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Dr Matthew Parry

(PhD Brown University, USA)Matthew Parry (2022)

Senior Lecturer
Course coordinator 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 & 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:

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.

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Publications

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

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. Advance online publication. 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

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

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

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

Journal - Research Article

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

Journal - Research Article

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. Advance online publication. doi: 10.1016/j.pathol.2021.04.001

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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. Cochrane Database of Systematic Reviews, 8, CD013699. doi: 10.1002/14651858.Cd013699

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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

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

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

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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

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

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

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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

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

Journal - Research Article

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

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

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

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

Journal - Research Article

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

Journal - Research Article

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

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

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

Journal - Research Article

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: 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 - 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: 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]

Conference Contribution - Published proceedings: 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: 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: Full paper

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

Conference Contribution - Published proceedings: Abstract

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/

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 - 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 - 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

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. (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 - 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.

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 driver of melanoma metastasis identified by genome-wide analysis. Poster session presented at the Queenstown Molecular Biology (QMB) Meetings, Queenstown, New Zealand.

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.

Conference Contribution - Poster Presentation (not in published proceedings)

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.

Conference Contribution - Verbal presentation and other Conference outputs

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