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Jeremy Sumner

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Jeremy Sumner

Lecturer
ARC DECRA Fellow

Room 407, Maths-Physics Building, Sandy Bay Campus

+61 3 6226 1765 (phone)

+61 3 6226 2410 (fax)

Jeremy.Sumner@utas.edu.au

Dr Jeremy Sumner is a Lecturer and ARC Discovery Early Career Fellow in the School of Physical Sciences and a member of the UTAS Theoretical Phylogenetics Research Group. His research interests revolve around applications of algebraic methods to phylogenetic models. Phylogenetics is concerned with the statistical inference of the evolutionary history of present-day organisms from molecular data, such as DNA. His specialty is exploiting the symmetries inherent in the problem by applying algebraic methods such as group representation theory to analyse and improve phylogenetic methodologies.

Career summary

Qualifications

DegreeThesis TitleUniversity Country Date of Award
PhDEntanglement, invariants,  and phylogeneticsUniversity of TasmaniaAustralia11/09/2007
BSc (1st Class Hons)Polar decomposition of a Dirac spinorUniversity of TasmaniaAustralia1/11/2001

Biography

Between March 2007 to May 2008, Jeremy held a post-doctoral position at the University of Sydney working under the supervision of A/Prof Michael Charleston (School of IT) and Prof Lars Jermiin (School of Biological Sciences). Between June 2008 and October 2011, he was awarded an ARC Post-Doctoral Fellowship working with Reader Peter Jarvis at UTAS on the Discovery Project 'Markov invariants and phylogenetic reconstruction'. The content of this project was a direct continuation of the research he conducted during his PhD on Markov invariants, which are group invariant polynomials useful to the context of Markov models of DNA evolution. In January 2012, he was appointed on a fixed-term basis as a lecturer in statistics and a post-doctoral researcher at UTAS. In November that year, he was awarded a highly-competitive ARC Discovery Early Career Research Award (DECRA) for the project 'Group theory and Phylogenetics: Using symmetry to uncover evolutionary history'. The project focuses on the development and implementation of the so-called 'Lie-Markov' models of DNA evolution, particularly those which respect the grouping of DNA nucleotides into purines and pyrimidines. Since December 2013, Jeremy has held a permanent position as a lecturer in the School of Physical Sciences.

Research Themes

Jeremy's research in phylogenetics has primarily been based around the introduction of new mathematical methods to molecular biology; in particular algebraic methods more usually applied in theoretical physics. Taken as a whole, phylogenetics is the suite of computational and statistical techniques used by biologists to infer the past evolutionary history of organisms given present-day molecular data such as DNA. With modern DNA sequencing methods producing ever increasing amounts of data at a fraction of previous costs, over the past few decades there has been a pressing need for the development of mathematical and statistical methods to analyse this data under the evolutionary presumption of decent from a common ancestor.

By far the most difficult problem in phylogenetics is the correct inference of the evolutionary tree that relates presently observed organisms. Fundamental to this problem is the correct estimation of the rate at which DNA mutations arise under the assumption of a random process. From the mathematical point of view, this entails assuming what is known as a Markov process which in turn boils down to the estimation of a 'matrix' of nucleotide substitution rates for random changes such as A (adenine) goes to C (cytosene). For reasons of statistical efficiency and tractability, these rates are for the most part assumed to be constant in time. Of course, the historical reality is that molecular evolution is more complicated than this and  one would like to ensure that the modelling simplifications made are at least consistent with this more complicated reality. Remarkably, the demand for consistency means that one must obtain a certain type of mathematical closure of the substitution matrices under standard algebraic operations of matrix addition and multiplication. Together with his co-authors, Jeremy has solved this problem through the development the so-called Lie-Markov models of DNA substitutions.  The development of these models, together with related algebraic methods applied to phylogenetics, has formed the foundation of his research career.

Memberships

Professional practice

  • 2013-2016: UTAS representative on the Australian Mathematical Society Council

Teaching

Statistics, Algebra, Group Theory, Representation Theory

Teaching responsibility

View more on Dr Jeremy Sumner in WARP

Expertise

  • Phylogenetic methods
  • Group representation theory

Collaboration

Jeremy is a member of the UTAS Theoretical Phylogenetic Research Group. The group organises the annual conference Phylomania: The UTAS theoretical phylogenetics meeting. This meeting brings together international researchers with a strong theoretical leaning, with the aim of discussing some of the more pressing problems in phylogenetics.

Current projects

Jeremy is currently chief investigator on two ARC Discovery projects:

  • 2015-2018: 'Algebraically informed models of biological sequence evolution'  
  • 2013-2016: 'Group theory and Phylogenetics: Using symmetry to uncover evolutionary history'

Fields of Research

  • Biological Mathematics (010202)
  • Physical Sciences (029999)
  • Phylogeny and Comparative Analysis (060309)
  • Molecular Evolution (060409)
  • Group Theory and Generalisations (010105)
  • Biostatistics (010402)
  • Biological Physics (029901)
  • Public Health and Health Services (111799)
  • Numerical Analysis (010301)
  • Statistical Theory (010405)
  • Genetic Immunology (060406)
  • Gene Expression (incl. Microarray and other genome-wide approaches) (060405)
  • Algebraic and Differential Geometry (010102)
  • Stochastic Analysis and Modelling (010406)
  • Applied Statistics (010401)

Research Objectives

  • Expanding Knowledge in the Mathematical Sciences (970101)
  • Expanding Knowledge in the Physical Sciences (970102)
  • Expanding Knowledge in the Biological Sciences (970106)
  • Expanding Knowledge in the Environmental Sciences (970105)
  • Computer Time Leasing, Sharing and Renting Services (890204)
  • Flora, Fauna and Biodiversity at Regional or Larger Scales (960805)

Publications

Total publications

28

Highlighted publications

(2 outputs)
YearTypeCitationAltmetrics
2012Journal ArticleSumner JG, Fernandez-Sanchez J, Jarvis PD, 'Lie Markov models', Journal of Theoretical Biology, 298 pp. 16-31. ISSN 1095-8541 (2012) [Refereed Article]

DOI: 10.1016/j.jtbi.2011.12.017 [eCite] [Details]

Citations: Scopus - 23Web of Science - 22

Co-authors: Jarvis PD

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2008Journal ArticleSumner JG, Charleston MA, Jermiin LS, Jarvis PD, 'Markov invariants, plethysms, and phylogenetics', Journal of Theoretical Biology, 253, (3) pp. 601-615. ISSN 0022-5193 (2008) [Refereed Article]

DOI: 10.1016/j.jtbi.2008.04.001 [eCite] [Details]

Citations: Scopus - 15Web of Science - 15

Co-authors: Jarvis PD

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Journal Article

(24 outputs)
YearCitationAltmetrics
2017Serdoz S, Egri-Nagy A, Sumner J, Holland BR, Jarvis PD, et al., 'Maximum likelihood estimates of pairwise rearrangement distances', Journal of Theoretical Biology, 423 pp. 31-40. ISSN 0022-5193 (2017) [Refereed Article]

DOI: 10.1016/j.jtbi.2017.04.015 [eCite] [Details]

Citations: Scopus - 1Web of Science - 1

Co-authors: Holland BR; Jarvis PD

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2017Sumner JG, 'Dimensional reduction for the General Markov Model on phylogenetic trees', Bulletin of Mathematical Biology, 79 pp. 619-634. ISSN 0092-8240 (2017) [Refereed Article]

DOI: 10.1007/s11538-017-0249-6 [eCite] [Details]

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2017Sumner JG, Taylor A, Holland BR, Jarvis PD, 'Developing a statistically powerful measure for quartet tree inference using phylogenetic identities and Markov invariants', Journal of Mathematical Biology pp. 1-36. ISSN 0303-6812 (2017) [Refereed Article]

DOI: 10.1007/s00285-017-1129-2 [eCite] [Details]

Co-authors: Holland BR; Jarvis PD

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2017Sumner JG, Jarvis PD, Francis AR, 'A representation-theoretic approach to the calculation of evolutionary distance in bacteria', Journal of Physics A: Mathematical and Theoretical, 50 Article 335601. ISSN 1751-8121 (2017) [Refereed Article]

DOI: 10.1088/1751-8121/aa7d60 [eCite] [Details]

Co-authors: Jarvis PD

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2016Jarvis PD, Sumner JG, 'Matrix group structure and Markov invariants in the strand symmetric phylogenetic substitution model', Journal of Mathematical Biology, 73 pp. 259-282. ISSN 0303-6812 (2016) [Refereed Article]

DOI: 10.1007/s00285-015-0951-7 [eCite] [Details]

Citations: Scopus - 2Web of Science - 2

Co-authors: Jarvis PD

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2015Fernandez-Sanchez J, Sumner JG, Jarvis PD, Woodhams MD, 'Lie Markov models with purine/pyrimidine symmetry', Journal of Mathematical Biology, 70, (4) pp. 855-891. ISSN 0303-6812 (2015) [Refereed Article]

DOI: 10.1007/s00285-014-0773-z [eCite] [Details]

Citations: Scopus - 3Web of Science - 1

Co-authors: Jarvis PD; Woodhams MD

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2015Woodhams MD, Fernandez-Sanchez J, Sumner JG, 'A new hierarchy of phylogenetic models consistent with heterogeneous substitution rates', Systematic Biology, 64, (4) pp. 638-650. ISSN 1063-5157 (2015) [Refereed Article]

DOI: 10.1093/sysbio/syv021 [eCite] [Details]

Citations: Scopus - 3Web of Science - 1

Co-authors: Woodhams MD

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2014Sumner JG, Jarvis PD, Holland BR, 'A tensorial approach to the inversion of group-based phylogenetic models', BMC Evolutionary Biology, 14 Article 236. ISSN 1471-2148 (2014) [Refereed Article]

DOI: 10.1186/s12862-014-0236-6 [eCite] [Details]

Co-authors: Jarvis PD; Holland BR

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2014Jarvis PD, Sumner JG, 'Adventures in invariant theory', ANZIAM Journal, 56, (2) pp. 105-115. ISSN 1446-1811 (2014) [Refereed Article]

DOI: 10.1017/S1446181114000327 [eCite] [Details]

Citations: Scopus - 2Web of Science - 2

Co-authors: Jarvis PD

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2013Allman ES, Jarvis PD, Rhodes JA, Sumner JG, 'Tensor rank, invariants, inequalities, and applications', Journal on Matrix Analysis and Applications, 34, (3) pp. 1014-1045. ISSN 0895-4798 (2013) [Refereed Article]

DOI: 10.1137/120899066 [eCite] [Details]

Citations: Scopus - 7Web of Science - 7

Co-authors: Jarvis PD

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2013Holland BR, Jarvis PD, Sumner JG, 'Low-parameter phylogenetic inference under the general Markov model', Systematic Biology, 62, (1) pp. 78-92. ISSN 1063-5157 (2013) [Refereed Article]

DOI: 10.1093/sysbio/sys072 [eCite] [Details]

Citations: Scopus - 9Web of Science - 9

Co-authors: Holland BR; Jarvis PD

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2013Sumner JG, 'Lie geometry of 2 x 2 Markov matrices', Journal of Theoretical Biology, 327 pp. 88-90. ISSN 0022-5193 (2013) [Refereed Article]

DOI: 10.1016/j.jtbi.2013.01.026 [eCite] [Details]

Citations: Scopus - 1Web of Science - 1

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2012Jarvis PD, Sumner JG, 'Markov Invariants for Phylogenetic Rate Matrices Derived from Embedded Submodels', IEEE/ACM Transactions on Computational Biology and Bioinformatics, 9, (3) pp. 828-836. ISSN 1545-5963 (2012) [Refereed Article]

DOI: 10.1109/TCBB.2012.24 [eCite] [Details]

Citations: Scopus - 2Web of Science - 2

Co-authors: Jarvis PD

Tweet

2012Sumner JG, Fernandez-Sanchez J, Jarvis PD, 'Lie Markov models', Journal of Theoretical Biology, 298 pp. 16-31. ISSN 1095-8541 (2012) [Refereed Article]

DOI: 10.1016/j.jtbi.2011.12.017 [eCite] [Details]

Citations: Scopus - 23Web of Science - 22

Co-authors: Jarvis PD

Tweet

2012Sumner JG, Holland BR, Jarvis PD, 'The Algebra of the General Markov Model on Phylogenetic Trees and Networks', Bulletin of Mathematical Biology, 74, (4) pp. 858-880. ISSN 1522-9602 (2012) [Refereed Article]

DOI: 10.1007/s11538-011-9691-z [eCite] [Details]

Citations: Scopus - 6Web of Science - 8

Co-authors: Holland BR; Jarvis PD

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2012Sumner JG, Jarvis PD, Fernandez-Sanchez J, Kaine BT, Woodhams MD, et al., 'Is the general time-reversible model bad for molecular phylogenetics?', Systematic Biology, 61, (6) pp. 1069-1074. ISSN 1063-5157 (2012) [Refereed Article]

DOI: 10.1093/sysbio/sys042 [eCite] [Details]

Citations: Scopus - 15Web of Science - 14

Co-authors: Jarvis PD; Kaine BT; Woodhams MD; Holland BR

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2010Sumner JG, Charleston M, 'Phylogenetic estimation with partial likelihood tensors', Journal of Theoretical Biology: An International Multidisciplinary Journal, 262, (3) pp. 413-424. ISSN 0022-5193 (2010) [Refereed Article]

DOI: 10.1016/j.jtbi.2009.09.037 [eCite] [Details]

Citations: Scopus - 4Web of Science - 4

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2009Sumner JG, Jarvis PD, 'Markov invariants and the isotropy subgroup of a quartet tree', Journal of Theoretical Biology, 258, (2) pp. 302-310. ISSN 0022-5193 (2009) [Refereed Article]

DOI: 10.1016/j.jtbi.2009.01.021 [eCite] [Details]

Citations: Scopus - 12Web of Science - 11

Co-authors: Jarvis PD

Tweet

2008Sumner JG, Charleston MA, Jermiin LS, Jarvis PD, 'Markov invariants, plethysms, and phylogenetics', Journal of Theoretical Biology, 253, (3) pp. 601-615. ISSN 0022-5193 (2008) [Refereed Article]

DOI: 10.1016/j.jtbi.2008.04.001 [eCite] [Details]

Citations: Scopus - 15Web of Science - 15

Co-authors: Jarvis PD

Tweet

2006Sumner JG, Jarvis PD, 'Using the tangle: A consistent construction of phylogenetic distance matrices for quartets', Mathematical Biosciences, 204, (1) pp. 49-67. ISSN 0025-5564 (2006) [Refereed Article]

DOI: 10.1016/j.mbs.2006.05.008 [eCite] [Details]

Citations: Scopus - 8Web of Science - 9

Co-authors: Jarvis PD

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2006Sumner JG, Jarvis PD, 'Erratum-Entanglement invariants and phylogenetic branching', Journal of Mathematical Biology, 53, (3) pp. 490. ISSN 0303-6812 (2006) [Letter or Note in Journal]

[eCite] [Details]

Co-authors: Jarvis PD

2005Jarvis PD, Bashford JD, Sumner JG, 'Path integral formulation and Feynman rules for phylogenetic branching models', Journal of Physics A: Mathematical and General, 38, (44) pp. 9621-9647. ISSN 0305-4470 (2005) [Refereed Article]

DOI: 10.1088/0305-4470/38/44/002 [eCite] [Details]

Citations: Scopus - 6Web of Science - 6

Co-authors: Jarvis PD; Bashford JD

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2005Sumner JG, Jarvis PD, 'Entanglement invariants and phylogenetic branching', Journal of Mathematical Biology, 51, (1) pp. 18-36. ISSN 0303-6812 (2005) [Refereed Article]

DOI: 10.1007/s00285-004-0309-z [eCite] [Details]

Citations: Scopus - 9Web of Science - 7

Co-authors: Jarvis PD

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2004Bashford JD, Jarvis PD, Sumner JG, Steel MA, 'U(1) U(1) U(1) symmetry of the Kimura 3ST model and phylogenetic branching processes', Journal of Physics A-Mathematical and General, 37, (8) pp. L81-L89. ISSN 0305-4470 (2004) [Refereed Article]

DOI: 10.1088/0305-4470/37/8/L01 [eCite] [Details]

Citations: Scopus - 10Web of Science - 2

Co-authors: Bashford JD; Jarvis PD

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Chapter in Book

(2 outputs)
YearCitationAltmetrics
2017Jarvis PD, Holland BR, Sumner JG, 'Phylogenetic Invariants and Markov Invariants', Reference Module in Life Sciences, Elsevier, BD Roitberg (ed), Amsterdam, Netherlands, pp. 1-3. ISBN 9780128096338 (2017) [Revised Book Chapter]

DOI: 10.1016/B978-0-12-809633-8.06903-X [eCite] [Details]

Co-authors: Jarvis PD; Holland BR

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2013Jarvis PD, Holland BR, Sumner JG, 'Phylogenetic Invariants', Brenner's Encyclopedia of Genetics, Academic Press Ltd Elsevier Science Ltd, S Maloy, K Hughes (ed), United Kingdom, pp. 321-323. ISBN 978-0-08-096156-9 (2013) [Other Book Chapter]

DOI: 10.1016/B978-0-12-374984-0.09001-X [eCite] [Details]

Co-authors: Jarvis PD; Holland BR

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Conference Publication

(1 outputs)
YearCitationAltmetrics
2012Humphries MA, Holland BR, Karpievitch YV, Sumner JG, 'To gamma or not to gamma? Testing the fit of rates-across-sites models', Phylomania 2012, 8-9 November 2012, University of Tasmania, Hobart, pp. 7. (2012) [Conference Extract]

[eCite] [Details]

Co-authors: Humphries MA; Holland BR; Karpievitch YV

Thesis

(1 outputs)
YearCitationAltmetrics
2006Sumner JG, 'Entanglement, Invariants, and Phylogenetics' (2006) [PhD]

[eCite] [Details]

Grants & Funding

Funding Summary

Number of grants

5

Total funding

$923,076

Projects

Algebraically informed models of biological sequence evolution (2015 - 2017)$310,700
Description
To make sense of the patterns they see in the natural world, biologists across fields as diverse as genetics, epidemiology and biogeography need an accurate picture of evolutionary history. DNA sequences provide an exciting means to establish this picture of the past, but to decode it successfully requires mathematical models of how DNA evolves. Our team has identified mathematical inconsistencies with current approaches. In particular, understanding the effect of natural selection in different parts of the Tree of Life requires models that behave robustly in the face of shifting evolutionary processes. This project will use insights from algebraic methods to construct mathematically consistent models of wide biological utility.
Funding
Australian Research Council ($310,700)
Scheme
Grant-Discovery Projects
Administered By
University of Tasmania
Research Team
Holland BR; Sumner JG; Jarvis PD
Period
2015 - 2017
Grant Reference
DP150100088
Group theory and phylogenetics: Exploiting symmetry to uncover evolutionary histories (2013 - 2015)$369,061
Description
Using advanced algebra, structural symmetries inherent in phylogenetic methods will be studied, and improved approaches will be derived. DNA sequences contain a wealth of information about evolutionary events that occurred millions of years ago, but extracting this information requires the application of robust methods.
Funding
Australian Research Council ($369,061)
Scheme
Fellowship-Discovery Early Career Researcher Award
Administered By
University of Tasmania
Research Team
Sumner JG
Period
2013 - 2015
Grant Reference
DE130100423
Phylogenetics: New Data, New Phylogenetic Challenges Follow-up Meeting - UK, 2011 (2010)$1,815
Funding
University of Tasmania ($1,815)
Scheme
Grant-Conference Support Scheme
Administered By
University of Tasmania
Research Team
Sumner JG
Year
2010
2008 R2 - Algebraic Methods in Systems Biology and Statistics: Molecular Evolution and Phylogenetics Workshop', Statistical and Applied Mathematical Sciences Institute (SAMSI), North Carolina, USA (2009)$1,500
Funding
University of Tasmania ($1,500)
Scheme
Grant-Conference Support Scheme
Administered By
University of Tasmania
Research Team
Sumner JG
Year
2009
Markov Invariants and Phylogenetic Tree Reconstruction (2008 - 2010)$240,000
Funding
Australian Research Council ($240,000)
Scheme
Grant-Discovery Projects
Administered By
University of Tasmania
Research Team
Jarvis PD; Sumner JG
Period
2008 - 2010
Grant Reference
DP0877447

Research Supervision

Current

4

Completed

1

Current

DegreeTitleCommenced
PhDA Scattering Approach to Gravitational Lensing2014
PhDQuadratic Lie Superalgebras in Mathematics and Physics2016
PhDUsing Rheological Equations as a Model of Fluid Turbulence2016
PhDRing Properties of Markov Invariants2017

Completed

DegreeTitleCompleted
PhDDistinguishing Convergence on Phylogenetic Networks
Candidate: Jonathan David Mitchell
2016