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von Kleist, M. and Raharinirina, Alexia and Gubela, Nils and Börnigen, Daniela and Smith, Maureen and Oh, Djin-Ye and Budt, Matthias and Mache, Christin and Schillings, Claudia and Fuchs, Stephan and Dürrwald, Ralf and Wolff, Thorsten and Hoelzer, Martin and Sofia, Paraskevopoulou (2023) SARS-CoV-2 Evolution on a Dynamic Immune Landscape. Biological Sciences . (Submitted)

Gupta, P. and Peter, S. and Jung, M. and Lewin, A. and Hemmrich-Stanisak, G. and Franke, A. and von Kleist, M. and Schütte, Ch. and Einspanier, R. and Sharbati, S. and zur Bruegge, J. (2019) Analysis of long non-coding RNA and mRNA expression in bovine macrophages brings up novel aspects of Mycobacterium avium subspecies paratuberculosis infections. Sci. Rep., 9 (1571). ISSN 2045-2322

Duwal, S. and Dickinson, L. and Khoo, S. and von Kleist, M. (2018) Hybrid stochastic framework predicts efficacy of prophylaxis against HIV: An example with different dolutegravir regimen. PLoS Computational Biology, 14 . e1006155. ISSN 1553-7358

Zhang, W. and Hartmann, C. and von Kleist, M. (2018) Optimal control of Markov jump processes: Asymptotic analysis, algorithms, and application to modelling of chemical reaction systems. Communications in Mathematical Sciences, 16 (2). pp. 293-331. ISSN 1539-6746

Smyth, R.P. and Smith, M. R. and Jousset, A-C. and Despons, L. and Laumond, G. and Decoville, T. and Cattenoz, P. and Moog, C. and Jossinet, F. and Mougel, M. and Paillart, J.-C. and von Kleist, M. and Marquet, R. (2018) In cell mutational interference mapping experiment (in cell MIME) identifies the 5' polyadenylation signal as a dual regulator of HIV - 1 genomic RNA production and packaging. Nucleic Acids Research, 46 (9). e57.

von Kleist, M. and Schütte, Ch. and Zhang, W. (2018) Statistical Analysis of the First Passage Path Ensemble of Jump Processes. Journal of Statistical Physics, 170 (4). pp. 809-843.

Gupta, Pooja and Gramatke, A and Einspanier, R and Schütte, Ch. and von Kleist, M. and Sharbati, J (2017) In silico cytotoxicity assessment on cultured rat intestinal cells deduced from cellular impedance measurements. Toxicology in Vitro, 41 . pp. 179-188. ISSN 08872333

Meixenberger, K. and Yousef, K. P. and Smith, M. and Somogyi, S. and Fiedler, S. and Bartmeyer, B. and Hamouda, O. and Bannert, N. and von Kleist, M. and Kücherer, C. (2017) Molecular evolution of HIV-1 integrase during the 20 years prior to the first approval of integrase inhibitors. Virology Journal, 14 . pp. 223-237.

Yousef, K. P. and Meixenberger, K. and Smith, M. and Jansen, K. and Bartmeyer, B. and Hamouda, O. and Kücherer, C. and von Kleist, M. (2016) Inferring HIV-1 transmission dynamics in Germany from recently transmitted viruses. Journal of Acquired Immunodeficiency Virus, 73 (3). pp. 356-363. ISSN 1525-4135

Smith, M. and Smyth, R.P. and Marquet, R. and von Kleist, M. (2016) MIMEAnTo – Profiling functional RNA in Mutational Interference Mapping Experiments. Bioinformatics, 32 (21). pp. 3369-3370. ISSN 1367-4803

Duwal, S. and von Kleist, M. (2016) Top-down and bottom-up modelling in system pharmacology to understand clinical efficacy : An example with NRTIs of HIV-1. European Journal of Pharmaceutical Sciences, 94 . pp. 72-83. ISSN 0928-0987

Duwal, S. and Sunkara, V. and von Kleist, M. (2016) Multiscale Systems-Pharmacology Pipeline to Assess the Prophylactic Efficacy of NRTIs Against HIV-1. CPT: Pharmacometrics & Systems Pharmacology, 5 (7). pp. 377-387. ISSN 2163-8306

Smyth, R.P. and Despons, L. and Huili, G. and Bernacchi, S. and Hijnen, M. and Mak, J. and Jossinet, F. and Weixi, L. and Paillart, J.-C. and von Kleist, M. and Marquet, R. (2015) Mutational Interference Mapping Experiment (MIME) for studying the relationship between RNA structure and function. Nature Methods, 12 . pp. 866-872. ISSN 1548-7091

Duwal, S. and Winkelmann, S. and Schütte, Ch. and von Kleist, M. (2015) Optimal treatment strategies in the context of 'treatment for prevention' against HIV-1 in resource-poor settings. PLOS Computational Biology, 11 . e1004200.

Yousef, K. P. and Streck, A. and Schütte, Ch. and Siebert, H. and Hengge, R. and von Kleist, M. (2015) Logical-continuous modelling of post-translationally regulated bistability of curli fiber expression in Escherichia coli. BMC Systems Biology, 9 . p. 39. ISSN 1752-0509

Meixenberger, K. and Yousef, K. P. and Somogyi, S. and Fiedler, S. and Bartmeyer, B. and von Kleist, M. and Kücherer, C. (2014) 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 (4 Suppl 3). p. 19746.

Muehlhans, S. and von Kleist, M. and Gretchuka, T and Martin, T. and Fegeler, U. and Maurer, W. and Namazova-Baranova, L. and Gaedicke, G. and Baranov, A. and Rath , B. (2014) Awareness and Utilization of Standards and Pathways for the Reporting of Adverse Events Following Immunization among Pediatricians in Russia and Germany. Pediatric Drugs, 16 (4). pp. 31-330. ISSN 1174-5878 (Print) 1179-2019 (Online)

Katchanov, J. and von Kleist, M. and Arasteh, K. and Stocker, H. (2014) “Time-to-Amphotericin B” in Cryptococcal Meningitis in a European Low-Prevalence Setting: Analysis of Diagnostic Delays. QJM: An International Journal of Medicine, 107 (10). pp. 799-803. ISSN 1460-2393

Chen, X. and Yousef, K. P. and Duwe, S. and Karsch, K. and Grover, S. and Wählisch, S. and Obermeier, P. and Tief, F. and Muehlhans, S. and Seeber, L. and von Kleist, M. and Schweiger, B. and Rath , B. (2014) Quantitative influenza follow-up testing (QIFT) - a novel biomarker for the monitoring of disease activity at the point-of-care. PLoS ONE, 9 (3). ISSN 1932-6203

Meixenberger, K. and Hauser, A. and Jansen, K. and Yousef, K. P. and Fiedler, S. and von Kleist, M. and Norley, S. and Somogyi, S. and Hamouda, O. and Bannert, N. and Bartmeyer, B. and Kücherer, C. (2014) Assessment of ambiguous base calls in HIV-1 pol population sequences as a biomarker to identify recent infections in HIV-1 incidence studies. Journal of Clinical Microbiology, 52 (8). pp. 2977-2983. ISSN 0095-1137

Winkelmann, S. and Schütte, Ch. and von Kleist, M. (2014) Markov Control Processes with Rare State Observation: Theory and Application to Treatment Scheduling in HIV-1. Communications in Mathematical Sciences, 12 (5). pp. 859-877. ISSN 1539-6746

Rath, B. A. and Yousef, K. P. and Katzenstein, D. K. and Shafer, R. W. and Schütte, Ch. and von Kleist, M. and Merigan, T. C. (2013) In vitro HIV-1 Evolution in Response to Triple Reverse Transcriptase Inhibitors & In Silico Phenotypic Analysis. PLoS ONE, 8 (4). e61102. ISSN 1932-6203

Rath, B. and von Kleist, M. and Castillo, M. E. and Kolevic, L. and Caballero, P. and Soto-Castellares, G. and Amedee, A. M. and Robinson, J.E. and Katzenstein, D. K. and Van Dyke, R.B. and Oberhelman, R. (2013) Antiviral Resistance and Correlates of Virologic Failure in the first Cohort of HIV-Infected Children Gaining Access to Structured Antiretroviral Therapy in Lima, Peru: A Cross-Sectional Analysis. BMC Infectious Diseases, 13 (1).

Winkelmann, S. and Schütte, Ch. and von Kleist, M. (2013) Markov Control Processes with Rare State Observation: Sensitivity Analysis with Respect to Optimal Treatment Strategies against HIV-1. International Journal of Biomathematics and Biostatistics, 2 (1). ISSN 0973-7340

Rath , B. and Tief, F. and Karsch, K. and Muehlhans, S. and Obermeier, P. and Adamou, E. and Chen, X. and Seeber, L. and Peiser, Ch. and Hoppe, Ch. and von Kleist, M. and Conrad, T. O. F. and Schweiger, B. (2013) 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 (1). pp. 25-33. ISSN 2212-3989

Duwal, S. and Schütte, Ch. and von Kleist, M. (2012) Pharmacokinetics and Pharmacodynamics of the Reverse Transcriptase Inhibitor Tenofovir & Prophylactic Efficacy against HIV-1 Infection. PLoS One, 7 (7). e40382.

von Kleist, M. and Metzner, Ph. and Marquet, R. and Schütte, Ch. (2012) Polymerase Inhibition by Nucleoside Analogs: Cellular- and Kinetic Parameters of Efficacy, Susceptibility and Resistance Selection. Plos Computational Biology, 8 (1). e1002359.

Rath, B. and von Kleist, M. and Tief, F. and Karsch, K. and Tuerk, E. and Muehlhans, S. and Louis, F. and Skopnik, H. and Schweiger, B. and Duwe, S. (2012) 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 (9). pp. 899-905.

von Kleist, M. and Menz, S. and Stocker, H. and Arasteh, K. and Huisinga, W. and Schütte, Ch. (2011) HIV Quasispecies Dynamics during Pro-active Treatment Switching: Impact on Multi-Drug Resistance and Resistance Archiving in Latent Reservoirs. Plos One, 6 (3). e18204.

Frank, M. and von Kleist, M. and Kunz, A. and Harms, G. and Schütte, Ch. and Kloft, Ch. (2011) 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 (12). pp. 5529-5540.

von Kleist, M. and Menz, S. and Huisinga, W. (2010) Drug-Class Specific Impact of Antivirals on the Reproductive Capacity of HIV. Plos Computational Biology, 6 (3). e1000720.

von Kleist, M. and Huisinga, W. (2009) Pharmacokinetic–pharmacodynamic relationship of NRTIs and its connection to viral escape: An example based on zidovudine. European Journal of Pharmaceutical Sciences, 36 . pp. 532-543.

von Kleist, M. and Huisinga, W. (2007) Physiologically Based Pharmacokinetic Modelling: A Sub-Compartmentalized Model of Tissue Distribution. J. Pharmacokin. Pharmacodyn., 34 (6). pp. 789-806.

Sunkara, V. and von Kleist, M. Coupling cellular phenotype and mechanics to understand extracellular matrix formation and homeostasis in osteoarthritis. IFAC-PapersOnLine, 49 (26). pp. 38-43.

Conference or Workshop Item

von Kleist, M. and Kloft, Ch. and Huisinga, W. (2007) Combining Systems Biology with Physiologically Based Pharmacokinetics to Support the Understanding of Drug Effects. In: Proceedings of the 2nd Foundations of Systems Biology in Engineering Conference, FOSBE 2007, 09.-12.09.2007, Stuttgart, Germany.

Telgmann, R. and von Kleist, M. and Huisinga, W. (2006) Software Supported Modelling in Pharmacokinetics. In: Computational Life Sciences II.