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Southern Cross Plant Science

Dr Abdul Baten

Abdul BatenResearch Fellow

t: +61 2 6620 3406
f: +61 2 6622 2080
e: abdul.baten@scu.edu.au

Education:
BSc. in Computer Science
PhD in Bioinformatics (University of Melbourne)

Research interests/background

Baten completed his PhD in Bioinformatics and Machine Learning from the University of Melbourne in 2009 and prior to that he completed his B.Sc. degree in Computer Science. He then worked at the Centre for Comparative Genomics (CCG) of Murdoch University where he worked in the wheat genome sequencing project. This was followed by a three years postdoctoral fellowship (Nov 2009-2012) at the University of Western Australia where he worked in the Centre for Diabetes Research (CDR) of The Western Australian Institute for Medical Research (WAIMR).

Baten's current research focus is the bioinformatics methods and the application of next generation sequencing in genomics, transcriptomics, epigenomics and metagenomics domain of various plants and animals. He is currently focusing on the denovo assembly and annotation of Macadamia, Corymbia and B. rapa R-o-18 genomes. Baten is also working with methods and databases to integrate genetic and omics data into a common framework, which will facilitate analysis, visualization and navigation of genetic data and omics data from multiple platforms. Here is a list of SCPS bioinformatics projects.

Grants/Awards

  • $1,250,000. Grains Research and Development Corporation "A consortium approach to assessing risk and biological impacts of herbicides in the grains industry" (2013-2017) (Dr L. van Zwieten, Dr M. Rose, Dr N. Seymour, Dr G. McGrath, Dr T. Vancov, Dr T. Rose, Dr A. Baten, Mr S. Kimber, Prof. I. Kennedy, Dr A. Crossan, Dr T. Cavagnaro, Ms A. Jenkins)
  • $5,000 SCU SEED research grant (2015) "Integrating genomic and genetic data to harness wheat improvement" (Dr. Abdul Baten, Professor Graham King)
  • $185,000. Horticulture Innovation Australia (2015-2019) "Establishing an open-source platform for unravelling the genetics of Macadamia: integration of linkage and genome maps " (Dr. Dr Catherine Nock, Dr. Abdul Baten, Prof. Graham King)
  • $66,000. Wound management innovation CRC (2015-2018) "Diabetic ulcers: Biofilm and treatment therapies " (A. Professor Kirsten Benkendorff, Dr. Abdul Baten, Dr. Joanne Bradbury, Dr. Paul Butterworth)
  • $10,000 SCU SEED research grant (2016) "CropSoreDB for post-genomic integration of major crop datasets: a public-domain resource to integrate wheat trait and (epi-)genome" (Dr. Abdul Baten, Professor Graham King)

Publications

  • 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
  • Ngangbam, A. K., Waters, D. L. E., Whalan, S., Baten, A., Benkendorff, K. (2015) "Indole producing bacteria from the biosynthetic organs of Muricid mollusc could contribute to Tyrian purple production" Journal of Shellfish Research (2015) 34(2):443-454
  • Rony, R. M. I. K., Baten, A., Bloomfield, J., Islam, Md. E.,Billah, Md. M.,Islam, K. D. (2015) "Inducing pluripotency in vitro: recent advances and highlights of iPSCs generation and pluripotent reprogramming" Cell Proliferation (2015) DOI: 10.1111/cpr.12162
  • 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
  • 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
  • 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.
  • Baten, A., Halgamuge, S. K., Chang, B. C. H., and Wickramarachchi N., (2008) "Biological Sequence Data Preprocessing for Classification: A Case Study in Splice Site Identification.". Lecture Notes in Computer Science(2007): 4492(1221-1230), Springer Verlag, June 2007
  • Shepherd, M., Baten, A., O. Bonfim da Silva Junior, D. J. Lee, J. Butler et al., 2015. UTowards a Corymbia reference genome: comparative efficiencies of Illumina, PacBio and hybrid de novo assemblies of a complex heterozygous genome, pp. in Tree Biotechnology Conference, Florence Italy, June 6-8, 2015
  • Baten, A., Nock, C.J., Kawamata, A., Furtado, A., Henry, R.J. and King, G.J. Unravelling the Gondwanan genome of macadamia. Plant and Animal Genome XXII Conference(PAG), San Diego, California. January 11-15, 2014
  • Nock, C.J., Baten, A., Hancock, W., Kawamata, A., Hardner, C.M., Topp, B., Henry, R.J. and King, G.J. Harvesting the macadamia genome. Plant and Animal Genome XXII Conference(PAG), San Diego, California. January 11-15, 2014
  • Bloomfield, JA., Rose, TJ., Kawamata, A., Nock C., Hopkins, C., Kurup, S., Wang, J., Baten, A., King GJ. Epigenetic profiling during Brassica rapa reproductive development. Poster abstract and poster. Plant Animal Genome Asia I. Singapore. March 2013
  • Baten, A., Ngangbam, A., Benkendorff, K. Preliminary genome sequencing, de novo assembly and annotation of the Neogastropoda Dicathais orbita. International Marine Biotechnology Conference, IMBC-2013, Nov 11-15, Brisbane
  • Baten, A., Halgamuge, S. K., Hybrid Methods for the Detection of Splice Sites in the Human Genome. 'Bioinformatics Australia 2009 conference (BA2009), Melbourne, Australia
  • Baten, A., Bellgard, M., Halgamuge, S. K. Comparative Analysis of Regular and Alternative Splice Site Strength in Several Eukaryotic Species. 'Bioinformatics Australia 2009 conference (BA2009), Melbourne, Australia
  • Baten, A., Halgamuge, S. K., Wickramarachchi, N., and Rajapakse, J. C., Splice Site Detection Using a Combination of Markov Model and Neural Network. 'International joint conference of InCoB, AASBi and KSBI (BIOINFO 2005)

Student supervision

  • Amin Ibrahim

PhD project: Bioinformatic approaches to unravel epigenetic basis of crop plasticity

  • Liliana Andres

PhD project: Knowledge representation and database integration to facilitate genetic analysis and development of underutilised crop plants

  • Sadaf Naz

Masters by research project: Development of interactive statistical modules to explore diverse crop phenotypic data

  • Jeanette Travis (Co-supervising with Dr Kirsten Benkendorff)

PhD project: Diabetic Ulcers-Investigation of biofilms and antimicrobial therapies

  • Ajit Kumar Ngangbam (Co-supervised with Dr Kirsten Benkendorff) (Completed in 2016)

PhD project: Putative role for bacterial symbionts in the biosynthetic origin of Tyrian purple in Dicathais orbita, a Muricidae mollusc