Publikationen von Ralf Herwig

Yalan Bi, Tom Lukas Lankenau, Matthias Lienhard, and Ralf Herwig, "IsoTools 2.0: Software for Comprehensive Analysis of Long-read Transcriptome Sequencing Data," Journal of Molecular Biology , Article 169049 (2025).

Michael Turewicz, Christine Skagen, Sonja Hartwig, Stephan Majda, Kristina Thedinga, Ralf Herwig, Christian Binsch , Delsi Altenhofen, D. Margriet Ouwens, Pia Marlene Förster, Thorsten Wachtmeister, Karl Köhrer, Torben Stermann, Alexandra Chadt, Stefan Lehr, Tobias Marschall , G. Hege Thoresen, and Hadi Al-Hasani, "Temporal phosphoproteomics reveals circuitry of phased propagation in insulin signaling," Nature Communications 16 (1), Article 1570 (2025).

Alicja Pacholewska, Matthias Lienhard, Mirko Brueggemann, Heike Haenel, Lorina Bilalli, Anja Koenigs, Felix Hess, Kerstin Becker, Karl Koehrer, Jesko Fabian Kaiser, Holger Gohlke, Norbert Gattermann, Michael Hallek, Carmen Diana Herling, Julian Koenig, Christina Grimm, Ralf Herwig, Kathi Zarnack, and Michal R. Schweiger, "Long-read transcriptome sequencing of CLL and MDS patients uncovers molecular effects of SF3B1 mutations," Genome Research 34 (11), 1832-1848 (2024).

F. J. Pardo-Palacios, D. Wang, F. Reese, M. Diekhans, S. Carbonell-Sala, B. Williams, J. E. Loveland, M. De Maria, M. S. Adams, G. Balderrama-Gutierrez, A. K. Behera, J. M. Gonzalez, T. Hunt, J. Lagarde, C. E. Liang, H. Li, M. Jerryd Meade, D. A. Moraga Amador, A. D. Prjibelski, I. Birol, H. Bostan, A. M. Brooks, M. Hasan Celik, Y. Chen, M. R. M. Du, C. Felton, J. Goke, S. Hafezqorani, R. Herwig, H. Kawaji, J. Lee, J. Liang Li, M. Lienhard, A. Mikheenko, D. Mulligan, K. Ming Nip, M. Pertea, M. E. Ritchie, A. D. Sim, A. D. Tang, Y. Kei Wan, C. Wang, B. Y. Wong, C. Yang, I. Barnes, A. Berry, S. Capella, N. Dhillon, J. M. Fernandez-Gonzalez, L. Ferrandez-Peral, N. Garcia-Reyero, S. Goetz, C. Hernandez-Ferrer, L. Kondratova, T. Liu, A. Martinez-Martin, C. Menor, J. Mestre-Tomas, J. M. Mudge, N. G. Panayotova, A. Paniagua, D. Repchevsky, E. Rouchka, B. Saint-John, E. Sapena, L. Sheynkman, M. Laird Smith, M. M. Suner, H. Takahashi, I. A. Youngworth, P. Carninci, N. D. Denslow, R. Guigo, M. E. Hunter, H. U. Tilgner, B. J. Wold, C. Vollmers, A. Frankish, K. Fai Au, G. M. Sheynkman, A. Mortazavi, A. Conesa, and A. N. Brooks, "Systematic assessment of long-read RNA-seq methods for transcript identification and quantification," Nature Methods 21 (7), 1349-1363 (2024).

Christian Springer, Christian Binsch, Deborah Weide, Laura Toska, Anna Lena Cremer, Heiko Backes, Anna K. Scheel, Lena Espelage, Jörg Kotzka, Sebastian Sill, Anette Kurowski, Kim Daebin, Sandra Karpinski, Theresia M. Schnurr, Torben Hansen, Sonja Hartwig, Stefan Lehr, Sandra Cames, Jens Brüning, Matthias Lienhard, Ralf Herwig, Stefan Börno, Bernd Timmermann, Hadi Al-Hasani, and Alexandra Chadt, "Depletion of TBC1D4 improves the metabolic exercise response by overcoming genetically induced peripheral insulin resistance," Diabetes 73 (7), 1058-1071 (2024).

Pedro A. Campana , Paul Prasse , Matthias Lienhard, Kristina Thedinga, Ralf Herwig, and Tobias Scheffer , "Cancer drug sensitivity estimation using modular deep Graph Neural Networks," NAR: Genomics and Bioinformatics 6 (2), Article lqae043 (2024).

Matthias Lienhard, Twan van den Beucken , Bernd Timmermann, Myriam Hochradel, Stefan Boerno, Florian Caiment , Martin Vingron, and Ralf Herwig, "IsoTools: a flexible workflow for long-read transcriptome sequencing analysis," Bioinformatics 39 (6), btad364 (2023).

Cyrine Bouabid, Sameh Rabhi, Kristina Thedinga, Gal Barel, Hedia Tnani, Imen Rabhi , Alia Benkahla, Ralf Herwig, and Lamia Guizani-Tabbane, "Host M-CSF induced gene expression drives changes in susceptible and resistant mice-derived BMdMs upon Leishmania major infection," Frontiers in immunology 14, 1111072 (2023).

C. Binsch, D. M. Barbosa, G. Hansen-Dille, M. Hubert, S. M. Hodge, M. Kolasa, K. Jeruschke, J. Weiß, C. Springer, S. Gorressen, J. W. Fischer, M. Lienhard, R. Herwig, S. Börno, B. Timmermann, A. L. Cremer, H. Backes, A. Chadt, and H. Al-Hasani, "Deletion of Tbc1d4/As160 abrogates cardiac glucose uptake and increases myocardial damage after ischemia/reperfusion," Cardiovascular Diabetology 22, 17 (2023).

Delsi Altenhofen, Jenny Minh-An Khuong, Tanja Kuhn, Sandra Lebek, Sarah Görigk, Katharina Kaiser, Christian Binsch, Kerstin Griess, Birgit Knebel, Bengt-Frederik Belgardt, Sandra Cames, Samaneh Eickelschulte, Torben Stermann, Axel Rasche, Ralf Herwig, Jürgen Weiss, Heike Vogel, Annette Schürmann, Alexandra Chadt, and Hadi Al-Hasani, "E96V Mutation in the Kdelr3 Gene Is Associated with Type 2 Diabetes Susceptibility in Obese NZO Mice," International Journal of Molecular Sciences 24 (1), 845 (2023).

Tanja Kuhn, Katharina Kaiser, Sandra Lebek, Delsi Altenhofen, Birgit Knebel, Ralf Herwig, Axel Rasche, Angela Pelligra, Sarah Görigk, Jenny Minh-An Khuong, Heike Vogel, Annette Schürmann, Matthias Blüher, Alexandra Chadt, and Hadi Al-Hasani, "Comparative genomic analyses of multiple backcross mouse populations suggest SGCG as a novel potential obesity-modifier gene," Human Molecular Genetics 31 (23), 4019-4033 (2022).

Daniel Thomalla, Laura Beckmann, Christina Grimm , Matteo Oliverio, Lydia Meder, Carmen Diana Herling, Pascal Nieper, Thorsten Feldmann, Olaf Merkel, Eva Lorsy, Alexandra da Palma Guerreiro , Jana von Jan, Ilmars Kisis, Elena Wasserburger, Julia Claasen, Elena Faitschuk-Meyer, Janine Altmüller, Peter Nürnberg, Tsun-Po Yang, Matthias Lienhard, Ralf Herwig, Karl-Anton Kreuzer, Christian P. Pallasch, Reinhard Buettner, Stephan Christian Schäfer, Jordan Hartley, Hinrich Abken, Martin Peifer, Hamid Kashkar, Gero Knittel, Barbara Eichhorst , Roland T. Ullrich, Marco Herling, Hans Christian Reinhardt, Michael Hallek, Michal R. Schweiger, and Lukas P. Frenzel, "Deregulation and epigenetic modification of BCL2-family genes cause resistance to venetoclax in hematologic malignancies," Blood 140 (20), 2113-2126 (2022).

Marcha Verheijen, Ugis Sarkans, Witold Wolski, Danyel Jennen, Florian Caiment , Jos Kleinjans, Consortium HeCaToS , Gal Barel, Stefan Boerno, Ralf Herwig, Matthias Lienhard, and Bernd et al Timmermann, "Multi-omics HeCaToS dataset of repeated dose toxicity for cardiotoxic & hepatotoxic compounds," Scientific Data 9, 699 (2022).

Paul Prasse, Pascal Iversen, Matthias Lienhard, Kristina Thedinga, Ralf Herwig, and Tobias Scheffer, "Pre-Training on In Vitro and Fine-Tuning on Patient-Derived Data Improves Deep Neural Networks for Anti-Cancer Drug-Sensitivity Prediction," Cancers / Molecular Diversity Preservation International (MDPI) 14 (16), 3950 (2022).

Kristina Thedinga and Ralf Herwig, "Gradient tree boosting and network propagation for the identification of pan-cancer survival networks," STAR Protocols 3 (2), 101353 (2022).

Nhan Nguyen, Matthias Lienhard, Ralf Herwig, Jos Kleinjans, and Danyel Jennen, "Epirubicin Alters DNA Methylation Profiles Related to Cardiotoxicity," Frontiers in Bioscience-Landmark 27 (6), 173 (2022).

Paul Prasse , Pascal Iversen , Matthias Lienhard, Kristina Thedinga, Chris Bauer, Ralf Herwig, and Tobias Scheffer, "Matching anticancer compounds and tumor cell lines by neural networks with ranking loss," NAR: genomics and bioinformatics 4 (1), lqab128 (2022).

Atanas Kamburov and Ralf Herwig, "ConsensusPathDB 2022: molecular interactions update as a resource for network biology," Nucleic Acids Research 50 (D1), D587-D595 (2022).

Kristina Thedinga and Ralf Herwig, "A gradient tree boosting and network propagation derived pan-cancer survival network of the tumor microenvironment," iScience 25 (1), 103617 (2021).

Alicja Pacholewska, Christina Grimm, Carmen D. Herling, Matthias Lienhard, Anja Königs, Bernd Timmermann, Janine Altmüller, Oliver Mücke, Hans Christian Reinhardt, Christoph Plass, Ralf Herwig, Michael Hallek, and Michal R. Schweiger, "Altered DNA Methylation Profiles in SF3B1 Mutated CLL Patients," International Journal of Molecular Sciences 22 (17), 9337 (2021).