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Journal Publications


  1. Näher A-F, …, Renard B, von Kleist M, Wieler LH, Grabenhenrich L. Secondary Data for Global Health Digitalization Lancet Digital Health, 2023 (in print) preprint.
  2. Bunse T, …, Von Kleist M, … , Schulte EC. T-cell dominated immune response resolves protracted SARS-CoV-2 infection in the absence of neutralizing antibodies (submitted)


  1. Ye L, Gribling-Burrer AS, Bohn P, Kibe A, Börtlein C, Ambi UB, Ahmad S, Olguin-Nava M, Smith M, Caliskan N, von Kleist M, Smyth RP. Short- and long-range interactions in the HIV-1 5′ UTR regulate genome dimerization and packaging. Nat Struct Mol Biol. 2022;29(4):306-319
  2. Oh DY, Hölzer M, Paraskevopoulou S, Trofimova M, …, Smith MR, …, Kröger S*, von Kleist M*, Wolff T* (*co-corresponding authorship); Advancing Precision Vaccinology by Molecular and Genomic Surveillance of Severe Acute Respiratory Syndrome Coronavirus 2 in Germany, 2021. Clin Infect Dis. 2022;75:S110-S120.
  3. Peppert F, Von Kleist M, Schütte C, Sunkara V. On the Sufficient Condition for Solving the Gap-Filling Problem Using Deep Convolutional Neural Networks. IEEE Trans Neural Netw Learn Syst. 2022;33(11):6194-6205
  4. Malysheva N, Wang J, von Kleist M. S̲tochastic S̲imulation A̲lgorithm For Effective Spreading Dynamics On T̲ime-Evolving A̲daptive N̲etworX̲ (SSATAN-X) Math. Model. Nat. Phenom. 2022; 17:35 (online)
  5. Baumgarte S, Hartkopf F, Hölzer M, von Kleist M, Neitz S, Kriegel M, Bollongino K. Investigation of a Limited but Explosive COVID-19 Outbreak in a German Secondary School. Viruses. 2022;14(1):87


  1. Smith MR, Trofimova M, Weber A, Duport Y, Kühnert D, von Kleist M. Rapid incidence estimation from SARS-CoV-2 genomes reveals decreased case detection in Europe during summer 2020. Nat Commun. 2021 Oct 14;12(1):6009
  2. Kiral FR, Dutta SB, Linneweber GA, Hilgert S, Poppa C, Duch C, von Kleist M, Hassan BA, Hiesinger PR. Brain connectivity inversely scales with developmental temperature in Drosophila. Cell Rep. 2021 Dec 21;37(12):110145
  3. Zhang L, Wang J, von Kleist M. Numerical approaches for the rapid analysis of prophylactic efficacy against HIV with arbitrary drug-dosing schemes. PLoS Comput Biol. 2021;17(12):e1009295
  4. van der Toorn W, Oh DY, Bourquain D, Michel J, Krause E, Nitsche A, von Kleist M; An intra-host SARS-CoV-2 dynamics model to assess testing and quarantine strategies for incoming travelers, contact management, and de-isolation. Patterns (N Y). 2021;2(6):100262
  5. van der Toorn W, Oh DY, von Kleist M; COVIDStrategyCalculator: A software to assess testing and quarantine strategies for incoming travelers, contact management, and de-isolation. Patterns (N Y). 2021 Jun 11;2(6):100264
  6. Oh DY, Buda S, Biere B, Reiche J, Schlosser F, Duwe S, Wedde M, von Kleist M, Mielke M, Wolff T, Dürrwald R. Trends in respiratory virus circulation following COVID-19-targeted nonpharmaceutical interventions in Germany, January September 2020: Analysis of national surveillance data. Lancet Reg Health Eur.
    2021 Jul;6:100112.
  7. Raharinirina NA, Peppert F, von Kleist M, Schütte C, Sunkara V. Inferring gene regulatory networks from single-cell RNA-seq temporal snapshot data requires higher-order moments. Patterns (N Y). 2021 Aug 18;2(9):100332
  8. Calvignac-Spencer S, Budt M, Huska M, Richard H, Leipold L, Grabenhenrich L, Semmler T, von Kleist M, Kröger S, Wolff T, Hölzer M. Rise and Fall of SARS-CoV-2 Lineage A.27 in Germany. Viruses. 2021;13(8):1491
  9. Iannuzzi S, von Kleist M. Mathematical Modelling of the Molecular Mechanisms of Interaction of Tenofovir with Emtricitabine against HIV. Viruses. 2021;13(7):1354
  10. Hufsky F, …, von Kleist M, …, Marz M. Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research. Brief Bioinform. 2021;22(2):642-663.
  11. Goettsch W, Beerenwinkel N, …, von Kleist M, …, Marz M. ITN-VIROINF: Understanding (Harmful) Virus-Host Interactions by Linking Virology and Bioinformatics. Viruses. 2021;13(5):766.


  1. F. R. Kiral, G. A. Linneweber, S. V. Georgiev, B. A. Hassan, M. von Kleist and P. R.
    Hiesinger. Kinetic restriction of synaptic partner choice through filopodial autophagy, Nature Communications 11 (2020), 1325
  2. M. von Kleist, G. Garcia-Lerma, A. Liu and P.L. Anderson. Pharmacokinetics and Pharmacodynamics of Pre-Exposure Prophylaxis against HIV, accepted in Frontiers in Pharmacol 11 (2020), 1288 (online)
  3. P. Gerletti, M. von Kleist, T. Kuhl, R. Pieper, M. Lahrssen-Wiederholt, J. Numata and H. Mielke. Transfer kinetics of fipronil into chicken (Gallus gallus domesticus) eggs. Computational Toxicology 15 (2020), 100131 (online)
  4. A.M. Richter, A. Possling, N. Malysheva, KP. Yousef, S. Herbst, M. von Kleist and R. Hengge. Local c-di-GMP signaling in the control of synthesis of the E. coli biofilm exopolysaccharide pEtN-cellulose. Journal of Molecular Biology 16 (2020), 4576


  1. M. Neset Özel, A. Kulkarni, A. Hasan, J. Schallau, M. Moldenhauer, I.-M. Daumann, H. Wolfenberg, V.J. Dercksen, F. R. Kiral, M. Weiser, S. Prohaska, M. von Kleist*, P. R. Hiesinger* (*shared corresponding authorship) Serial synapse formation through filopodial competition for synaptic seeding factors, Developmental Cell 50 (2019), 447–61
  2. A. Rittig, T. Haase, A. Pletnyov, B. Kohl, W. Ertel, M. von Kleist, V. Sunkara. SLCV -A supervised learning-computer vision combined strategy for automated muscle fibre detection in cross sectional images, PeerJ 7 (2019), e7053
  3. S. Duwal*, D. Seeler*, L. Dickinson, S. Khoo and M. von Kleist. The utility of efavirenz-based PrEP against HIV infection. A systems pharmacological analysis. Frontiers in Pharmacol 19 (2019), 199 (online)
  4. T. Haase, V. Sunkara, B. Kohl, C. Meier, P. Bussmann, J. Becker, M. Jagielski, M. von Kleist*, W. Ertel* (*shared corresponding authorship) Discerning the spatio-temporal disease patterns of surgically induced OA mouse models, PLoS One 14 (2019), e0213734
  5. S. Duwal, L. Dickinson, S. Khoo and M. von Kleist. Mechanistic framework predicts drug-class specific utility of antiretrovirals for HIV prophylaxis, PLoS Computational Biology 15(2019), e1006740
  6. K. Hanke, N. Rodriguez Faria, D. Kühnert, K. P. Yousef, A. Hauser, K. Meixenberger, A. Hofmann, V. Bremer, B. Bartmeyer, O. Pybus, C. Kücherer, M. von Kleist and N. Bannert. Reconstruction of the genetic history and the current spread of HIV-1 subtype A in Germany. Journal of Virology 93 (2019), e02238-18
  7. P. Gupta, S. Peter, M. Jung, A. Lewin, G. Hemmrich-Stanisak, A. Franke, M. von Kleist, C. Schütte, R. Einspanier, S. Sharbati, J. zur Bruegge Analysis of long non-coding RNA and mRNA expression in bovine macrophages brings up novel aspects of Mycobacterium avium subspecies paratuberculosis infections, Scientific Reports 8 (2019), 1571


  1. R.P. Smyth*, M. Smith, A.-C. Jousset, L. Despons, G. Laumond, T. Decoville, P. Cattenoz, C. Moog, F. Jossinet, M. Mougel, J.-C. Paillart, M. von Kleist*, Roland Marquet* (*shared corresponding authorship) In cell Mutational Interference Mapping Experiment (in cell MIME) identifies the 5’ PolyA signal as a dual regulator of HIV-1 genomic RNA production and packaging, Nucleic Acids Research 46 (2018), e57
  2. W. Zhang, C. Hartmann and M. von Kleist. Optimal control of markov jump processes: Asymptotic analysis, algorithms and application to modelling of chemical reaction systems, Communications in Mathematical Sciences 16 (2018), 293


  1. K. Meixenberger, K. P. Yousef, S. Somogyi, Sybille, S. Fiedler, B. Bartmeyer, O. Hamouda, N. Bannert, M. von Kleist, C. Kücherer. Molecular evolution of HIV-1 integrase during the 20 years prior to the first approval of integrase inhibitors, Virology Journal, 14 (2017), 223
  2. M. von Kleist, Ch. Schütte, W. Zhang. Statistical analysis of the first passage path ensemble of jump processes. Journal of Statistical Physics 170 (2017), 809
  3. P. Gupta, A. Gramatke, R. Einspanier, C. Schütte, M. von Kleist* and Jutta Sharbati* (*equally contributed). In silico cytotoxicity assessment on cultured rat intestinal cells deduced from cellular impedance measurements, Toxicology in vitro, 41 (2017), 179
  4. M. R. Smith, R. P. Smyth, R. Marquet and M. von Kleist. MIMEAnTo-Profiling functional RNA in Mutational Interference Mapping Experiments, Bioinformatics, 32 (2016), 3369
  5. S. Duwal, V. Sunkara and M. von Kleist. Multi-scale Systems-Pharmacology pipeline to assess the prophylactic efficacy of NRTIs against HIV-1. CPT: Pharmacometrics & Systems Pharmacology, 5 (2016), 377
  6. V. Sunkara, M. von Kleist, Coupling cellular phenotype and mechanics to understand extracellular matrix formation and homeostasis in osteoarthritis, in IFAC-PapersOnLine, 49(2016), 38
  7. K. P. Yousef, K. Meixenberger, M. R. Smith, S. Somogyi, S. Gromöller, D. Schmidt, B. Gunsenheimer-Bartmeyer. O. Hamouda, C. Kücherer and M. von Kleist. Inferring HIV-1 transmission dynamics in Germany from recently transmitted viruses, Journal of Acquired Immune Deficiency Syndromes, 73 (2016), 356
  8. K.P. Yousef, A. Streck, C. Schütte, H. Siebert, R. Hengge and Max von Kleist. Logical- continuous modelling of post-translationally regulated bistability of curli fiber expression in Escherichia coli, BMC Systems Biology, 9 (2015), 39
  9. R.P. Smyth*, L. Despons, G. Huili, S. Bernacchi, M. Hijnen, J. Mak, F. Jossinet, L. Weixi, J.-C. Paillart, Max von Kleist* and R. Marquet* (*shared corresponding authorship). Mutational Interference Mapping Experiment (MIME) for studying the relationship between RNA structure and function, Nature Methods, 12 (2015), 866
  10. S. Duwal, M. von Kleist. Top-down and bottom-up modelling in system pharmacology to understand clinical efficacy : An example with NRTIs of HIV-1, Eur J Parm Sci, 94 (2016), 72
  11. S. Duwal, S. Winkelmann, C. Schütte and Max von Kleist. Optimal treatment strategies in the context of ’treatment for prevention’ against HIV/1 in resource-poor settings, PLoS Computational Biology, 11(2015), e1004200
  12. S. Winkelmann, C. Schütte and M. von Kleist. Markov Control Processes with Rare State Observation: Theory and Application to Treatment Scheduling in HIV-1. Communications in Mathematical Sciences 12 (2014), 859
  13. K Meixenberger, KP Yousef, S Somogyi, S Fiedler, B Bartmeyer, M von Kleist, C
    Kücherer. Characterization of natural polymorphic sites of the HIV-1 integrase before the introduction of HIV-1 integrase inhibitors in Germany. J Int AIDS Soc, 17 (2014), 19746
  14. J. Katchanov, M. von Kleist, K. Arasteh and H. Stocker. ”Time-to-Amphotericin B” in Cryptococcal Meningitis in a European Low-Prevalence Setting: Analysis of Diagnostic Delays. QJM: An International Journal of Medicine, 107 (2014), 799-803
  15. S. Muehlhans, M. von Kleist, T. Gretchukha, T. Martin, U. Fegeler, W. Maurer, L.
    Namazova-Baranova, G. Gaedicke, A. Baranov and B. Rath. Awareness and Utilization of Standards and Pathways for the Reporting of Adverse Events Following Immunization among Pediatricians in Russia and Germany. Pediatric Drugs, 16(2014), 321-30
  16. K. Meixenberger, A. Hauser, K. Jansen, K. P. Yousef, S. Fiedler, S. Somogyi, S. Norley, M von Kleist, O. Hamouda, N. Bannert, B. Bartmeyer and C. Kücherer. Assessment of ambiguous base calls in HIV-1 pol population sequences as biomarker to identify recent HIV-1 infections in incidence studies. Journal of Clinical Microbiology, 52 (2014), 2977-83
  17. X. Chen, K. P. Yousef, S. Duwe, K. Karsch, S. Grover, S. Wählisch, P. Obermeier, F. Tief, S. Muehlhans, L. Seeber, M von Kleist, B. Schweiger and B. Rath. Quantitative influenza follow-up testing (QIFT) – a novel biomarker for the monitoring of disease activity at the point-of-care. Plos One 9 (2014), e92500
  18. B. Rath, F. Tief, K. Karsch, S. Muehlhans, P. Obermeier, E. Adamou, X. Chen, L. Seeber, C. Peiser, C. Hoppe, M. von Kleist, T. Conrad and B. Schweiger Towards a personalized approach to managing of influenza infections in infants and children – food for thought and a note on oseltamivir Infectious Disorders – Drug Targets 13 (2013), 25
  19. B. Rath, K. P. Yousef, D. K. Katzenstein, R. W. Shafer, Ch. Schütte, M. von Kleist and T. C. Merigan. In vitro HIV-1 Evolution in Response to Triple Reverse Transcriptase Inhibitors & in silico Phenotypic Analysis. PLoS One 8 (2013), e61102
  20. S. Winkelmann, C. Schütte and M. von Kleist. ”Markov Control with Rare State Observation”: Sensitivity Analysis with Respect to Optimal Treatment Strategies against HIV-1. International Journal of Biomathematics and Biostatistics 2 (2013), 1
  21. B. A. Rath, M. von Kleist, M. E. Castillo, L. Kolevic, P. Caballero, G. Soto-Castellares, A. M. Amedee, J. E. Robinson, D. K. Katzenstein, R. B. Van Dyke and R. A. Oberhelman. Antiviral Resistance and Predictors of Virologic Failure in the first Cohort of HIV-Infected Children Receiving Highly-Active Antiretroviral Therapy in Lima, Peru: A Cross-Sectional Analysis. BMC Infect Dis 13 (2013), 1
  22. S. Duwal, C. Schütte and M. von Kleist. Pharmacokinetics and pharmacodynamics of the reverse transcriptase inhibitor tenofovir & prophylactic efficacy against HIV-1 infection. PLoS One 8 (2012), e40382
  23. B. Rath, M. von Kleist, F. Tief, K. Karsch, E. Türk, S. Mühlhans, F. Louis, H. Skopnik, B. Schweiger and S. Duwe. Virus Load Kinetics and Resistance Development during Oseltamivir Treatment in Infants and Children Infected with Influenza A (H1N1) 2009 and Influenza B Viruses. Pediatr Infect Dis J 31 (2012), 899
  24. M. von Kleist, P. Metzner, R. Marquet and C. Schütte. Polymerase inhibition by nucleoside analogs: Cellular- and kinetic parameters of efficacy, susceptibility and resistance selection. PLoS Comput. Biol. 8 (2012), e1002359
  25. M. Frank*, M. von Kleist*, A. Kunz, G. Harms, C. Schütte and C. Kloft (*equally contributed). Quantifying the impact of nevirapine-based prophylaxis strategies to prevent mother-to-child transmission of HIV-1: A combined pharmacokinetic, pharmaco- and viral dynamic analysis to predict clinical outcomes. Antimicrob. Agents Chemother. 55 (2011), pp. 5529-40
  26. M. von Kleist, Stephan Menz, Hartmut Stocker, Kaikawus Arasteh, Christof Schütte and Wilhelm Huisinga. HIV quasi-species dynamics during pro-active treatment switching: impact on multi-drug resistance and resistance archiving in latent reservoirs. PLoS One 6 (2011), e18204
  27. M. von Kleist, Stephan Menz and W. Huisinga. Drug-Class specific impact of antivirals on the reproductive capacity of HIV PLoS Comput. Biol. 6 (2010), e1000720
  28. M. von Kleist and W. Huisinga. Pharmacokinetic-Pharmacodynamic relationship of NRTIs and its connection to viral escape: An example based on Zidovudine Eur. J. Pharm. Sci. 36 (2009), 532-543
  29. M. von Kleist and W. Huisinga. Physiologically based pharmacokinetic modelling: A sub-compartmentalized model of tissue distribution J. Pharmacokinet. Pharmacodyn. 34 (2007), pp 789-806

Publication in German

  1. Oh DY, Böttcher S, Kröger S, von Kleist M. SARS-CoV-2-Übertragungswege und Implikationen für den Selbst- und Fremdschutz [SARS-CoV-2 transmission routes and implications for self- and non-self-protection]. Bundesgesundheitsblatt Gesundheitsforschung Gesundheitsschutz. 2021;64(9):1050-1057
  2. Grote U, Arvand M, Brinkwirth S, Brunke M, Buchholz U, Eckmanns T, von Kleist M, Niebank M, Ruehe B, Schulze K, Stoliaroff-Pépin A, Thanheiser M, Schaade L, Said D, Haas W. Maßnahmen zur Bewältigung der COVID-19-Pandemie in Deutschland: nichtpharmakologische und pharmakologische Ansätze [Measures to cope with the COVID-19 pandemic in Germany: nonpharmaceutical and pharmaceutical interventions]. Bundesgesundheitsblatt Gesundheitsforschung Gesundheitsschutz. 2021 ;64(4):435-445.
  3. Seifried J, Böttcher S, von Kleist M, Jenny M, Antão E-M, Oh DY, Jung-Sendzik T, Broich K, Denkinger C, Bartenschlager R, Schaade L, Hamouda O, Mielke M. Antigentests als ergänzendes Instrument in der Pandemiebekämpfung Epidemiologisches Bulletin 2021, 17:3-14 (online)
  4. Oh DY, Kröger S, Wedde M, …, Schaade L, Mielke M, von Kleist M, Fuchs S, Wieler LH, Wolff T. SARS-CoV-2-Varianten: Evolution im Zeitraffer, Deutsches Ärzteblatt 2021, 9:9 (online)
  5. von Kleist M, Ruehe B, Oh DY, …, van der Toorn W, Jenny M, Mielke M, Herzog C, Wieler LH. Abwägung der Dauer von Quarantäne und Isolierung bei COVID-19 Epidemiologisches Bulletin 2020, 39:3-11 (online)

Proceedings and book chapters

  1. M. von Kleist, C. Kloft and W. Huisinga. Combining Systems Biology with physiologically-based pharmacokinetics to support the understanding of drug effects Proceedings of Foundations of Systems Biology in Engeneering FOSBE, (2007), pp. 231-236.
  2. R. Telgmann, M. von Kleist, and W. Huisinga. Software Supported Modelling in Pharmacokinetics Computational Life Sciences II, Lecture Notes in Computer Science 4216 (2006), M.R. Berthold, R. Glen, and I. Fischer (Eds.), Springer, pp. 216-225.
  3. D. Franke, J. Pavlovic, T. S. Utesch, M. von Kleist, J. Schultz, G. Dollenmaier and K.
    Moelling. chapter: Update on Antiviral DNA Vaccine Research (2000-2003) in Novel Vaccination Strategies, Stefan H. E. Kaufmann (ed.), Wiley 2004

Consortium Publications

  1. Walker A, …, Dilthey AT; (as part of DeCOI) Characterization of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infection Clusters Based on Integrated Genomic Surveillance, Outbreak Analysis and Contact Tracing in an Urban Setting. Clin Infect Dis. 2022;74(6):1039-1046
  2. Houwaart T, …, Walker A, Dilthey AT; (as part of DeCOI) Integrated genomic surveillance enables tracing of person-to-person SARS-CoV-2 transmission chains during community transmission and reveals extensive onward transmission of travel-imported infections, Germany, June to July 2021. Euro Surveill. 2022;27(43):2101089
  3. Schulte-Schrepping J, …, Schultze JL, Aschenbrenner AC, Li Y, Nattermann J, Sawitzki B, Saliba AE, Sander LE; (as part of DeCOI). Severe COVID-19 Is Marked by a Dysregulated Myeloid Cell Compartment. Cell. 2020;182(6):1419-1440.e23.
  4. Bernardes JP, … , Schultze JL, Rosenstiel P; (as part of DeCOI) Longitudinal Multi-omics Analyses Identify Responses of Megakaryocytes, Erythroid Cells, and Plasmablasts as Hallmarks of Severe COVID-19. Immunity, 2020 ;53(6):1296-1314.e9.
  5. Krämer B, …, Kurth F, Sander LE, Sawitzki B, Aschenbrenner AC, Schultze JL, Nattermann J.; (as part of DeCOI) Early IFN-α signatures and persistent dysfunction are distinguishing features of NK cells in severe COVID-19. Immunity. 2021;54(11):2650-2669.e14.
  6. Warnat-Herresthal S, … , Breteler MMB, Giamarellos-Bourboulis EJ, Kox M, Becker M, Cheran S, Woodacre MS, Goh EL, Schultze JL.; (as part of DeCOI) Swarm Learning for decentralized and confidential clinical machine learning. Nature. 2021 Jun;594(7862):265-270. doi: 10.1038/s41586-021-03583-3.
  7. 5: Aschenbrenner AC, …, Nattermann J, Koutsoukou A, Giamarellos-Bourboulis EJ, Ulas T; (as part of DeCOI). Disease severity-specific neutrophil signatures in blood transcriptomes stratify COVID-19 patients. Genome Med. 2021 ;13(1):7.
  8. Alm E, …, O’Toole Á, Pereyaslov D; (as part of the GISAID EpiCoV group) Geographical and temporal distribution of SARS-CoV-2 clades in the WHO European Region, January to June 2020. Euro Surveill. 2020;25(32):2001410.


M. von Kleist and Christof Schütte. Reduction technique for pharmacological models to support planning, execution and analysis of clinical studies (2010). German patent office. Pat.Nr.: 10 2010 060 311