Publications

    Journal articles

  • Waterkamp, Christoph; Hoffmann, Daniel
    BAYAS : simplifying access to Bayesian analysis for biologists
    In: Bioinformatics, Vol. 41, 2025, Nr. 6, btaf276
    DOI, Online Full Text (Open Access)
  • Neu, Christoph; Wülling, Manuela; Waterkamp, Christoph; Hoffmann, Daniel; Vortkamp, Andrea
    Bath : A Bayesian approach to analyze epigenetic transitions reveals a dual role of H3K27me3 in chondrogenesis
    In: Epigenetics and Chromatin, Vol. 18, 2025, Nr. 1, 38
    DOI (Open Access)
  • Schwarz, Tatjana; Ptok, Johannes; Damagnez, Maximilian; Menne, Christopher; Alizei, Elahe Salimi; Lang-Meli, Julia; Maas, Michelle; Habermann, Daniel; Hoffmann, Daniel; Schulze zur Wiesch, Julian; Lauer, Georg; Kefalakes, Helenie; Cornberg, Markus; Kraft, Anke RM.; Gliga, Smaranda; Bock, Hans H.; Horn, Peter A.; Maini, Mala K.; Thimme, Robert; Wedemeyer, Heiner; Nattermann, Jacob; Heinemann, Falko M.; Luedde, Tom; Neumann-Haefelin, Christoph; Walker, Andreas; Timm, Jörg
    HBV shows different levels of adaptation to HLA class I-associated selection pressure correlating with markers of replication
    In: Journal of Hepatology, Vol. 82, 2025, Nr. 5, pp. 805 – 815
    DOI (Open Access)
  • Lei, Kuan Cheok; Srinivas, Nalini; Chandra, Mitalee; Serobyan, Vahan; Ugurel, Selma; Hoffmann, Daniel; Kervarrec, Thibault; Lui, Weng-Onn; Becker, Jürgen C.
    High-resolution spatial transcriptomics uncover epidermal-dermal divergences in Merkel cell carcinoma : Spatial context reshapes the gene expression landscape
    In: Oncogene, Vol. 44, 2025, Nr. 47, pp. 4615 – 4625
    DOI (Open Access)
  • Ttoouli, Dimitris; Hoffmann, Daniel
    Multiplets in scRNA-seq data : Extent of the problem and efficacy of methods for removal
    In: PLoS ONE, Vol. 20, 2025, Nr. 10, e0333687
    DOI (Open Access)
  • Kitanovski, Simo; Wollek, Kai; Hoffmann, Daniel
    Quantitative Visualisierung von HTseq-Daten
    In: Biospektrum, Vol. 31, 2025, Nr. 1, pp. 49 – 51
    DOI (Open Access)
  • Wang, Jun; Li, Qian; Qiu, Yuanwang; Kitanovski, Simo; Wang, Chen; Zhang, Chenxia; Li, Fahong; Li, Xiaoguang; Zhang, Zhenfeng; Huang, Lihua; Zhang, Jiming; Hoffmann, Daniel; Lu, Mengji; Lu, Hongzhou
    Cell-type-specific expression analysis of liver transcriptomics with clinical parameters to decipher the cause of intrahepatic inflammation in chronic hepatitis B
    In: iMeta, Vol. 3, 2024, Nr. 4, e221
    DOI (Open Access)
  • Porfetye, Arthur T.; Stege, Patricia; Rebollido-Rios, Rocio; Hoffmann, Daniel; Schrader, Thomas; Vetter, Ingrid R.
    How Do Molecular Tweezers Bind to Proteins? : Lessons from X-ray Crystallography
    In: Molecules: A Journal of Synthetic Chemistry and Natural Product Chemistry, Vol. 29, 2024, Nr. 8, 1764
    DOI (Open Access)
  • Lei, Kuan Cheok; Srinivas, Nalini; Chandra, Mitalee; Kervarrec, Thibault; Coyaud, Etienne; Spassova, Ivelina; Peiffer, Lukas; Houben, Roland; Shuda, Masahiro; Hoffmann, Daniel; Schrama, David; Becker, Jürgen
    Merkel cell polyomavirus pan-T antigen knockdown reduces cancer cell stemness and promotes neural differentiation independent of RB1
    In: Journal of Medical Virology, Vol. 96, 2024, Nr. 7, e29789
    DOI (Open Access)
  • Tuz, Ali A.; Ghosh, Susmita; Karsch, Laura; Ttoouli, Dimitris; Sata, Sai P.; Ulusoy, Özgür; Kraus, Andreas; Hoerenbaum, Nils; Wolf, Jan-Niklas; Lohmann, Sabrina; Zwirnlein, Franziska; Kaygusuz, Viola; Lakovic, Vivian; Tummes, Hannah-Lea; Beer, Alexander; Gallert, Markus; Thiebes, Stephanie; Qefalia, Altea; Cibir, Zülal; Antler, Medina; Korste, Sebastian; Haj Yehia, Elias; Michel, Lars; Rassaf, Tienush; Kaltwasser, Britta; Abdelrahman, Hossam; Mohamud Yusuf, Ayan; Wang, Chen; Yin, Dongpei; Haeusler, Lars; Lueong, Smiths; Richter, Mathis; Engel, Daniel R.; Stenzel, Martin; Soehnlein, Oliver; Frank, Benedikt; Solo-Nomenjanahary, Mialitiana; Ho-Tin-Noé, Benoît; Siveke, Jens T.; Totzeck, Matthias; Hoffmann, Daniel; Grüneboom, Anika; Hagemann, Nina; Hasenberg, Anja; Desilles, Jean-Philippe; Mazighi, Mikael; Sickmann, Albert; Chen, Jianxu; Hermann, Dirk M.; Gunzer, Matthias; Singh, Vikramjeet
    Stroke and myocardial infarction induce neutrophil extracellular trap release disrupting lymphoid organ structure and immunoglobulin secretion
    In: Nature Cardiovascular Research, Vol. 3, 2024, Nr. 5, pp. 525 – 540
    DOI (Open Access)
  • Kitanovski, Simo; Cao, Yingying; Ttoouli, Dimitris; Farahpour, Farnoush; Wang, Jun; Hoffmann, Daniel
    scBubbletree: computational approach for visualization of single cell RNA-seq data
    In: BMC Bioinformatics, Vol. 25, 2024, Nr. 1, 302
    DOI (Open Access)
  • Waterkamp, Christoph; von Kortzfleisch, V T; Neu, Ch; Kitanovski, Simo; Richter, S H; Hoffmann, Daniel
    Increasing information gain in animal research by improving statistical model accuracy
    In: Journal of Physics: Conference Series (JPCONF), Vol. 2514, 2023, Nr. 1, 012021
    DOI (Open Access)
  • Magvan, Battur; Kloeble, Anne Alina; Ptok, Johannes; Hoffmann, Daniel; Habermann, Daniel; Gantumur, Anuujin; Paluschinski, Martha; Enebish, Gerelmaa; Balz, Vera; Fischer, Johannes C.; Chimeddorj, Battogtokh; Walker, Andreas; Timm, Jörg
    Sequence diversity of hepatitis D virus in Mongolia
    In: Frontiers in Medicine, Vol. 10, 2023, 1108543
    DOI (Open Access)
  • Karakoese, Zehra; Le-Trilling, Vu Thuy Khanh; Schuhenn, Jonas; Francois, Sandra; Lu, Mengji; Liu, Jia; Trilling, Mirko; Hoffmann, Daniel; Dittmer, Ulf; Sutter, Kathrin
    Targeted mutations in IFNα2 improve its antiviral activity against various viruses
    In: mBio, Vol. 14, 2023, Nr. 6, e02357-23
    DOI, Online Full Text (Open Access)
  • Spassova, Ivelina; Ugurel, Selma; Kubat, Linda; Zimmer, Lisa; Terheyden, Patrick; Mohr, Annalena; Björn Andtback, Hannah; Villabona, Lisa; Leiter, Ulrike; Eigentler, Thomas; Loquai, Carmen; Hassel, Jessica C.; Gambichler, Thilo; Haferkamp, Sebastian; Mohr, Peter; Pfoehler, Claudia; Heinzerling, Lucie; Gutzmer, Ralf; Utikal, Jochen S.; Horny, Kai; Schildhaus, Hans-Ulrich; Habermann, Daniel; Hoffmann, Daniel; Schadendorf, Dirk; Becker, Jürgen
    Clinical and molecular characteristics associated with response to therapeutic PD-1/PD-L1 inhibition in advanced Merkel cell carcinoma
    In: Journal for ImmunoTherapy of Cancer, Vol. 10, 2022, Nr. 1, e003198
    DOI, Online Full Text (Open Access)
  • Rafieiolhosseini, Neda; Killa, Matthias; Neumann, Thorben; Tötsch, Niklas; Grad, Jean-Noël; Höing, Alexander; Dirksmeyer, Thies; Niemeyer, Jochen; Ottmann, Christian; Knauer, Shirley K; Giese, Michael; Voskuhl, Jens; Hoffmann, Daniel
    Computational model predicts protein binding sites of a luminescent ligand equipped with guanidiniocarbonyl-pyrrole groups
    In: Beilstein Journal of Organic Chemistry, Vol. 18, 2022, pp. 1322 – 1331
    DOI (Open Access)
  • Gravemeyer, Jan; Spassova, Ivelina; Verhaegen, Monique E.; Dlugosz, Andrzej A.; Hoffmann, Daniel; Lange, Anja; Becker, Jürgen
    DNA-methylation patterns imply a common cellular origin of virus- and UV-associated Merkel cell carcinoma
    In: Oncogene, Vol. 41, 2022, Nr. 1, pp. 37 – 45
    DOI (Open Access)
  • Streeck, Hendrik; Maestri, Alvino; Habermann, Daniel; Crowell, Trevor A.; Esber, Allahna L.; Son, Gowoon; Eller, Leigh Anne; Eller, Michael A.; Parikh, Ajay P.; Horn, Peter; Maganga, Lucas; Bahemana, Emmanuel; Adamu, Yakubu; Kiweewa, Francis; Maswai, Jonah; Owuoth, John; Robb, Merlin L.; Michael, Nelson L.; Polyak, Christina S.; Hoffmann, Daniel; Ake, Julie A.
    Dissecting drivers of immune activation in chronic HIV-1 infection
    In: eBioMedicine, Vol. 83, 2022, 104182
    DOI (Open Access)
  • Höing, Alexander; Struth, Robin; Beuck, Christine; Rafieiolhosseini, Neda; Hoffmann, Daniel; Stauber, Roland H.; Bayer, Peter; Niemeyer, Jochen; Knauer, Shirley
    Dual activity inhibition of threonine aspartase 1 by a single bisphosphate ligand
    In: RSC Advances, Vol. 12, 2022, Nr. 53, pp. 34176 – 34184
    DOI (Open Access)
  • Habermann, Daniel; Kharimzadeh, Hadi; Walker, Andreas; Li, Yang; Yang, Rongge; Kaiser, Rolf; Brumme, Zabrina L.; Timm, Jörg; Roggendorf, Michael; Hoffmann, Daniel
    HAMdetector : A Bayesian regression model that integrates information to detect HLA-associated mutations
    In: Bioinformatics, Vol. 38, 2022, Nr. 9, pp. 2428 – 2436
    DOI (Open Access)
  • Walker, Andreas; Schwarz, Tatjana; Brinkmann-Paulukat, Janine; Wisskirchen, Karin; Menne, Christopher; Alizei, Elahe Salimi; Kefalakes, Helenie; Theißen, Martin; Hoffmann, Daniel; Schulze zur Wiesch, Julian; Maini, Mala K.; Cornberg, Markus; Kraft, Anke RM; Keitel, Verena; Bock, Hans H.; Horn, Peter; Thimme, Robert; Wedemeyer, Heiner; Heinemann, Falko M.; Luedde, Tom; Neumann-Haefelin, Christoph; Protzer, Ulrike; Timm, Jörg
    Immune escape pathways from the HBV core₁₈₋₂₇ CD8 T cell response are driven by individual HLA class I alleles
    In: Frontiers in Immunology, Vol. 13, 2022, 1045498
    DOI (Open Access)
  • Reinold, Johanna; Farahpour, Farnoush; Fehring, Christian; Dolff, Sebastian; Konik, Margarethe; Korth, Johannes; van Baal, Lukas; Hoffmann, Daniel; Buer, Jan; Witzke, Oliver; Westendorf, Astrid; Kehrmann, Jan
    A Pro-Inflammatory Gut Microbiome Characterizes SARS-CoV-2 Infected Patients and a Reduction in the Connectivity of an Anti-Inflammatory Bacterial Network Associates With Severe COVID-19
    In: Frontiers in Cellular and Infection Microbiology, Vol. 11, 2021, 747816
    DOI, Online Full Text (Open Access)
  • Pfeiffer, Lukas; Farahpour, Farnoush; Sriram, Ashwin; Spassova, Ivelina; Hoffmann, Daniel; Kubat, Linda; Stoitzner, Patrizia; Gambichler, Thilo; Sucker, Antje; Ugurel, Selma; Schadendorf, Dirk; Becker, Jürgen C.
    BRAF and MEK inhibition in melanoma patients enables reprogramming of tumor infiltrating lymphocytes
    In: Cancer Immunology, Immunotherapy, Vol. 70, 2021, Nr. 6, pp. 1635 – 1647
    DOI (Open Access)
  • Gravemeyer, Jan; Lange, Anja; Ritter, Cathrin; Spassova, Ivelina; Song, Lina; Picard, Daniel; Remke, Marc; Horny, Kai; Sriram, Ashwin; Gambichler, Thilo; Schadendorf, Dirk; Hoffmann, Daniel; Becker, Jürgen
    Classical and Variant Merkel Cell Carcinoma Cell Lines Display Different Degrees of Neuroendocrine Differentiation and Epithelial-Mesenchymal Transition
    In: Journal of Investigative Dermatology, Vol. 141, 2021, Nr. 7, pp. 1675 – 1686.e4
    DOI (Open Access)
  • Tötsch, Niklas; Hoffmann, Daniel
    Classifier uncertainty : Evidence, potential impact, and probabilistic treatment
    In: PeerJ Computer Science, Vol. 7, 2021, pp. e398
    DOI (Open Access)
  • Cao, Yingying; Xu, Xintian; Kitanovski, Simo; Song, Lina; Wang, Jun; Hao, Pei; Hoffmann, Daniel
    Comprehensive Comparison of RNA-Seq Data of SARS-CoV-2, SARS-CoV and MERS-CoV Infections : Alternative Entry Routes and Innate Immune Responses
    In: Frontiers in Immunology, Vol. 12, 2021, 656433
    DOI, Online Full Text (Open Access)
  • Wülling, Manuela; Neu, Christoph; Thiesen, Andrea M.; Kitanovski, Simo; Cao, Yingying; Lange, Anja; Westendorf, Astrid; Hoffmann, Daniel; Vortkamp, Andrea
    Epigenetic mechanisms mediating cell state transitions in chondrocytes
    In: Journal of Bone and Mineral Research (JBMR), Vol. 36, 2021, Nr. 5, pp. 968 – 985
    DOI, Online Full Text (Open Access)
  • Li, Qian; Wang, Jun; Islam, Heba; Kirschning, Carsten Jürgen; Lu, Hongzhou; Hoffmann, Daniel; Dittmer, Ulf; Lu, Mengji
    Hepatitis B virus particles activate B cells through the TLR2–MyD88–mTOR axis
    In: Cell Death and Disease, Vol. 12, 2021, Nr. 1, 34
    DOI, Online Full Text (Open Access)
  • Budeus, Bettina; Kibler, Artur; Brauser, Martina; Homp, Ekaterina; Bronischewski, Kevin; Ross, J. Alexander; Görgens, Andre; Weniger, Marc; Dunst, Josefine; Kreslavsky, Taras; da Conceição Castro, Symone Vitoriano; Murke, Florian; Oakes, Christopher C.; Rusch, Peter; Andrikos, Dimitrios; Kern, Peter; Köninger, Angela; Lindemann, Monika; Johansson, Patricia; Hansen, Wiebke; Lundell, Anna-Carin; Rudin, Anna; Dürig, Jan; Giebel, Bernd; Hoffmann, Daniel; Küppers, Ralf; Seifert, Marc
    Human cord blood b cells differ from the adult counterpart by conserved ig repertoires and accelerated response dynamics
    In: The Journal of Immunology (JI), Vol. 206, 2021, Nr. 12, pp. 2839 – 2851
    DOI
  • Duhan, Vikas; Khairnar, Vishal; Kitanovski, Simo; Hamdan, Thamer A.; Klein, Andrés D.; Lang, Judith; Ali, Murtaza; Adomati, Tom; Bhat, Hilal; Friedrich, Sarah-Kim; Li, Fanghui; Krebs, Philippe; Futerman, Anthony H.; Addo, Marylyn M.; Hardt, Cornelia; Hoffmann, Daniel; Lang, Philipp A.; Lang, Karl S.
    Integrin Alpha E (CD103) Limits Virus-Induced IFN-I Production in Conventional Dendritic Cells
    In: Frontiers in Immunology, Vol. 11, 2021, 607889
    DOI, Online Full Text (Open Access)
  • Krysztofiak, Adam; Szymonowicz, Klaudia; Hlouschek, Julian; Xiang, Kexu; Waterkamp, Christoph; Larafa, Safa; Goetting, Isabell; Vega-Rubin-de-Celis, Silvia; Theiss, Carsten; Matschke, Veronika; Hoffmann, Daniel; Jendrossek, Verena; Matschke, Johann
    Metabolism of cancer cells commonly responds to irradiation by a transient early mitochondrial shutdown
    In: iScience, Vol. 24, 2021, Nr. 11, 103366
    DOI (Open Access)
  • Kitanovski, Simo; Horemheb-Rubio, Gibran; Adams, Ortwin; Gärtner, Barbara; Lengauer, Thomas; Hoffmann, Daniel; Kaiser, Rolf
    Rhinovirus prevalence as indicator for efficacy of measures against SARS-CoV-2
    In: BMC Public Health, Vol. 21, 2021, Nr. 1, 1178
    DOI, Online Full Text (Open Access)
  • Meiners, Annika; Bäcker, Sandra; Hadrovic, Inesa; Heid, Christian; Beuck, Christine; Ruiz-Blanco, Yasser B.; Mieres-Perez, Joel; Pörschke, Marius; Grad, Jean-Noël; Vallet, Cecilia; Hoffmann, Daniel; Bayer, Peter; Sánchez-García, Elsa; Schrader, Thomas; Knauer, Shirley
    Specific inhibition of the Survivin–CRM1 interaction by peptide-modified molecular tweezers
    In: Nature Communications, Vol. 12, 2021, Nr. 1, pp. 1505
    DOI, Online Full Text (Open Access)
  • Cao, Yingying; Kitanovski, Simo; Küppers, Ralf; Hoffmann, Daniel
    UMI or not UMI, that is the question for scRNA-seq zero-inflation
    In: Nature Biotechnology, Vol. 39, 2021, Nr. 2, pp. 158 – 159
    DOI, Online Full Text (Open Access)
  • 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
    DOI (Open Access)
  • 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
    DOI (Open Access)
  • 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
    DOI (Open Access)
  • 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
    DOI (Open Access)
  • 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, Vol. 39, 2020, pp. 43 – 59
    DOI (Open Access)
  • 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
    DOI, Online Full Text (Open Access)
  • Kitanovski, Simo; Hoffmann, Daniel
    IgGeneUsage : differential gene usage in immune repertoires
    In: Bioinformatics, Vol. 36, 2020, Nr. 11, pp. 3590 – 3591
    DOI
  • 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 C.
    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
    DOI (Open Access)
  • 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
    DOI
  • 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
    DOI (Open Access)
  • Cao, Yingying; Kitanovski, Simo; Hoffmann, Daniel
    intePareto : an R package for integrative analyses of RNA-Seq and ChIP-Seq data
    International Conference on Intelligent Biology and Medicine (ICIBM 2020), 9.-10.08.2020, Virtual,
    In: BMC Genomics, Vol. 21, 2020, Nr. Supplement 11, pp. 802
    DOI (Open Access)
  • 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
    DOI, Online Full Text (Open Access)
  • 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: ChemComm, Vol. 55, 2019, Nr. 1, pp. 111 – 114
    DOI
  • Schröder, Nadine; Wülling, Manuela; Hoffmann, Daniel; Brand-Saberi, Beate; Vortkamp, Andrea
    Atoh8 acts as a regulator of chondrocyte proliferation and differentiation in endochondral bones
    In: PLoS ONE, Vol. 14, 2019, Nr. 8, pp. e0218230
    DOI, Online Full Text (Open Access)
  • 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
    DOI (Open Access)
  • 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 (JID), Vol. 219, 2019, Nr. 3, pp. 497 – 508
    DOI (Open Access)
  • 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
    DOI (Open Access)
  • 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
    DOI
  • 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
    DOI
  • 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, e01891-17
    DOI, Online Full Text (Open Access)
  • 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
    DOI (Open Access)
  • 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
    DOI
  • 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 (IJEST), Vol. 15, 2018, Nr. 6, pp. 1139 – 1158
    DOI
  • 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
    DOI, Online Full Text (Open Access)
  • 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
    DOI (Open Access)
  • Ehlers, Martin; Grad, Jean-Noël; Mittal, Sumit; Bier, David; Mertel, Marcel; Ohl, Ludwig; Bartel, Maria; Briels, Jeroen; Heimann, Marius; Ottmann, Christian; Sánchez-García, 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
    DOI
  • 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
    DOI (Open Access)
  • Farahpour, Farnoush; Saeedghalati, Mohammadkarim; Brauer, Verena S.; Hoffmann, Daniel
    Trade-off shapes diversity in eco-evolutionary dynamics
    In: eLife, Vol. 7, 2018, pp. e36273
    DOI (Open Access)
  • 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
    DOI (Open Access)
  • 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, 42
    DOI (Open Access)
  • Nemec, Mike; Hoffmann, Daniel
    Quantitative Assessment of Molecular Dynamics Sampling for Flexible Systems
    In: Journal of Chemical Theory and Computation (JCTC), Vol. 13, 2017, Nr. 2, pp. 400 – 414
    DOI
  • 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, e1005362
    DOI, Online Full Text (Open Access)
  • 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
    DOI (Open Access)
  • 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
    DOI (Open Access)
  • Budeus, Bettina; Timm, Jörg; Hoffmann, Daniel
    SeqFeatR for the Discovery of Feature-Sequence Associations
    In: PLoS ONE, Vol. 11, 2016, Nr. 1, pp. e0146409
    DOI (Open Access)
  • 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
    DOI (Open Access)
  • 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
    DOI, Online Full Text (Open Access)
  • 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 (PNAS), Vol. 112, 2015, Nr. 38, pp. E5281 – E5289
    DOI (Open Access)
  • 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
    DOI (Open Access)
  • 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
    DOI (Open Access)
  • 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
    DOI (Open Access)
  • 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
    DOI (Open Access)
  • 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
    DOI
  • 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
    DOI
  • 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
    DOI (Open Access)
  • 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
    DOI (Open Access)
  • 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
    DOI, Online Full Text (Open Access)
  • 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
    DOI
  • 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
    DOI (Open Access)
  • 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
    DOI, Online Full Text (Open Access)
  • 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
    DOI
  • 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
    DOI (Open Access)
  • 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
    DOI
  • 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
    DOI (Open Access)
  • 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: The Journal of Biological Chemistry (JBC), Vol. 287, 2012, Nr. 52, pp. 43708 – 43719
    DOI
  • 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
    DOI, Online Full Text (Open Access)
  • 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
    DOI (Open Access)
  • 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
    DOI (Open Access)
  • 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
    DOI
  • 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
    DOI (Open Access)
  • 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
    DOI
  • 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
    DOI, Online Full Text (Open Access)
  • Heider, Dominik; Hoffmann, Daniel
    Interpol : An R package for preprocessing of protein sequences
    In: BioData Mining, Vol. 4, 2011, pp. 16
    DOI, Online Full Text (Open Access)
  • Heider, Dominik; Verheyen, Jens; Hoffmann, Daniel
    Machine learning on normalized protein sequences
    In: BMC Research Notes, Vol. 4, 2011, pp. 94
    DOI, Online Full Text (Open Access)
  • 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 (EJMG), Vol. 54, 2011, Nr. 1, pp. 19 – 24
    DOI
  • 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
    DOI, Online Full Text (Open Access)
  • 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
    DOI (Open Access)
  • 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
    DOI (Open Access)
  • Heider, Dominik; Verheyen, Jens; Hoffmann, Daniel
    Predicting Bevirimat resistance of HIV-1 from genotype
    In: BMC Bioinformatics, Vol. 11, 2010, pp. 37
    DOI (Open Access)
  • 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
    DOI (Open Access)
  • 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 (PNAS), Vol. 107, 2010, Nr. 12, pp. 5522 – 5527
    DOI
  • 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
    DOI, Online Full Text (Open Access)
  • 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
    DOI
  • 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
    DOI
  • Jakuschev, Stanislav; Hoffmann, Daniel
    A novel algorithm for macromolecular epitope matching
    In: Algorithms, Vol. 2, 2009, Nr. 1, pp. 498 – 517
    DOI
  • Verheyen, Jens; Knops, Elena; Kupfer, Bernd; Hamouda, Osamah; Somogyi, Sybille; Schuldenzucker, Ulrike; Hoffmann, Daniel; Kaiser, Rolf; Pfister, Herbert; Kücherer, Claudia
    Prevalence of C-terminal gag cleavage site mutations in HIV from therapy-naïve patients
    In: Journal of Infection, Vol. 58, 2009, Nr. 1, pp. 61 – 67
    DOI
  • Balduin, Melanie; Oette, Mark; Däumer, Martin P.; Hoffmann, Daniel; Pfister, Herbert J.; Kaiser, Rolf
    Prevalence of minor variants of HIV strains at reverse transcriptase position 103 in therapy-naïve patients and their impact on the virological failure
    In: Journal of Clinical Virology, Vol. 45, 2009, Nr. 1, pp. 34 – 38
    DOI
  • Fischer, Sven; Kohlhase, Jürgen; Böhm, Detlef; Schweiger, Bernd; Hoffmann, Daniel; Heitmann, Melanie; Horsthemke, Bernhard; Wieczorek, Dagmar
    Biallelic loss of function of the promyelocytic leukaemia zinc finger (PLZF) gene causes severe skeletal defects and genital hypoplasia
    In: Journal of Medical Genetics (eJMG), Vol. 45, 2008, Nr. 11, pp. 731 – 737
    DOI
  • Hoffmann, Daniel
    Evolution : von der Biologie zur Mathematik und wieder zurück ; die Ergebnisse der Evolutionstheorie sind heute nicht nur Naturbeschreibung, sondern auch mathematisches Werkzeug
    In: Unikate: Berichte aus Forschung und Lehre, 2008, Nr. 33: Mathematik: eine lebendige Wissenschaft, pp. 54 – 65
    DOI, Online Full Text (Open Access)
  • Gronwald, Wolfram; Hohm, Tim; Hoffmann, Daniel
    Evolutionary Pareto-optimization of stably folding peptides
    In: BMC Bioinformatics, Vol. 9, 2008, pp. 109
    DOI (Open Access)
  • Albert, Thilo; Egler, Christian; Jakuschev, Stanislav; Schuldenzucker, Ulrike; Schmitt, Alexandra; Brokemper, Oliver; Zabe-Kuhn, Martin; Hoffmann, Daniel; Oldenburg, Johannes; Schwaab, Rainer
    The B-cell epitope of the monoclonal anti-factor VIII anti- body ESH8 characterized by peptide array analysis
    In: Thrombosis and Haemostasis, Vol. 99, 2008, Nr. 3, pp. 634 – 637
    DOI
  • Hohm, Tim; Limbourg, Philipp; Hoffmann, Daniel
    A multiobjective evolutionary method for the design of peptidic mimotopes
    In: Journal of Computational Biology, Vol. 13, 2006, Nr. 1, pp. 113 – 125
    DOI
  • Verheyen, Jens; Litau, Elena; Sing, Tobias; Däumer, Martin; Balduin, Melanie; Oette, Mark; Fätkenheuer, Gerd; Rockstroh, Jürgen K.; Schuldenzucker, Ulrike; Hoffmann, Daniel; Pfister, Herbert; Kaiser, Rolf
    Compensatory mutations at the HIV cleavage sites p7/p1 and p1/p6-gag in therapy-naive and therapy-experienced patients.
    In: Antiviral Therapy, Vol. 11, 2006, Nr. 7, pp. 879 – 887
  • Wefing, Stephan; Schnaible, Volker; Hoffmann, Daniel
    SearchXLinks : A program for the identification of disulfide bonds in proteins from mass spectra
    In: Analytical Chemistry, Vol. 78, 2006, Nr. 4, pp. 1235 – 1241
    DOI
  • Wendeler, Michaela; Werth, Norbert; Maier, Timm; Schwarzmann, Guenter; Kolter, Thomas; Schoeniger, Maike; Hoffmann, Daniel; Lemm, Thorsten; Saenger, Wolfram; Sandhoff, Konrad
    The enzyme-binding region of human GM2-activator protein
    In: The FEBS Journal, Vol. 273, 2006, Nr. 5, pp. 982 – 991
    DOI
  • 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
    DOI (Open Access)
  • Beerenwinkel, Niko; Däumer, Martin; Sing, Tobias; Rahnenführer, Jörg; Lengauer, Thomas; Selbig, Joachim; Hoffmann, Daniel; Kaiser, Rolf
    Estimating HIV evolutionary pathways and the genetic barrier to drug resistance
    In: Journal of Infectious Diseases, Vol. 191, 2005, Nr. 11, pp. 1953 – 1960
    DOI (Open Access)
  • Balduin, Melanie; Sierra, Saleta; Daumer, Martin P.; Rockstroh, Jürgen K.; Oette, Mark; Fätkenheuer, Gerd; Kupfer, Bernd; Beerenwinkel, Niko; Hoffmann, Daniel; Selbig, Joachim; Pfister, Herbert J.; Kaiser, Rolf
    Evolution of HIV resistance during treatment interruption in experienced patients and after restarting a new therapy
    In: Journal of Clinical Virology, Vol. 34, 2005, Nr. 4, pp. 277 – 287
    DOI
  • Beerenwinkel, Niko; Rahnenführer, Jörg; Däumer, Martin; Hoffmann, Daniel; Kaiser, Rolf; Selbig, Joachim; Lengauer, Thomas
    Learning multiple evolutionary pathways from cross-sectional data
    In: Journal of Computational Biology, Vol. 12, 2005, Nr. 6, pp. 584 – 598
    DOI
  • 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
    DOI (Open Access)
  • Wendeler, Michaela; Hoernschemeyer, Joerg; Hoffmann, Daniel; Kolter, Thomas; Schwarzmann, Guenter; Sandhoff, Konrad
    Photoaffinity labelling of the Human GM2-activator protein Mechanistic insight into ganglioside GM2 degradation
    In: EJB: the FEBS Journal, Vol. 271, 2004, Nr. 3, pp. 614 – 627
    DOI
  • Beerenwinkel, Niko; Däumer, Martin; Oette, Mark; Korn, Klaus; Hoffmann, Daniel; Kaiser, Rolf; Lengauer, Thomas; Selbig, Joachim; Walter, Hauke
    Geno2pheno : Estimating phenotypic drug resistance from HIV-1 genotypes
    In: Nucleic Acids Research, Vol. 31, 2003, Nr. 13, pp. 3850 – 3855
    DOI
  • 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, pp. i16 – i25
    DOI (Open Access)
  • Albrecht, Mario; Hoffmann, Daniel; Evert, Bernd O.; Schmitt, Ina; Wüllner, Ullrich; Lengauer, Thomas
    Structural modeling of ataxin-3 reveals distant homology to adaptins
    In: Proteins: Structure, Function and Genetics, Vol. 50, 2003, Nr. 2, pp. 355 – 370
    DOI
  • Wolf, Katharina; Walter, Hauke; Beerenwinkel, Niko; Keulen, Wilco; Kaiser, Rolf; Hoffmann, Daniel; Lengauer, Thomas; Selbig, Joachim; Vandamme, Anne-Mieke; Korn, Klaus; Schmidt, Barbara
    Tenofovir Resistance and Resensitization
    In: Antimicrobial Agents and Chemotherapy, Vol. 47, 2003, Nr. 11, pp. 3478 – 3484
    DOI, Online Full Text (Open Access)
  • 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 (PNAS), Vol. 99, 2002, Nr. 12, pp. 8271 – 8276
    DOI
  • Schnaible, Volker; Wefing, Stephan; Bücker, Anne; Wolf-Kümmeth, Sybille; Hoffmann, Daniel
    Partial reduction and two-step modification of proteins for identification of disulfide bonds
    In: Analytical Chemistry, Vol. 74, 2002, Nr. 10, pp. 2386 – 2393
    DOI
  • Schnaible, Volker; Wefing, Stephan; Resemann, Anja; Suckau, Detlev; Bücker, Anne; Wolf-Kümmeth, Sybille; Hoffmann, Daniel
    Screening for disulfide bonds in proteins by MALDI in-source decay and LIFT-TOF/TOF-MS
    In: Analytical Chemistry, Vol. 74, 2002, Nr. 19, pp. 4980 – 4988
    DOI
  • Hoffmann, Daniel
    Web Site : The Protein Information Resource
    In: Angewandte Chemie International Edition, Vol. 41, 2002, Nr. 6, pp. 1075 – 1075
    DOI
  • Beerenwinkel, Niko; Lengauer, Thomas; Selbig, Joachim; Schmidt, Barbara; Walter, Hauke; Korn, Klaus; Kaiser, Rolf; Hoffmann, Daniel
    Geno2pheno : Interpreting Genotypic HIV Drug Resistance Tests
    In: IEEE Intelligent Systems, Vol. 16, 2001, Nr. 6, pp. 35 – 41
    DOI, Online Full Text (Open Access)
  • Beerenwinkel, Niko; Däumer, Martin; Hoffmann, Daniel; Kaiser, Rolf; Korn, Klaus; Lengauer, Thomas; Schmidt, Barbara; Walter, Hauke; Selbig, Joachim
    Neue Wege zur Optimierung von Anti-HIV-Therapien : Erste Analysen mit bioinformatischen Methoden
    In: BIOforum, Vol. 24, 2001, Nr. 12, pp. 912 – 914
  • Jacob, Joël; Geßler, Katrin; Hoffmann, Daniel; Sanbe, Haruyo; Koizumi, Kyoko; Smith, Steven M.; Takaha, Takeshi; Saenger, Wolfram; Geβler, Katrin
    Band-flip and kink as novel structural motifs in α-(1→4)-D-glucose oligosaccharides. Crystal structures of cyclodeca- and cyclotetradecaamylose
    In: Carbohydrate Research, Vol. 322, 1999, Nr. 3-4, pp. 228 – 246
    DOI
  • Hoffmann, Daniel; Kramer, B.; Washio, T.; Steinmetzer, T.; Rarey, M.; Lengauer, T.
    Two-Stage Method for Protein-Ligand Dockin
    In: (J. Med. Chem.), Vol. 42, 1999, pp. 4422 – 4433
  • Hoffmann, Daniel; Kramer, Bernd; Washio, Takumi; Steinmetzer, Torsten; Rarey, Matthias; Lengauer, Thomas
    Two-stage method for protein-ligand docking
    In: Journal of Medicinal Chemistry, Vol. 42, 1999, Nr. 21, pp. 4422 – 4433
    DOI
  • Hoffmann, Daniel; Flörke, Holger
    A structural role for glycosylation : Lessons from the hp model
    In: Folding and Design, Vol. 3, 1998, Nr. 5, pp. 337 – 343
    DOI (Open Access)
  • Hoffmann, Daniel; Flörke, H.
    A structural role for glycosylation: lessons from the hp-mode
    In: Folding & Design, Vol. 3, 1998, pp. 337 – 343
  • 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
    DOI
  • 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
  • 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
    DOI
  • Hoffmann, Daniel; Knapp, Ernst-Walter
    Folding Pathways of a Helix-Turn-Helix Model Protein
    In: Journal of Physical Chemistry B: Condensed Matter, Materials, Surfaces, Interfaces & Biophysical Chemistry, Vol. 101, 1997, Nr. 34, pp. 6734 – 6740
    DOI, Online Full Text (Open Access)
  • Hoffmann, Daniel; Knapp, Ernst-Walter
    Polypeptide folding with-off lattice Monte Carlo dynamics : The method
    In: European Biophysics Journal, Vol. 24, 1996, Nr. 6, pp. 387 – 403
    DOI
  • Hoffmann, Daniel; Knapp, Ernst-Walter
    Protein dynamics with off-lattice monte carlo moves
    In: Physical Review E: Statistical, nonlinear, and soft matter physics, Vol. 53, 1996, Nr. 4, pp. 4221 – 4224
    DOI, Online Full Text (Open Access)

    • Book articles / Proceedings papers

  • Roomp, Kirsten; Beerenwinkel, Niko; Sing, Tobias; Schülter, Eugen; Büch, Joachim; Sierra-Aragon, Saleta; Däumer, Martin; Hoffmann, Daniel; Kaiser, Rolf; Lengauer, Thomas; Selbig, Joachim
    Arevir : A Secure Platform for Designing Personalized Antiretroviral Therapies Against HIV
    In: Data Integration in the Life Sciences / Third International Workshop (DILS), July 20-22, 2006, Hinxton, UK, / Leser, Ulf; Naumann, Felix; Eckman, Barbara (Eds.). Berlin: Springer, 2006, pp. 185 – 194
    DOI
  • Hohm, Tim; Hoffmann, Daniel
    A multi-objective evolutionary approach to peptide structure redesign and stabilization
    In: Proceedings of the 7th annual conference on Genetic and evolutionary computation / GECCO 2005 - Genetic and Evolutionary Computation Conference, 25-29 June 2005, Washington D.C., United States / Beyer, Hans-Georg (Eds.). New York: ACM, 2005, pp. 423 – 429
    DOI
  • Sing, Tobias; Svicher, Valentina; Beerenwinkel, Niko; Ceccherini-Silberstein, Francesca; Däumer, Martin; Kaiser, Rolf; Walter, Hauke; Korn, Klaus; Hoffmann, Daniel; Oette, Mark; Rockstroh, Jürgen K.; Fätkenheuer, Gert; Perno, Carlo-Federico; Lengauer, Thomas
    Characterization of Novel HIV Drug Resistance Mutations Using Clustering, Multidimensional Scaling and SVM-Based Feature Ranking
    In: Knowledge Discovery in Databases: PKDD 2005: th European Conference on Principles and Practice of Knowledge Discovery in Databases, Porto, Portugal, October 3-7, 2005. Proceedings / 9th European Conference on Principles and Practice of Knowledge Discovery in Databases (PKDD 2005), 3-7 October 2005, Porto, Portugal / Jorge, Alípio Mário; Torgo, Luís; Brazdil, Pavel; Camacho, Rui; Gama, João (Eds.). Berlin: Springer, 2005, pp. 285 – 296
    DOI
  • Hoffmann, Daniel
    Computergestützte molekulare Modellierung für die Suche nach neuen Wirkstoffen gegen HIV/AIDS
    In: Resistenz in der HIV-Therapie: Diagnostik und Management / Oette, Mark; Kaiser, Rolf; Häussinger, Dieter (Eds.). Bremen: Uni-Med. Verlag, 2003, pp. 62 – 65
  • Hoffmann, Daniel; Schnaible, V.; Wefing, S.; Albrecht, M.; Hanisch, D.; Zimmer, R.
    A New Method for the Fast Solution of Protein-3D-Structures, combining Experiments and Bioinformatics
    In: Coupling of Biological and Electronic Systems: Proceedings of the 2nd Caesarium / 2nd Caesarium, Bonn, November 1–3, 2000 / Hoffmann, Karl-Heinz (Eds.). Berlin: Springer, 2002, pp. 59 – 78
    DOI
  • Beerenwinkel, Niko; Schmidt, Barbara; Walter, Hauke; Kaiser, Rolf; Lengauer, Thomas; Hoffmann, Daniel; Korn, Klaus; Selbig, Joachim
    Identifying Drug Resistance-Associated Patterns in HIV Genotypes
    In: Computer science and biology: proceedings of the German Conference on Bioinformatics / German Conference on Bioinformatics (GCB '01), 7.-10. October 2001, Braunschweig / Wingender, Edgar (Eds.). Braunschweig: German Research Center for Biotechnology, 2001, pp. 126 – 130
  • Rabenstein, Björn; Hoffmann, Daniel; Knapp, Ernst-Walter
    Simulation of oligopeptide folding or how do residues talk
    In: Biological Physics: Third International Symposium ; Santa Fe, NM, September 1998 / Third International Symposium on Biological Physics ; September 20-24, 1998, Santa Fe, New Mexico, USA / Frauenfelder, Hans; Hummer, Gerhard; Garcia, Roderick (Eds.). Melville: American Institute of Physics, 1999, pp. 54 – 68
    DOI
  • Hoffmann, Daniel; Washio, Takashi; Gessler, Katrin; Jacob, Jean-Paul
    Tackling Concrete Problems in Molecular Biophysics Using Monte Carlo and Related Methods : Glycosylation, Folding, Solvation
    In: Workshop on Monte Carlo Approach to Biopolymers and Protein Folding / Workshop on Monte Carlo Approach to Biopolymers and Protein, 3 - 5 December 1997 , Jülich, Germany / Grassberger, P.; Barkema, G.; Nadler, W. (Eds.). Singapore: World Scientific, 1998, pp. 153 – 170
    Online Full Text
  • Hoffmann, Daniel; Knapp, E.W.
    A Monte Carlo method for simulations of protein folding with detailed protein models
    In: Perspectives on protein engineering: a comprehensive on-line access tool for Web-based resources, papers from Perspectives on Protein Engineering '96 / Perspectives on Protein Engineering Conference 5 (POPE5), 2-6 March 1996, Montpellier. Bingham: Biodigm, 1996

    • Books, Collections, Proceedings

  • Hoffmann, Daniel
    Monte Carlo Methoden zur Simulation der Langzeitdynamik von Proteinen
    Berlin: Köster, 1996(Bioinformatik)