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The Bioinformatics Hub currently has two full-time staff members, and one position held in conjunction with the Robinson Research Institute.

Co-ordinator - Steve Pederson

As the inaugural co-ordinator of the Bioinformatics Hub, Steve began the position in 2014. He has been involved as an educator outside of Science for over 20 years, and brings this experience to the training workshops run at regular intervals. With a strong background in genetics and statistics, Steve is proficient in R, C and bash scripting. His research interests include regulation of gene expression, and downstream analysis of gene sets.

Select Publications:

  1. Nina I. Schwensow, Harald Detering, Stephen Pederson, Camila Mazzoni, Ron Sinclair, David Peacock, John Kovaliski, Brian Cooke, Jörns Fickel, Simone Sommer (2017) Resistance to RHD virus in wild Australian rabbits: Comparison of susceptible and resistant individuals using a genomewide approach. Molecular Ecology 26 (17) 4551–4561
  2. Lu Zeng, Stephen Pederson, Dan Feng Cao, Zhi Peng Qu, Zhi Qiang Hu, David Adelson, Chao Chun Wei (2017) Genome-Wide Analysis Of Repetitive Elements Associated With Gene Regulation. Bioarxiv doi: https://doi.org/10.1101/142018
  3. Kym D. Perry, Stephen M. Pederson, Simon W. Baxter (2017) Genome-Wide SNP Discovery In Field And Laboratory Colonies Of Australian Plutella Species. Bioarxiv doi: https://doi.org/10.1101/141606
  4. Sinny Delacroix, Ramesh G Chokka, Adam J Nelson, Dennis T Wong, Samuel Sidharta, Stephen M Pederson, Adil Rajwani, Joanne Nimmo, Karen S Teo, Stephen G Worthley (2017) Renal sympathetic denervation increases renal blood volume per cardiac cycle: a serial magnetic resonance imaging study in resistant hypertension. International Journal of Nephrology and Renovascular Disease 10: 243-249 doi: 10.2147/IJNRD.S131220
  5. McInnes N, Sadlon TJ, Brown CY, Pederson S, Beyer M, Schultze JL, McColl S, Goodall GJ, Barry SC (2012) FOXP3 and FOXP3-regulated microRNAs suppress SATB1 in breast cancer cells. Oncogene 31(8):1045-54. doi: 10.1038/onc.2011.293
  6. Hill D, Eastaff-Leung N, Bresatz-Atkins S, Warner N, Ruitenberg J, Krumbiegel D, Pederson S, McInnes N, Brown CY, Sadlon T, Barry SC. Inhibition of activation induced CD154 on CD4+ CD25- cells: a valid surrogate for human Treg suppressor function. Immunol Cell Biol. 90(8):812-21. doi: 10.1038/icb.2012.18
  7. Sadlon TJ, Wilkinson BG, Pederson S, Brown CY, Bresatz S, Gargett T, Melville EL, Peng K, D'Andrea RJ, Glonek GG, Goodall GJ, Zola H, Shannon MF, Barry SC (2010) Genome-wide identification of human FOXP3 target genes in natural regulatory T cells. J Immunol. 185(2):1071-81. doi: 10.4049/jimmunol.1000082.

Post Doctoral Bioinformatician - Hien To

With a strong background in applied mathematics, Dr To received her PhD in 2011 from Université Paris Diderot - Paris 7. She has been working on algorithm aspects of constructing phylogenies, reconciling gene trees within species phylogenies to predict gene losses, duplications or transfers; and on molecular dating methods. Her research interests include of developments of algorithms, and modelling in bioinformatics.

Select Publications:

  1. Michel Habib, Thu-Hien To: Level-k Phylogenetic Networks Are Constructable from a Dense Triplet Set in Polynomial Time. CPM 2009: 275-288
  2. Michel Habib, Thu-Hien To: On a Conjecture about Compatibility of Multi-states Characters. WABI 2011: 116-127
    Michel Habib, Thu-Hien To: Constructing a Minimum phylogenetic Network from a Dense triplet Set. J. Bioinformatics and Computational Biology 10(5) (2012)
  3. Thu-Hien To, Matthieu Jung, Samantha Lycette, and Olivier Gascuel, Fast Dating Using Least-squares Criteria and Algorithms, Systematic Biology 2015; doi: 10.1093/sysbio/syv068
  4. Thu-Hien To, Celine Scornavacca, Efficient algorithms for reconciling gene trees and species networks via duplication and loss events, BMC Genomics 2015, 16(Suppl 10):S6
  5. Thu-Hien To, Edwin Jacox, Vincent Ranwez, and Celine Scornavacca, Fast methods for Calculating Event Supports in Gene Tree Reconciliations, accepted for BMC Bioinformatics.

Post Doctoral Bioinformatician - Jimmy Breen

Jimmy is a Bioinformatician and genomic researcher with 10 years expertise. Starting research life in agricultural genomics, he gained his PhD in assembling complex (>16Gb/>70% repetitive DNA) plant genomes as part of the International Wheat Genome Sequencing Consortium. His Post doctoral position in Switzerland (plant/fungal disease resistance genes and physical map assembly) was followed by QC and data analysis for AGRF in Brisbane.

His previous role was at the Australian Centre for Ancient DNA and School of Agriculture, Food and Wine, working with Professor Alan Cooper on a range of projects including:

  • ancient DNA sequencing of 5,000 year old plant material from Armenia
  • metagenomics and NGS pipeline development for the analysis of dental calculus from Neandertals and other ancient Hominins,
  • developing an ancient human genome data repository called the Online Ancient Genome Repository (OAGR; https://www.oagr.org.au)
  • epigenetic profiling of fungal pathogens (Botrytis cinerea) and Shiraz plants in the Barossa Valley.

Jimmy is also the lecturer for the University of Adelaide’s Bioinformatics and Systems Modelling unit as part of the Master of Biotechnology course.

Select Publications:

  1. Czechowski P, Clarke LJ, Breen J, Cooper A, Stevens MI. (2016). Exploration of the Prince Charles Mountains, East Antarctica: Eukaryotic soil diversity investigated by high throughput sequencing. Soil Biology and Biochemistry. Accepted 18/12/2015
  2. Ellison A, Rodríguez López CM, Moran P, Breen J, Swain M, Megias M, Hegarty M, Wilkinson M, Pawluk R and Consuegra S. (2015). Epigenetic regulation of sex-ratios may explain natural variation in self-fertilisation rates. Proceedings of the Royal Society B, Accepted 09/10/2015
  3. Hurni S, Scheuermann D, Krattinger SG, Kessel B, Wicker T, Herren G, Fitze MN, Breen J, Presterl T, Ouzunova M, Keller, B. (2015). The maize disease resistance gene Htn1 against northern corn leaf blight encodes a wall-associated receptor-like kinase. Proceedings of the National Academy of Sciences, 112(28): 8780-8785
  4. Young J, Weyrich LS, Breen J, Macdonald LM, Cooper A. (2015). Predicting the origin of soil evidence: high throughput eukaryote sequencing and MIR spectroscopy applied to a crime scene scenario. Forensic Science International. Accepted March 2015
  5. Mago R, Tabe L, Vautrin S, Simková H, Kubaláková M, Upadhyaya N, Berges H, Kong XY, Breen J, Dolezel J, Appels R, Ellis J, Spielmeyer W. (2015). Major haplotype divergence including multiple germin-like protein genes, at the wheat Sr2 adult plant stem rust resistance locus. BMC Plant Biology. Accepted February 2015.
  6. Breen J, Wicker T, Shatalina M, Frenkel Z, Bertin I, Phillippe R, Spielmeyer W, Doležel J, Simková H, Scalabrin S, Vautrin S, Bergès H, International Wheat Genome Sequencing Consortium, Paux E, Fahima T, Korol A, Feuillet C and Keller B. (2013). A Physical Map of the Short Arm of Wheat Chromosome 1A. PLoS ONE, 8(11), e80272
Bioinformatics Hub
Address

Level 4,
Santos Petroleum Engineering Building,
North Terrace Campus
The University of Adelaide
SA 5005
Australia

Contact

T: +61 8 8313 1207
Email