Anna Syme

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Research

Links to publications, presentations, and training resources developed.

Bioinformatician, Australian BioCommons

Melbourne Bioinformatics, Melbourne University, October 2020 to present

Workforce transition and user-upskilling for the Australian BioCommons Bring-Your-Own-Data project.

A nice welcome here from Melbourne Bioinformatics!



Research Scientist, Bioinformatics

Royal Botanic Gardens Victoria, February 2019 to September 2020

I worked on the Genomics for Australian Plants project (Bioplatforms Australia), as lead for the working groups: Bioinformatics (Reference Genomes), and Bioinformatics Training. A focus was the genome for the golden wattle, Acacia pycnantha, with sequencing data from Illumina, Oxford Nanopore, and 10X. A manuscript for assemblies of the chloroplast and mitochondrial genomes is in prep. Long sequencing reads have been particularly informative regarding the structural complexity of the mitome.

mitome-paths

Investigating paths through the mitochondrial assembly to understand genomic structure

The training webpage for the Australian plant genomics research community has been set up and will expand over the next few years.

training-webpage-snapshot

Snapshot of training webpages, Feb 2020: https://plant-genomics.github.io/training/

New training will be developed using both the Galaxy Australia platform and command-line tools. A recent publication aims to make bioinformatics software development easier and more user-friendly with the Bionitio tool:

bionitio

Overview of the automated process for creating new projects performed by the Bionitio bootstrap script. From: Peter Georgeson, Anna Syme, Clare Sloggett, Jessica Chung, Harriet Dashnow, Michael Milton, Andrew Lonsdale, David Powell, Torsten Seemann, Bernard Pope. (2019) Bionitio: demonstrating and facilitating best practices for bioinformatics command-line software, GigaScience.

Bioinformatician

Melbourne Bioinformatics, May 2016 to January 2019

Bacterial genome assembly for Bioplatforms Australia project on antibiotic resistance. Development and presentation of bioinformatics training. Galaxy Australia Training Manager (2018). Contributor to the Galaxy Training Network. Subject coordinator for Elements of Bioinformatics (Masters level, University of Melbourne)(2018).

training-examples

Training examples: Galaxy Australia training webpage snapshot, https://galaxy-au-training.github.io/tutorials/; Development of long-read genome assembly workshop (command-line, presented at Melbourne Bioinformatics).

Molecular Systematist

Royal Botanic Gardens Victoria, September 2010 to December 2012

Molecular analyses of grasses (Stipeae) and fungi (Agaricaceae), including studies on diversification rates, and the evolution of morphological features. Molecular Lab Manager.

Austrostipa

From Syme, A. E. (2012). Diversification rates in the Australasian endemic grass Austrostipa - 15 million years of constant evolution. Plant Systematics and Evolution; and Syme, A. E., Murphy, D. J., Holmes, G. D., Gardner, S., Fowler, R. and Cantrill, D. C. (2012). An expanded phylogenetic analysis of Austrostipa (Poaceae: Stipeae) to test infrageneric relationships. Australian Systematic Botany, 25:1-10.

fungi-phylogeny

From Lebel, T. and Syme, A. E. (2012). Sequestrate Agaricus and Macrolepiota from Australia: new combinations and species, and their position in a calibrated phylogeny. Mycologia, 104:496-520.

Postdoctoral Researcher

UC Santa Barbara, California, April 2007 to April 2008

At the Oakley Evolution Lab. Evolutionary dynamics of ostracods including modeling gain/loss of the lateral eye and modeling speciation/extinction rates. Phylogenetics of vision genes in Pancrustacea.

Ostracod-eye-evolution

From Syme A. E. and Oakley T. H. (2012). Dispersal between shallow and abyssal seas and evolutionary loss and re-gain of ostracod compound eyes in cylindroleberidid ostracods: conflicting conclusions from different comparative methods. Systematic Biology, 61(2): 314-336.

chupacabra

From Lum, K. E., Syme, A. E., Schwab, A. K. and Oakley, T. H. (2008). Euphilomedes chupacabra (Ostracoda: Myodocopida: Philomedidae), a new demersal marine species from coastal Puerto Rico with male-biased vespertine swimming activity. Zootaxa, 1684: 35–57.

gene-duplication

From Rivera, A. S, Pankey, M. S., Plachetzki, D. C., Villacorta, C., Syme, A. E., Serb, J. M., Omilian, A. R. and Oakley, T. H. (2010). Gene duplication and the origins of morphological complexity in pancrustacean eyes, a genomic approach. BMC Evolutionary Biology, 10:123.

PhD (Zoology)

The University of Melbourne, Australia, January 2003 - January 2007

Systematics, taxonomy, evolution of the ostracod family Cylindroleberididae (Crustacea). Co-author on marine field guides.

new-species

From Syme, A. E. and Poore, G. C. B. (2006). Three new species of the Cylindroleberididae from coastal Australian waters (Crustacea: Ostracoda). Zootaxa, 1305: 51–67.

type-species-redescription

From Syme and Poore (2008) PLoS ONE, A Supplementary Description of Cypridina mariae and Rediagnosis of the Genus Cylindroleberis (Ostracoda: Myodocopa: Cylindroleberididae) https://doi.org/10.1371/journal.pone.0001960.

leuroleberis-and-asteropterygion

Leuroleberis mackenziei and Asteropterygion magnum. Collected Victoria, Australia, 2004.

books

Wilson, R., Norman, M. and Syme, A. E. (2007). An Introduction to Marine Life. Museum Victoria; CSIRO Publishing. Poore, G. C. B. and Syme, A. E. (2009). Barnacles. Museum Victoria; CSIRO Publishing.