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Southern Cross Plant Science

Bioinformatics and Computational Biology

Scope

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 Brassica (Bloomfield, Baten, King)
  • Re-sequencing
  • Meta-genomics
    • Dicathais orbita (Ajit, Baten, Benkendorff)
    • Soil herbicide (Baten, Rose, NSW DPI)
  • Omics data integration
  • Crop species data integration and online delivery (King, Baten)

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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

Nock, C.J., Baten, A., King, G.J. (2014) "Complete chloroplast genome of Macadamia integrifolia confirms position of the early-diverging eudicot Gondwanan plant family Proteaceaes" BMC Genomics (2014), 15(Suppl 9):S13

Liu S, Liu Y, Yang X, Tong C, Edwards D, Parkin IA,….King GJ et al (2014) The Brassica oleracea genome reveals the asymmetrical evolution of polyploid genomes. Nature Communications 5: 3930.

Chaloub B …...King GJ….et al (2014) Early allopolyploid evolution in the post-neolithic Brassica napus oilseed genome. Science. 345:950-953

Isobel AP Parkin, Chushin Koh, Haibao Tang, Stephen J Robinson, Sateesh Kagale, … Graham King, Ian Bancroft and Andrew G Sharpe (2014) Transcriptome and methylome profiling reveals relics of genome dominance in the mesopolyploid Brassica oleracea. Genome Biology. 15:R77 doi:10.1186/gb-2014-15-6-r77

Nguyen, C., Baten, A., Morahan, G. (2014) "Comparison of sequence variants in transcriptomic control regions across 17 mouse genomes" Database Vol. 2014: article ID bau020; doi:10.1093/database/bau020

Rony, R. M. I. K., Baten, A., Bloomfield, J., Islam, Md. E.,Billah, Md. M.,Islam, K. D. (2014) "Inducing pluripotency in vitro: recent advances and highlights of iPSCs generation and pluripotent reprogramming" Cell Proliferation doi: 10.1111/cpr.12162. [ePub ahead of print]

Baten, A., Halgamuge, S. K., and Chang, B. C. H., (2008) "Fast splice site detection using information content and feature reduction " BMC Bioinformatics (2008), 9 (suppl 12): S8

Baten, A., Chang, B. C. H., Halgamuge, S. K., and Li, Jason., (2006). "Splice site identification using probabilistic parameters and SVM classification" BMC Bioinformatics (2006),7(suppl 5):S15.

Wang N, Li F, Chen B....King GJ et al. (2014) Genome-wide investigation of genetic changes during modern breeding of Brassica napus. Theoretical & Applied Genetics DOI 10.1007/s00122-014-2343-6

Nock C.J., Elphinstone, M.S., Ablett, G., Kawamata, A., Hancock, W., Hardner, C.M. and King, G.J. (2014) Whole genome shotgun sequences for microsatellite discovery and application in cultivated and wild Macadamia (Proteaceae). Applications in Plant Sciences. 2: 1300089.

Shapter FM, Cross M, Ablett G, Malory S, Chivers IH, King GJ, Henry RJ (2013) High-throughput sequencing and mutagenesis to accelerate the domestication of Microlaena stipoides as a new food crop. PLoS ONE. 8:e82641. DOI: 10.1371/journal.pone.0082641

Amoah, S, Kurup S, Rodriguez Lopez CM, Welham SJ, Powers SJ, Hopkins CJ, Wilkinson MJ, King GJ (2012) A Hypomethylated Population of Brassica rapa for Forward and Reverse Epi-Genetics. BMC Plant Biology.12:193

Love CG, Andongabo AE, Wang J, Carion PWC, Rawlings CJ, King GJ (2012) InterStoreDB: a generic integration resource for genetic and genomic data. J.Integrative Plant Biology. 54:345-355.

Gilks W, Welham S, Wang J, King GJ (2012) Three-point appraisal of genetic linkage maps. Theor. Appl. Genet.125: 1393-402.

Chapman NH, Bonnet J, Grivet L, Lynn J, Graham N, Smith R, Sun G, Walley PG, King GJ, Baxter C, Seymour GB (2012) High Resolution Mapping of a Fruit Firmness-Related QTL in Tomato Reveals Epistatic Interactions Associated with a Complex Combinatorial Locus. Plant Physiology 159:1644-1657.

The Brassica rapa Genome Consortium (2011). The genome of the mesopolyploid crop species Brassica rapa. Nature Genetics. 43: 1035-1039

Hammond JP, Mayes S, Bowen HC, Graham NS, Hayden RMm Love CG, Spracklen WP, Wang J, Welham SJ, White PJ, King GJ, Broadley MR. (2011) Regulatory hotspots are associated with plant gene expression under varying soil phosphorus (P) supply in Brassica rapa. Plant Physiology. 156: 1230-1241.

Wang J, Lydiate DJ, Parkin IAP, Falentin C, Delourme R, Carion P, King GJ (2011) Integration of Linkage Maps for the Amphidiploid Brassica napus and Comparative Mapping with Arabidopsis and Brassica rapa. BMC Genomics 12:101. doi:10.1186/1471-2164-12-101

Love CG, Graham NS, Ó Lochlainn S, Bowen HC, May ST, White PJ, Broadley MR, Hammond JP, King GJ (2010) A Brassica Exon Array for Whole-Transcript Gene Expression Profiling. PLOS One5(9): e12812

Østergaard L, King GJ (2008) Standardized gene nomenclature for the Brassica genus. Plant Methods. 4:10

King, GJ (2007) Utilization of Arabidopsis and Brassica Genomic Resources to Underpin Genetic Analysis and Improvement of Brassica crops. In: Model Plants : Crop Improvement. Eds. R.K. Varshney & R.M.D. Koebner, CRC Press, Boca Ratan (FL), USA. pp33-69.

King GJ (2004) Bioinformatics: Harvesting Information for Plant and Crop Science. Seminars in Cell & Developmental Biology. 15:721-731.

King, G.J. & Lynn, J.R. (1996) Constraints on mutability in a multi-gene family. J Molecular Evolution. 41:732-740

King, G.J. (1993). Stability, structure and complexity of yeast chromosome III. Nucleic Acids Research 21(18):4239-4245.

King, G.J. (1989). ELBAMAP: software for management of electrophoresis banding patterns. Computer Applications in the Biosciences 5: 313-317.

King, G.J. & Ingrouille, M.J. (1987). Genome heterogeneity and classification of the Poaceae. New Phytologist 107, 633-644. (used a Cray 1-S)

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