Bioinformatics

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Bioinformatics can be defined as the mathematical, statistical and computing methods that aim to solve biological problems and derive knowledge using data generated from various omics platforms and related sources. Research in bioinformatics includes method development for the analysis of the data as well as data storage and retrieval.

SCPS has a wide range of bioinformatics projects and excellent facilities for bioinformatics research and development. We collaborate with researchers in crop and soil science, zoology and marine ecology.

Research opportunities

For Masters/PhD opportunities or for further information please contact Dr. Abdul Baten

Current projects

  • De novo sequencing and annotation projects - complex plant genomes
    • Macadamia (Baten, Nock)
    • Corymbia (spotted gum; Baten, Shepherd, U. Tas, Embrapa Brazil)
    • Melaleuca (tea tree; Baten, Shepherd)
  • Transcriptome analysis
    • Macadamia (Baten, Nock)
    • Brassica Rapa (Baten, Bloomfield, King)
    • Rice (Jeong, Baten, Rose)
    • Corymbia (Baten, Shepherd, U. Tas, Embrapa Brazil)
    • Dicathais orbita (Baten, Ajit, Benkendorff)
  • Epigenome
    • Methylome WGBS (5mC) mapping in Brassicsa(Bloomfield, Baten, King)
  • Re-sequencing
    • Bush tomato(Bundock, Baten)
    • Hybrid rice (Baten)
  • Meta-genomics
    • Dicathais orbita (Ajit, Baten, Benkendorff)
    • Soil herbicide (Baten, Rose, NSW DPI)
  • Omics data integration
    • Integration of transcriptomics, proteomics and metabolomics data of Mesembryanthemum crystallinum (Bronwyn Barkla, Baten)
  • Crop species data integration and online delivery (King, Baten)
    • CropStoreDB platform (part of InterStoreDB)
      •  (+other in UK)

Computing resources

  • HP Blade server with 512GB RAM and 32CPUs (RedHat Linux)
  • 50+ TB 3PAR SAN storage
  • TimeLogic Decypher server (Hardware accelerated sequence alignment)
  • As a member of Intersect we have access to NSW state funded high performance computing infrastructure. Each year we receive a large HPC quota in the Orange, which is a large memory cluster featuring 100 cluster nodes with 1600 cores powered by the Intel® Xeon® E5-2600 processor series. It also includes 200TB local scratch disk space, 101TB of usable shared storage delivering 30+ TFlops.

Selected Publications

Calvert, J., Baten, A., Butler, J., Barkla, B., and Shepherd, M. “Terpene synthase genes in Melaleuca alternifolia: comparative analysis of lineage- specific subfamily variation within Myrtaceae”, Plant Systematics and Evolution (2017), DOI: 10.1007/s00606-017-1454-3

Butler, J. B., Vaillancourt, R. E., Potts, B. M.,  King, G. J., Baten, A., Shepherd, M., and Freeman, J.,  “Comparative genomics of Eucalyptus and Corymbia reveals low rates of genome structural rearrangement”BMC Genomics  (2017), DOI 10.1186/s12864-017-3782-7

Das, A., Ahmed, O., Baten, A., Bushra, S., Islam, T., Sabah, A., Islam, R., and Khan, H. Draft Genome Sequence of Grammothele lineata SDL- CO-2015-1, a Jute Endophyte with a Potential for Paclitaxel Biosynthesis”, Genome Announcements (2017), DOI: 10.1128/genomea.00825-17

Grover, Jeffrey., Kendall, Timmy., Baten, Abdul., King, J. Graham., Mosher, A. Rebecca. “Maternal RNA-directed DNA methylation is required for seed development in Brassica rapa”, bioRxiv (preprint), doi: https://doi.org/10.1101/174805

Didier, L., Anand, S., Santos, R., Mayes, S., Ray, R., Al-Azri, M., Baten, A., King, G., Karunaratne, A., Azam-Ali, S., Jackson, M. Geospatial binding for transdiciplinary research in crop science: the GRASPgfs initiative”, Open Geospatial Data, Software and Standards  (2017), DOI: 10.1186/s40965-017-0034-3

Nock, C.J., Baten, A., Barkla, B, J., Furtado, A., Henry, R.J. and King, G.J. (2016) "Genome and transcriptome sequencing characterises the gene space of Macadamia integrifolia (Proteaceae)" BMC Genomics (2016) DOI: 10.1186/s12864-016-3272-3

Baten, A., Ngangbam, A. K., Waters, D., Benkendorff, K. (2016) "Transcriptome of the Australian mollusc Dicathais orbita provides insights in the biosynthesis of indoles and choline esters" Marine Drugs (2016) 14(7), 135; doi:10.3390/md14070135

Jeong, K; Baten, A; Waters, D; Pantoja, O; Julia, C; Wissuwa, M; Heuer, S; Kretzschmar, T; Rose, T (2016) "Phosphorus remobilisation from rice flag leaves during grain filling: an RNA-seq study" plant biotechnology journal (2016) DOI: 10.1111/pbi.12586

Waters, D. L. E., Gopala, K. S., Mani, E., Singh, S., Vaddadi, S., Baten, A., Henry, R. J. (2015) "Genome wide polymorphisms and yield heterosis in rice (Oryza sativa subsp. indica)" Tropical Plant Biology (2015) DOI 10.1007/s12042-015-9156-x

Ngangbam, A. K.,Baten, A.,., Waters, D. L. E., Whalan, S., Benkendorff, K. (2015) "Characterization of Bacterial Communities Associated with the Tyrian Purple Producing Gland in a Marine Gastropod" PLoS ONE (2015) DOI: 10.1371/journal.pone.0140725

Jiang, F. X., Mishina, Y., Baten, A., Morahan, G., Harrison, L. (2015) "Transcriptome of pancreas-specific Bmpr1a-deleted islets links to TPH1-5-HT axis" Biology Open (2015) 00, 1-8 doi:10.1242/bio.011858