I’ve been doing academic research in biology since 2007, when I started an undergrad research project in the Gregory Lab at the University of Guelph. Since then I have been lucky to collaborate on a variety of projects with researchers around the world, the details of which can be found in the carousel below this section.
You can hear me talking about transposons with my colleague Dr. Beth Clare in her BioAudio podcast here!
To get a sense of the impact of my research, please see my Google Scholar and Impact Story profiles. If you would like access to any of my papers, please check my ResearchGate or Academia profiles, or contact me directly.
I have presented my research at venues around the world, a list of which can be found here.
For ease of access, here are links to the TE Hub and my Repeat Resources
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Ecology of the Genome
Thinking of the genome like an ecosystem has been a useful tool to understand the patterns of TE abundance and distribution across the Tree of Life. This work has involved collaborating with researchers from a variety of disciplines at the University of Guelph.
S.C. Kremer, S. Linquist, B. Saylor, T.A. Elliott, T.R. Gregory, K. Cottenie. 2021. Long-term TE persistence even without beneficial insertion. BMC Genomics. 22: 260
S.C. Kremer, S. Linquist, B. Saylor, T.A. Elliott, T.R. Gregory, K. Cottenie. 2020. Transposable element persistence via potential genome-level ecosystem engineering. BMC Genomics. 21: 367
S. Linquist, K. Cottenie, T.A. Elliott, B. Saylor, S.C. Kremer, T.R, Gregory. 2015. Applying ecological models to communities of genetic elements: the case of neutral theory. Molecular Ecology. 24(13): 3232-3242
B. Saylor, T.A. Elliott, S. Linquist, S.C. Kremer, T.R. Gregory, K. Cottenie. 2013. A novel application of ecological analyses to assess transposable element distributions in the genome of the domestic cow, Bos taurus. Genome. 56(9): 521-533
B. Saylor, S. Linquist, K. Cottenie, T.A. Elliott, S.C. Kremer, T.R. Gregory. 2013. Distinguishing ecological from evolutionary approaches to transposable elements. Biological Reviews. 88: 573-584
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Transposable Element Evolution
At the heart of it, my interest in TEs stems from trying to understand the diversity and evolution of these fascinating replicators.
M. Ibrahim, B. Al-Shomrani, S. Alharbi, T.A. Elliott, F. Alqahtani, M. Manee. 2021. Genome-wide comparative analysis of transposable elements in Palmae genomes. Frontiers in Bioscience-Landmark. 26(11): 1119-1131
T.A. Elliott. Conceptual and empirical investigations of eukaryotic transposable element evolution. 2016. PhD Thesis. Department of Integrative Biology, University of Guelph
T.A. Elliott*, D.E. Stage*, T.J. Crease, T.H. Eickbush. 2013. In and out of rRNA genes: characterization of Pokey elements in the sequenced Daphnia genome. Mobile DNA. 4: 20
R. Vergilino, T.A. Elliott, P. Desjardins-Proulx, T.J. Crease, F. Dufresne. 2013. Evolution of a transposon in Daphnia hybrid genomes. Mobile DNA, 4: 7
T.A. Elliott. The activity and evolution of the Daphnia DNA transposon Pokey. 2011. MSc Thesis. Department of Integrative Biology, University of Guelph
* indicates co-first authorship
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Biology and Philosophy
Understanding the history and philosophical issues of your discipline is the job of every scientist, I feel. I have been lucky to collaborate with Dr. Stefan Linquist throughout the years on the philosophical issues inherent in TE research.
S. Linquist, T.R. Gregory, T.A. Elliott, B. Saylor, S.C. Kremer and K. Cottenie. 2016. Yes! There are resilient generalizations (or ‘”laws”) in ecology. The Quarterly Review of Biology. 91(2): 119-131
T.A. Elliott, S. Linquist, T.R. Gregory. 2014. Conceptual and empirical challenges of ascribing functions to transposable elements. The American Naturalist. 184(1): 14-24
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DNA Barcoding
In my position as a Research Associate in the Adamowicz Lab, and previously as the Data Management Lead for BOLD, I have had the privilege to play a part in several barcoding papers.
S. E. Majoros et al. 2024. Building a collaborative DNA barcode library for the Diptera of Churchill, Canada: A resource for northern research In review
D.S.J. Nowosad, I.D. Hogg, K. Cottenie, C. Lear, T.A. Elliott, J.R. deWaard, D. Steinke, S.J. Adamowicz. 2024. High diversity of freshwater invertebrates on Inuinnait Nuna, the Canadian Arctic, revealed using mitochondrial DNA barcodes. Polar Biology.
C.A. Hempel, S.E.E. Carson, T.A. Elliott, S.J. Adamowicz, D. Steinke. 2022. Reconstruction of small subunit ribosomal RNA from high-throughput sequencing data: A comparative study of metagenomics and total RNA sequencing. Methods in Ecology and Evolution.
P.R. Shashank, N.L. Naveena, N.N. Rajgopal, T.A. Elliott, K. Sreedevi, Sunil, N.N. Meshram. 2022. DNA barcoding of insects in India: Current status and future perspectives. Molecular Biology Reports.
T. Roslin et al. 2022. A molecular-based identification resource for the arthropods of Finland. Molecular Ecology Resources. 22(2) 803-822
C.-H. Lue et al.. 2021. DROP: Molecular voucher database for identification of Drosophila parasitoids. Molecular Ecology Resources. 21 (7): 2437-2354
C. Nugent, T.A. Elliott, S. Ratnasingham, P. Hebert, S.J. Adamowicz. 2021. debar, a sequence-by-sequence denoiser for COI-5P barcode data. Molecular Ecology Resources.
C.M. Nugent, T.A. Elliott, S. Ratnasingham, S.J. Adamowicz. 2020. coil: an R package for cytochrome C oxidase I (COI) DNA barcode data cleaning, translation, and error evaluation. Genome. 63(6): 291-305
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Book Chapters and Reviews
T.R. Gregory, T.A. Elliott, S. Linquist. 2016. Why genomics needs multi-level evolutionary theory. In “Evolutionary Theory: A Hierarchical Perspective”. Eds. Niles Eldredge, Telmo Pievani, Emanuele Serrelli, Ilya Temkin. The University of Chicago Press
T.A. Elliott*, J.A. Ågren*. 2016. A naturalists guide to mobile genetic elements. Evolution: Education and Outreach. 9:6
* indicates co-first authorship
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Resources for Transposable Elements
I have always been interested in improving the access to transposable element information, most recently in supporting the TE Hub project. More information can be found here and in the paper below.
The TE Hub Consortium, T.A. Elliott*, T. Heitkam*, R. Hubley*, H. Quesneville*, A. Suh*, T.J. Wheeler*. 2021. TE Hub: a community-oriented space for sharing and connecting tools, data, resources, and methods for transposable element annotation. Mobile DNA. 12: 16
I also maintain Repeat Resources , which mirrors much of the information on TE Hub, as well as some other catalogs of information I am working on.
If you work on Transposons/Mobile Genetic Elements and wish to connect with other researchers, please consider joining the TransposonsWorldwide Slack created by Dr. Rebecca Berrens
I also started my Transposon Library several years ago, where I collect books on Mobile Genetic Elements.
* indicates co-first authorship
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Genomes and Transposable Elements
To sequence and understand genomes is to tackle the annotation and classification of TEs and other repeats, both for the sake of understanding the elements themselves, but also how they have affected the evolution of their hosts.
S. Ou, W. Su, Y. Liao, K. Chougule, J.R.A. Agda, A.J. Hellinga, C.S.B. Lugo, T.A. Elliott, D. Ware, T. Peterson, N. Jiang, C.N. Hirsch, M.B. Hufford. 2019. Benchmarking transposable element annotation methods for creation of a streamlined, comprehensive pipeline. Genome Biology. 20: 275
T.A. Elliott and T.R. Gregory. 2015. What’s in a genome? The C-value enigma and the evolution of eukaryotic genome content. Philosophical Transactions of the Royal Society B: Biological Sciences. 370: 20140331
T.A. Elliott and T.R. Gregory. 2015. Do larger genomes contain more diverse transposable elements? BMC Evolutionary Biology. 15: 69
