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Dr Steffen Docken
Research Fellow

Dr Steffen Docken

BA (Phys and Math), MSc (Applied Math), MSc (Pharmacology and Toxicology), PhD (Applied Math)

Medicine & Health
The Kirby Institute

Steffen is an Applied Mathematician broadly interested in understanding the mechanisms underlying diseases. His current research is on the growth and persistence of pathogens within a host and immune responses towards these pathogens. The primary pathogens he focuses on are HIV and Simian Immunodeficiency Virus (SIV), but Steffen has also worked on Malaria and COVID-19. In his research, Steffen works closely with experimental collaborators from the fields of virology and immunology.

Previously, Steffen's dissertation research focused on modelling the effects of anti-arrhythmic drugs on electrical signalling in the heart, which he completed at the University of California, Davis, receiving his Ph.D. in applied mathematics in 2018.
E-mail
sdocken@kirby.unsw.edu.au
Location
Kirby Institute, L6 Wallace Wurth Building UNSW Sydney
  • Journal articles | 2023
    Bauer A; Lindemuth E; Marino FE; Krause R; Joy J; Docken SS; Mallick S; McCormick K; Holt C; Georgiev I; Felber B; Keele BF; Veazey R; Davenport MP; Li H; Shaw GM; Bar KJ, 2023, 'Adaptation of a transmitted/founder simian-human immunodeficiency virus for enhanced replication in rhesus macaques', PLoS Pathogens, 19, http://dx.doi.org/10.1371/journal.ppat.1011059
    Journal articles | 2023
    Docken SS; Clancy CE; Lewis TJ, 2023, 'Rate-dependent effects of state-specific sodium channel blockers in cardiac tissue: Insights from idealized models', Journal of Theoretical Biology, 573, pp. 111595 - 111595, http://dx.doi.org/10.1016/j.jtbi.2023.111595
    Journal articles | 2023
    Khoury DS; Docken SS; Subbarao K; Kent SJ; Davenport MP; Cromer D, 2023, 'Predicting the efficacy of variant-modified COVID-19 vaccine boosters', Nature Medicine, 29, pp. 574 - 578, http://dx.doi.org/10.1038/s41591-023-02228-4
    Journal articles | 2023
    Pinkevych M; Docken SS; Okoye AA; Fennessey CM; Del Prete GQ; Pino M; Harper JL; Betts MR; Paiardini M; Keele BF; Davenport MP, 2023, 'Timing of initiation of anti-retroviral therapy predicts post-treatment control of SIV replication', PLoS Pathogens, 19, http://dx.doi.org/10.1371/journal.ppat.1011660
    Journal articles | 2023
    Statzu M; Jin W; Fray EJ; Wong AKH; Kumar MR; Ferrer E; Docken SS; Pinkevych M; McBrien JB; Fennessey CM; Keele BF; Liang S; Harper JL; Mutascio S; Franchitti L; Wang H; Cicetti D; Bosinger SE; Carnathan DG; Vanderford TH; Margolis DM; Garcia-Martinez JV; Chahroudi A; Paiardini M; Siliciano J; Davenport MP; Kulpa DA; Siliciano RS; Silvestri G, 2023, 'CD8+ lymphocytes do not impact SIV reservoir establishment under ART', Nature Microbiology, 8, pp. 299 - 308, http://dx.doi.org/10.1038/s41564-022-01311-9
    Journal articles | 2022
    2022, 'OP 2.5 – 00048 Targeting the SIV reservoir with Alemtuzumab', Journal of Virus Eradication, 8, pp. 100153 - 100153, http://dx.doi.org/10.1016/j.jve.2022.100153
    Journal articles | 2022
    2022, 'OP 8.6 – 00166 Autologous neutralizing antibody responses in bnAb-treated rhesus macaques', Journal of Virus Eradication, 8, pp. 100280 - 100280, http://dx.doi.org/10.1016/j.jve.2022.100280
    Journal articles | 2022
    2022, 'PP 2.3 – 00034 CD8+ T-Cell Sieving During SIV Reactivation from Latency', Journal of Virus Eradication, 8, pp. 100159 - 100159, http://dx.doi.org/10.1016/j.jve.2022.100159
    Journal articles | 2021
    Docken SS; Clancy CE; Lewis TJ, 2021, 'Rate-dependent effects of lidocaine on cardiac dynamics: Development and analysis of a low-dimensional drug-channel interaction model', PLoS Computational Biology, 17, http://dx.doi.org/10.1371/journal.pcbi.1009145
    Journal articles | 2021
    Eustaquio PC; Docken SS; Leyritana KT; Wulandari LPL, 2021, 'HIV care cascade among cisgender men who have sex with men in a key population-led community center in the Philippines', International Journal of STD and AIDS, 32, pp. 718 - 728, http://dx.doi.org/10.1177/0956462420987435
    Journal articles | 2020
    Corder RM; de Lima ACP; Khoury DS; Docken SS; Davenport MP; Ferreira MU, 2020, 'Quantifying and preventing plasmodium vivax recurrences in primaquine-untreated pregnant women: An observational and modeling study in Brazil', PLoS Neglected Tropical Diseases, 14, pp. 1 - 16, http://dx.doi.org/10.1371/journal.pntd.0008526
    Journal articles | 2020
    DeMarino C; Cowen M; Pleet ML; Pinto DO; Khatkar P; Erickson J; Docken SS; Russell N; Reichmuth B; Phan T; Kuang Y; Anderson DM; Emelianenko M; Kashanchi F, 2020, 'Differences in Transcriptional Dynamics Between T-cells and Macrophages as Determined by a Three-State Mathematical Model', Scientific Reports, 10, http://dx.doi.org/10.1038/s41598-020-59008-0
    Journal articles | 2019
    Ciocanel MV; Docken SS; Gasper RE; Dean C; Carlson BE; Olufsen MS, 2019, 'Cardiovascular regulation in response to multiple hemorrhages: analysis and parameter estimation', Biological Cybernetics, 113, pp. 105 - 120, http://dx.doi.org/10.1007/s00422-018-0781-y
    Journal articles | 2016
    Yang PC; Boras BW; Jeng MT; Docken SS; Lewis TJ; McCulloch AD; Harvey RD; Clancy CE, 2016, 'A Computational Modeling and Simulation Approach to Investigate Mechanisms of Subcellular cAMP Compartmentation', PLoS Computational Biology, 12, http://dx.doi.org/10.1371/journal.pcbi.1005005
    Journal articles | 2015
    Walcott S; Docken S; Harris SP, 2015, 'Effects of cardiac myosin binding protein-C on actin motility are explained with a drag-activation-competition model', Biophysical Journal, 108, pp. 10 - 13, http://dx.doi.org/10.1016/j.bpj.2014.11.1852
  • Conference Posters | 2022
    Bar K; Viox E; Krause R; Lindemuth E; Jin W; Docken S; Mallick S; Paiardini M, 2022, 'OP 8.6 – 00166 Autologous neutralizing antibody responses in bnAb-treated rhesus macaques', Vol. 8, pp. 100280 - 100280, http://dx.doi.org/10.1016/j.jve.2022.100280
    Preprints | 2022
    Bauer A; Lindemuth E; Joy J; Marino FE; Docken SS; Krause R; Mallick S; McCormick K; Holt C; Georgiev I; Felber B; Keele BF; Veazey R; Davenport MP; Li H; Shaw GM; Bar KJ, 2022, Adaptation of a transmitted/founder simian-human immunodeficiency virus for enhanced replication in rhesus macaques, , http://dx.doi.org/10.1101/2022.12.12.520031
    Conference Posters | 2022
    Docken S; McCormick K; Pampena M; Pinkevych M; Viox E; Keele B; Paiardini M; Betts M; Bar K; Davenport M; Samer S; Cromer D; Schlub T, 2022, 'PP 2.3 – 00034 CD8+ T-Cell Sieving During SIV Reactivation from Latency', Vol. 8, pp. 100159 - 100159, http://dx.doi.org/10.1016/j.jve.2022.100159
    Preprints | 2022
    Khoury D; Docken S; Subbarao K; Kent S; Davenport M; Cromer D, 2022, Predicting the efficacy of variant-modified COVID-19 vaccine boosters, , http://dx.doi.org/10.1101/2022.08.25.22279237
    Conference Papers | 2022
    Statzu M; Wong A; McBrien J; Choe Y; Enemuo C; Ngo J; Jimenez L; Wang J; Pinkevych M; Docken S; Davenport M; Keele B; Vanderford T; Paiardini M; Silvestri G; Kulpa D, 2022, 'CD8(+) T cell depletion does not affect viral reservoir size, but influences the rebound after ART interruption in SIV-infected rhesus macaques', in JOURNAL OF MEDICAL PRIMATOLOGY, WILEY, pp. 323 - 324, https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000852720100075&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=891bb5ab6ba270e68a29b250adbe88d1
    Conference Posters | 2022
    Varco-Merth B; Chaunzwa M; Duell D; Marenco A; Docken S; Smedley J; Axthelm MK; Hansen SG; Davenport MP; Estes JD; Keele B; Lifson JD; Lewin SR; Okoye AA; Picker LJ, 2022, 'OP 2.5 – 00048 Targeting the SIV reservoir with Alemtuzumab', Vol. 8, pp. 100153 - 100153, http://dx.doi.org/10.1016/j.jve.2022.100153
    Conference Abstracts | 2022
    Viox E; Samer S; Nguyen K; Docken S; Lindemuth E; Mampe F; Pinkevych M; Keele B; Betts M; Davenport M; Paiardini M; Bar K, 2022, 'Impact of CD4 binding-site bNAb therapy on viral rebound in barcoded TF-SHIV-D-infected rhesus macaques at ATI', in JOURNAL OF MEDICAL PRIMATOLOGY, WILEY, Vol. 51, pp. 301 - 302, https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000852720100028&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=891bb5ab6ba270e68a29b250adbe88d1
    Preprints | 2021
    Docken SS; Clancy CE; Lewis TJ, 2021, Rate-dependent effects of lidocaine on cardiac dynamics: Development and analysis of a low-dimensional drug-channel interaction model, , http://dx.doi.org/10.48550/arxiv.2102.02342
    Conference Abstracts | 2019
    Furutani K; Docken S; Vorobyov IV; Clancy CE; Lewis TJ; Sack JT, 2019, 'A Kinetic Mechanism Underlying hERG Facilitation by a Blocker', in Biophysical Journal, Elsevier BV, Vol. 116, pp. 245a - 245a, http://dx.doi.org/10.1016/j.bpj.2018.11.1343
    Conference Abstracts | 2018
    Docken SS; Lewis TJ; Clancy CE, 2018, 'Mechanisms Underlying Rate-Dependent Effects of State-Specific Binding of Sodium Channel Blockers in Cardiac Tissue: Insights from Idealized Models', in Biophysical Journal, Elsevier BV, Vol. 114, pp. 489a - 489a, http://dx.doi.org/10.1016/j.bpj.2017.11.2682
    Conference Abstracts | 2016
    Yang P-C; Boras B; Jeng M-T; Docken S; Lewis T; McCulloch A; Harvey R; Clancy C, 2016, 'A Computational Investigation Predicts Mechanisms of Subcellular cAMP Compartmentation', in Biophysical Journal, Elsevier BV, Vol. 110, pp. 590a - 590a, http://dx.doi.org/10.1016/j.bpj.2015.11.3151
    Conference Abstracts | 2015
    Walcott S; Docken S; Harris SP, 2015, 'Effects of Cardiac Myosin Binding Protein-C on Actin Motility are Explained with a Drag-Activation-Competition Model', in Biophysical Journal, Elsevier BV, Vol. 108, pp. 339a - 339a, http://dx.doi.org/10.1016/j.bpj.2014.11.1849

UNSW Values in Action Award Winner in the Heroes-Team category (2022)

I am broadly interested in utilising mathematical modelling to further our understanding of diseases and aid in the development of new therapies. Currently, I am focusing on the interaction between the immune system and evolution of HIV or Simian Immunodeficiency Virus (SIV) within a host, especially in the context of viral rebound following treatment interruption. I am also examining the kinetics of viral production by individual infected cells.

In my research, I use a variety of mathematical techniques, such as differential equations and dynamical systems, probabilistic modelling, singular perturbation analysis, and model selection.