Publications
2023
March
Next-generation humanized NSG-SGM3 mice are highly susceptible to Staphylococcus aureus infection. Sophia Hung, Amelie Kasperkowitz, Florian Kurz, Liane Dreher, Joachim Diessner, Eslam S. Ibrahin, Stefan Schwarz, Knut Ohlsen, Tobias Hertlein. Frontiers in Immunology
April
PRO-Simat: Protein network simulation and design tool. Rana Salihoglu, Mugdha Srivastava, Chunguang Liang, Klaus Schilling, Aladar Szalay, Elena Bencurova, Thomas Dandekar. Computational and Structural Biotechnology Journal.
June
Optimized cell type signatures revealed from single-cell data by combining principal feature analysis, mutual information, and machine learning. Aylin Caliskan, Deniz Caliskan, Lauritz Rasbach, Weimeng Yu, Thomas Dandekar, Tim Breitenbach. Computational and Structural Biotechnology Journal.
October
Metadata integrity in bioinformatics: Bridging the gap between data and knowledge. Aylin Caliskan, Seema Dangwal, Thomas Dandekar. Computational and Structural Biotechnology Journal.
Mitochondrial dysfunction promotes the transition of precursor to terminally exhausted T cells through HIF-1α-mediated glycolytic reprogramming. Hao Wu, Xiufeng Zhao, Sophia Hochrein, Miriam Eckstein, Gabriela Gubert, Konrad Knöpper, Ana Mansilla, Arman Öner, Remi Doucet-Ladevèze, Werner Schmitz, Bart Ghesquiére, Sebastian Theurich, Jan Dudek, Georg Gasteiger, Alma Zernecke, Sebastian Kobold, Wolfgang Kastenmüller, Martin Vaeth. nature communications.
December
Signaling network analysis reveals fostamatinib as a potential drug to control platelet hyperactivation during SARS-CoV-2 infection. Özge Osmanoglu, Shishir Gupta, Anna Almasi, Seray Yagci, Mugdha Srivastava, Gabriel Araujo, Zoltan Nagy, Johannes Balkenhol, Thomas Dandekar. Frontiers in Immunology.
Same yet different - how lymph node heterogeneity affects immune responses. Paulina Cruz de Casas, Konrad Knöpper, Rupak Dey Sarkar, Wolfgang Kastenmüller. nature reviews immunology.
2024
January
How to make DNA data storage more applicable. Aman Akash, Elena Bencurova, Thomas Dandekar. Trends in Biotechnology.
Circulating NK cells establish tissue residency upon acute infection of skin and mediate accelerated effector responses to secondary infection. Tommaso Torcellan, Christin Friedrich, Rémi Doucet-Ladevèze, Thomas Ossner, Virgínia Visaconill Solé, Sofie Riedmann, Milas Ugur, Fabian Imdahl, Stephan Rosshart, Sebastian Arnold, Mercedes Gomez de Agüero, Nicola Gagliani, Richard Flavell, Simone Backes, Wolfgang Kastenmüller, Georg Gasteiger. Immunity.
February
Mechanisms underlying immunosuppression by regulatory cells. Oliver Goldmann, Obiageli Vivian Nwofor, Qian Chen, Eva Medina. Frontiers in Immunology.
Correcting 4sU induced quantification bias in nucleotide conversion RNA-seq data. Kevin Berg, Manivel Lodha, Isabel Delazer, Karolina Bartosik, Yilliam Cruz Garcia, Thomas Hennig, Elmar Wolf, Lars Dölken, Alexandra Lusser, Bhupesh Prusty, Florian Erhard. Nucleic Acids Research.
Human cytomegalovirus exploits STING signaling and counteracts IFN/ISG induction to facilitate infection of dendritic cells. Bibiana Costa, Jennifer Becker, Tobias Krammer, Felix Mulenge, Verónica Durán, Andreas Pavlou, Olivia Gern, Xiaojing Chu, Yang Li, Luka Čičin-Šain, Britta Eiz-Vesper, Martin Messerle, Lars Dölken, Antoine-Emmanuel Saliba, Florian Erhard, Ulrich Kalinke. nature communications.
March
Cat-E: A comprehensive web tool for exploring cancer targeting strategies. Rana Salihoglu, Johannes Balkenhol, Gudrun Dandekar, Chunguang Liang, Thomas Dandekar, Elena Bencurova. Computational and Structural Biotechnology Journal.
April
An orchestra of machine learning methods reveals landmarks in single-cell data exemplified with aging fibroblasts. Lauritz Rasbach, Aylin Caliskan, Fatemeh Saderi, Thomas Dandekar, Tim Breitenbach. PLOS ONE
Decoding spatiotemporal transcriptional dynamics and epithelial fibroblast crosstalk during gastroesophageal junction development through single cell analysis. Naveen Kumar, Pon Ganish Prakash, Christian Wentland, Shilpa Mary Kurian, Gaurav Jethva, Volker Brinkmann, Hans-Joachim Mollenkopf, Tobias Krammer, Christophe Toussaint, Antoine-Emmanuel Saliba, Matthias Biebl, Christian Jürgensen, Bertram Wiedenmann, Thomas F. Meyer, Rajendra Kumar Gurumurthy, Cindrilla Chumduri. nature communications.
August
Infection of human organoids supports an intestinal niche for Chlamydia trachomatis. Pargev Hovhannisyan, Kathrin Stelzner, Markus Keicher, Kerstin Paprotka, Mastura Neyazi, Mindaugas Pauzuolis, Waled Mohammed Ali, Karthika Rajeeve, Sina Bartfeld, Thomas Rudel. PLOS Pathogens.
September
A clinical protocol for a German birth cohort study of the Maturation of Immunity Against respiratory viral Infections (MIAI). Carina R. Hartmann, Robin Koch, Jennifer Schöning, Maximilian Richter, Maike Willers, Sabine Pirr, Julia Heckmann, Johannes Dirks, Henner Morbach, Monika Konrad, Elena Fries, Magdalena Winkler, Johanna Büchel, Silvia Seidenspinner, Jonas Fischer, Claudia Vollmuth, Martin Meinhardt, Janina Marissen, Mirco Schmolke Sibylle Haid, Thomas Pietschmann, Simone Backes, Lars Dölken, Ulrike Löber, Thomas Keil, Peter U. Heuschmann, Achim Wöckel, Sagar, Thomas Ulas, Sofia K. Forslund-Startceva, Christoph Härtel, Dorothee Viemann. Frontiers in Immunology.
October
Postnatal supplementation with alarmins S100a8/a9 ameliorates malnutrition-induced neonate enteropathy in mice. Lisa Perruzza, Julia Heckmann, Tanja Rezzonico Jost, Matteo Raneri, Simone Guglielmetti, Giorgio Gargari, Martina Palatella, Maike Willers, Beate Fehlhaber, Christopher Werlein, Thomas Vogl, Johannes Roth, Fabio Grassi, Dorothee Viemann. nature communications.
November
Beyond-local neural information processing in neuronal networks. Johannes Balkenhol, Barbara Händel, Sounak Biswas, Johannes Grohmann, Jóakim v. Kistowski, Juan Prada, Conrado A. Bosman, Hannelore Ehrenreich, Sonja M. Wojcik, Samuel Kounex, Robert Blum, Thomas Dandekar. Computational and Structural Biotechnology Journal