nic geard

Associate Professor, School of Computing and Information Systems, Faculty of Engineering and Information Technology

Director, Melbourne Data Analytics Platform

The University of Melbourne

Email: ngeard@unimelb.edu.au

Office: Melbourne Connect, The University of Melbourne, Parkville VIC 3010, Australia

Research

I create computational models to investigate the transmission and control of infectious diseases such as influenza, group A Streptococcus, and COVID-19. I'm interested in how rich computational models can capture the influence of demographic, behavioural, and pathogen heterogeneity on the spread of diseases, and what this means for the design of effective control strategies.

I am a CI on a National Health & Medical Research Council Centre of Research Excellence (SPECTRUM; 2020-2024) aimed at enhancing national and regional decision making to improve the control of infectious diseases, strengthen health systems and reduce these risks in Australia and the Asia Pacific region through collaboration, partnerships, and model-based evidence to aid decision making.

More broadly, I am interested in the application of simulation models to the study of complex biological, social, and artificial systems.  Past areas of research interest have included the structure and dynamics of gene regulatory networks, the interplay between developmental and evolutionary processes, and the co-evolution of state and topology in dynamic networks.


Biography

I am currently an Associate Professor with the School of Computing and Information Systems at The University of Melbourne, and Director of the Melbourne Data Analytics Platform.

I joined the School of Computing and Information Systems in 2016. Prior to that, I was an ARC DECRA Fellow (2013-2016) with the Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, where I first began to develop and apply computational models of infectious disease transmission and control with Jodie McVernon and James McCaw. Before arriving in Melbourne, I worked with Seth Bullock in the School of Electronics and Computer Science, University of Southampton, on modelling the dynamics of social networks. Between Southampton and Melbourne, I spent some time on a bike. I obtained my BSc and PhD in computer science at the School of Information Technology and Electrical Engineering, University of Queensland. My PhD, on modelling the evolution of gene regulatory networks, was supervised by Janet Wiles.


Teaching


Team

current research staff

current PhD students

former research staff

completed PhD students

Prospective research students: Please note that I do not currently have capacity to take on additional PhD students. I do not take on international interns. Inquiries that are outside the scope of my research will not be responded to. 


Publications

submitted / preprints

Lydeamore MJ*, Zachreson C*, Conway E, Shearer FM, Baker C, Ross J, Miller JC, McCaw JM, Geard N#, McVernon J#, Price DJ#. Border quarantine, vaccination and public health measures to mitigate the impact of COVID-19 importations: a modelling study  (medRxiv preprint) (*,# equal contribution) .

Kollepara P, Dey S, Tomko M, Martino E, Bentley R, Tizzoni M, Geard N, Zachreson C. Socioeconomic correlates of urban mobility trends in two Australian cities during transitional periods of the COVID-19 pandemic (medRxiv preprint).

Lydeamore MJ, Donker T, Wu D, Gorrie C, Turner A, Easton M, Hennessey D, Geard N, Howden BP, Cooper BS, Wilson A, Peleg AY, Stewardson AJ. Carbapenemase-producing Enterobacterales colonisation status does not lead to more frequent admissions: a linked patient study (medRxiv preprint).

Zachreson C, Tobin R, Walker J, Conway E, Shearer FM, McVernon J, Geard N. A model-based assessment of social isolation practices for COVID-19 outbreak response in residential care facilities (arXiv preprint).

Moreira da Silva B, Ascher DB, Geard N, Pires DEV. AI driven B-cell Immunotherapy Design (arXiv preprint).

Pham A, Baker C, Geard N. Multiscale modelling of invasive species control: the cane toad in Australia (bioRxiv preprint).

Garrett P, White JP, Luo Y, Dennis S, Geard N, ..., Kashima Y. COVID-19, national culture, and privacy calculus: factors predicting the cross-cultural acceptance and uptake of contact-tracing technologies (PsyArXiv preprint).

Chisholm RH, Lacey JA, Kokko J, Campbell PT, McDonald MI, Corander J, Davies MR, Tong SYC, McVernon, Geard N. Unravelling the immune response to Group A Streptococcus from population-level observations of prevalence and strain diversity (arXiv preprint).


journal articles

Chen J, Goudey B, Geard N, Verspoor K (2024) Integration of background knowledge for automatic detection of inconsistencies in gene ontology annotation. Bioinformatics (accepted 8 April 2024).

Zachreson C, Savulescu J, Plank MJ, Coghlan S, Miller JC, Ainslie KEC, Geard N (2024) Ethical frameworks should be applied to computational modelling of infectious disease interventions. PLoS Computational Biology 20(3):e1011933 .

Pedrana A et al (2024) Priority populations’ experiences of isolation, quarantine and distancing for COVID-19: protocol for a longitudinal cohort study (Optimise Study). BMJ Open 14(1):e076907.

Zachreson C, Tobin R, Szanyi J, Walker C, Cromer D, Shearer F, Conway E, Ryan G, Cheng A, McCaw J, Geard N (2023) Individual variation in vaccine immune response can produce bimodal distributions of protection. Vaccine 41:6630-6636.

Abell I, Zachreson C, Conway E, Geard N, McVernon J, Waring T, Baker C (2023) Rapid prototyping of models for COVID-19 outbreak detection in workplaces. BMC Infectious Diseases 23:213.

Tellioglu N, Chisholm RH, Campbell PT, Collinson S, Timothy J, Kollie K, Zayzay S, Devine A, McVernon J, Marks M, Geard N (2023) Modelling mass drug administration strategies for reducing scabies burden in Monrovia, Liberia. Epidemiology & Infection 151:e23.

Conway E, Walker C, Baker C, Lydeamore M, Ryan G, Campbell PT, Miller J, Yeung M, Kabashima G, Rebuli N, Geard N, Wood J, McCaw J, McVernon J, Golding N, Price D, Shearer F (2023) COVID-19 vaccine coverage targets to inform reopening plans in a low incidence setting. Proceedings of the Royal Society B 290:20231437.

Lacey JA, Marcato AJ, Chisholm RH, Campbell PT, Zachreson C, ..., Geard N, McVernon J, Tong S (2023) Evaluating the role of asymptomatic throat carriage of Streptococcus pyogenes in impetigo transmission in remote Aboriginal communities in Northern Territory, Australia: a retrospective genomic analysis. The Lancet Microbe 4(7):524-533.

Eze PU, Geard N, Mueller I, Chades I (2023) Anomaly detection in endemic disease surveillance data using machine learning techniques. Healthcare 11(13):1896.

Eze PU, Geard N, Baker CM, Campbell PT, Chades I (2023) Value of Information analysis for pandemic response: intensive care unit preparedness at the onset of COVID-19. BMC Health Systems Research 23:485.

Harris T, Geard N, Zachreson C (2023) Correlation of viral loads in disease transmission chains could bias early estimates of the reproduction number. Journal of the Royal Society Interface 20(202):20220827.

Geard N, Bradhurst R, Tellioglu N, Oktaria V, McVernon J, Handley A, Bines JE (2022) Model-based estimation of RV3-BB vaccine impact under infant and neonatal schedules. Human Vaccines & Immunotherapeutics 18(6).

Goldsmith JJ, Campvell PT, Villanueva Cabezas JP, Chisholm RH, McKinnon M, Gurruwiwi GG, Dhurrkay RG, Dockery AM, Geard N, Tong SYC, McVernon J, Gibney K. Capturing household structure and mobility within and between remote Aboriginal communities in northern Australia using longitudinal data: A pilot study (2022) International Journal of Environmental Research and Public Health 19(19):12002.

Roy GG, Geard N, Verspoor K, He S. MPVNN: Mutated Pathway Visible Neural Network architecture for interpretable prediction of cancer-specific survival risk (2022) Bioinformatics 38(22):5025-5032.

Goudey B, Geard N, Verspoor K, Zobel J (2022) Propagation, detection, and correction of errors using the sequence database network. Briefings in Bioinformatics 23(6):bbac416.

Chen J, Goudey B, Zobel J, Geard N, Verspoor K (2022) Exploring automatic inconsistency detection for literature-based Gene Ontology Annotation. Bioinformatics 38(Supp 1):i273-i281.

Tellioglu N, Geard N, Chisholm RH (2022) Modelling the effect of within-host dynamics on the diversity of a multi-strain pathogen. Journal of Theoretical Biology 548: 111185.

Tellioglu N, Chisholm RH, McVernon J, Geard N, Campbell PT (2022) The efficacy of sampling strategies for estimating scabies prevalence. PLoS Neglected Tropical Diseases 16(6): e0010456.

Zachreson C, Shearer FM, Price DJ, Lydeamore MJ, McVernon J, McCaw J, Geard N (2022) COVID-19 in low-tolerance border quarantine systems: impact of the Delta variant of SARS-CoV-2. Science Advances 8(14):eabm3624.

Shearer F, Walker J, Tellioglu N, McCaw JM, McVernon J, Black A, Geard N (2022) Rapid assessment of the risk of SARS-CoV-2 importation: case study and lessons learned. Epidemics 38:100549.

Chen J, Geard N, Zobel J, Verspoor K. (2021) Automatic consistency assurance for literature-based Gene Ontology annotation. BMC Bioinformatics 22:565.

Zachreson C, Martino E, Tomko M, Shearer FM, Bentley R, Geard N (2021) Mapping internet activity during COVID-19 lockdown to identify occupartion-related inequalities. Scientific Reports 11:21054.

Hui BB, Brown D, Chisholm RH, Geard N, McVernon J, Regan D (2021) Modelling testing and response strategies for COVID-19 outbreaks in remote Australian Aboriginal communities. BMC Infectious Diseases 21:929. 

Roy GG, He S, Geard N, Verspoor K (2021) Bow-tie architecture of gene regulatory networks in species of varying complexity. Journal of the Royal Society Interface 18(179):20210069.

Garrett P, White JP, Lewandowsky S, Kashima Y, Perfors A, Little D, Geard N, Mitchell L, Tomko M, Dennis S (2021) The acceptability and uptake of smartphone tracking for COVID-19 in Australia. PLoS ONE 16(1):e024482.

Zachreson C, Mitchell L, Lydeamore M, Rebuli N, Tomko M, Geard N (2021) Risk mapping for COVID-19 outbreaks in Australia using mobility data. Journal of the Royal Society Interface 18(174):20200657.

Blakely T, Moss R, Collins J, Mizdrak A, Singh A, Carvalho N, Wilson N, Geard N, Flaxman A (2020) Multistate lifetable modelling of preventative interventions: concepts and worked examples. International Journal of Epidemiology 49(5):1624–1636.

Campbell PT, Geard N, Hogan AB (2020) Modelling the household-level impact of a maternal respiratory syncytial virus (RSV) vaccine in a high-income setting. BMC Medicine 18:319.

Campbell PT, Tong SYC, Geard N, Davies MR, Worthing KA, Lacey JA, Smeesters PR, Batzloff MR, Kado J, Jenney AWJ, McVernon J, Steer AC (2020) Longitudinal analysis of group A Streptococcus emm types and emm clusters in a high-prevalence setting: relationship between past and future infections . Journal of Infectious Diseases 9(1):1429-1437.

Chisholm RH, Crammond B, Wu Y, Campbell PT, Tong SYC, McVenon J, Geard N (2020) A model of population dynamics with complex household structure and mobility: implications for transmission and control of communicable diseases. PeerJ 8:e10203.

Chisholm RH, Sonenberg N, Lacey JA, McDonald MI, Pandey M, Davies MR, Tong SYC, McVernon J, Geard N (2020) Epidemiological consequences of enduring strain-specific immunity requiring repeated episodes of infection. PLoS Computational Biology 16(6):e1007182.

Roy GG, Geard N, Verspoor K, He S (2020) PoLoBag: Polynomial Lasso Bagging for signed gene regulatory network inference from expression data. Bioinformatics 36(21):5187–5193.

Cuningham W, Geard N, Fielding J, Braat S, ..., McVernon J, Moss R (2019) Optimal timing of influenza vaccination during pregnancy: a systematic review and meta-analysis. Influenza and Other Respiratory Viruses 13:438-452.

Moss R, Naghizade E, Tomko M, Geard N (2019) What can urban mobility data reveal about the spatial distribution of infection in a single city? BMC Public Health 19:656.

Ragonnet R, Trauer JM, Geard N, Scott N, McBryde, ES (2019) Profiling Mycobacterium tuberculosis transmission and the resulting disease burden in the five highest tuberculosis burden countries. BMC Medicine 17:208.

Xu Z, Graves PM, Lau C, Clements A, Geard N, Glass K (2019) GEOFIL: A spatially-explicit agent-based modelling framework for predicting the long-term transmission dynamics of lymphatic filariasis in American Samoa. Epidemics 27:19-27.

Campbell PT, Frost H, Smeesters PR, Kado J, Good MF, Batzloff MR, Geard N, McVernon J, Steer AC (2018) Investigation of group A Streptococcus immune responses in an endemic setting, with a particular focus on J8. Vaccine 36(50):7618-7624.

Chisholm RH, Campbell PT, Wu Y, Tong SYC, McVernon J, Geard N (2018) Implications of asymptomatic carriers for infectious disease transmission and control. Royal Society Open Science 5:172341.

Dias A, Geard N, Campbell PT, Warr D, McVernon J (2018) Quantity or quality? Assessing relationships between perceived social connectedness and recorded encounters. PLoS ONE 13(11): e0208083.

Black AJ, Geard N, McCaw JM, McVernon J, Ross JV (2017) Characterising pandemic severity and transmissibility from data collected during first few hundred studies. Epidemics 19:61-73.

Campbell PT, McVernon J, Shrestha N, Nathan PM, Geard N (2017) Who's holding the baby? A prospective diary study of the contact patterns of mothers with an infant. BMC Infectious Diseases 17:634.

Campbell PT, McVernon J, Geard N (2017) Determining best strategies for maternally-targeted pertussis vaccination using an individual based model. American Journal of Epidemiology 186 (1):109-117.

Vino T, Singh GR, Davison B, Campbell PT, Lydeamore M, Robinson A, McVernon J, Tong SYC, Geard N (2017) Indigenous Australian household structure: a simple data collection tool and implications for close contact transmission of communicable diseases. PeerJ 5:e3958.

Xu Z, Glass K, Lau C, Geard N, Graves PM, Clements A (2017) A synthetic population for modelling the dynamics of infectious disease transmission in American Samoa. Scientific Reports 7:16725.

Campbell PT, McVernon J, McIntyre P, Geard N (2016) Influence of population demography and immunization history on the impact of an antenatal pertussis program. Clinical Infectious Diseases 63 (suppl 4):S213-S220.

Moss R, Hickson R, Hort K, Black J, McCaw JM, Tran N, McVernon J, Madden J, McBryde ES, Geard N (2016) Model-informed risk assessment and decision making for an emerging infectious disease in the Asia-Pacific region. PLoS Neglected Tropical Diseases 10(9):e0005018.

Geard N, Glass K, McCaw JM, McBryde E, Korb, K, Keeling MJ, McVernon J (2015) The effects of demographic change on disease transmission and vaccine impact in a household structured population. Epidemics 13:56-64.

Ragonnet R, Trauer JM, Denholm JT, Geard N, Hellard M, McBryde ES (2015) Vaccination programs for endemic infections: modelling real versus apparent impacts of vaccine and infection characteristics. Scientific Reports 5:15468.

Rolls D*, Geard N*, Warr DJ, Nathan PM, Robins GL, Pattison PE, McCaw JM, McVernon J (2015) Social encounter profiles of greater Melbourne residents, by location – a telephone survey. BMC Infectious Diseases 15:494. (* equal contribution)

Dorin A, Geard N (2014) The practice of agent-based model visualisation. Artificial Life 20(2): 271-289.

Geard N, McCaw J, Dorin A, Korb KB, McVernon J (2013) Synthetic population dynamics: a model of household demography. Journal of Artificial Societies and Social Simulation 16(1):8.

Jacyno M, Bullock S, Geard N, Payne TR, Luck M (2013) Self-organising agent communities for autonomic resource management. Adaptive Behavior 21(1):3-28.

Geard N, Bullock S, Lohaus R, Azevedo RBR, Wiles J (2011) Developmental motifs reveal complex structure in cell lineages. Complexity 16(4):48-57.

Bryden J*, Funk S*, Geard N*, Bullock S, Jansen V (2011) Stability in flux: Community structure in dynamic networks. Journal of the Royal Society Interface 8(60):1031-1040. (* equal contribution)

Bullock S, Geard N (2011) Spatial embedding as an enabling constraint. Complexity 16(2):8-10.

Geard N, Bullock S (2010) Competition and the dynamics of group affiliation. Advances in Complex Systems 13(4):501-517.

Geard N, Willadsen K (2009) Dynamical approaches to modeling developmental gene regulatory networks. Birth Defects Research C: Embryo Today 87(2):131-142.

Geard N, Wiles J (2008) LinMap: visualising complexity gradients in evolutionary landscapes. Artificial Life 14(3):277-297.

Lohaus R, Geard N, Wiles J, Azevedo RBR (2007) A generative bias towards average complexity in artificial cell lineages. Proceedings of the Royal Society of London, Series B 274(1619):1741-1750.

Copren KA, Geard N (2005) An individual based model examining the emergence of cooperative recognition in a social insect. Sociobiology 46(2):349-361.

Geard N, Wiles J (2005) A gene network model for developing cell lineages. Artificial Life 11(3):249-268.

Watson J, Geard N, Wiles J (2004) Towards more biological mutation operators in gene regulation studies. BioSystems 76(1-3):239-248.


full conference papers

Wickramaarachchi H, Kirley M, Geard N (2024) Cooperative multi-agent reinforcement learning with dynamic target localization: a reward sharing approach. In: AI 2023: Advances in Artificial Intelligence - Australasian Joint Conference on Artificial Intelligence, pp 310-324, Springer.

Eccles D, Kurnia S, Dingler T, Geard N (2021) Three preventative interventions to address the fake news phenomenon on social media. Australasian Conference on Information Systems 2021, 6–10 December 6-10, 2021, Sydney, Australia

Buckland E, Tanin E, Geard N, Zachreson C, Xie H, Samet, H (2021) Managing trajectories and interactions during a pandemic: a trajectory similarity-based approach (Demo Paper). In: ACM SIGSPATIAL 2021, 2-9 November, 2021, Beijing, China.

Silverman E, Geard N, Wood I (2016) Job insecurity in academic research employment: an agent-based model. In: ALIFE XV: The 15th International Conference on the Synthesis and Simulation of Living Systems, 4-8 July, 2016, Cancún, Mexico.

Geard N, McCaw J, Dorin A, Korb KB, McVernon J (2012) Modelling household dynamics for epidemiological simulation. In: 4th World Congress on Social Simulation, 4-7 September, 2012, Taipei, Taiwan.

Geard N, Noble J (2010) Modelling academic research funding as a resource allocation problem. In: 3rd World Congress on Social Simulation, 6-9 September, 2010, Kassel, Germany.

Geard N, Bullock S (2009) Homophily and competition: a model of group affiliation. In: The Sixth Conference of the European Social Simulation Association, 14-18 September, 2009, Guildford, UK.

Jacyno M, Bullock S, Payne TR, Geard N, Luck M (2008) Autonomic resource management through self-organising agent communities. In: Second IEEE International Conference on Self-Adaptive and Self-Organizing Systems, October 20-24, 2008, Venice, Italy.

Geard N, Bullock S (2008) Group formation and social evolution: a computational model. In: Artificial Life XI: Proceedings of the Eleventh International Conference on the Simulation and Synthesis of Living Systems, pp. 197-203, MIT Press, Cambridge, MA.

Geard N, Wiles J (2007) Directed evolution of an artificial cell lineage. In: Progress in Artificial Life, Third Australian Conference, ACAL 2007, Proceedings, pp. 144-155, Springer-Verlag.

Geard N, Bullock S (2007) Milieu and function: toward a multilayer framework for understanding social networks. In: the Ninth European Conference on Artificial Life; Workshop: The Emergence of Social Behaviour, Lisbon, Portugal.

Geard N, Wiles J (2006) Investigating ontogenetic space with developmental cell lineages. In: Artificial Life X: Proceedings of the Tenth International Conference on the Simulation and Synthesis of Living Systems, pp. 55-62, MIT Press.

Rudge T, Geard N (2005) Evolving gene regulatory networks for cellular morphogenesis. In: Recent Advances in Artificial Life, Second Australian Conference, ACAL 2005, Proceedings, pp. 239-252, World Scientific Publishing.

Geard N, Willadsen K, Wiles J (2005) Perturbation analysis: a complex systems pattern. In: Recent Advances in Artificial Life, Second Australian Conference, ACAL 2005, Proceedings, pp. 69-84, World Scientific Publishing.

Skellett B, Cairns B, Geard N, Tonkes B, Wiles J (2005) Rugged NK landscapes contain the highest peaks. In: Genetic and Evolutionary Computation Conference, GECCO 2005, Proceedings, pp. 579-584, ACM Press.

Wiles J, Geard N, Watson J, Willadsen K, Mattick J, Bradley D, Hallinan J (2005) There's more to a model than code: understanding and formalizing in silico modeling experience. In: Workshop on Scalable, Evolvable, Emergent Design and Developmental Systems at The Genetic and Evolutionary Computation Conference, GECCO 2005, Washington DC, USA. pp. 281-288.

Geard N, Wiles J (2003) A gene regulatory network for cell differentiation in Caenorhabditis elegans. In: Proceedings of the First Australian Conference on Artificial Life, pp. 86-100, University of New South Wales.

Geard N, Wiles J (2003) Structure and dynamics of a gene network model incorporating small RNAs. In: Proceedings of the 2003 Congress on Evolutionary Computation, CEC 2003, Volume 1, pp. 199-206, IEEE Press.

Watson J, Geard N, Wiles J (2003) Towards more biological mutation operators in gene regulation studies. In: Information Processing in Cells and Tissues (IPCAT2003), Lausanne, Switzerland.

Geard N, Wiles J, Hallinan J, Tonkes B, Skellett B (2002) A comparison of neutral landscapes - NK, NKp and NKq. In: Proceedings of the 2002 Congress on Evolutionary Computation, pp. 205-210, IEEE Press.

Geard N, Wiles J (2002) Diversity maintenance on neutral landscapes: an argument for recombination. In: Proceedings of the 2002 Congress on Evolutionary Computation, pp. 211-213, IEEE Press.

Watson J, Geard N, Wiles J (2002) Stability and task complexity: a neural network model of genetic assimilation. In: Artificial Life VIII: Proceedings of the Eighth International Conference on Artificial Life, p. 153, MIT Press.


book chapters

Geard, N, Madden, JR, McBryde, E, Moss, R and Tran, NH (2020) Modelling the economic impacts of epidemics in developing countries under alternative intervention strategies. In: JR Madden, H Shibusawa, Y Higano (eds) Environmental Economics and Computable General Equilibrium Analysis, pp. 193-214, Springer.

Korb KB, Geard N, Dorin A (2013) A Bayesian approach to the validation of agent-based models. In: A Tolk (ed) Ontology, Epistemology, and Teleology for Modeling and Simulation, pp. 255-269, Springer.


miscellanea: reviews, reports and theses

Geard N (2010) Book review of Thilo Gross and Hiroki Sayama's "Adaptive Networks: Theory, Models and Applications". Artificial Life, 16(4):329-331.

Geard N (2006) Artificial Ontogenies: A Computational Model of the Control and Evolution of Development. PhD thesis, The University of Queensland.

Geard N (2006) Two design patterns for visualising the parameter space of complex systems. Technical Report ACCS-TR-06-02, ARC Centre for Complex Systems, The University of Queensland.

Geard N (2004) Modelling gene regulatory networks: systems biology to complex systems. Technical Report ACCS-TR-04-01, School of Information Technology and Electrical Engineering, The University of Queensland.

Fischer W, Geard N (2002) Reconstructing phylogeny from RNA secondary structure via simulated evolution. In: Santa Fe Institute Complex Systems Summer School 2002, June 2002, Santa Fe, NM.

Geard N (2001) An Exploration of NK Landscapes with Neutrality. BSc (Hons) thesis, The University of Queensland.