Pironti, Alejandro; Heider, Dominik; Güney, Lisa; Thielen, Alex; Reuter, Stefan; Esser, Stefan; Fätkenheuer, Gerd; Lengauer, Thomas; Hoffmann, Daniel; Pfister, Herbert; Jensen, Björn; Kaiser, Rolf
    Parameters influencing baseline HIV-1 genotypic tropism testing related to clinical outcome in patients on maraviroc
    In: PLoS ONE Vol. 10 (2015) Nr. 5, pp. e0125502
    ISSN: 1932-6203
  • Klammer, Martin; Dybowski, Jan Nikolaj; Hoffmann, Daniel; Schaab, Christoph
    Pareto optimization identifies diverse set of phosphorylation signatures predicting response to treatment with dasatinib
    In: PLoS ONE Vol. 10 (2015) Nr. 6, pp. e0128542
    ISSN: 1932-6203
  • Merches, Katja; Khairnar, Vishal; Knuschke, Torben; Shaabani, Namir; Honke, Nadine; Duhan, Vikas; Recher, Mike; Navarini, Alexander A.; Hardt, Cornelia; Häussinger, Dieter; Tümmler, Burkhard; Gulbins, Erich; Futerman, Anthony H.; Hoffmann, Daniel; Lang, Florian; Lang, Philipp A.; Westendorf, Astrid; Lang, Karl S.
    Virus-induced type i interferon deteriorates control of systemic pseudomonas aeruginosa infection
    In: Cellular Physiology and Biochemistry Vol. 36 (2015) Nr. 6, pp. 2379 - 2392
    ISSN: 1015-8987; 1421-9778
  • Heider, Dominik; Dybowski, Jan Nikolaj; Wilms, Christoph; Hoffmann, Daniel
    A simple structure-based model for the prediction of HIV-1 co-receptor tropism
    In: BioData Mining Vol. 7 (2014) pp. 14
    ISSN: 1756-0381
  • Dang, S.; Wang, Yan; Budeus, Bettina; Verheyen, Jens; Yang, R.; Hoffmann, Daniel
    Differential selection in HIV-1 gp120 between subtype B and East Asian variant B'
    In: Virologica Sinica Vol. 29 (2014) Nr. 1, pp. 40 - 47
    ISSN: 1674-0769; 1995-820X
  • 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
  • Klammer, Martin; Dybowski, Jan Nikolaj; Hoffmann, Daniel; Schaab, Christoph
    Identification of Significant Features by the Global Mean Rank Test
    In: PLoS ONE Vol. 9 (2014) Nr. 8, pp. e104504
    ISSN: 1932-6203
  • Rebollido-Rios, Rocio; Bandari, Shyam; Wilms, Christoph; Jakuschev, Stanislav; Vortkamp, Andrea; Grobe, Kay; Hoffmann, Daniel
    Signaling Domain of Sonic Hedgehog as Cannibalistic Calcium-Regulated Zinc-Peptidase
    In: PLoS Computational Biology Vol. 10 (2014) Nr. 7, pp. e1003707
    ISSN: 1553-7358; 1553-734X
  • Wang, Yan; Rawi, Reda; Wilms, Christoph; Heider, Dominik; Yang, Rongge; Hoffmann, Daniel
    A Small Set of Succinct Signature Patterns Distinguishes Chinese and Non-Chinese HIV-1 Genomes
    In: PLoS ONE Vol. 8 (2013) Nr. 3, pp. e58804
    ISSN: 1932-6203
  • Jiang, Qian-Qian; Bartsch, Lina; Sicking, Wilhelm; Wich, Peter R.; Heider, Dominik; Hoffmann, Daniel; Schmuck, Carsten
    A new approach to inhibit human β-tryptase by protein surface binding of four-armed peptide ligands with two different sets of arms
    In: Organic and Biomolecular Chemistry Vol. 11 (2013) Nr. 10, pp. 1631 - 1639
    ISSN: 1477-0539; 1477-0520
  • Wang, Yan; Rawi, Reda; Wilms, Christoph; Heider, Dominik; Yang, Rongge; Hoffmann, Daniel
    Correction: A Small Set of Succinct Signature Patterns Distinguishes Chinese and Non-Chinese HIV-1 Genomes.
    In: PLoS ONE Vol. 8 (2013) Nr. 12,
    ISSN: 1932-6203
  • Grum, Daniel; Franke, Stefan; Kraff, Oliver; Heider, Dominik; Schramm, Alexander; Hoffmann, Daniel; Bayer, Peter
    Design of a Modular Protein-Based MRI Contrast Agent for Targeted Application
    In: PLoS ONE Vol. 8 (2013) Nr. 6, pp. e65346
    ISSN: 1932-6203
  • Wang, Yan; Rawi, Reda; Hoffmann, Daniel; Sun, Binlian; Yang, Rongge
    Inference of global HIV-1 sequence patterns and preliminary feature analysis
    In: Virologica Sinica Vol. 28 (2013) Nr. 4, pp. 228 - 238
    ISSN: 1674-0769; 1995-820X
  • Sowa, Jan-Peter; Heider, Dominik; Bechmann, Lars Peter; Gerken, Guido; Hoffmann, Daniel; Canbay, Aliekber
    Novel Algorithm for Non-Invasive Assessment of Fibrosis in NAFLD
    In: PLoS ONE Vol. 8 (2013) Nr. 4, pp. e62439
    ISSN: 1932-6203
  • Qin, Bo; Budeus, Bettina; Cao, Liang; Wu, Chunchen; Wang, Yun; Zhang, Xiaoyong; Rayner, Simon; Hoffmann, Daniel; Lu, Mengji; Chen, Xinwen
    The amino acid substitutions rtP177G and rtF249A in the reverse transcriptase domain of hepatitis B virus polymerase reduce the susceptibility to tenofovir
    In: Antiviral Research Vol. 97 (2013) Nr. 2, pp. 93 - 100
    ISSN: 0166-3542; 1872-9096
  • Matena, Anja; Sinnen, Christian; van den Boom, Johannes; Wilms, Christoph; Dybowski, Jan Nikolaj; Maltaner, Ricarda; Müller, Jonathan W.; Link, Nina M.; Hoffmann, Daniel; Bayer, Peter
    Transient domain interactions enhance the affinity of the mitotic regulator pin1 toward phosphorylated peptide ligands
    In: Structure Vol. 21 (2013) Nr. 10, pp. 1769 - 1777
    ISSN: 1878-4186
  • Ohlig, Stefanie; Pickhinke, Ute; Sirko, Svetlana; Bandari, Shyam; Hoffmann, Daniel; Dreier, Rita; Farshi, Pershang; Götz, Magdalena; Grobe, Kai
    An emerging role of sonic hedgehog shedding as a modulator of heparan sulfate interactions
    In: Journal of Biological Chemistry Vol. 287 (2012) Nr. 52, pp. 43708 - 43719
    ISSN: 0021-9258; 1083-351X
  • Ruhl, Marianne; Chhatwal, Patrick; Strathmann, Heiko; Kuntzen, Thomas; Bankwitz, Dorothea; Skibbe, Kathrin; Walker, Andreas; Heinemann, Falko M.; Horn, Peter; Allen, Todd M.; Hoffmann, Daniel; Pietschmann, Thomas; Timm, Jörg
    Escape from a dominant hla-b*15-restricted cd8+ t cell response against hepatitis c virus requires compensatory mutations outside the epitope
    In: Journal of Virology Vol. 86 (2012) Nr. 2, pp. 991 - 1000
    ISSN: 0022-538X; 1098-5514
  • Genheden, Samuel; Kuhn, Oliver; Mikulskis, Paulius; Hoffmann, Daniel; Ryde, Ulf
    The Normal-Mode Entropy in the MM/GBSA Method : Effect of System Truncation, Buffer Region, and Dielectric Constant
    In: Journal of Chemical Information and Modeling Vol. 52 (2012) Nr. 8, pp. 2079 - 2088
    ISSN: 1549-9596; 1520-5142; 0021-9576; 0095-2338
  • Neumann, Lisa; Markaki, Yolanda; Mladenov, Emil; Hoffmann, Daniel; Buiting, Karin; Horsthemke, Bernhard
    The imprinted NPAP1/C15orf2 gene in the Prader-Willi syndrome region encodes a nuclear pore complex associated protein
    In: Human Molecular Genetics Vol. 21 (2012) Nr. 18, pp. 4038 - 4048
    ISSN: 1460-2083; 0964-6906
  • Haferkamp, Patrick; Kutschki, Simone; Treichel, Jenny; Hemeda, Hatim; Sewczyk, Karsten; Hoffmann, Daniel; Zaparty, Melanie; Siebers, Bettina
    An additional glucose dehydrogenase from Sulfolobus solfataricus : fine-tuning of sugar degradation?
    In: Biochemical Society Transactions Vol. 39 (2011) Nr. 1, pp. 77 - 81
    ISSN: 0300-5127; 1470-8752
  • 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
  • Dybowski, Jan Nikolaj; Riemenschneider, Mona; Hauke, Sascha; Pyka, Martin; Verheyen, Jens; Hoffmann, Daniel; Heider, Dominik
    Improved Bevirimat resistance prediction by combination of structural and sequence-based classifiers
    In: BioData Mining Vol. 4 (2011) Nr. 1, pp. 26
    ISSN: 1756-0381
  • Heider, Dominik; Hoffmann, Daniel
    Interpol : An R package for preprocessing of protein sequences
    In: BioData Mining Vol. 4 (2011) pp. 16
    ISSN: 1756-0381
  • Heider, Dominik; Verheyen, Jens; Hoffmann, Daniel
    Machine learning on normalized protein sequences
    In: BMC Research Notes Vol. 4 (2011) pp. 94
    ISSN: 1756-0500
  • Horsthemke, Bernhard; Wawrzik, Michaela; Groß, Stephanie; Lich, Christina; Sauer, Birgitta; Rost, Imma; Krasemann, Ernst; Kosyakowa, Nadezda; Liehr, Thomas; Weise, Anja; Dybowski, Jan Nikolaj; Hoffmann, Daniel; Wieczorek, Dagmar
    Parental origin and functional relevance of a de novo UBE3A variant
    In: European Journal of Medical Genetics Vol. 54 (2011) Nr. 1, pp. 19 - 24
    ISSN: 1769-7212
  • Lederer, Christoph; Heider, Dominik; van den Boom, Johannes; Hoffmann, Daniel; Müller, Jonathan W.; Bayer, Peter
    Single-Domain Parvulins Constitute a Specific Marker for Recently Proposed Deep-Branching Archaeal Subgroups
    In: Evolutionary Bioinformatics Vol. 7 (2011) pp. 135 - 148
    ISSN: 1176-9343
  • Ohlig, Stefanie; Farshi, Pershang; Pickhinke, Ute; van den Boom, Johannes; Höing, Susanne; Jakuschev, Stanislav; Hoffmann, Daniel; Dreier, Rita; Schöler, Hans R.; Dierker, Tabea; Bordych, Christian; Grobe, Kay
    Sonic hedgehog shedding results in functional activation of the solubilized protein
    In: Developmental Cell Vol. 20 (2011) Nr. 6, pp. 764 - 774
    ISSN: 1534-5807; 1878-1551
  • Franke, Stefan; Herfurth, Julia; Hoffmann, Daniel
    Estimating affinities of calcium ions to proteins
    In: Advances and Applications in Bioinformatics and Chemistry Vol. 3 (2010) Nr. 1, pp. 1 - 6
    ISSN: 1178-6949
  • Heider, Dominik; Verheyen, Jens; Hoffmann, Daniel
    Predicting Bevirimat resistance of HIV-1 from genotype
    In: BMC Bioinformatics Vol. 11 (2010) pp. 37
    ISSN: 1471-2105
  • Dybowski, Jan Nikolaj; Heider, Dominik; Hoffmann, Daniel
    Prediction of Co-Receptor Usage of HIV-1 from Genotype
    In: PLoS Computational Biology Vol. 6 (2010) Nr. 4, pp. e1000743
    ISSN: 1553-7358; 1553-734X
  • 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
  • Dybowski, Jan Nikolaj; Heider, Dominik; Hoffmann, Daniel
    Structure of HIV-1 quasi-species as early indicator for switches of co-receptor tropism.
    In: AIDS Research and Therapy Vol. 7 (2010) pp. 41
    ISSN: 1742-6405
  • Drogan, Daniel; Rauch, Pia; Hoffmann, Daniel; Walter, Hauke; Metzner, Karin J.
    The antiretroviral potency of emtricitabine is approximately 3-fold higher compared to lamivudine in dual human immunodeficiency virus type 1 infection/competition experiments in vitro
    In: Antiviral Research Vol. 86 (2010) Nr. 3, pp. 312 - 315
    ISSN: 1872-9096
  • Schirling, Corinna; Heseding, Christiane; Heise, Franziska; Kesper, Dörthe; Klebes, Ansgar; Klein-Hitpaß, Ludger; Vortkamp, Andrea; Hoffmann, Daniel; Saumweber, Harald; Ehrenhofer-Murray, Ann
    Widespread regulation of gene expression in the Drosophila genome by the histone acetyltransferase dTip60
    In: Chromosoma Vol. 119 (2010) Nr. 1, pp. 99 - 113
    ISSN: 0009-5915; 1432-0886

ZMB Research Programme

Prof. Daniel Hoffmann participates in the ZMB research programme III, Molecular and Chemical Cell Biology.