Publications
2023
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
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.