Matthew Parry, Our people, Department of Mathematics and Statistics

(PhD Brown University, USA)

Associate Professor
Course co‑ordinator for BAppSc in Data Science

Office: Science III, room 236
Tel +64 3 479 7780
Email matthew.parry@otago.ac.nz

About

My PhD was in physics but I moved into statistics courtesy of an EPSRC (UK) Statistics Mobility Fellowship. I have been a member of the Department of Mathematics and Statistics since 2011.

I am currently a principal investigator at Te Pūnaha Matatini Centre for Research Excellence. I am deputy leader of NZ Science Group, which is part of the Laser Interferometer Space Antenna (LISA) Consortium. I am also a past President of the NZ Statistical Association (2020–2022).

Teaching responsibilities

My teaching responsibilities include:

STAT 312 Modelling High Dimensional Data
STAT 372 Stochastic Modelling
STAT 405 Probability and Random Processes
INFO 420 Statistical Techniques for Data Science

Research interests

My research expertise is mathematical and statistical modelling. My research is currently focused on applications of scoring rules in statistics, modelling epidemics in plants and human populations, analysis of solar storms and geomagnetic events, statistical analysis of gravitational waves, modelling of methylation and epigenetic modification, and the development of new algorithms for statistical inference. These activities are strongly influenced by my background in physics and computational methods.

I am actively looking for Honours and postgraduate students to work on projects in these areas. I value mathematical and computational ability as much as I do statistical background.

Publications

Arnold, R., Binny, R. N., Lumley, T., Lustig, A., Parry, M., & Plank, M. J. (2024). Estimating the risk of SARS-CoV-2 infection in New Zealand border arrivals. BMC Global & Public Health, 2, 27. doi: 10.1186/s44263-024-00057-2 Journal - Research Article

Wang, T., Parry, M., Rodger, C., Allen, J., & Petersen, T. (2023). Forecasting extreme geomagnetic storms using different statistical models. Proceedings of the European Geosciences Union (EGU) General Assembly. EGU23-11294. doi: 10.5194/egusphere-egu23-11294 Conference Contribution - Published proceedings: Abstract

Easterbrook-Clarke, L., Hardie, S., Petersen, T., Wang, T., Parry, M., Davison, A., … Rodger, C. J., … Oliver, W., & Williams, C. (2023). Digitising historical New Zealand paper magnetograms to extract one-minute data as input for modelling geomagnetic storms [Invited]. Proceedings of the 28th General Assembly of the International Union of Geodesy and Geophysics (IUGG). doi: 10.57757/IUGG23-0757 Conference Contribution - Published proceedings: Abstract

Nanayakkara, S., Zeng, J., Turner, R., Parry, M., & Sywak, M. (2023). Development and internal validation of clinical risk prediction models for structural recurrence disease of thyroid cancer. Proceedings of the New Zealand Biostatistics Conference. Retrieved from https://events.otago.ac.nz/2023-biostatistics-conference Conference Contribution - Published proceedings: Abstract

Yassi, M., Chatterjee, A., & Parry, M. (2023). Application of deep learning in cancer epigenetics through DNA methylation analysis. Briefings in Bioinformatics, 24(6). doi: 10.1093/bib/bbad411 Journal - Research Other

2024

Journal - Research Article

2023

Journal - Research Article

Fletcher, D., Dillingham, P. W., & Parry, M. (2023). A simple and robust approach to Bayesian modelling of overdispersed data. Environmental & Ecological Statistics, 30, 289-308. doi: 10.1007/s10651-023-00567-6

Richter, M. E., Leonard, G. H., Smith, I. J., Langhorne, P. J., Mahoney, A. R., & Parry, M. (2023). Accuracy and precision when deriving sea-ice thickness from thermistor strings: A comparison of methods. Journal of Glaciology, 69(276), 879-898. doi: 10.1017/jog.2022.108

Journal - Research Other

Yassi, M., Chatterjee, A., & Parry, M. (2023). Application of deep learning in cancer epigenetics through DNA methylation analysis. Briefings in Bioinformatics, 24(6). doi: 10.1093/bib/bbad411

Conference Contribution - Published proceedings: Abstract

Richter, M. E., Leonard, G. H., Smith, I. J., Langhorne, P. J., & Parry, M. (2023). Interannual variability of fast-ice thickness in McMurdo Sound: Drivers and trends. Proceedings of the New Zealand-Australia Antarctic Science Conference (NZAASC): Latitudes of Change. (pp. 84). Retrieved from https://www.nzaasc.org

2022

Journal - Research Article

Binny, R. N., Priest, P., French, N. P., Parry, M., Lustig, A., Hendy, S. C., … Plank, M. J. (2022). Sensitivity of RT-PCR tests for SARS-CoV-2 through time. Journal of Infectious Diseases. doi: 10.1093/infdis/jiac317

Baeumer, B., Kovács, M., & Parry, M. (2022). A higher order resolvent-positive finite difference approximation for fractional derivatives on bounded domains. Fractional Calculus & Applied Analysis, 25, 299-319. doi: 10.1007/s13540-021-00013-z

2021

Journal - Research Article

Ahn, A., Rodger, E. J., Motwani, J., Gimenez, G., Stockwell, P. A., Parry, M., … Chatterjee, A., & Eccles, M. R. (2021). Transcriptional reprogramming and constitutive PD-L1 expression in melanoma are associated with dedifferentiation and activation of interferon and tumour necrosis factor signalling pathways. Cancers, 13, 4250. doi: 10.3390/cancers13174250

Craigie, A., McGregor, R., Whitcombe, A. L., Carlton, L., Harte, D., Sutherland, M., Parry, M., … Ussher, J., … Jack, S., & Upton, A. (2021). SARS-CoV-2 antibodies in the southern region of New Zealand, 2020. Pathology, 53(5), 645-651. doi: 10.1016/j.pathol.2021.04.001

Cao, Z., Bryant, D., Molteno, T. C. A., Fox, C., & Parry, M. (2021). V-spline: An adaptive smoothing spline for trajectory reconstruction. Sensors, 21, 3215. doi: 10.3390/s21093215

2020

Journal - Research Article

Wilson, N., Schwehm, M., Verrall, A. J., Parry, M., Baker, M. G., & Eichner, M. (2020). Detecting the re-emergent COVID-19 pandemic after elimination: Modelling study of combined primary care and hospital surveillance. New Zealand Medical Journal, 133(1524), 28-39. Retrieved from https://www.nzma.org.nz/journal

Martin, A., Parry, M., Soundy, A. W. R., Panckhurst, B. J., Brown, P., Molteno, T. C. A., & Schumayer, D. (2020). Improving real-time position estimation using correlated noise models. Sensors, 20, 5913. doi: 10.3390/s20205913

Anglemyer, A., Moore, T. H. M., Parker, L., Chambers, T., Grady, A., Chiu, K., Parry, M., … Bero, L. (2020). Digital contact tracing technologies in epidemics: A rapid review (Review). Cochrane Database of Systematic Reviews, 8, CD013699. doi: 10.1002%2F14651858.CD013699

Bowden, S. A., Stockwell, P. A., Rodger, E. J., Parry, M. F., Eccles, M. R., Stayner, C., & Chatterjee, A. (2020). Extensive inter-cyst DNA methylation variation in autosomal dominant polycystic kidney disease revealed by genome scale sequencing. Frontiers in Genetics, 11, 348. doi: 10.3389/fgene.2020.00348

Bender, C. M., Brody, D. C., & Parry, M. F. (2020). Making sense of the divergent series for reconstructing a Hamiltonian from its eigenstates and eigenvalues. American Journal of Physics, 88(2), 148-152. doi: 10.1119/10.0000215

Brownlie, T., Bishop, T., Parry, M., Salmon, S. E., & Hunnam, J. C. (2020). Predicting the periodic risk of anthrax in livestock in Victoria, Australia, using meteorological data. International Journal of Biometeorology, 64, 601-610. doi: 10.1007/s00484-019-01849-0

Afroz, F., Parry, M., & Fletcher, D. (2020). Estimating overdispersion in sparse multinomial data. Biometrics, 76, 834-842. doi: 10.1111/biom.13194

Conference Contribution - Published proceedings: Full paper

Deng, J. D., & Parry, M. (2020). Data Science programmes: Is there an ideal design? Proceedings of the 62nd International Statistics Institute (ISI) World Statistics Congress: Special Topic Session. Vol. 3, (pp. 66-73). Putrajaya, Malaysia: Department of Statistics Malaysia. Retrieved from www.isi2019.org

Conference Contribution - Published proceedings: Abstract

Ahn, A., Rodger, E. J., Stockwell, P. A., Parry, M., Motwani, J., Gallagher, S. J., … Chatterjee, A., & Eccles, M. R. (2020). mRNA and long non-coding RNA expression defines constitutive and inducible PD-L1 expression in melanoma and associated with treatment resistance and response. Proceedings of the Genetics Otago (GO) Epigenetics User Group (EUG) Symposium. Retrieved from https://blogs.otago.ac.nz/go/2020-3/

Parry, M. (2020). Statistical issues of methylation analysis [Invited]. Proceedings of the Genetics Otago (GO) Epigenetics User Group (EUG) Symposium. Retrieved from https://blogs.otago.ac.nz/go/2020-3/

Working Paper; Discussion Paper; Technical Report

Anglemyer, A., Parker, L., Chiu, K., Chambers, T., Wilczynska, M., Grady, A., … Parry, M. (2020). Contact tracing technologies in epidemics: A rapid review [CRD42020188946]. PROSPERO. Retrieved from https://www.crd.york.ac.uk/prospero

2019

Journal - Research Article

Moffat, S., Fritz, Z., Slowther, A.-M., Parry, M., & Barclay, S. (2019). ‘Do not attempt CPR’ in the community: The experience of ambulance clinicians. Journal of Paramedic Practice, 11(5), 198-204. doi: 10.12968/jpar.2019.11.5.198

Conference Contribution - Published proceedings: Abstract

Chatterjee, A., Rodger, E. J., Ahn, A., Stockwell, P. A., Parry, M., Gallagher, S., … Eccles, M. (2019). Methylome and transcriptome programme segregates PD-L1 expressing and non-expressing melanoma. Proceedings of the 16th Asian Conference on Transcription. (pp. 38-39). Retrieved from http://act2019.p.events4you.currinda.com/days/2019-12-02/

Parry, M. F., & Calvacanti, P. P. (2019). Archetypal analysis as an autoencoder with application to data imputation. Proceedings of the New Zealand Statistical Association Conference. (pp. 34). Retrieved from https://www.otago.ac.nz/nzsa/programme-and-speakers/

Chatterjee, A., Ahn, A., Rodger, E. J., Stockwell, P. A., Parry, M., Motwani, J., … Eccles, M. R. (2019). Global DNA methylation levels regulate PD-L1 expression in melanoma. Cancer Research, 79(13, Suppl.). doi: 10.1158/1538-7445.Am2019-826

Working Paper; Discussion Paper; Technical Report

Bender, C. M., Brody, D. C., & Parry, M. F. (2019). Making sense of the divergent series for reconstructing a Hamiltonian from its eigenstates and eigenvalues. arXiv. Retrieved from https://arxiv.org/abs/1906.03017

2018

Journal - Research Article

Torres, U., Godsoe, W., Buckley, H. L., Parry, M., Lustig, A., & Worner, S. P. (2018). Using niche conservatism information to prioritize hotspots of invasion by non-native freshwater invertebrates in New Zealand. Diversity & Distributions, 24(12), 1802-1815. doi: 10.1111/ddi.12818

Craig, H. J. B., Stachowicz, K., Black, M., Parry, M., Burke, C. R., Meier, S., & Amer, P. R. (2018). Genotype by environment interactions in fertility traits in New Zealand dairy cows. Journal of Dairy Science, 101, 10991-11003. doi: 10.3168/jds.2017-14195

Chatterjee, A., Rodger, E. J., Ahn, A., Stockwell, P. A., Parry, M., Motwani, J., … Eccles, M. R., & Hersey, P. (2018). Marked global DNA hypomethylation is associated with constitutive PD-L1 expression in melanoma. iScience, 4, 312-325. doi: 10.1016/j.isci.2018.05.021

Craig, A. P., Cunniffe, N. J., Parry, M., Laranjeira, F. F., & Gilligan, C. A. (2018). Grower and regulator conflict in management of the citrus disease Huanglongbing in Brazil: A modelling study. Journal of Applied Ecology, 55(4), 1956-1965. doi: 10.1111/1365-2664.13122

Conference Contribution - Poster Presentation (not in published proceedings)

Ahn, A., Rodger, E. J., Stockwell, P. A., Parry, M., Motwani, J., Gallagher, S. J., … Chatterjee, A., & Eccles, M. R. (2018, August). Investigating the role of DNA methylation, gene expression, long non-coding RNA and transposable elements in constitutive PD-L1 expression in melanoma cell lines. Poster session presented at the Queenstown Molecular Biology (QMB) Meetings, Queenstown, New Zealand.

Conference Contribution - Verbal presentation and other Conference outputs

Chatterjee, A., Rodger, E., Ahn, A., Stockwell, P., Parry, M., Motwani, J., … Eccles, M., & Hersey, P. (2018, August). Striking loss of global DNA methylation levels and constitutive PD-L1 expression in melanoma. Verbal presentation at the Queenstown Molecular Biology (QMB) Meetings, Queenstown, New Zealand.

2017

Journal - Research Article

Cameron, C., Iosua, E., Parry, M., Richards, R., & Jaye, C. (2017). More than just numbers: Challenges for professional statisticians. Statistics Education Research Journal, 16(2), 362-375. Retrieved from http://iase-web.org/Publications.php?p=SERJ

Chatterjee, A., Macaulay, E. C., Ahn, A., Ludgate, J. L., Stockwell, P. A., Weeks, R. J., Parry, M. F., Foster, T. J., … Eccles, M. R., & Morison, I. M. (2017). Comparative assessment of DNA methylation patterns between reduced representation bisulfite sequencing and Sequenom EpiTyper methylation analysis. Epigenomics, 9(6), 823-832. doi: 10.2217/epi-2016-0176

Conference Contribution - Published proceedings: Full paper

Martin, A. D., Soundy, A. W. R., Panckhurst, B. J., Brown, C. P., Schumayer, D., Molteno, T. C. A., & Parry, M. (2017). Real-time uncertainty quantification using correlated noise models for GNSS positioning. Proceedings of the IEEE Sensors Conference. IEEE. doi: 10.1109/ICSENS.2017.8233899

Conference Contribution - Poster Presentation (not in published proceedings)

Eccles, M. R., Chatterjee, A., Rodger, E. J., Ahn, A., Leichter, A., Motwani, J., Stockwell, P., & Parry, M. (2017, September). Epigenetic drivers of melanoma metastasis identified by genome-wide reduced-representation bisulphite sequencing (RRBS) analysis. Poster session presented at the Queenstown Molecular Biology (QMB) Meetings, Queenstown, New Zealand.

Eccles, M. R., Chatterjee, A., Rodger, E. J., Ahn, A., Leichter, A., Motwani, J., Stockwell, P., & Parry, M. (2017, September). Epigenetic driver of melanoma metastasis identified by genome-wide analysis. Poster session presented at the Queenstown Molecular Biology (QMB) Meetings, Queenstown, New Zealand.

Conference Contribution - Verbal presentation and other Conference outputs

Eccles, M. R., Chatterjee, A., Rodger, E. J., Ahn, A., Leichter, A., Motwani, J., Stockwell, P., Parry, M., … Gardner, J., … Sarwar, M., … multiple other members of The Maurice Wilkins Centre. (2017, September). Can research involving NZ melanoma patient participation and extensive networking by researchers help reduce the melanoma burden in NZ? Verbal presentation at the Queenstown Molecular Biology (QMB) Meetings, Queenstown, New Zealand.

Parry, M. (2017, July). Scoring rules for probabilistic binary classification. Verbal presentation at the International Statistical Institute (ISI) 61st World Statistics Congress, Marrakech, Morocco.

2016

Journal - Research Article

Roigé, M., Parry, M., Phillips, C., & Worner, S. (2016). Self-organizing maps for analysing pest profiles: Sensitivity analysis of weights and ranks. Ecological Modelling, 342, 113-122. doi: 10.1016/j.ecolmodel.2016.10.003

Whigham, P. A., Dick, G., & Parry, M. (2016). Network rewiring dynamics with convergence towards a star network. Proceedings of the Royal Society A, 472(2194), 20160236. doi: 10.1098/rspa.2016.0236

Chatterjee, A., Stockwell, P. A., Rodger, E. J., Parry, M. F., & Eccles, M. R. (2016). scan_tcga tools for integrated epigenomic and transcriptomic analysis of tumor subgroups. Epigenomics, 8(10), 1315-1330. doi: 10.2217/epi-2016-0063

Parry, M. (2016). Linear scoring rules for probabilistic binary classification. Electronic Journal of Statistics, 10(1), 1596-1607. doi: 10.1214/16-EJS1150

Parry, M. (2016). Extensive scoring rules. Electronic Journal of Statistics, 10(1), 1098-1108. doi: 10.1214/16-EJS1132

Chatterjee, A., Macaulay, E. C., Rodger, E. J., Stockwell, P. A., Parry, M. F., Roberts, H. E., Slatter, T. L., Hung, N. A., Devenish, C. J., & Morison, I. M. (2016). Placental hypomethylation is more pronounced in genomic loci devoid of retroelements. Genes Genomes Genetics, 6(7), 1911-1921. doi: 10.1534/g3.116.030379

Hiscott, G., Fox, C., Parry, M., & Bryant, D. (2016). Efficient recycled algorithms for quantitative trait models on phylogenies. Genome Biology & Evolution, 8(5), 1338-1350. doi: 10.1093/gbe/evw064

Conference Contribution - Published proceedings: Full paper

Patrick, M., Craig, A. P., Cunniffe, N. J., Parry, M., & Gilligan, C. A. (2016). Testing stochastic software using pseudo-oracles. Proceedings of the 25th International Symposium on Software Testing and Analysis (ISSTA). (pp. 235-246). New York, NY: ACM. doi: 10.1145/2931037.2931063

Conference Contribution - Published proceedings: Abstract

Casey, B., McDonald, J., Matthaei, C., Fletcher, D., Parry, M., Cameron, C., & Dakson, C. (2016). Postgraduate peer statistics advisers: A pilot programme. Proceedings of the Tertiary Education Research in New Zealand (TERNZ) Conference. Retrieved from http://herdsa.org.nz/ternz/2016

Conference Contribution - Poster Presentation (not in published proceedings)

Macaulay, E. C., Chatterjee, A., Rodger, E. J., Stockwell, P. A., Parry, M. F., Roberts, H. E., Slatter, T. L., Hung, N. A., & Morison, I. M. (2016, March). Placental hypomethylation is more pronounced in genomic loci devoid of retroelements. Poster session presented at the Keystone Symposia on Molecular and Cellular Biology: Chromatin and Epigenetics, Whistler, Canada.

2015

Journal - Research Article

Chatterjee, A., Stockwell, P. A., Rodger, E. J., Duncan, E. J., Parry, M. F., Weeks, R. J., & Morison, I. M. (2015). Genome-wide DNA methylation map of human neutrophils reveals widespread inter-individual epigenetic variation. Scientific Reports, 5, 17328. doi: 10.1038/srep17328

2014

Journal - Research Article

Parry, M., Gibson, G. J., Parnell, S., Gottwald, T. R., Irey, M. S., Gast, T. C., & Gilligan, C. A. (2014). Bayesian inference for an emerging arboreal epidemic in the presence of control. PNAS, 111(17), 6258-6262. doi: 10.1073/pnas.1310997111

Conference Contribution - Published proceedings: Full paper

Martin, A. D., Molteno, T. C. A., & Parry, M. (2014). Measuring the performance of sensors that report uncertainty. Proceedings of the 21st Electronics New Zealand Conference (ENZCon). (pp. 57-61). University of Waikato, New Zealand: Electronics New Zealand. [Full Paper]

Parry, M. (2014). Local scoring rules and statistical inference in unnormalized models. In J. Rissanen, P. Myllymäki, T. Roos & N. P. Santhanam (Eds.), Proceedings of the Seventh Workshop on Information Theoretic Methods in Science and Engineering [Department of Computer Science: Series of Publications B: Report B-2014-4]. (pp. 13-15). [Full Paper]

Conference Contribution - Published proceedings: Abstract

Roigé, M., Worner, S., Parry, M., & Phillips, C. (2014). Using pest assemblages to predict invasions: Validation tests for the self-organizing map approach. Proceedings of the New Zealand Ecological Society (NZES) Annual Conference. (pp. 73). Retrieved from http://newzealandecology.org/node/40

Conference Contribution - Verbal presentation and other Conference outputs

Deaker, L., Harraway, J., Wang, T., Parry, M., Schofield, M., Cox, N., & Davie, G. (2014, August). Where is Statistics heading? What should we be doing to future proof the profession? Invited presentation at the Box Plot II Symposium, Dunedin, New Zealand.

Working Paper; Discussion Paper; Technical Report

Martin, A. D., Molteno, T. C. A., & Parry, M. (2014). Measuring the performance of sensors that report uncertainty. arXiv. Retrieved from http://arxiv.org/abs/1411.4354v1

2013

Conference Contribution - Published proceedings: Full paper

Parry, M. (2013). Multidimensional local scoring rules. Proceedings of the 59th ISI World Statistics Congress of the International Statistical Institute. (pp. 1453-1458). The Hague, The Netherlands: International Statistical Institute. Retrieved from http://2013.isiproceedings.org/

Conference Contribution - Published proceedings: Abstract

Parry, M. (2013). Randomization and approximation in MCMC. Proceedings of the Joint New Zealand Statistical Association (NZSA) and Operations Research Society of New Zealand (ORSNZ) Conference: Analytics for a Changing World: From Data to Decisions. (pp. 57). Retrieved from https://secure.orsnz.org.nz/conf47/index.php

2012

Journal - Research Article

Brody, D. C., Meister, B. K., & Parry, M. F. (2012). Informational inefficiency in financial markets. Mathematics & Financial Economics, 6(3), 249-259. doi: 10.1007/s11579-012-0078-1

Parry, M., Dawid, A. P., & Lauritzen, S. (2012). Proper local scoring rules. Annals of Statistics, 40(1), 561-592. doi: 10.1214/12-AOS971

Dawid, A. P., Lauritzen, S., & Parry, M. (2012). Proper local scoring rules on discrete sample spaces. Annals of Statistics, 40(1), 593-608. doi: 10.1214/12-AOS972

2011

Working Paper; Discussion Paper; Technical Report

Dawid, A. P., Lauritzen, S., & Parry, M. (2011). Proper local scoring rules on discrete sample spaces. arXiv. Retrieved from http://arxiv.org/abs/1104.2224v1

Parry, M., Dawid, A. P., & Lauritzen, S. (2011). Proper local scoring rules. arXiv. Retrieved from http://arxiv.org/abs/1101.5011v1

2010

Journal - Research Article

Brody, D. C., Hughston, L. P., & Parry, M. F. (2010). Effects of quantum entanglement in phase transitions. Physics Letters A, 374(24), 2424-2428. doi: 10.1016/j.physleta.2010.03.060

Working Paper; Discussion Paper; Technical Report

Brody, D. C., Brody, J., Meister, B. K., & Parry, M. F. (2010). Outsider trading. arXiv. Retrieved from http://arxiv.org/abs/1003.0764v2

2006

Journal - Research Article

Parry, M. (2006). A rule of thumb for cosmological backreaction. Journal of Cosmology & Astroparticle Physics, 2006, 016. doi: 10.1088/1475-7516/2006/06/016