Thomas Harrop


I am a post-doctoral researcher with a background in bioinformatics, genetics and molecular biology and interests in data science and research relating to agriculture. I mainly work with R, Python and shell scripts. I have experience in molecular, plant, animal and medical laboratories and installing, maintaining and using computers running Unix, Linux and macOS.


Personal information

Nationalities
Australian and British
Research
My research interests include plant and insect research related to agronomy, tools and techniques in bioinformatics and evolutionary and comparative biology.
Technical
My main tools are R, Python and bash. I use git and GitHub for version control and follow the principles of reproducible research when coding. I also use Markdown, TeX, html and css.
I have experience with workload managers for high-performance computing (HPC) including SGE, LSF and SLURM.
I have built and used workstations and servers that run macOS, Ubuntu and FreeBSD, and run jobs in HPC environments running Debian and CentOS.
I have skills in molecular biology techniques including quantitative real-time PCR, cloning, nucleic acid extraction and cDNA library preparation, as well as classical genetic approaches with live organisms, such as transformation, crosses, microdissection and bioassays.
Languages
English (native), German (TELC Level B2) and French (TELC Level B1)

Education

2006–2012
Doctor of Philosophy, Department of Genetics, the University of Melbourne, Parkville, Australia.
Thesis: The functions of cytochrome P450s in Drosophila.
During my Ph.D. I used classical genetics and modern molecular biology, including transgenic manipulation of gene expression and comparative studies of gene function, to investigate the functions of cytochrome P450 genes in the Drosophila genus.
2002–2005
Bachelor of Science with Honours (first class), the University of Melbourne, Parkville, Australia.
Awards
2006–2009, Australian Postgraduate Award

Experience

Research positions

2017–Present

Post-doctoral researcher, Laboratory for Evolution and Development, Biochemistry Department, University of Otago, Dunedin, New Zealand.
I am currently working on a project to develop and apply tools to integrate genomic selection to breeding programmes to improve honeybee performance.

2016–2017

Post-doctoral researcher, Laboratory for Evolution and Development, Biochemistry Department, University of Otago, Dunedin, New Zealand.
In this project, I worked on a bioprotection project investigating the resistance of Argentine stem weevil to its biological control agent.

2014–2016
Post-doctoral researcher, UMR DIADE, Institut de Recherche pour le Développement (IRD), Montpellier, France.
I used machine learning, data mining, statistical analyses and other bioinformatic techniques to study the development of inflorescence architecture in rice, which affects crop yield. We used laser microdissection and RNA sequencing to characterise molecular events that occur in the developing inflorescence, and applied these results to study the effects of selection on gene expression during the parallel domestications of African and Asian rice.
2013–2014
Post-doctoral researcher, Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, Germany.
At the Max Planck Institute I worked on a bioinformatic and molecular biology project to compare the transcriptional response of different land plants to UV-B exposure, which acts as an environmental signal.

Professional positions

2004–2007
Medical scientist, Network Pathology, the Austin Hospital, Heidelberg, Australia.
2001–2004
Laboratory assistant, Network Pathology, the Austin Hospital, Heidelberg, Australia.

Teaching

2007–2011
3rd Year Genetics, Department of Genetics, The University of Melbourne, Parkville, Australia.
2006–2009
High School Biology, Department of Genetics, The University of Melbourne, Parkville, Australia.
2006–2008
High School Biology, Gene Technology Access Centre, The University High School, Parkville, Australia.
2005–2008
1st Year Genetics, The University of Melbourne, Parkville, Australia.

Students co-supervised

Marissa Le Lec
Bachelor of Science with Honours, Genetics, University of Otago, Dunedin, New Zealand.
Swarit Jaisal
Master of Science, Life Science Informatics, Universität Bonn, Germany.
Axel Verdier
Master of Science, Sciences et Technologies de l’Information et de la Communication pour la Santé, Université de Montpellier, France.

Publications

Peer-reviewed journals

Lamichhane, R., Schneider, M., Harpe, S.M. de la, Harrop, T.W.R., Hannaway, R.F., Dearden, P.K., Kirman, J.R., Tyndall, J.D.A., Vernall, A.J., and Ussher, J.E. (2019). TCR- or Cytokine-Activated CD8+ Mucosal-Associated Invariant T Cells Are Rapid Polyfunctional Effectors That Can Coordinate Immune Responses. Cell Reports 28, 3061-3076.e5. doi:10.1016/j.celrep.2019.08.054.

Harrop, T.W.R., Mantegazza, O., Luong, A.M., Béthune, K., Lorieux, M., Jouannic, S., and Adam, H. (2019). A set of AP2-like genes is associated with inflorescence branching and architecture in domesticated rice. Journal of Experimental Botany 70, 5617–5629. doi:10.1093/jxb/erz340

Guerrero, F.D., Bendele, K.G., Ghaffari, N., Guhlin, J., Gedye, K.R., Lawrence, K.E., Dearden, P.K., Harrop, T.W.R., Heath, A.C.G., Lun, Y., et al. (2019). The Pacific Biosciences de novo assembled genome dataset from a parthenogenetic New Zealand wild population of the longhorned tick, Haemaphysalis longicornis Neumann, 1901. Data in Brief 27, 104602. doi:10.1016/j.dib.2019.104602.

Harrop, T.W.§, Denecke, S.§, Yang, Y.T., Chan, J., Daborn, P.J., Perry, T., Batterham, P., (2018). Evidence for activation of nitenpyram by a mitochondrial cytochrome P450 in Drosophila melanogaster. Pest Management Science 74, 1616–1622. doi:10.1002/ps.4852.

Ta, K. N., Adam. H., Staedler, Y.M., Schönenberger, J., Harrop. T.W.R., Tregear, J., Do, N.V.,Gantet, P., Ghesquière, A., and Jouannic, S. (2017). Differences in meristem size and expression of branching genes are associated with variation in panicle phenotype in wild and domesticated African rice. EvoDevo 8: 2. doi:10.1186/s13227-017-0065-y.

Harrop, T.W.R.§, Ud Din, I.§, Gregis, V., Osnato, M., Jouannic, S., Adam, H. and Kater, M. (2016). Gene expression profiling of reproductive meristem types in early rice inflorescences by laser microdissection. The Plant Journal 86, 75–88. doi:10.1111/tpj.13147.

Harrop, T.W.R.§, Pearce, S.L.§, Daborn, P.J. and Batterham, P. (2014). Whole-genome expression analysis in the third instar larval midgut of Drosophila melanogaster. G3 (Bethesda) 4, 2197–2205. doi:10.1534/g3.114.013870.

Harrop, T.W.R., Sztal, T., Lumb, C., Good, R.T., Daborn, P.J., Batterham, P. and Chung, H. (2014). Evolutionary changes in gene expression, coding sequence and copy-number at the Cyp6g1 locus contribute to resistance to multiple insecticides in Drosophila. Plos One 9, e84879. doi:10.1371/journal.pone.0084879.

Daborn, P.J., Lumb, C., Harrop, T.W.R., Blasetti, A., Pasricha, S., Morin, S., Mitchell, S.N., Donnelly, M.J., Müller, P. and Batterham, P. (2012). Using Drosophila melanogaster to validate metabolism-based insecticide resistance from insect pests. Insect Biochemistry and Molecular Biology 42, 918–924. doi:10.1016/j.ibmb.2012.09.003.

§ Equal contribution

Book chapters

Cridge, A., Harrop, T. W. R., Lovegrove, M., Remnant, E. & Dearden, P. (2017). Nutrition and Epigenetic Change in Insects: Evidence and Implications, in Advances in Insect Physiology (ed. Verlinden, H.) 53, 31–54 (Academic Press). doi:10.1016/bs.aiip.2017.06.001

Selected scientific presentations

The genomes of three invasive social wasps. Oral presentation at the Annual Conference of the Genetics Society of Australasia (GSA), Melbourne, Australia, 2019. Symposium chair: Genomics & bioinformatics.

Comparative genomics of sexual and asexual parasitoid wasps from the Microctonus genus. Poster presentation at the 7th meeting of the European Society for Evolutionary Developmental Biology, Galway, Ireland, 2018.

Genomics of a weevil pest and its parasitoid biocontrol agent. Poster presentation at the Annual Conference of the Genetics Society of Australasia (GSA) with the New Zealand Society for Biochemistry and Molecular Biology (NZSBMB), Dunedin, New Zealand, 2017.

De novo sequencing of Argentine stem weevil and its parasitoid wasp biocontrol agent. Poster presentation at the 10th Annual Arthropod Genomics Symposium, Notre Dame University, South Bend, U.S.A., 2017.

Sequencing and community annotation of the Vespula vulgaris genome. Oral presentation at the Entomological Society of NZ Conference, Wellington, New Zealand, 2017.

Genes controlling transition of reproductive meristem identity during inflorescence development. Oral presentation at the 14th International Symposium on Rice Functional Genomics, Montpellier, France, 2016.

Mechanisms underlying the parallel evolution of inflorescence phenotype during independent domestication of African and Asian rice. Contributed oral presentation at the 6th meeting of the European Society for Evolutionary Developmental Biology, Uppsala, Sweden, 2016. Joint symposium chair: Branching across the tree of life.

Gene expression during O. sativa panicle development. Invited seminar at the Agricultural Genetics Institute, Hanoi, Vietnam, 2015.

Molecular mechanisms underlying the phenotypic convergence of inflorescence architecture in domesticated rice species. Poster presentation at the Society for Molecular Biology and Evolution annual meeting, Vienna, Austria, 2015.

Transcriptomic analysis of early developmental stages of the rice panicle. Poster presentation at the Workshop in Molecular Mechanisms Controlling Flowering, Aiguablava, Spain, 2015

RNA interference of the Cytochrome P450 redox partners Cpr and dare uncovers novel P450 functions in Drosophila melanogaster. Poster presentation at the 50th Annual Drosophila Research Conference, Chicago, USA, 2009.


· tomharrop.io

Dunedin, NEW ZEALAND