Sara C. Käufler, Henri Schmidt, Martin Jürgens, Gunnar W. Klau, Palash Sashittal, Benjamin J. Raphael. “POTTR: Identifying Recurrent Trajectories in Evolutionary and Developmental Processes using Posets.” Preprint, bioRxiv, February 26, 2026. https://doi.org/10.64898/2026.02.25.707960
Hugo Magalhaes, Jonas Weber, Gunnar W. Klau, Tobias Marschall, Timofey Prodanov. “Sequence-to-Graph Alignment Based Copy Number Calling Using a Network Flow Formulation.” Preprint, bioRxiv, February 24, 2026. https://doi.org/10.1101/2025.11.21.689771.
Nguyen Khoa Tran, My Ky Huynh, Alexander D Kotman, Martin Jürgens, Thomas Kurz, Sascha Dietrich, Gunnar W Klau, Nan Qin. “VUScope: a mathematical model for evaluating image-based drug response measurements and predicting long-term incubation outcomes.” Bioinformatics, Volume 42, Issue 2, February 2026, btaf679, https://doi.org/10.1093/bioinformatics/btaf679
Jonathan Bobak, Philipp Spohr, Sarah Richter, Alexander Streuer, Felicitas Isabel Schulz, Corinna Strupp, Catharina Gerhards, Nanni Schmitt, Thomas Luft, Sascha Dietrich, Ulrich Germing, Gunnar W. Klau. "Dynamic Mortality Risk Prediction in Myelodysplastic Syndromes Using Longitudinal Clinical Data." JCO Clin Cancer Inform9, e2500236(2025), Volume 9 DOI: 10.1200/CCI-25-00236
Nguyen Khoa Tran and Gunnar W. Klau. “Drug Response Prediction: A Critical Systematic Review of Current Datasets and Methods.” Pattern Recognition Letters, ahead of print, October 30, 2025. https://doi.org/10.1016/j.patrec.2025.10.016
Martin Papenberg, Martin Breuer, Max Diekhoff, Nguyen K. Tran, Gunnar W. Klau. Extending the Bicriterion Approach for Anticlustering: Exact and Hybrid Approaches. Psychometrika. Published online 2025:1-43. https://doi.org/10.1017/psy.2025.10052
Philipp Spohr, Rebecca C Fröhlich, Sebastian Scharf, Anna Rommerskirchen, Jonathan Bobak, Sarah Schweier, Paul Jäger, Guido Kobbe, Sascha Dietrich, Alexander T Dilthey, Birgit Henrich, Klaus Pfeffer, Rainer Haas, Gunnar W Klau. Dynamic prediction of mortality risk following allogeneic hematopoietic stem cell transplantation. Machine Learning: Health. Vol 1, No 1 (2025) https://iopscience.iop.org/article/10.1088/3049-477X/adf74e
Martin Papenberg, Cheng Wang, Maïgane Diop, Syed Hassan Bukhari, Boris Oskotsky, Brittany R. Davidson, Kim Chi Vo, Binya Liu, Juan C. Irwin, Alexis J. Combes, Brice Gaudilliere, Jingjing Li, David K. Stevenson, Gunnar W. Klau,Linda C. Giudice, Marina Sirota, Tomiko T. Oskotsky. Anticlustering for sample allocation to minimize batch effects. Cell Reports Methods, Vol. 5, Issue 8, (2025) https://dx.doi.org/10.1016/j.crmeth.2025.101137
Sara C. Schulte, Wolfgang Peter, Georg Rosenberger, Moritz Schäfer, Cecile L. Maire, Alessandra Rünger, Alice Ryba, Kristoffer Riecken, Krystian D. Fita, Jakob Matschke, Nuray Akyüz, Judith Dierlamm, Gunnar W. Klau, Franz L. Ricklefs, Jens Gempt, Manfred Westphal, Katrin Lamszus, Alexander Dilthey, Malte Mohme. Somatic mutations in HLA class genes and antigen presenting molecules in malignant glioma. Cancer Immunol Res (2025) https://doi.org/10.1158/2326-6066.CIR-24-0419
Sebastian Jeising, Ann-Christin Nickel, Johanna Trübel, Jörg Felsberg, Daniel Picard, Gabriel Leprivier, Marietta Wolter, My Ky Huynh, Marlene B. Olivera, Kerstin Kaulich, Lena Häberle, Irene Esposito, Gunnar W. Klau, Julia Steinmann, Thomas Beez, Marion Rapp, Michael Sabel, Sascha Dietrich, Marc Remke, Jan F. Cornelius, Guido Reifenberger, Nan Qin. "A clinically compatible in vitro drug-screening platform identifies therapeutic vulnerabilities in primary cultures of brain metastases" Journal of Neuro-Oncology 2024, https://doi.org/10.1007/s11060-024-04763-7
Philipp Spohr, Max Ried, Laura Kühle, Alexander Dilthey. "SWGTS—a platform for stream-based host DNA depletion" Bioinformatics40(6), 2024, https://doi.org/10.1093/bioinformatics/btae332
Philipp Spohr, Sebastian Scharf, Anna Rommerskirchen, Birgit Henrich, Paul Jäger, Gunnar W. Klau, Rainer Haas, Alexander Dilthey, Klaus Pfeffer. "Insights into gut microbiomes in stem cell transplantation by comprehensive shotgun long-read sequencing" Scientific Reports 14:4068, https://doi.org/10.1038/s41598-024-53506-1
Rebecca Serra Mari, Sven Schrinner, Richard Finkers, Freya Maria Rosemarie Ziegler, Paul Arens, Maximilian H.-W. Schmidt, Björn Usadel, Gunnar W. Klau, and Tobias Marschall. “Haplotype-Resolved Assembly of a Tetraploid Potato Genome Using Long Reads and Low-Depth Offspring Data.” Genome Biology 25, no. 1 (January 19, 2024): 26. https://doi.org/10.1186/s13059-023-03160-z
Nguyen Khoa Tran, Laura C. Kühle, Gunnar W. Klau. "A critical review of multi-output support vector regression" Pattern Recognition Letters 178, pp. 68-75 (2024). DOI: 10.1016/j.patrec.2023.12.007
Sara C. Schulte, Alexander T. Dilthey, Gunnar W. Klau. “HOGVAX: Exploiting epitope overlaps to maximize population coverage in vaccine design with application to SARS-CoV-2.” Cell Systems 14 (2023). https://doi.org/10.1016/j.cels.2023.11.001
Eline S. van Mantgem, Johanna Hillebrand, Lukas Rose, and Gunnar W. Klau. “Coco: Conservation Design for Optimal Ecological Connectivity.” Frontiers in Ecology and Evolution 11 (2023). https://www.frontiersin.org/articles/10.3389/fevo.2023.1149571.
Lukas Becker, Philipp Spohr, Gunnar W. Klau, Ilka M. Axmann, Sebastian Fraune, and Nicolas M. Schmelling. “CATHI: An Interactive Platform for Comparative Genomics and Homolog Identification.” bioRxiv, September 6, 2023. https://doi.org/10.1101/2023.09.04.556229.
Nick D. Bergkamp, Jeffrey R. van Senten, Hendrik J. Brink, Maarten P. Bebelman, Jelle van den Bor, Tuğçe S. Çobanoğlu, Kasper Dinkla, Johannes Köster, Gunnar W. Klau, Marco Siderius, Martine Smit. “A Virally Encoded GPCR Drives Glioblastoma through Feed-Forward Activation of the SK1-S1P1 Signaling Axis.” Science Signaling 16, no. 798 (August 15, 2023): eade6737. doi.org/10.1126/scisignal.ade6737.
Martin Stroet, Bertrand Caron, Martin S. Engler, Jimi van der Woning, Aude Kauffmann, Marc van Dijk, Mohammed El-Kebir, Koen Visscher, Josef Holownia, Callum Macfarlane, Brian Bennion, Sveltlana Geipi-Dominguez, Felice Lightstone, Tijs van der Storm, Daan Geerke, Alan Mark and Gunnar W. Klau. “OFraMP: A Fragment-Based Tool to Facilitate the Parametrization of Large Molecules.” Journal of Computer-Aided Molecular Design, June 13, 2023. https://doi.org/10.1007/s10822-023-00511-7.
F. Kretschmer, J. Seipp, M. Ludwig, G. W. Klau, S. Boecker. Small molecule machine learning: All models are wrong, some may not even be useful. bioRxiv 2023.03.27.534311; doi: https://doi.org/10.1101/2023.03.27.534311, 2023.
Spohr, P., Scharf, S., Rommerskirchen, A., Henrich, B., Jäger, P., Klau, G. W., Haas, R., Dilthey, A., Pfeffer, K. MetaGut: Insights into gut microbiomes in stem cell transplantation by comprehensive shotgun long-read sequencing. bioRxiv 2023.03.10.531901; doi: https://doi.org/10.1101/2023.03.10.531901, 2023
S. Schulte, A. Dilthey, and G. W. Klau. HOGVAX: Exploiting Peptide Overlaps to Maximize Population Coverage in Vaccine Design with Application to SARS-CoV-2. bioRxiv, 2023.01. 09.523288; doi: https://doi.org/10.1101/2023.01.09.523288. 2023
McGuinness, K.N., Klau, G.W., Morrison, S.M., Moore, E.K., Seipp, J., Falkowski, P.G., Nanda, V. Evaluating Mineral Lattices as Evolutionary Proxies for Metalloprotein Evolution. Orig Life Evol Biosph (2022). https://doi.org/10.1007/s11084-022-09630-x
Eline van Mantgem and Gunnar W. Klau. Boolean network inference at different levels of logical complexity. To appear in Proc. Computational Intelligence Methods for Bioinformatics and Biostatistics (CIBB 2021).
Sven Schrinner, Manish Goel, Michael Wulfert, Philipp Spohr, Korbinian Schneeberger and Gunnar W. Klau. Using the longest run subsequence problem within homology-based scaffolding. Algorithms for Molecular Biology 16, 11 (2021), https://doi.org/10.1186/s13015-021-00191-8.
Julia Hesse, Christoph Owenier, Tobias Lautwein, Ria Zalfen, Jonas F. Weber, Zhaoping Ding, Christina Alter, Alexander Lang, Maria Grandoch, Norbert Gerdes, Jens W. Fischer, Gunnar W. Klau, Christoph Dieterich, Karl Köhrer, Jürgen Schrader. Single-cell transcriptomics defines heterogeneity of epicardial cells and fibroblasts within the infarcted heart. eLife 2021;10:e65921 DOI: 10.7554/eLife.65921
Martin Papenberg and Gunnar W. Klau. Using anticlustering to partition data sets into equivalent parts. Psychological Methods, 26(2), 161–174. https://doi.org/10.1037/met0000301, 2021
Tae Yoon Park, Mark D.M. Leiserson, Gunnar W. Klau, Benjamin J. Raphael. Integrating genetic dependencies and genomic alterations across pathways and cancer types. bioRxiv. 2020.07.13.184697; doi: https://doi.org/10.1101/2020.07.13.184697, July 2020
Sven Schrinner, Manish Goel, Michael Wulfert, Philipp Spohr, Korbinian Schneeberger and Gunnar W. Klau. The Longest Run Subsequence Problem. To appear in Proc. WABI 2020.
Maren Brand, Nguyen Khoa Tran, Philipp Spohr, Sven Schrinner, and Gunnar W. Klau. The Homo-Edit Distance Problem. bioRxiv. 2020.05.27.118273; doi: https://doi.org/10.1101/2020.05.27.118273, May 2020
Martin S. Engler, Bertrand Caron, Lourens Veen, Daan Geerke, Alan Mark, Gunnar W. Klau. Multiple-choice knapsack for assigning partial atomic charges in drug-like molecules. In Proc. WABI 2018, pp. 16:1-16:13, vol. 113 of Leibniz International Proceedings in Informatics (LIPIcs), doi 10.4230/LIPIcs.WABI.2018.16, 2018
Simone Zaccaria, Mohammed El-Kebir, Gunnar W. Klau, Ben Raphael. Phylogenetic Copy-Number Factorization of Multiple Tumor Samples. Journal of Computational Biology, https://doi.org/10.1089/cmb.2017.0253, 2018
Filipe Branco dos Santos, Brett G. Olivier, Joost Boele, Vincent Smessaert, Philippe De Rop, Petra Krumpochova, Gunnar W. Klau, Martin Giera, Philippe Dehottay, Bas Teusink, Philippe Goffin. Probing the genome-scale metabolic landscape of Bordetella pertussis, the causative agent of whooping cough. Appl. Environ. Microbiol. doi:10.1128/AEM.01528-17, accepted, 2017
Martin S. Engler, Mohammed El-Kebir, Jelmer Mulder, Alan E. Mark, Daan P. Geerke, Gunnar W. Klau. Enumerating common molecular substructures. In Proc. German Bioinformatics Conference (GCB 2017). PeerJ Preprints 5:e3250v1.
Gunnar W. Klau, Tobias Marschall. A Guided Tour to Computational Haplotyping. In Proc. of CiE 2017 (Computability in Europe). LNCS 10307, pp. 50-63, Springer, 2017.
Simone Zaccaria, Mohammed El-Kebir, Gunnar W. Klau, Ben J. Raphael. The Copy-Number Tree Mixture Deconvolution Problem and Applications to Multi-sample Bulk Sequencing Tumor Data. In: Sahinalp S. (eds) Research in Computational Molecular Biology. RECOMB 2017. LNCS 10229. Springer, 2017
Martin S. Engler, Kerstin Scheubert, Ulrich S. Schubert and Sebastian Böcker: Exploring the Limits of the Geometric Copolymerization Model. Polymers, 9:101, 2017. www.mdpi.com/2073-4360/9/3/101
