• Publications

    1. Mathematical modelling of the molecular mechanisms of interaction of tenofovir with emtricitabine against HIV. S. Iannuzzi*, M. von Kleist, submitted , 2021
    2. Rapid incidence estimation from SARS-CoV-2 genomes reveals decreased case detection in Europe during summer 2020. M.R. Smith*, M. Trofimova*, A. Weber, Y. Duport, D. Kühnert, M. von Kleist, submitted , 2021, (preprint)
    3. Variable brain wiring trough scalable and relative synapse formation in Drosophila. F. Kiral, S. Dutta, L. Linneweber, C. Poppa, M. von Kleist, B. Hassan and R.P. Hiesinga , submitted , 2021,
    4. ITN-VIROINF: Understanding (harmful) virus-host Interactions by linking Virology and Bioinformatics. W. Goettsch, N. Beerenwinkel, L. Deng, L. Dölken, B. E. Dutilh, F. Erhard, L. Kaderali, M. von Kleist, R. Marquet, J. Matthijnssens, S. McCallin, D. McMahon, T. Rattei, R. Van Rij, D. L. Robertson, M. Schwemmle, N. Stern-Ginossar and M. Marz , Viruses , 2021, 13, 766, (online)
    5. COVIDStrategyCalculator: A software to assess testing- and quarantine strategies for incoming travelers, contact person management and de-isolation W. van der Toorn, DY Oh, M. von Kleist, accepted in Patterns (Cell press) , 2021 (online)
    6. Rapid and pronounced effect of COVID-19-targeted nonpharmaceutical interventions on respiratory virus circulation in Germany D.-Y. Oh, S. Buda, B. Biere, J. Reiche, F. Schlosser, S. Duwe, M. Wedde, M. von Kleist, M. Mielke, T. Wolff, R. Dürrwald , accepted in The Lancet Regional Health -Europe 6: 100112 , 2021 (online)
    7. An intra-host SARS-CoV-2 dynamics model to assess testing- and quarantine strategies for incoming travelers, contact person management and de-isolation W. van der Toorn, DY Oh, D Bourquain, J Michel, E Krause, A Nitsche, M. von Kleist, accepted in Patterns (Cell press) , 2021 (online)
    8. Inferring Gene Regulatory Networks from Single Cell RNA-seq Temporal Snapshot Data Requires Higher Order Moments N. A. Raharinirina, F. Peppert, M. von Kleist, C. Schütte, V. Sunkara , submitted , 2021
    9. Pharmacokinetics and Pharmacodynamics of Pre-Exposure Prophylaxisagainst HIV M. von Kleist, G. García-Lerma, A. Liu and P.L. Anderson , Frontiers in Pharmacology,  11, 1288, 2020 (online)
    10. On the Sufficient Condition for Solving the Gap-Filling Problem Using Deep Convolutional Neural Networks F. Peppert, M. von Kleist, Ch. Schütte, Vikram Sunkara, IEEE Transactions on Neural Networks and Learning Systems, 2020 (online)
    11. Computer fighting SARS-CoV-2: Useful tools to advance Coronavirus research. F. Hufsky, K. Lamkiewicz, A. Almeida, A. Aouacheria, C. Arighi, A. Bateman, J. Baumbach, N. Beerenwinkel, C.Brandt, M.Cacciabue, S. Chuguransky, O. Drechsel, R. D. Finn, A. Fritz, S. Fuchs, D. Heider, M. Hoffmann, M. Hölzer, S. Hoops, L- Kaderali, Max von Kleist, R. Kmiecinski, D.Kühnert, U. Kummer, G.Lasso, P. Libin, M. List, M. J. Martin, J. Matschinske, A. McHardy, P. Mendes, J Mistry, V. Navratil, A. N. O’Toole, A. I. Petrov, G. Rangel-Pineros, N. Redaschi, S. Reimering, K. Reinert, A. Reyes, L. Richardson, S. Sadegh, K. Theys, C. Upton, L. Williams and M. Marz, Briefings in Bioinformatics, bbaa232, 2020 (online)
    12. Kinetic restriction of synaptic partner choice through filopodial autophagy. F. R. Kiral, G. A. Linneweber, S. V. Georgiev, B. A. Hassan, M. von Kleist and P. R. Hiesinger, Nature Communications,  11, 1325, 2020 (online)
    13. Transfer kinetics of fipronil into hen (Gallus gallus domesticus) eggs. P. Gerletti,  Max von Kleist, T Kuhl, R Pieper, M Lahrssen-Wiederholt, J Numata and H Mielke, Computational Toxicology,  15, 100131, 2020. (online)
    14. Local c-di-GMP signaling in the control of synthesis of the E. coli biofilm exopolysaccharide pEtN-cellulose. A.M. Richter, A. Possling, N. MalyshevaKP. Yousef, S. Herbst, M. von Kleist and R. Hengge, Journal of Molecular Biology432, 4576 (online) , 2020
    15. Serial synapse formation through filopodial competition for synaptic seeding factors. M.N. Ozel, A. Kulkarni, A. Hasan, J. Brummer, M. Moldenhauer, I.-M. Daumann, H. Wolfenberg, V. Dercksen, F.R. Kiral, M. Weiser, S. Prohaska, M. von Kleist*, P.R. Hiesinger*, Developmental Cell50, 447-61, 2019 (online, bioRXiv), recommended by F1000
    16. Reconstruction of the genetic history and the current spread of HIV-1 subtype A in Germany. K. Hanke, N. R. 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, Journal of Virology, 93, e02238-18, 2019 (online)
    17. SLCV -A supervised learning-computer vision combined strategy for automated muscle fibre detection in cross sectional images. A. Rittig, T. Haase, A. Pletnyov, B. Kohl, W. Ertel, M. von Kleist, V. Sunkara, PeerJ 7e7053, 2019 (online, open access)
    18. Discerning the spatio-temporal disease patterns of surgically induced OA mouse models. T. Haase+, V. Sunkara+, B. Kohl, C. Meier, P. Bußmann, J. Becker, M. Jagielski, M. von Kleist*, W. Ertel* (+shared first- , *shared corresponding authorship),Plos One, 14, e0213734, 2019 (online, open access)
    19. The utility of efavirenz-based prophylaxis against HIV infection. A systems pharmacological analysis. S. Duwal*, D. Seeler*, L. Dickinson, S. Khoo and M. von Kleist, Frontiers in Pharmacology, 10, 199, 2019 (online, open access)
    20. Mechanistic framework predicts drug-class specific utility of antiretrovirals for HIV prophylaxis, S. Duwal, L. Dickinson, S. Khoo and M. von Kleist, PLoS Computational Biology, 15, e1006740, 2019 (online, open access)
    21. Analysis of long non-coding RNA and mRNA expression in bovine macrophages brings up novel aspects of Mycobacterium avium subspecies paratuberculosis infections. P. Gupta, S. Peter, M. Jung, A. Lewin, G. Hemmrich-Stanisak, A. Franke, M. von Kleist, C. Schütte, R. Einspanier, S. Sharbati and J. zur Bruegge, Scientific Reports, 9, 1571, 2019 (online, open access)
    22. Hybrid stochastic framework predicts efficacy of prophylaxis against HIV: An example with different dolutegravir regimen, S. Duwal, L. Dickinson, S. Khoo and M. von Kleist, PLoS Computational Biology14, e1006155, 2018 (online, open access)
    23. In cell Mutational Interference Mapping Experiment (in cell MIME) identifies 5’ PolyA as a dual regulator of HIV-1 genomic RNA production and packaging, R.P. Smyth*$, M.R. Smith$, A-C. Jousset, L. Despons, G. Laumond, T. Decoville, P. Cattenoz, C. Moog, F. Jossinet, M. Mougel, J.-C. Paillart, M. von Kleist*, R. Marquet*Nucleic Acids Research, 46, e57, 2018 (online, open access)(*shared corresponding authorship)
    24. Statistical analysis of the first passage path ensemble of jump processes. M.  von Kleist, Ch. Schütte, W. Zhang, Journal of Statistical Physics, 170, 809, 2018 (ArXiv final version)
    25. Optimal control of markov jump processes: Asymptotic analysis, algorithms and application to modelling of chemical reaction systems. W. Zhang, C. Hartmann and M. von Kleist, Communications in Mathematical Sciences, 16, 293, 2018 (ArXiv, online)
    26. Molecular evolution of HIV-1 integrase during the 20 years prior to the first approval of integrase inhibitors. K. Meixenberger, K.P. Yousef, M.R. Smith, S. Somogyi, Sybille, S. Fiedler, B. Bartmeyer, O.  Hamouda, N. Bannert, M.  von Kleist, C. Kücherer, Virology Journal, 14, 223, 2017 (open access)
    27. In silico cytotoxicity assessment on cultured rat intestinal cells deduced from cellular impedance measurements. P. Gupta, A. Gramatke, R. Einspanier, C. Schütte, M. von Kleist*, J. Sharbati*Toxicology in vitro, 41, 179, 2017 (online)*equally contributed
    28. Coupling cellular phenotype and mechanics to understand extracellular matrix formation and homeostasis in osteoarthritis. V. Sunkara, M. von Kleist,
      IFAC-PapersOnLine 49(26), 38, 2016 (online,preprint)
    29. MIMEAnTo-Profiling functional RNA in Mutational Interference Mapping Experiments. M. Smith, R. P. Smyth, R. Marquet and M. von KleistBioinformatics, 32, 3369, 2016 (open access)
    30. Multi-scale Systems-Pharmacology pipeline to assess the prophylactic efficacy of NRTIs against HIV-1. S. Duwal, V. Sunkara and M. von Kleist, CPT: Pharmacometrics & Systems Pharmacology, 5, 377, 2016 (open access)
    31. Inferring HIV-1 transmission dynamics in Germany from recently transmitted viruses. 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, Journal of Acquired Immune Deficiency Syndromes, 73, 356, 2016 (online)
    32. Top-down and bottom-up modelling in system pharmacology to understand clinical efficacy : An example with NRTIs of HIV-1. S. Duwal, M. von Kleist, Eur J Parm Sci, 94, 72, 2016 (online)
    33. Mutational Interference Mapping Experiment (MIME) for studying the relationship between RNA structure and function. R.P. Smyth*, L. Despons, G. Huili, S. Bernacchi, M. Hijnen, J. Mak, F. Jossinet, L. Weixi, J-C. Paillart, M. von Kleist*, R. Marquet*, Nature Methods+, 12, 866 , 2015 (online) *shared corresponding authorship. +see also cover of the september issue
    34. Logical-continuous modelling of post-translationally regulated bistability of curli fiber expression in Echerichia coli. K. P. Yousef, A. Streck, C. Schütte, H. Siebert, R. Hengge and M. von Kleist, BMC Systems Biology, 9, 39, 2015 (open access)
    35. Optimal treatment strategies in the context of ‘treatment for prevention’ against HIV-1 in resource-poor settings. S. Duwal, S. Winkelmann, C. Schütte and M. von Kleist, PLoS Comput. Biol., 11, e1004200, 2015 (open access)
    36. Characterization of natural polymorphic sites of the HIV-1 integrase before the introduction of HIV-1 integrase inhibitors in Germany. K. Meixenberger, K. P. Yousef, S. Somogyi, S. Fiedler, B. Bartmeyer, M. von Kleist, C. Kücherer. Journal of the International AIDS Society 11/2014; 17(4(Suppl 3)):19746.
    37. Assessment of ambiguous base calls in HIV-1 pol population sequences as a biomarker to indentify recent infections in HIV-1 incidence studies. K. Meixenberger, A. Hauser, K. Jansen, K. P. Yousef, S. Fiedler, M. von Kleist, S. Norley, S.Somogyi, O. Hamouda, N. Bannert, B. Bartmeyer, C. Kücherer. Journal of Clinical Microbiology52, 2977, 2014 (online)
    38. Awareness and Utilization of Standards and Pathways for the Reporting of Adverse Events Following Immunization among Pediatricians in Russia and Germany. S. Muehlhans, M. von Kleist, T. Gretchukha, T. Martin, U. Fegeler, W. Maurer, L. Namazova-Baranova, G. Gaedicke, A. Baranov, B. Rath. Pediatric Drugs16, 321, 2014 (online)
    39. “Time-to-Amphotericin B” in Cryptococcal Meningitis in a European Low-Prevalence Setting: Analysis of Diagnostic Delays. J. Katchanov, M. von Kleist, K. Arasteh, H. Stocker QJM: An International Journal of Medicine, 107, 799, 2014 (online)
    40. Quantitative influenza follow-up testing (QIFT) – a novel biomarker for the monitoring of disease activity at the point-of-care. 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, B. Rath. Plos One 9, e92500, 2014 (open access)
    41. Markov Control Processes with Rare State Observation: Theory and Application to Treatment Scheduling in HIV-1 S. Winkelmann, C. Schütte and M. von KleistCommunications in Mathematical Sciences 12, 859, 2014 (online)
    42. “Markov Control with Rare State Observation”: Sensitivity Analysis with Respect to Optimal Treatment Strategies against HIV-1. S. Winkelmann, C. Schütte and M. von Kleist. International Journal of Biomathematics and Biostatistics 2, 1, 2013 (pdf of preprint)
    43. Towards a personalized approach to managing of influenza infections in infants and children – food for thought and a note on oseltamivir 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, B. Schweiger. Infectious Disorders – Drug Targets 13 , 25, 2013 (online)
    44. In Vitro HIV-1 Evolution in Response to Triple Reverse Transcriptase Inhibitors & In Silico Phenotypic Analysis
      B. Rath, K. P. Yousef, D. K. Katzenstein, R. W. Shafer, Ch. Schütte, M. von Kleist and T. C. Merigan. PLoS One 8 , e61102, 2013 (open access)
    45. Antiviral Resistance and Predictors of Virologic Failure in the first Cohort of HIV-infected Children Gaining Access to Structured Antiretroviral Therapy in Lima, Peru: A Cross-Sectional Analysis B. 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. Oberhelman BMC Infect Dis 13, 1, 2013 (open access)
    46. Pharmacokinetics and Pharmacodynamics of the Reverse Transcriptase Inhibitor Tenefovir and Prophylactic Efficacy against HIV-1 Infection. S. Duwal, C. Schütte and M. von Kleist. PLoS One 8, e40382, 2012 (open access)
    47. Virus Load Kinetics and Resistance Development during Oseltamivir Treatment in Infants and Children Infected with Influenza A (H1N1) 2009 and Influenza B Viruses B. Rath, M. von Kleist, F. Tief, K. Karsch, E. Türk, S. Mühlhans, F. Louis, H. Skopnik, B. Schweiger and S. Duwe. Pediatr Infect Dis J. 31, 9, 2012(online)
    48. HIV-1 polymerase inhibition by nucleoside analogs: Cellular- and kinetic parameters of efficacy, susceptibility and resistance selection M. von Kleist, P. Metzner, R. Marquet and C. Schütte. PLoS Comput. Biol.8, e1002359, 2012 (open access)
    49. 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. M. Frank*, M. von Kleist*, A. Kunz, G. Harms, C. Schütte and C. Kloft. Antimicrob. Agents Chemother 55, 5529, 2011 (open access)* equally contributed
    50. Reduction technique for pharmacological models to support planning, execution and analysis of clinical studies (patent).
      M. von Kleist (67%) and Christof Schutte (33%) . German patent office. Pat.Nr.: 10 2010 060 311, 2010 (link)
    51. HIV quasi-species dynamics during pro-active treatment switching: impact on multi-drug resistance and resistance archiving in latent reservoirs. M. von Kleist, S. Menz, H. Stocker, K. Arasteh, C. Schütte and W. Huisinga. PLoS ONE 6, e18204, 2011 (open access)
    52. A Drug-Class specific impact of antivirals on the reproductive capacity of HIV. M. von Kleist, Stephan Menz and W. Huisinga. PLoS Comput. Biol. 6, e1000720, 2010 ( open access )
    53. Pharmacokinetic-Pharmacodynamic relationship of NRTIs and its connection to viral escape: An example based on Zidovudine M. von Kleist and W. Huisinga Eur J Pharm Sci 36, 532, 2009 (online)
    54. Combining Systems Biology with physiologically-based pharmacokinetics to support the understanding of drug effects. M. von Kleist, C. Kloft and W. Huisinga. Proceedings of Foundations of Systems Biology in Engeneering FOSBE, 231, 2007 (pdf of preprint)
    55. Physiologically based pharmacokinetic modelling: A sub-compartmentalized model of tissue distribution
      M. von Kleist and W. Huisinga. J. Pharmakokinet. Pharmacodyn. 34, 789, 2007 (online)
    56. Software Supported Modelling in Pharmacokinetics R. Telgmann, M. von Kleist, and W. Huisinga LNCS 4216, 216, 2006 (online)
    57. Update on Antiviral DNA Vaccine Research (2000-2003) D. Franke, J. Pavlovic, T. S. Utesch, M. von Kleist, J. Schultz, G. Dollenmaier and K. Moelling. in Novel Vaccination Strategies Stefan H. E. Kaufmann (ed.), Wiley 2004 (online)
    58. Consortium Publications

    59. Severe COVID-19 is marked by a dysregulated myeloid cell compartment Schulte-Schreppning et al. ( Max von Kleist as part of deCOI) Cell , 182: 1419, 2020
    60. (online)
    61. Geographical and temporal distribution of SARS-CoV-2 clades in the WHO European Region, January to June 2020 Alm et al. ( Max von Kleist as part of the GISAID EpiCoV Group) Eurosurveillance , 25,2001410, 2020
    62. (online)

      Publications in German

    63. SARS-CoV-2 Transmission Routes: Implications for self- and non-self protection [in german] DY. Oh, S. Böttcher, S. Kröger, M. von Kleist , submitted, 2021
    64. Measures to cope with the COVID-19 pandemic in Germany: nonpharmaceutical and pharmaceutical interventions [in german] U. Grote, M. Arvand, S. Brinkwirth, M. Brunke, U. Buchholz, T. Eckmanns, M. von Kleist, M. Niebank, B. Ruehe, K. Schulze, A. Stoliaroff-Pépin, M. Thanheiser, L. Schaade, D. Said, W. Haas , Bundesgesundheitsblatt, 1437-1588, 2021 (online)
    65. Antigen tests as a supplementary tool for fighting the pandemic [in german] J. Seifried, S. Böttcher, M. von Kleist, M.A. Jenny, E. Antao, D.Y. Oh, T. Jung-Sendzik, K. Broich, C. Denkinger, T. Bartenschlager, L. Schade, O. Hamouda, M. Mielke , Epid Bull,  17, 3-14, 2021 (online)
    66. SARS-CoV-2 Varianten: Evolution im Zeitraffer D-Y. Oh, S. Kröger, M. Wedde, F. Hartkopf, M. Budt, J. Seifried, A. Radonic, E. Belarbi, M. Hölzer, S. Böttcher, G. Schubert, S. Kaiser, T. Domaszewska, A. Sachse, O. Drechsel, R. Grajcar, M. Huska, L. Zhang, A. Brinkmann, K. Yahosseini, L. Grabenhenrich, O. Hamouda, R. Dürrwald, W. Haas, S. Calvignac-Spencer, T. Semmler, L. Schaade, M. Mielke, M. von Kleist, S. Fuchs, LH. Wieler, T. Wolff, Dtsch Arztebl ,  118, A-460 / B-388, 2021 (open access)
    67. Corona-Schnelltests – die Prävalenz macht’s! [in german] C. Leuker, I. Lein, E.-M.a Antão, M. von Kleist , M. A. Jenny Ärztezeitung , 2020 (open access)
    68. SARS-CoV-2: Testergebnisse richtig einordnen [in german] I. Lein, C. Leuker, E.-M. Antão, M. von Kleist , M. A. Jenny Dtsch Arztebl , 117(47): A-2304/B-1944, 2020 (open access)
    69. Balancing the duration of quarantine and Isolation for COVID-19 [in german] M. von Kleist, B. Ruehe, DY Oh, A. Nitsche, W. Haas, A. Stoliaroff-Pépin, T. Eckmanns, M. Abu Sin, W. van der Toorn W, M. Jenny, M. Mielke, C. Herzog, LH. Wieler , Epid Bull,  39, 3-11, 2020 (online)