[1] Cervantes F, Murgatroyd M, Allan D, Farwig N, Kemp R, Krüger S, Maude G, Mendelsohn J, Rösner S, Schabo D, Tate G, Wolter K, Amar A. (2023 Jan). A utilization distribution for the global population of Cape Vultures (Gyps coprotheres) to guide wind energy development. doi.org/10.1002/eap.2809

[2] Patten G, Euvrard J, Anderegg N, Boulle A, Arendse K, von der Heyden E, Ford N, Davies M. (2023 Mar). Advanced HIV disease and engagement in care among patients on antiretroviral therapy in South Africa: results from a multi-state model. doi.org/10.1097/qad.0000000000003442

[3] Patten G, Sipambo N, Technau K, Euvrard J, Ford N, Davies M. (2023 Apr). Ongoing High Prevalence of Severe Immune Suppression Among Children in South Africa. doi.org/10.1097/qai.0000000000003137

[4] Eribo O, Naidoo C, Theron G, Walzl G, du Plessis N, Chegou N. (2023 Feb). An Archetypical Model for Engrafting Bacteroides fragilis into Conventional Mice Following Reproducible Antibiotic Conditioning of the Gut Microbiota. doi.org/10.3390/microorganisms11020451

[5] Nyawo G, Naidoo C, Wu B, Sulaiman I, Clemente J, Li Y, Minnies S, Reeve B, Moodley S, Rautenbach C, Wright C, Singh S, Whitelaw A, Schubert P, Warren R, Segal L, Theron G. (2023 Mar). More than Mycobacterium tuberculosis: site-of-disease microbial communities, and their functional and clinical profiles in tuberculous lymphadenitis. doi.org/10.1136/thorax-2022-219103

[6] Shekhar V, von Klemperer C, Langdon G. (2023 Jan). The Damage and Impulse Transfer Characteristics of Flexible Steel V-Structures with Large Bend Radii. doi.org/10.3390/app13031293

[7] Jatu T, Bello-Ochende T. (2023 Mar). Entropy Generation of Two-Phase Flow Boiling in Elliptical U-Bend Tube Heat Exchanger. doi.org/10.1080/01457632.2023.2185490

[8] Kalita S, Uniyal A. (2023 May). Constraining Fundamental Parameters in Modified Gravity Using Gaia-DR2 Massive White Dwarf Observations. doi.org/10.3847/1538-4357/accf1c

[9] Bejrajh N, Jayalath S. (2023). Impact of a Titanium Tibial Implant on the Wireless Charging of a Biomedical Knee Sensor. doi.org/10.1109/WPTCE56855.2023.10216023

[10] Kalita S, Bhatporia S, Weltman A (2023 Nov). Gravitational lensing in modified gravity: a case study for Fast Radio Bursts. doi.org/10.1088/1475-7516/2023/11/059

[11] Uniyal A, Kalita S, Chakrabarti S (2023 Oct). Effect of temperature on measurement of fundamental constants using white dwarfs in Gaia-EDR3 survey. doi.org/10.1093/mnras/stad3123

[12] Meyer F, Buys J (2023 Jul). Subword Segmental Machine Translation: Unifying Segmentation and Target Sentence Generation. 10.18653/v1/2023.findings-acl.175

[13] Toledo E, Buys J, Shock J (2023 May). Policy-based Reinforcement Learning for Generalisation in Interactive Text-based Environments. 10.18653/v1/2023.eacl-main.88

[14] Katsanikas M, Hillebrand M, Skokos Ch, Wiggins S (2023 May). A new type of dynamical matching in an asymmetric Caldera potential energy surface. doi.org/10.1016/j.cplett.2022.140208

[15] Zimper S, Ngapasare A, Hillebrand M, Katsanikas M, Wiggins S, Skokos Ch (2023 Nov). A new type of dynamical matching in an asymmetric Caldera potential energy surface. doi.org/10.1016/j.physd.2023.133833

[16] Dika A (2023 June). Analytical perspectives on localized solutions of the φ4 theory. hdl.handle.net/11427/39378

[17] Ssozi E (2023 Feb). Anomaly Detection in Laboratory Tests Subject to Gatekeeping in Selected Health Facilities. hdl.handle.net/11427/39743

[18] Odidi M (2023 May). Comparison of Non-reactive Solute Transport Models for the Evaluation of Fluid Flow in Leaching Beds. hdl.handle.net/11427/38530

[19] Kootbodien T (2023 Jun). Epidemiology and Genetic Risk Factors of Suicidal Behaviours in South Africa. hdl.handle.net/11427/39682

[20] Carew L (2023). Application of CNN-gcForestCS to cassava leaf image classification. hdl.handle.net/11427/39293

[21] Steyn T (2023). Investigating cestode modulation of host neuronal excitability and cell-type-specific gene expression in an ex vivo mouse model of neurocysticercosis. hdl.handle.net/11427/39864

[1] Okendo J, Okanda D. (2022 Apr). Investigating expressed RNA variants that are related to disease severity in SARS-CoV-2-infected patients with mild-to-severe disease. doi.org/10.1186/s43042-022-00299-5

[2] Okendo J, Musanabaganwa C, Mwangi P, Nyaga M, Onywera H. (2022 Aug). SARS-CoV-2-positive patients display considerable differences in proteome diversity in urine, nasopharyngeal, gargle solution and bronchoalveolar lavage fluid samples. doi.org/10.1371/journal.pone.0271870

[3] Namalomba P. (2022). Towards a material damage model using the logarithmic strain, with von Mises plasticity considerations. dx.doi.org/10.13140/RG.2.2.28037.63205

[4] Kawuma AN, Wasmann RE, Dooley KE, Boffito M, Maartens G, Denti P. (2022 May). Population Pharmacokinetic Model and Alternative Dosing Regimens for Dolutegravir Coadministered with Rifampicin. doi.org/10.1128/aac.00215-22

[5] Gausi K, Chirehwa M, Ignatius EH, Court R, Sun X, Moran L, Hafner R, Wiesner L, Rosenkranz SL, De Jager V, De Vries N, Harding J, Gumbo T, Swindells S, Diacon AH, Dooley KE, McIlleron H, Denti P. (2022). Pharmacokinetics of standard versus high-dose isoniazid for treatment of multidrug-resistant tuberculosis. doi.org/10.1093/jac/dkac188

[6] Jatu T, Bello-Ochende T. (2022 Oct). Numerical investigation and entropy generation for flow boiling evaporation in U-bend tube heat exchanger with elliptical and circular cross-sections. doi.org/10.1016/j.tsep.2022.101480

[7] Hepworth E, MessoriG, Vichi M. (2022 Mar). Association Between Extreme Atmospheric Anomalies Over Antarctic Sea Ice, Southern Ocean Polar Cyclones and Atmospheric Rivers. doi.org/10.1029/2021JD036121

[8] Jatu T, Bello-Ochende T. (2022 Dec). Minimization of entropy generation in U-bend tube heat exchanger during flow boiling of R134a. doi.org/10.1016/j.ijthermalsci.2022.108032

[9] Richardson N, Kuttel M, Ravenscroft N. (2022 Aug). Modeling of pneumococcal serogroup 10 capsular polysaccharide molecular conformations provides insight into epitopes and observed cross-reactivity. doi.org/10.3389/fmolb.2022.961532

[10] Hao Li, Kuttel M, Ravenscroft N, Thompson A, Prasad A, Gangolli S, Tan C, Cooper D, Watson W, Liberator P, Pride M, Jansen K, Anderson A, Scully I. (2022 Jul). Streptococcus pneumoniae serotype 15B polysaccharide conjugate elicits a cross-functional immune response against serotype 15C but not 15A. doi.org/10.1016/j.vaccine.2022.06.041

[11] Kuttel M. (2022 Feb). Comparative Molecular Modelling of Capsular Polysaccharide Conformations in Streptococcus suis Serotypes 1, 2, 1/2 and 14 Identifies Common Epitopes for Antibody Binding. doi.org/10.3389/fmolb.2022.830854

[12] Lazar R, Akher F, Ravenscroft N, Kuttel M. (2022 Jan). Carbohydrate Force Fields: The Role of Small Partial Atomic Charges in Preventing Conformational Collapse. doi.org/10.1021/acs.jctc.1c00534

[13] Nurmahomed Y. (2022 Oct). Hospital readmission prediction with long clinical notes. hdl.handle.net/11427/37712

[14] Alheit B, Bargmann S, Reddy BD. (2022 Oct). How suture networks improve the protective function of natural structures: A multiscale investigation. doi.org/10.1016/j.actbio.2022.03.037

[15] Marquart R. (2022 Sep). Computational modelling of ice floe dynamics in the Antarctic marginal ice zone. hdl.handle.net/11427/38051

[16] Heekes A. (2022). Investigation of HIV-TB co-infection through analysis of the potential impact of host genetic variation on host-pathogen protein interactions. hdl.handle.net/11427/36779

[17] Furman G, Toledo E, Shock J, Buys J. (2022 Jul). A Sequence Modelling Approach to Question Answering in Text-Based Games. 10.18653/v1/2022.wordplay-1.4

[18] Acton S, Buys J. (2022 Nov). From GNNs to Sparse Transformers: Graph-based architectures for Multi-hop Question Answering. doi.org/10.1007/978-3-031-22321-1_11

[19] Meyer F, Buys J. (2022 Dec). Subword Segmental Language Modelling for Nguni Languages. 10.18653/v1/2022.findings-emnlp.494

[20] Elmadani K, Meyer F, Buys J. (2022 Dec). University of Cape Town’s WMT22 System: Multilingual Machine Translation for Southern African Languages. aclanthology.org/2022.wmt-1.101

[21] Lazar R. (2022 Jan). Comparative evaluation of two carbohydrate force fields for modelling polysaccharide conformation. hdl.handle.net/11427/37461

[22] Dames N. (2022 Jan). Short-term dynamics of nano and picoplankton in the southern Benguela upwelling system. hdl.handle.net/11427/36679

[23] Senyage B, Skokos Ch. (2022 Apr). Identifying localized and spreading chaos in nonlinear disordered lattices by the Generalized Alignment Index (GALI) method. doi.org/10.48550/arXiv.2107.14635

[24] Many Manda B, Chaunsali R, Theocharis G, Skokos Ch. (2022 Mar). Nonlinear topological edge states: From dynamic delocalization to thermalization. doi.org/10.1103/PhysRevB.105.104308

[25] Katsanikas M, Hillebrand M, Skokos Ch, Wiggins S. (2022 Mar). The Influence of Asymmetry on the Dynamics Associated with a Caldera Potential Energy Surface. dx.doi.org/10.1142/S0218127422300300

[26] Hillebrand M, Zimper S, Ngapasare A, Katsanikas M, Wiggins S, Skokos Ch. (2022 Dec). Quantifying chaos using Lagrangian descriptors. doi.org/10.1063/5.0120889

[27] Clark A. (2022 Oct). Fast and Efficient Approaches to Large-Scale Occupancy Models. hdl.handle.net/11427/37138

[28] Ndadza A. (2022 Oct). Pharmacogenomics of Warfarin: Comprehensive Evaluation of Important Warfarin Genomic Response Factors. hdl.handle.net/11427/38521

[29] Abotsi R. (2022 Apr). The effect of long-term azithromycin treatment on the respiratory microbiota of HIV-infected children with chronic lung disease. hdl.handle.net/11427/36998

[30] Nkwentsha X. (2022 Jun). Semi-Supervised Transfer Learning for medical images as an alternative to ImageNet Transfer Learning. hdl.handle.net/11427/37687

[31] Dunn J. (2022 Feb). Evaluating Automated and Hybrid Neural Disambiguation for African Historical Named Entities. hdl.handle.net/11427/36921

[32] Taylor B. (2022 Jun). Small-Scale Distributed Machine Learning in R. hdl.handle.net/11427/37331

[33] Kamuli S. (2022 Aug). The Molecular Genetics of Familial Cardiomyopathy. hdl.handle.net/11427/37985

[34] Czech D. (2022 Aug). Word Sense Disambiguation in the domain of Sentiment Analysis through Deep Learning. hdl.handle.net/11427/30071

[35] Du Toit C. (2022). Cape Town road traffic accident analysis: Utilising supervised learning techniques and discussing their effectiveness. hdl.handle.net/11427/37335

[36] Beetar C. (2022). Artificial Neural Networks as a Probe of Many-Body Localization in Novel Topologies. hdl.handle.net/11427/37059

[37] Geza E. (2022 Sep). Investigating local ancestry inference models in mixed ancestry individual genomes. hdl.handle.net/11427/37276

[1] Ignatius E, Abdelwahab M, Hendricks B, Gupte N, Narunsky K, Wiesner L, Barnes G, Dawson R, Dooley K, Denti P. (2021 Jan). Pretomanid Pharmacokinetics in the Presence of Rifamycins: Interim Results from a Randomized Trial among Patients with Tuberculosis. doi.org/10.1128/AAC.01196-20

[2] Kuttel M, Berti F, Ravenscoft N. (2021 Mar). Molecular modeling provides insights into the loading of sialic acid-containing antigens onto CRM197: the role of chain flexibility in conjugation efficiency and glycoconjugate architecture. doi.org/10.1007/s10719-021-09991-x

[3] Senyage B. (2021 Apr). Chaotic behaviour of disordered nonlinear lattices. hdl.handle.net/11427/34029

[4] Richardson N, Ravenscroft N, Arato V, Oldrini D, Micoli F, Kuttel M. (2021 Apr). Conformational and Immunogenicity Studies of the Shigella flexneri Serogroup 6 O-Antigen: The Effect of O-Acetylation. doi.org/10.3390/vaccines9050432

[5] Onywera H, Anejo-Okopi J, Mwapagha LM, Okendo J, Williamson AL. (2021 Jun). Predictive functional analysis reveals inferred features unique to cervicovaginal microbiota of African women with bacterial vaginosis and high-risk human papillomavirus infection. doi.org/10.1371/journal.pone.0253218

[6] Abdelwahab M, Court R, Everitt D, Diacon A, Dawson R, Svensson E, Maartens G, Denti P. (2021 Jun). Effect of Clofazimine Concentration on QT Prolongation in Patients Treated for Tuberculosis. doi.org/10.1128/AAC.02687-20

[7] Abdelwahab M, Wasserman S, Brust J, Dheda K, Wiesner L, Gandhi N, Warren R, Sirgel A, Meintjies G, Maartens G, Denti P . (2021 Sep). Linezolid population pharmacokinetics in South African adults with drug-resistant tuberculosis. doi.org/10.1128/AAC.01381-21

[8] Gausi K, Ignatius E, Sun X, Kim S, Moran L, Wiesner L, von Groote-Bidlingmaier F, Hafner R, Donahue K, Vanker N, Rosenkranz S, Swindells S, Diacon A, Nuermberger E, Dooley K, Denti P. (2021 Oct). A Semi-Mechanistic Model of the Bactericidal Activity of High-Dose Isoniazid Against Multi-Drug-Resistant Tuberculosis. doi.org/10.1164/rccm.202103-0534OC

[9] Francis J, Mngqibisa R, McIlleron H, Kendall M, Wu X, Dooley K, Firnhaber C, Godfrey C, Cohm S, Denti P. (2021 Jun). A Semimechanistic Pharmacokinetic Model for Depot Medroxyprogesterone Acetate and Drug–Drug Interactions With Antiretroviral and Antituberculosis Treatment. doi.org/10.1002/cpt.2324

[10] Fouefack J. (2021). Towards a framework for multi class statistical modelling of shape, intensity, and kinematics in medical images. hdl.handle.net/11427/33746

[11] Hlozek J. (2021). Molecular modeling of bacterial polysaccharide antigens to inform future vaccine development. hdl.handle.net/11427/33811

[12] Salaam-Dreyer Z. (2021). The Epidemiology and Evolution of Rifampicin Mono Resistant Tuberculosis in Khayelitsha, Cape Town, South Africa. hdl.handle.net/11427/33896

[13] Richardson N, Kuttel M, Michael F, Cairns C, Cox A, Ravenscroft N. (2021 Sep). Cross-reactivity of Haemophilus influenzae type a and b polysaccharides: molecular modeling and conjugate immunogenicity studies. doi.org/10.1007/s10719-021-10020-0

[14] Denti P, Wasmann R, van Rie A, Winckler J, Bekker A, Rabie H, Hesseling A, van der Laan L, Gonzalez-Martinez C, Zar H, Davies G, Wiesner L, Svensson E, McIlleron H. (2021 Oct). Optimizing dosing and fixed-dose combinations of rifampicin, isoniazid, and pyrazinamide in pediatric patients with tuberculosis: a prospective population pharmacokinetic study. doi.org/10.1093/cid/ciab908

[15] Dey S, Vichi M, Fearon G, Seyboth E, Findlay K, Meynecke J, de Bie J, Lee S, Samanta S, Barraqueta J, Roychoudhury A, Mackey B. (2021 Oct). Oceanographic anomalies coinciding with humpback whale super-group occurrences in the Southern Benguela. doi.org/10.1038/s41598-021-00253-2

[16] Wright M, Gambioli F, Malan A. (2021 Nov). CFD Based Non-Dimensional Characterization of Energy Dissipation Due to Verticle Slosh. doi.org/10.3390/app112110401

[17] Jatu T, Bello-Ochende T. (2021 Nov). Heat transfer and flow pattern map development of R134A in a U-bend tube for flow boiling evaporation. doi.org/10.1016/j.icheatmasstransfer.2021.105629

[18] Mielke D, Bandawe G, Zheng J, Jones J, Abrahams M, Bekker V, Ochsenbauer C, Garrett N, Karim S, Moore P, Morris L, Montefiori D, Anthony C, Ferrari G, Williamson C. (2021 Nov). ADCC-mediating non-neutralizing antibodies can exert immune pressure in early HIV-1 infection. doi.org/10.1371/journal.ppat.1010046

[19] Singini I. (2021). Diagnostics for joint models for longitudinal and survival data. hdl.handle.net/11427/36070

[20] Blake K. (2021). The Brain Age Gap in Social Anxiety Disorder. hdl.handle.net/11427/35635

[21] Rogan M. (2021). The application of spatial capture-recapture models to investigate leopard ecology and conservation in South Africa. hdl.handle.net/11427/36055

[22] Chirehwa MT, Court R, de Kock M, Wiesner L, de Vries N, Harding J, Gumbo T, Maartens G, Warren R, Denti P, McIlleron H. (Sep 2021). Effect of Isoniazid Intake on Ethionamide Pharmacokinetics and Target Attainment in Multidrug-Resistant Tuberculosis Patients. doi.org/10.1128/aac.00278-21

[23] Tikiso T. (2021). Population pharmacokinetic modelling to address the gaps in knowledge of commonly used HIV and TB drugs in children. hdl.handle.net/11427/36177

[24] van der Laan LE, Garcia-prats AJ, Schaaf HS, Winckler JL, Draper H, Norman J, Wiesner L, McIlleron H, Denti P, Hesseling AC. (2021). Pharmacokinetics and Drug-Drug Interactions of Abacavir and Lamuvudine Co-administered With Antituberculosis Drugs in HIV-Positive Children Treated for Multidrug-Resistant Tuberculosis. doi.org/10.3389/fphar.2021.722204

[25] Gausi K, Ignatius EH, Sun X, Kim S, Moran L, Wiesner L, von Groote-Bidlingmaier F, Hafner R, Donahue K, Vanker N, Rosenkranz SL, Swindells S, Diacon AH, Nuermberger EL, Dooley KE, Denti P. (2021). A Semimechanistic Model of the Bactericidal Activity of High-Dose Isoniazid against Multidrug-Resistant Tuberculosis: Results from a Randomized Clinical Trial. doi.org/10.1164/rccm.202103-0534OC

[26] Marquart R, Bogaers A, Skatulla S, Alberello A, Toffoli A, Schwarz C, Vichi M. (2021 Apr). A Computational Fluid Dynamics Model for the Small-Scale Dynamics of Wave, Ice Floe and Interstitial Grease Ice Interaction. doi.org/10.3390/fluids6050176

[27] Alheit B, Bargmann S, Reddy BD. (2021). Dynamic mechanical behaviour of suture interfaces as inspiration for architectured hierarchical interlocking composites. doi.org/10.1016/j.jmps.2021.104620

[28] Campbell M. (2021). Investigation of the Shared Genetic Influences on Bipolar Disorder, Borderline Personality Disorder and Regional Brain Structures. hdl.handle.net/11427/36881

[29] Many Manda B. (2021 Feb). Nonlinear dynamics and chaos in multidimensional disordered Hamiltonian systems. hdl.handle.net/11427/33780

[30] Mithun T, Maluckov A, Many Manda B, Skokos Ch, Bishop A, Saxena A, Khare A, Kevrekidis P. (2021 Mar). Thermalization in the one-dimensional Salerno model lattice. doi.org/10.1103/PhysRevE.103.032211

[31] Moges H, Manos T, Skokos Ch. (2021 Dec). Anomalous diffusion in single and coupled standard maps with extensive chaotic phase spaces. doi.org/10.48550/arXiv.2107.14635

[32] Fearon G. (2021 Jul). The influence of the land-sea breeze on coastal upwelling systems. hdl.handle.net/11427/35480

[33] Kadish S. (2021 Dec). Traditional Image Processing and Modern Computer Vision Techniques for the Study of Two-Phase CO2 Flow. hdl.handle.net/11427/37382

[34] Nebel C. (2021 Mar). A Mechanistic Approach to Understanding the Colour Polymorphism in Black Sparrowhawks (Accipter Melanoleucus). hdl.handle.net/11427/36022

[1] Laubscher R, Rousseau P. (2020 Jan). Numerical investigation on the impact of variable particle radiation properties on the heat transfer in high ash pulverized coal boiler through co-simulation. doi.org/10.1016/j.energy.2020.117006

[2] Onywera H, Meiring T. (2020 Jan). Comparative analyses of Ion Torrent V4 and Illumina V3-V4 16S rRNA gene metabarcoding methods for characterization of cervical microbiota: taxonomic and functional profiling. doi.org/10.1016/j.sciaf.2020.e00278

[3] Nyangahu D, Darby M, Havyarimana E, Brown B, Horsnell W, Jaspan H. (2020 Mar). Preconception helminth infection alters offspring microbiota and immune subsets in a mouse model. doi.org/10.1111/pim.12721

[4] Onywera H, Williamson A, Cozzuto L, Bonnin S, Mbulawa Z, Coetzee D, PonomarenkoJ, Meiring T. (2020 Apr). The penile microbiota of Black South African men: relationship with human papillomavirus and HIV infection. doi.org/10.1186/s12866-020-01759-x

[5] Hlozek J, Ravenscroft N, Kuttel M. (2020 Apr). Effects of Glucosylation and O-Acetylation on the Conformation of Shigella flexneri Serogroup 2 O-Antigen Vaccine Targets. doi.org/10.1021/acs.jpcb.0c01595

[6] Rocke E, Cheung S, Gebe Z, Dames N, Liu H, Moloney C. (2020 Apr 22). Marine Microbial Community Composition During the Upwelling Season in the Southern Benguela. doi.org/10.3389/fmars.2020.00255

[7] Kuttel M, Casadevall A, Oscarson S. (2020 Jun 04). Cryptococcus neoformans Capsular GXM Conformation and Epitope Presentation: A Molecular Modelling Study. doi.org/10.3390/molecules25112651

[8] Hlozek J, Owen S, Ravenscroft N, Kuttel M (2020 Jun 04). Molecular Modeling of the Shigella flexneri Serogroup 3 and 5 O-Antigens and Conformational Relationships for a Vaccine Containing Serotypes 2a and 3a. dx.doi.org/10.3390/vaccines8040643

[9] Awine T, Sital S. (2020 Nov 23). Accounting for regional transmission variability and the impact of malaria control interventions in Ghana: a population level mathematical modelling approach. doi.org/10.1186/s12936-020-03496-y

[10] Distiller G, Borchers D, Foster R, Harmsen B. (2020 Oct). Using Continuous‐Time Spatial Capture–Recapture models to make inference about animal activity patterns. doi.org/10.1002/ece3.6822

[11] Wootton L. (2020). Reassessment of species limits and diversification process in the Cape grass genus Ehrharta Thunb. hdl.handle.net/11427/32733

[12] Douglas R. (2020). Avoiding data mining bias when testing technical analysis strategies – a methodological study. hdl.handle.net/11427/32620

[13] Oladele T. (2020 Oct). A study of impact breakage of single rock specimen using discrete element method. hdl.handle.net/11427/32903

[14] Chirehwa M, Court R, de Kock M, Wiesner L, de Vries N, Harding J, Gum T. (2020 Oct). Population Pharmacokinetics of Cycloserine and Pharmacokinetic/Pharmacodynamic Target Attainment in Multidrug-Resistant Tuberculosis Patients Dosed with Terizidone. doi.org/10.1128/AAC.01381-20

[15] Francis J, Barnes K, Workman L, Kredo T, Vestergaard L, Hoglund R, Byakika-Kibwika P, Lamorde M, Walimbwa S, Chijioke-Nwauche I, Sutherland C, Concepta M, Scarsi K, Nyagonde N, Lemnge M, Khoo S, Bygbjerg I, Parikh S, Aweeka F, Tarning J, Denti P. (2020 Apr). An Individual Participant Data Population Pharmacokinetic Meta-analysis of Drug-Drug Interactions between Lumefantrine and Commonly Used Antiretroviral Treatment. doi.org/10.1128/AAC.02394-19

[16] Gausi K, Wiesner L, Norman J, Wallis C, Onyango-Makumbi C, Chipato T, Haas D, Browning R, Chakhtoura N, Montepiedra G, Aaron L, McCarthy K, Bradford S, Vhembo T, Stranix-Chibanda L, Masheto G, Violari A, Mmbaga B, Aurpibul L, Bhosale R, Nevrekhar N, Rouzier V, Kabugho E, Mutambanengwe M, Chanaiwa V, Nyati M, Mhembere T, Tongprasert F, Hesseling A, Shin K, Zimmer B, Costello D, Jean-Philippe P, Sterling T, Theron G, Weinberg A, Gupta A, Denti P. (2020 Sep). Pharmacokinetics and Drug-Drug Interactions of Isoniazid and Efavirenz in Pregnant Women Living With HIV in High TB Incidence Settings. doi.org/10.1002/cpt.2044

[17] Gambu T. (2020 Feb). The mobility of oxygen containing species (OCS*) over Pt-based catalyst surfaces: Impact on the oxygen reduction reaction (ORR) activity. hdl.handle.net/11427/32705

[18] Alheit B, Bargmann S, Reddy BD. (2020). Computationally modelling the mechanical behaviour of turtle shell sutures-A natural interlocking structure. doi.org/10.1016/j.jmbbm.2020.103973

[19] Fourie A. (2020 Feb). Computational Analysis of Escherichia coli O25 and O25b Carbohydrate Antigens using the CHARMM36 and GLYCAM06 Force Fields. hdl.handle.net/11427/32264

[20] Senyage B, du Plessis JJ, Many Manda B, Skokos H (2020 Oct). Effect of temperature on measurement of fundamental constants using white dwarfs in Gaia-EDR3 survey. doi.org/10.33581/1561-4085-2020-23-2-165-171

[21] Goosen K. (2020). Calibrating High Frequency Trading Data to Agent Based Models using Approximate Bayesian Computation. hdl.handle.net/11427/33699

[22] Hillebrand M. (2020). Chaotic Dynamics of Polyatomic Systems with an Emphasis on DNA Models. hdl.handle.net/11427/33834

[23] Moges H. (2020 Mar). Investigating Chaos by the Generalized Alignment Index (GALI) Method. hdl.handle.net/11427/32284

[24] Many Manda B, Senyage B, Harris Ch. (2020 Mar). Chaotic wave-packet spreading in two-dimensional disordered nonlinear lattices. doi.org/10.1103/PhysRevE.101.032206

[25] Hillebrand M, Many Manda B, Senyage B, Kalosakas G, Gerlach E, Harris Ch. (2020 Jun). Chaotic dynamics of graphene and graphene nanoribbons. doi.org/10.1063/5.0007761

[26] Moges H, Manos T, Harris Ch. (2020 Jan). On the Behavior of the Generalized Alignment Index (GALI) Method for Regular Motion in Multidimensional Hamiltonian Systems. doi.org/10.48550/arXiv.2001.00803

[27] Senyage B, du Plessis J, Harris Ch. (2020 Jan). Properties of Normal Modes in a Modified Disordered Klein–Gordon Lattice: From Disorder to Order. doi.org/10.48550/arXiv.2001.01465

[28] Hillebrand M, Kalosakas G, Skokos Ch, Bishop A. (2020 Dec). Distributions of bubble lifetimes and bubble lengths in DNA. doi.org/10.1103/PhysRevE.102.062114

[29] Bountis A, Kaloudis K, Oikonomou T, Many Manda B, Skokos Ch. (2020 Apr). Stability Properties of 1-Dimensional Hamiltonian Lattices with Nonanalytic Potentials. dx.doi.org/10.1142/S0218127420300475

[30] Hague M. (2020 Oct). Ice – Ocean – Atmosphere Interactions in the Southern Ocean and Implications for Phytoplankton Phenology. hdl.handle.net/11427/33708

[31] Griffiths E. (2020 Jul). Micromechanical modelling of advanced hierarchical composites. hdl.handle.net/11427/32222

[32] Claassen-Weitz S, Gardner-Lubbe S, Mwaikono K, du Toit E, Zar H, Nicol M. (2020). Optimizing 16S rRNA gene profile analysis from low biomass nasopharyngeal and induced sputum specimens. doi.org/10.1186/s12866-020-01795-7

[33] Atuhaire F. (2020 Aug). Reconstruction of three-dimensional facial geometric features related to fetal alcohol syndrome using adult surrogates. hdl.handle.net/11427/32579

[34] Spracklen T. (2020 Dec). Whole-exome sequencing of cases with familial cardiomyopathy. hdl.handle.net/11427/33999

[1] Govender S, Gambu T, van Heerden T, Steen E (2019 Feb). Mechanistic pathways for oxygen removal on Pt-doped Co(111) in the Fischer-Tropsch reaction. doi.org/10.1016/j.cattod.2019.02.001

[2] Kuttel M, Ravenscroft N. (2019 Feb). Conformation and Cross-Protection in Group B Streptococcus Serotype III and Streptococcus pneumoniae Serotype 14: A Molecular Modeling Study. doi.org/10.3390/ph12010028

[3] Onywera H., Williamson A.L., Mbulawa Z.Z.A., Coetzee D., Meiring T.L. (2019 Jun). The cervical microbiota in reproductive-age South African women with and without human papillomavirus infection. doi.org/10.1016/j.pvr.2019.04.006

[4] Hitria K, Kuttel M, De Benedetto G, Lockyer K, Gao F, Hansal P, Rudd T, Beamish E, Rijpkema S, Ravenscroft N, Bolgiano B. (2019 Jul). O-acetylation of typhoid capsular polysaccharide confers polysaccharide rigidity and immunodominance by masking additional epitopes. doi.org/10.1016/j.vaccine.2019.05.050

[5] Nnene O, Joubert J, Zuidgeest M. (2019 Apr). An agent-based evaluation of transit network design. doi.org/10.1016/j.procs.2019.04.102

[6] Nnene O, Joubert J, Zuidgeest M. (2019 Apr). Transit network design with meta-heuristic algorithms and agent based simulation. doi.org/10.1016/j.ifacol.2019.06.003

[7] Onywera H, Williamson A, Mbulawa ZZA, Coetzee D, Meiring TL. (2019 Aug). Factors associated with the composition and diversity of the cervical microbiota of reproductive-age Black South African women: a retrospective cross-sectional study. doi.org/10.7717/peerj.7488

[8] Willis JR, Gonzalez-Torres P, Pittis AA, Bejarano LA, Cozzuto L, Andreu-Somavilla N, Alloza-Trabado M, Valentin A, Ksiezopolska E, Company C, Onywera H, Montfort M, Hermoso A, Iraola-Guzman S, Saus E, Labeeuw A, Carolis C, Hecht J, Ponomarenko J, Gabaldon T. (2018 Dec). Citizen science charts two major “stomatotypes” in the oral microbiome of adolescents and reveals links with habits and drinking water composition. doi.org/10.1186/s40168-018-0592-3

[9] du Plessis J. (2019 Sep). Chaotic Diffusion in Disordered Nonlinear Lattices. Hons thesis

[10] Omatuku E, Skatulla S. (2019). Phase field modeling of dynamic brittle fracture at finite strains. hdl.handle.net/11427/30172  – Acknowledgement incorrectly attributed.

[11] Laubscher R, Rousseau P. (2019 Jul). CFD study of pulverized coal-fired boiler evaporator and radiant superheaters at varying loads. doi.org/10.1016/j.applthermaleng.2019.114057

[12] Laubscher R, Rousseau P. (2019 Sep). Numerical investigation into the effect of burner swirl direction on furnace and superheater heat absorption for a 620 MWe opposing wall-fired pulverized coal boiler. doi.org/10.1016/j.ijheatmasstransfer.2019.03.150

[13] Hlozek J, Ravenscroft N, Kuttel M. (2019 Dec). Modeling the conformations of Neisseria meningitidis serogroup A CPS and a carba-analogue: implications for vaccine development. doi.org/10.1016/j.carres.2019.107838

[14] Geza E, Mulder N, Chimusa E, Mazandu G. (2019 Nov). FRANC: a unified framework for multi-way local ancestry deconvolution with high density SNP data. doi.org/10.1093/bib/bbz117

[15] Oje S. (2019 Nov). Breast Cancer Prediction using Machine Learning Algorithms – A Deep Learning Approach. PDF

[16] de Moor CL. (2019 Jul). Is OMP-18 robust to alternative assumptions about anchovy dynamics?. hdl.handle.net/11427/30819

[17] Parker T. (2019 Oct). An integrative taxonomic approach using genome-wide SNP data resolves variation in the Dimorphotheca pluvialis-sinuata species complex (Calenduleae: Asteraceae) in South Africa. Hons thesis

[18] Elsheikh S, Chimusa E, Mulder N, Crimi A. (2019 Dec). Genome-Wide Association Study of Brain Connectivity Changes for Alzheimer’s Disease. doi.org/10.1101/342436

[19] Elsheikh S, Bakas S, Mulder N, Chimusa E. (2019 Jan). Multi-stage Association Analysis of Glioblastoma Gene Expressions with Texture and Spatial Patterns. doi.org/10.1007/978-3-030-11723-8_24

[20] Lilla A. (2019 Oct). AI-based Hybrid Optimisation of Multi-Megawatt Scale Permanent Magnet Synchronous Generators for Offshore Wind Energy Capture. hdl.handle.net/11427/31667

[21] Yelibi L. (2019 Jun 20). Introduction to fast Super-Paramagnetic Clustering. hdl.handle.net/11427/31332

[22] Bleki Z. (2019 Feb). Efficient Bayesian Analysis of Spatial Occupancy Models. hdl.handle.net/11427/32469

[23] Francis J, Zvada S, Denti P, Hatherill M, Charalambous S, Mungofa S, Dawson R, Dorman S, Gupte N, Wiesner L, Jindani A, Harrison T, Olagunju A, Egan D, Owen A, McIlleron H. (2019 Mar). A Population Pharmacokinetic Analysis Shows that Arylacetamide Deacetylase (AADAC) Gene Polymorphism and HIV Infection Affect the Exposure of Rifapentine. doi.org/10.1128/AAC.01964-18

[24] Viljoen C. (2019). Machine learning for particle identification; deep generative models towards fast simulations for the Alice Transition Radiation Detector at CERN. hdl.handle.net/11427/31781

[25] Mielke D, Bandawe1 G, Pollara J, Abrahams M, Nyanhete T, Moore P, Thebus R, Yates N, Kappes J, Ochsenbauer C, Garrett N, Karim S, Tomaras G, Montefiori D, Morris L, Ferrari G, Williamson C. (2019 Dec). Antibody-Dependent Cellular Cytotoxicity (ADCC)-Mediating Antibodies Constrain Neutralizing Antibody Escape Pathway. doi.org/10.3389/fimmu.2019.02875

[26] Koziol T. (2019 Jun). Heterogeneous agent models to determine spillover effects in the context of Quantitative Easing. open.uct.ac.za/handle/11427/31762

[27] Danieli C, Many Manda B, Mithun T, Skokos Ch. (2019 May). Computational efficiency of numerical integration methods for the tangent dynamics of many-body Hamiltonian systems in one and two spatial dimensions. doi.org/10.3934/mine.2019.3.447

[28] Knutsen C. (2019 Dec). Thermal analysis of the internal climatic condition of a house using a computational model. hdl.handle.net/11427/32740

[29] Shaik Z. (2019 Feb). Species delimitation and speciation process in the Seriphium plumosum L. complex (Gnaphalieae: Asteraceae) in South Africa. hdl.handle.net/11427/31236

[30] Koopowitz S. (2019 Feb). Neuroimaging and Neurocognitive Assessment of PTSD and MDD in a South African Community Setting. hdl.handle.net/11427/30409

[31] de Klerk D. (2019 Oct). Investigating Multi-Directional Inhomogeneous Granular Suspensions. hdl.handle.net/11427/31229

[32] van der Merwe D. (2019 Jul). Investigating the effects of environmental variables on martial eagle breeding performance in the Kruger National Park. hdl.handle.net/11427/31813

[1] Illig S, Cadier E, Bachèlery M, Kersalé M. (2018). Subseasonal Coastal Trapped Wave Propagations in the Southeastern Pacific and Atlantic Oceans: 1. A New Approach to Estimate Wave Amplitude doi.org/10.1029/2017JC013539

[2] Illig S, Cadier E, Bachèlery M. (2018). Subseasonal Coastal Trapped Wave Propagations in the Southeastern Pacific and Atlantic Oceans: 2. Wave Characteristics and Connection With Equatorial Variability doi.org/10.1029/2017JC013540

[3] Hlozek J, Kuttel M, Ravenscroft N. (2018). Conformations of Neisseria meningitidis serogroup A and X polysaccharides: The effects of chain length and O-acetylation doi.org/10.1016/j.carres.2018.06.007

[4] Oladele T, Lawrence B, Weatehrley D. (2018). DEM simulations of crack propagation during single particle impact

[5] Nickless A, Rayner P, Engelbrecht F, Brunke E, Erni B, Scholes R . (2018). Estimates of CO2 fluxes over the city of Cape Town, South Africa, through Bayesian inverse modelling. doi.org/10.5194/acp-18-4765-2018

[6] van der Laan L, Garcia-Prats A, Schaaf H, Tikiso T, Wiesner L, de Kock M, Winckler J, Norman J, McIlleron H, Denti P, Hesseling A. Pharmacokinetics and Drug-Drug Interactions of Lopinavir-Ritonavir Administered with First- and Second-Line Antituberculosis Drugs in HIV-Infected Children Treated for Multidrug-Resistant Tuberculosis. doi.org/10.1128/AAC.00420-17

[7] Nyangahu D, Lennard K, Brown B, Darby M, Wendoh J, Havyarimana E, Smith P, Butcher J, Stintzi A, Mulder N, Horsnell W, Jaspan H. Disruption of maternal gut microbiota during gestation alters offspring microbiota and immunity. doi.org/10.1186/s40168-018-0511-7

[8] Hawthorne R, Grzybowski L. Benefits from competition in a high-inequality economy: The case of mobile telephony in South Africa. ACER conference papers

[9] Flaviani F, Declan D, Lebret K, Balestreri C, Highfield A, Schroeder J, Thorpe S, Moore K, Pasckiewicz K, Pfaff M, Rybicki E. Distinct Oceanic Microbiomes From Viruses to Protists Located Near the Antarctic Circumpolar Current. doi.org/10.1186/s40168-018-0511-7

[10] Ghoor I. The response of concave singly curved fibre reinforced moulded sandwich and laminated composite panels to blast loading. hdl.handle.net/11427/27811

[11] Kuttel M, Ravenscroft N. The Role of Molecular Modeling in Predicting Carbohydrate Antigen Conformation and Understanding Vaccine Immunogenicity in Carbohydrate-Based Vaccines: From Concept to Clinic. Chapter 7, 139-173 ACS Symposium Series, Vol. 1290. (2018). doi:10.1021/bk-2018-1290.ch007

[12] Baichoo S, Souilmi Y, Panji S, Botha G, Meintjes A, Hazelhurst S, Bendou H, de Beste E, Mpangase P, Souiai O, Alghali M, Yi L, O’Connor B, Crusoe M, Armstrong D, Aron S, Joubert F, Ahmed A, Mbiyavanga M, Heusden P, Magosi L, Zermeno J, Mainzer L, Fadlelmola F, Jongeneel C and Mulder N. Developing reproducible bioinformatics analysis workflows for heterogeneous computing environments to support African genomics (2018 Oct). doi:10.1186/s12859-018-2446-1

[13] Ragoo Y, Mahmood T. Determining the Surface Energies of MAX Phase Surfaces Using DFT. 

[14] Gabin M, Gandhi S. The promotional effect of water on O2-dissociation over Pt (111). 

[15] Moodley M, Mutataguta T. Segregation behaviour in Binary and Ternary alloy systems. 

[16] Okendo J. Analysis of within-host evolution of Plasmodium Falciparum during treatment (2018). hdl.handle.net/11427/29305

[17] Alexeeva N, Barashenkov I, Saxena A. Spinor solitons and their PT-symmetric offspring (Nov 2018). doi.org/10.1016/j.aop.2018.11.010

[18] Innes S, van der Laan L, Anderson PL, Cotton M, Denti P. Can We Improve Stavudine’s Safety Profile in Children? Pharmacokinetics of Intracellular Stavudine Triphosphate with Reduced Dosing. (Nov 2018). doi.org/10.1128/AAC.00761-18

[19] Balle C, Lennard K, Dabee S, Barnabas S, Jaumdally S, Gasper M, Maseko V,Mbulawa Z, Williamson A, Bekker L, Lewis D, Passmore J, Jaspan H. Endocervical and vaginal microbiota in South African adolescents with asymptomatic Chlamydia trachomatis infection (Jul 2018). doi.org/10.1038/s41598-018-29320-x

[20] Balle C. Effects of hormonal contraceptives on the female genital tract microbiota in South African adolescents. (2018). hdl.handle.net/11427/36414

[21] Nyoni B. Thermo-chemo-mechanical modelling of hydropower structures affected by alkali silica reaction. (2018). hdl.handle.net/11427/29367

[22] Fouefack J. Geometric morphometrics for 3D dense surface correspondence: population comparisons of shoulder bone morphology. (2018). hdl.handle.net/11427/30024

[23] Manyisa N. Whole exome sequencing to investigate genetic variants of non-syndromic hearing impairment in a population of African ancestry. (2018). hdl.handle.net/11427/29272

[24] Chirehwa M. Population/ Nonlinear mixed-effects modelling of pharmacokinetics and pharmacodynamics of tuberculosis treatment. (2018). hdl.handle.net/11427/28429

[25] Blumenthal M, Schutz C, Meintjes G, Mohamed Z, Mendelson M, Ambler J, Whitby D, Mackelprang R, Carse S, Katz A, Schäfer G. (2018 Oct). EPHA2 sequence variants are associated with susceptibility to Kaposi’s sarcoma-associated herpesvirus infection and Kaposi’s sarcoma prevalence in HIV-infected patients. doi.org/10.1016/j.canep.2018.08.005

[26] Elsheikh S, Chimusa E, Mulder N, Crimi A. (2018 Apr). Relating connectivity changes in brain networks to genetic information in Alzheimer patients. doi.org/10.1109/ISBI.2018.8363831

[27] de Kock M, Tarning J, Workman L, Allen EN, Tekete MM, Djimde AA, Bell DJ, Ward SA, Barnes KI, Denti P (2018). Population Pharmacokinetic Properties of Sulfadoxine and Pyrimethamine: a Pooled Analysis To Inform Optimal Dosing in African Children with Uncomplicated Malaria. doi.org/10.1128/aac.01370-17

[28] Nickless A. (2018 Feb). Regional CO2 Flux Estimates for South Africa through Inverse Modelling. hdl.handle.net/11427/29703

[29] Senyage B, Many Manda B, Skokos Ch. (2018 Nov). Characteristics of chaos evolution in one-dimensional disordered nonlinear lattices. doi.org/10.1103/PhysRevE.98.052229

[30] Vrancken C. (2018 Aug). An application of climate change ensemble averaging methods to fisheries management. hdl.handle.net/11427/29404

[31] Dilmahamod F. (2018 Aug). The biophysical processes controlling the South-East Madagascar Bloom. hdl.handle.net/11427/29265

[32] Shakuntala B, Mpangase P, Botha G, Meintjies A, Mulder N, et al. (2018). Developing reproducible bioinformatics analysis workflows for heterogeneous computing environments to support African genomics. doi.org/10.1186/s12859-018-2446-1

[33] Engelbrecht H. (2018). Elucidating the Genetic Aetiology of Bipolar Disorder. hdl.handle.net/11427/36751

[34] Bussiere E. (2018 Nov). Camera Traps as Sensor Networks for Space-Time Exploration of Terrestrial Mammal Communities. hdl.handle.net/11427/30184

[1] Ahnert, T., & Georg, C. P. (2017). Information contagion and systemic risk. Journal of Financial Stability. doi.org/10.1016/j.jfs.2017.05.009

[2] Alexeeva, N. V., Barashenkov, I. V., & Kivshar, Y. S. (2017). Solitons in-symmetric ladders of optical waveguides. New Journal of Physics, 19(11), 113032. doi: 10.1088/1367-2630/aa8fdd

[3] Davids, S. A., Langdon, G. S., & Nurick, G. N. (2017). The influence of charge geometry on the response of partially confined right circular stainless steel cylinders subjected to blast loading. International Journal of Impact Engineering. doi.org/10.1016/j.ijimpeng.2017.02.015

[4] de Moor, C. L., Butterworth, D. S., & van der Lingen, C. (2017). The Quantitative Use of Parasite Data in Multi-Stock Modelling of South African Sardine (Sardinops sagax). Canadian Journal of Fisheries and Aquatic Sciences, 74(11): 1895-1903, doi.org/10.1139/cjfas-2016-0280

[5] Dheda, K., Limberis, J. D., Pietersen, E., Phelan, J., Esmail, A., Lesosky, M., … & Dolby, T. (2017). Outcomes, infectiousness, and transmission dynamics of patients with extensively drug-resistant tuberculosis and home-discharged patients with programmatically incurable tuberculosis: a prospective cohort study. The Lancet Respiratory Medicine, 5(4), 269-281. doi:10.1016/S2213-2600(16)30433-7

[6] Flaviani, F., Schroeder, D. C., Balestreri, C., Schroeder, J. L., Moore, K., Paszkiewicz, K., … & Rybicki, E. P. (2017). A Pelagic Microbiome (Viruses to Protists) from a Small Cup of Seawater. Viruses, 9(3), 47. doi:10.3390/v9030047

[7] Kuttel, M. M., Cescutti, P., Distefano, M., & Rizzo, R. (2017). Fluorescence and NMR spectroscopy together with molecular simulations reveal amphiphilic characteristics of a Burkholderia biofilm exopolysaccharide. Journal of Biological Chemistry, jbc-M117. doi.org/10.1074/jbc.M117.785048

[8] Kuttel, M., Timol, Z., Ravenscroft, N. (2017). Cross-protection in Neisseria meningitidis serogroups Y and W polysaccharides: A comparative conformational analysis, In Carbohydrate Research, 446-447. doi.org/10.1016/j.carres.2017.05.004

[9] Lennard, K., Dabee, S., Barnabas, S. L., Havyarimana, E., Blakney, A., Jaumdally, S. Z., … & Gray, G. (2018). Microbial Composition Predicts Genital Tract Inflammation and Persistent Bacterial Vaginosis in South African Adolescent Females. Infection and immunity, 86(1), e00410-17. doi: 10.1128/IAI.00410-17

[10] Malahe, M. (2017). A High-Performance Crystal Plasticity Solver for CPU-GPU Architectures. Conference paper. XIV International Conference on Computational Plasticity.

[11] Ngandu, N. K., Carlson, J. M., Chopera, D. R., Ndabambi, N., Abdool Karim, Q., Abdool Karim, S., & Williamson, C. (2017). Brief Report: Selection of HIV-1 Variants With Higher Transmission Potential by 1% Tenofovir Gel Microbicide. Journal of Acquired Immune Deficiency Syndromes (1999), 76(1), 43–47. doi.org/10.1097/QAI.0000000000001458

[12] Ramanathan V. (2017). Measuring cross-section data for prompt gammas emitted during proton-nucleus collisions. PHD thesis.

[13] Ravenscroft, N., Omar, A., Hlozek, J., Edmonds-Smith, C., Follador, R., Serventi, F., … & Faridmoayer, A. (2017). Genetic and structural elucidation of capsular polysaccharides from Streptococcus pneumoniae serotype 23A and 23B, and comparison to serotype 23F. Carbohydrate research, 450, 19-29. doi.org/10.1016/j.carres.2017.08.006

[14] Sewpersad, T. (2017). Efficient Large-Scale Vegetation Simulation. Research Paper.

[15] Smuts, E. M., Deglon, D. A., & Meyer, C. J. (2017). A coupled CFD-DEM model for simulating the rheology of particulate suspensions. Progress in Computational Fluid Dynamics, an International Journal, 17(5), 290-301. doi.org/10.1504/PCFD.2017.086340

[16] Blumenthal, M. The impact of EPHA2 polymorphism on KSHV infectivity and KS prevalence among HIV/AIDS patients in South Africa.MSC Thesis

[17] Timol, Z. (2017). Chemical and conformational studies of bacterial cell surface polysaccharide repeating units (Doctoral dissertation, University of Cape Town). hdl.handle.net/11427/25484

[18] van Rooyen, J. (2017). Computational fluid dynamic based optimization of an industrial axial fan for rapid prototyping. PhD thesis

[19] Gambu T, Petersen M, Steen E. (2017). Probing the edge effect on the ORR activity using platinum nanorods: A DFT study. doi.org/10.1016/j.cattod.2017.12.026

[20] Shorten D. (2017). Spectral analysis of neutral evolution. hdl.handle.net/11427/27420

[21] Mugo J, Geza E, Joel Defo, Elsheikh S, Mazandu G, Mulder N, Chimusa E. (2017). A multi-scenario genome-wide medical population genetics simulation framework. doi.org/10.1093/bioinformatics/btx369

[22] Amato M, Carreno J. (Nov 2017). DFT Study of Diatomic Oxygen Adsorption on Pt(100) and Pt(111). Hons project

[23] Lennard K, Dabee S , Barnabas S, Havyarimana E, Jaumdally S, Botha G, Mkhize N, Bekker L, Gray G, Mulder N, PassmoreJ, Jaspan H. (2017). High rates of bacterial vaginosis and Chlamydia in a low-income, high-population-density community in Cape Town. dx.doi.org/10.4102/satnt.v36i1.1484

[24] Nyangahu D. (2017). Alterations in preconception, antenatal, and postnatal maternal gut microbiota influence offspring intestinal microbiota and immunity. hdl.handle.net/11427/25479

[25] Changfoot D. (2017 Aug). Towards a hybrid CFD platform for investigating aircraft trailing vortices. hdl.handle.net/11427/26905

[26] Currie J. (2017 May). Historical baselines and a century of change in the demersal fish assemblages on South Africa’s Agulhas Bank. hdl.handle.net/11427/27385

[27] Chavula J. (2017 Oct). Improving Pan-African Research and Education Networks Through Traffic Engineering: A LISP/SDN Approach. hdl.handle.net/11427/27021

[1] Bernardo, P *., Muhire, B., François, S., Deshoux, M., Hartnady, P., Farkas, K., Kraberger, S., Filloux, D., Fernandez, E. and Galzi, S. Molecular characterization and prevalence of two capulaviruses: Alfalfa leaf curl virus from France and Euphorbia caput-medusae latent virus from South Africa. Virology, 493 (2016), 142-153. doi: 10.1016/j.virol.2016.03.016

[2] Davids, S. The Influence of charge geometry on the structural response of right circular cylinders to internal air blasting. Masters’ thesis, University of Cape Town, 2016. http://hdl.handle.net/11427/20400

[3] Kuttel, M. M., Ståhle, J. and Widmalm, G. CarbBuilder: Software for building molecular models of complex oligo‐and polysaccharide structures. Journal of Computational Chemistry, 37, 22 (2016), 2098-2105. doi:10.1002/jcc.24428

[4] Potgieter, M. G., Nakedi, K. C., Ambler, J. M., Nel, A. J., Garnett, S., Soares, N. C., Mulder, N. and Blackburn, J. M. Proteogenomic analysis of Mycobacterium smegmatis using high resolution mass spectrometry. Frontiers in microbiology, 7 (2016). doi:10.3389/fmicb.2016.00427

[5] Ross-Gillespie, A., Butterworth, D. Modelling cannibalism and inter-species predation for the Cape hake species Merluccius capensis and M. paradoxus. Research paper, University of Cape Town, 2016. http://hdl.handle.net/11427/18916

[6] Ross-Gillespie, A. Modelling cannibalism and inter-species predation for the Cape hake species Merluccius capensis and M. paradoxus. Research paper, University of Cape Town, 2016. http://hdl.handle.net/11427/18916

[7] Schomaker, M., Davies, M.-A., Malateste, K., Renner, L., Sawry, S., N’Gbeche, S., Technau, K.-G., Eboua, F., Tanser, F. and Sygnaté-Sy, H. Growth and mortality outcomes for different antiretroviral therapy initiation criteria in children ages 1–5 Years: a causal modeling analysis. Epidemiology, 27, 2 (2016), 237-246. doi: 10.1097/EDE.0000000000000412

[8] Schomaker, M., Leroy, V., Wolfs, T., Technau, K.-G., Renner, L., Judd, A., Sawry, S., Amorissani-Folquet, M., Noguera-Julian, A. and Tanser, F. Optimal timing of antiretroviral treatment initiation in HIV-positive children and adolescents: a multiregional analysis from Southern Africa, West Africa and Europe. International Journal of Epidemiology (2016), doi: 10.1093/ije/dyw097

[9] van Rooyen, J., Malan, A., Raad, E. High performance industrial fan optimization. Conference paper. European Congress on Computational Methods in Applied Sciences and Engineering (ECCOMAS 2016). Institute of Structural Analysis and Antiseismic Research, School of Civil Engineering, National Technical University of Athens (NTUA), Athens, 2016. https://www.eccomas2016.org/proceedings/pdf/6442.pdf

[10] Viljoen, J.-A. Ecological influences in the biogeography of the Austral sedges. Masters’ thesis, University of Cape Town, 2016. http://hdl.handle.net/11427/20302

[11] Williams, T. C. The impact of increased grid resolution on the mixed layer depth variability in the South Atlantic Ocean and Southern Ocean. Masters’ thesis, University of Cape Town, 2016. http://hdl.handle.net/11427/20814

[12] van Heerden, T. Metal support interactions on cobalt based FT catalysts – a DFT study of model inverse catalysts, 2016. DOI: 10.1039/C6FD00201C

[13] Vasic, L., Mudley T, Direct CO dissociation on B5 and B6 sites of fcc cobalt Fischer-Tropsch catalyst nanocrystals, 2016. Report

[14] Matsutsu, M, Pt₃₈ cluster on OH- and COOH-functionalised graphene as a model for Pt/C-catalysts, 2016. DOI: 10.1039/C6CP04111F

[15] Deeplal, R, Stochastic Differentials Mixed Effect Models, 2016. PDF

[16] Venter, G, Catalytic enantioselective acyl transfer: the case for 4-PPY with a C-3 carboxamide peptide auxiliary based on synthesis and modelling studies, 2016. DOI: 10.1039/C6OB01991A

[17] Moodley K, A Proper Orthogonal Decomposition-based Inverse Material Parameter Optimization Method with Applications to Cardiac Mechanics, 2016. hdl.handle.net/11427/22777

[18] Profe W, Adolescent’s Responses to the Distress of Others: The Influence of Multiple Attachment Figures Via Empathic Concern, 2016. hdl.handle.net/11427/22999

[1] Ross-Gillespie, A. and Butterworth, D.S. (2015) Implementing the 2014 three-stock model for Southern Hemisphere Breeding Stocks E1, Oceania and G. International Whaling Commission document: SC/66a/SH/05: 17pp

[2] Ross-Gillespie, A. and Butterworth, D.S. (2015) Modelling cannibalism and inter-species predation for Cape hake Merluccius capensis and M. paradoxus: Model specifications and preliminary results. International Stock Assessment Review Workshop document. open.uct.ac.za/handle/11427/21481

[3] Evan Smuts. A Methodology for Coupled CFD-DEM Modelling of Particulate Suspension Rheology *

[4] Andrew van Rooyen. Determining the optimal protocols for transfer of large data files. Dec 2015.

[5] Emmanuel Omatuku Ngongo. Modelling of Residual Stresses of Blood Vessels. 23 Nov 2015.

[6] Simeon Solomons. Proper Orthogonal Decomposition – Based Material Parameter Identification. Nov 2015. *

[7] Dezire Mikael Ettienne. Computational Inverse Analysis of Prestressed Concrete Structures. Nov 2015. *

[8] Jamie Hewland, Geoff Nitschke. The Benefits of Adaptive Behavior and Morphology for Cooperation in Robot Teams. Nov 2015.

[9] Jae Jang. An empirical evaluation of evolutionary controller design methods for collective gathering task. Nov 2015.

[10] Vinay Ramaswami Shekhar. The effect of bend radius on the impulse transfer characteristics of V-hulls. 2015 Nov.

[11] Chimusa ER, Mbiyavanga M, Mazandu GK, Mulder NJ.  ancGWAS: a post genome-wide association study method for interaction, pathway and ancestry analysis in homogeneous and admixed populations. 27 Oct 2015.

[12] Robert Spencer. Tensor Networks and Emergent Geometry. 2015 Oct 17.

[13] Renata Briarjaj. Simulating Blast Disruptions. 6 Oct 2015.

[14] Jarred de Beer. Accelerating automated extraction of radio astronomical sources from observations with GPU accelerators. Oct 2015.

[15] Gorden Thobani Gambu. A DFT study of the interaction of Ox with Pt nanorod edge sites: A model for the ORR activity on Pt nanoparticle edges. Oct 2015.

[16] Hassan Sadiq. A Topic Model-Based Approach to Inferring Episodic Directional Selection in Protein Coding Sequences. July 2015. http://hdl.handle.net/11427/20013

[17] Alexander Antrobus. Achieving baseline states in sparsely connected spiking-neural networks. July 2015

[18] Lubbe, S., Dube, F., Nicol, M. and Zar, H. Functional Data Analysis for the Investigation of Longitudinal Response Patterns in Health Care. Presentation presented at the International Federation of Classification Societies Conference, Bologna, Italy. July 2015

[19] S.J. Perkins, P.C. Marais, J.T.L. Zwart, I. Natarajan, C. Tasse, O. Smirnov. GPU accelerated radio interferometer measurement equations in support of Bayesian inference for radio observations. 19 June 2015.

[20] J. Gain, B. Merry, P. Marais. Parallel, Realistic and Controllable Terrain Synthesis. May 2015.

[21] Bevan W.S. Jones. Mesh Adaptation through r-refinement using a Truss Network Analogy. 4 May 2015

[22] Nathan Geffen. Optimising partner matching for microsimulations of the HIV epidemic. 24 March 2015.

[23] CL de Moor, DS Butterworth. Assessing the South African Sardine Resource. 16 March 2015.

[24] Shareefa Dalvie. Genetic Analysis of Bipolar Disorder and Alcohol Use Disorder. March 2015.

[25] Mayuresh Kulkarni. Simulation of x-rays using slot scanning technique. 2015.

[26] Bevan W.S. Jones, Arnaud G. Malan, Jacobus A. van Rooyen. A Ball-Vertex Approach to r-Refinement for Accuracy Enhancements in CFD Calculations. 2 May 2015.

[27] Michelle Lochner, Iniyan Natarajan, Jonathan T. L. Zwart, Oleg Smirnov, Bruce A. Bassett, Nadeem Oozeer and Martin Kunz. Bayesian inference for radio observations. 25 March 2015.

[28] Michelle M. Kuttel, Graham E. Jackson, Mpho Mafata, Neil Ravenscroft. Capsular polysaccharide conformations in pneumococcal serotypes 19F and 19A. 14 January 2015. 

[29] Dube F. Longitudinal colonisation by Streptococcus pneumoniae and nasopharyngeal microbial interactions in health and disease: A South African birth cohort study. 2015. hdl.handle.net/11427/20649.

[30] Jack K, Smith G. Pay as You Go: Prepaid Metering and Electricity Expenditures in South Africa. 2015 May. dx.doi.org/10.1257/aer.p20151096.

[1] Bierman A. Mapping and survey sequencing of Dn resistance genes in Triticum aestivum L. December 2014. hdl.handle.net/10019.1/96912

[2] Muhire B. Molecular diversity of Chickpea chlorotic dwarf virus in Sudan: High rates of intra-species recombination – a driving force in the emergence of new strains. 2014 Nov doi:10.1016/j.meegid.2014.11.024 *

[3] Combrink J. A Sensitivity Analysis of Model Structure in Stochastic Differential Equation and Agent-Based Epidemiological Models. 2014 Nov hdl.handle.net/11427/21645

[4] Mandikumba W. New nonreversible nucleotide substitution models to describe evolution of viral and cellular genome. 26 October 2014. Hons thesis

[5] Bantom M. An assessment of the contribution of a satellite laser ranging station at Matjiesfontein. 15 October 2014.BSc thesis

[6] Mongwane B. Problems in Cosmology and Numerical Relativity. October 2014. PhD thesis

[7] Hunt N. Development of an equivalent mechanical model for fuel slosh in the wing of an aircraft. October 2014. *

[8] Hussen J. Industrial Research. October 2014. *

[9] Le Clezio S. Rigid wing-mast design for a small sailing vessel. October 2014. *

[10] Lochner M. New Applications of Statistics in Astronomy and Cosmology. September 2014. PhD thesis

[11] Muhire B, Varsani A, Martin D. SDT: A Virus Classification Tool Based on Pairwise Sequence Alignment and Identity Calculation. 26 September 2014. doi.org/10.1371/journal.pone.0108277

[12] Febraury S. Evolution of linear perturbations in spherically symmetric dust spacetimes. 19 August 2014. PhD thesis

[13] Muhire B. Revealing a Hidden Viral Infection with Deep Sequencing in a Plant Quarantine Context. 25 July 2014. doi.org/10.1371/journal.pone.0102945 *

[14] Govind R. Multi-technique Space Geodesy Analysis Centre at the University of Cape Town. 9 Jul 2014. Presentation

[15] Muhire B. Pigeon circoviruses display patterns of recombination, genomic secondary structure and selection similar to those of beak and feather disease viruses. 1 Jun 2014 dx.doi.org/10.1099/vir.0.063917-0 *

[16] Ross-Gillespie A. Report of the Sub-Committee on Other Southern Hemisphere Whale Stocks. 12 May 2014. Report

[17] Ross-Gillespie A. Assessment results for humpback breeding stocks. 10 May 2014. open.uct.ac.za/handle/11427/17837

[18] Golden M. Identification of evolutionarily conserved nucleic acid secondary structures within viral genomes. 2014. open.uct.ac.za/handle/11427/5972

[19] Kuttel M, Gordon M, Ravenscroft N. Comparative simulation of pneumococcal serogroup 19 polysaccharide repeating units with two carbohydrate force fields. 2014. doi-org.ezproxy.uct.ac.za/10.1016/j.carres.2014.02.026

[1] Olivier C, Alexeeva N. The direct scattering study of the parametrically driven nonliner Schroeding equation. 2013. arxiv.org/pdf/1312.7655.pdf

[2] Golden M. Identification of evolutionarily conserved nucleic acid secondary structures within viral genomes. 23 December 2013. hdl.handle.net/11427/5972

[3] Muasya A, Viljoen J, Dludlu M, Demissew S. Phylogenetic position of Cyperus clandestinus (Cypereae, Cyperaceae) clarified by morphological and molecular evidence. 12 December 2013. hdl.handle.net/11427/21206

[4] Viljoen J, Muasya A, Barrett R, Bruhl J, Gibbs A, Slingsby J, Wilson K, Verboom G. Radiation and Repeated Transoceanic Dispersal of Schoeneae (Cyperaceae) Through the Southern Hemisphere. Dec 2013. hdl.handle.net/11427/21215

[5] Robinson W. Modelling the impact of the South African small pelagic Fishery on African penguin dynamics. November 2013. hdl.handle.net/11427/18162

[6] Muhire B, Golden M, Murrell B, Lefeuvre P, Lett J, Gray A, Poon A, Ngandu N, Semegni Y, Tanov E, Monjane A, Harkins G, Varsani A, Shepherd D, Martin D. Evidence of pervasive biologically functional secondary-structures within the genomes of eukaryotic single-stranded DNA viruses. 27 November 2013. hdl.handle.net/11427/21202

[7] Kerry Kalweit. Prioritisation of candidate genes for psychiatric disorders. 25 October 2013. open.uct.ac.za/handle/11427/21223

[8] Hugo B. Fast online predictive compression of radio astronomy data. 25 October 2013. open.uct.ac.za/handle/11427/21225

[9] Bures P, Muasya A, Lipnerova I, Zedek F, Bauters K, Smarda P, Viljoen J, Elizondo M, Barrett R, Goetghebeur P, Bruhl J, Mwachala G, Prychid C, Hroudova Z, Thomas W, Wilson K. The evolution of genome size and base composition in Cyperid clade. July 2013. Conference paper

[10] Munyai R. A Systematic Study of South African Genus Prionium (Thurniaceae). May 2013. hdl.handle.net/11427/14030

[11] February S, Clarkson C, Maartens R. Galaxy correlations and the BAO in a void universe: structure formation as a test of the Copernican Principle. 19 March 2013. hdl.handle.net/11427/21222

[12] Muhire B, Martin D, Brown J, Navas-Castillo J , Moriones E, Zerbini F, Rivera-Bustamante R, Malathi V, Riddon R, Varsani A. A genome-wide pairwise-identity-based proposal for the classification of viruses in the genus Mastrevirus (family Geminiviridae). 23 January 2013. hdl.handle.net/11427/21221

[13] Fadly Isaacs F. Spatial Transitions: Cape Town Case Study. January 2103. hdl.handle.net/11427/21224

[1] Bell L. High throughput proteomic analysis of Mycobacterium tuberculosis associated Immune Reconstitution Inflammatory Syndrome (TB-IRIS). December 2012. open.uct.ac.za/handle/11427/4397

[2] Tshiila A. Systematics of Ficinia clade December 2012 MSc dissertation. African Studies Collection – BUT 580 TSHI

[3] Dlodlo O. Rhizobia diversity and their effect on the distribution of indigenous legumes in the Cape Floristic Region. December 2012 MSc dissertation. African Studies Collection – BUT 580 DLOD

[4] Stephen Marquard. Improving Searchability of Automatically Transcribed Lectures Through Dynamic Language Modelling. December 2012. Thesis

[5] Alexeeva N, Barashenkov I, Sukhorukov A, Kivshar Y. Optical solitons in Parity Time symmetric nonlinear couplers with gain and loss. 28 June 2012.  open.uct.ac.za/handle/11427/21216

[6.] Home-grown high-performance computing at ICTS. UCT Monday Paper – Volume 31.14 – 17 September 2012

[7] Lee-Thorp J. Spectral continuation study of the temporally periodic solitons of the damped-driven nonlinear Schodinger equations. 22 August 2012 hdl.handle.net/11427/11261

[8] Olivier C, Herbst B, Molchan M. A numerical study of the large-period limit of a Zakharov-Shabat eigenvalue problem with periodic potentials. 31 May 2012. hdl.handle.net/11427/21200