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Otago Medical School staff profiles

Dr Ambarish Biswas

PositionResearch Fellow
DepartmentDepartment of Microbiology and Immunology
QualificationsPhD
Research summaryBioinformatics, environmental microbiology, microbial interactions

Research

Bioinformatics software development, analysis of (meta)genomic NGS data and building pipelines. CRISPR-Cas analysis.

Publications

Oo, K. M., Myat, T. O., Htike, W. W., Biswas, A., Hannaway, R. F., Murdoch, D. R., Crump, J. A., & Ussher, J. E. (2019). Molecular mechanisms of antimicrobial resistance and phylogenetic relationships of Salmonella enterica isolates from febrile patients in Yangon, Myanmar. Transactions of the Royal Society of Tropical Medicine & Hygiene. Advance online publication. doi: 10.1093/trstmh/trz053

Morales, S. E., Biswas, A., Herndl, G. J., & Baltar, F. (2019). Global structuring of phylogenetic and functional diversity of pelagic fungi by depth and temperature. Frontiers in Marine Science, 6, 131. doi: 10.3389/fmars.2019.00131

Centanni, M., Ferguson, S. A., Sims, I. M., Biswas, A., & Tannock, G. W. (2019). Bifidobacterium bifidum ATCC 15696 and Bifidobacterium breve 24b metabolic interaction based on 2'-O-fucosyl-lactose studied in steady-state cultures in a Freter-style chemostat. Applied & Environmental Microbiology. Advance online publication. doi: 10.1128/aem.02783-18

Ney, B., Ahmed, F. H., Carere, C. R., Biswas, A., Warden, A. C., Morales, S. E., … Greening, C. (2017). The methanogenic redox cofactor F420 is widely synthesized by aerobic soil bacteria. ISME Journal, 11, 125-137. doi: 10.1038/ismej.2016.100

Wolf, P. G., Biswas, A., Morales, S. E., Greening, C., & Gaskins, H. R. (2016). H2 metabolism is widespread and diverse among human colonic microbes. Gut Microbes, 7(3), 235-245. doi: 10.1080/19490976.2016.1182288

Chapter in Book - Research

Biswas, A., Fineran, P. C., & Brown, C. M. (2015). Computational detection of CRISPR/crRNA targets. In M. Lundgren, E. Charpentier & P. C. Fineran (Eds.), CRISPR: Methods in molecular biology (Vol. 1311). (pp. 77-89). New York, NY: Humana Press. doi: 10.1007/978-1-4939-2687-9_5

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Journal - Research Article

Oo, K. M., Myat, T. O., Htike, W. W., Biswas, A., Hannaway, R. F., Murdoch, D. R., Crump, J. A., & Ussher, J. E. (2019). Molecular mechanisms of antimicrobial resistance and phylogenetic relationships of Salmonella enterica isolates from febrile patients in Yangon, Myanmar. Transactions of the Royal Society of Tropical Medicine & Hygiene. Advance online publication. doi: 10.1093/trstmh/trz053

Centanni, M., Ferguson, S. A., Sims, I. M., Biswas, A., & Tannock, G. W. (2019). Bifidobacterium bifidum ATCC 15696 and Bifidobacterium breve 24b metabolic interaction based on 2'-O-fucosyl-lactose studied in steady-state cultures in a Freter-style chemostat. Applied & Environmental Microbiology. Advance online publication. doi: 10.1128/aem.02783-18

Morales, S. E., Biswas, A., Herndl, G. J., & Baltar, F. (2019). Global structuring of phylogenetic and functional diversity of pelagic fungi by depth and temperature. Frontiers in Marine Science, 6, 131. doi: 10.3389/fmars.2019.00131

Ney, B., Ahmed, F. H., Carere, C. R., Biswas, A., Warden, A. C., Morales, S. E., … Greening, C. (2017). The methanogenic redox cofactor F420 is widely synthesized by aerobic soil bacteria. ISME Journal, 11, 125-137. doi: 10.1038/ismej.2016.100

Wolf, P. G., Biswas, A., Morales, S. E., Greening, C., & Gaskins, H. R. (2016). H2 metabolism is widespread and diverse among human colonic microbes. Gut Microbes, 7(3), 235-245. doi: 10.1080/19490976.2016.1182288

Biswas, A., Staals, R. H. J., Morales, S. E., Fineran, P. C., & Brown, C. M. (2016). CRISPRDetect: A flexible algorithm to define CRISPR arrays. BMC Genomics, 17, 356. doi: 10.1186/s12864-016-2627-0

Greening, C., Biswas, A., Carere, C. R., Jackson, C. J., Taylor, M. C., Stott, M. B., Cook, G. M., & Morales, S. E. (2016). Genomic and metagenomic surveys of hydrogenase distribution indicate H2 is a widely utilised energy source for microbial growth and survival. ISME Journal, 10, 761-777. doi: 10.1038/ismej.2015.153

Staals, R. H. J., Jackson, S. A., Biswas, A., Brouns, S. J. J., Brown, C. M., & Fineran, P. C. (2016). Interference-driven spacer acquisition is dominant over naive and primed adaptation in a native CRISPR–Cas system. Nature Communications, 7, 12853. doi: 10.1038/ncomms12853

Samad, M. S., Biswas, A., Bakken, L. R., Clough, T. J., de Klein, C. A. M., Richards, K. G., … Morales, S. E. (2016). Phylogenetic and functional potential links pH and N2O emissions in pasture soils. Scientific Reports, 6, 35990. doi: 10.1038/srep35990

Biswas, A., Fineran, P. C., & Brown, C. M. (2014). Accurate computational prediction of the transcribed strand of CRISPR noncoding RNAs. Bioinformatics, 30(13), 1805-1813. doi: 10.1093/bioinformatics/btu114

Biswas, A., & Brown, C. M. (2014). Scan for Motifs: A webserver for the analysis of post-transcriptional regulatory elements in the 3’ untranslated regions (3’ UTRs) of mRNAs. BMC Bioinformatics, 15, 174. doi: 10.1186/1471-2105-15-174

Biswas, A., Gagnon, J. N., Brouns, S. J. J., Fineran, P. C., & Brown, C. M. (2013). CRISPRTarget: Bioinformatic prediction and analysis of crRNA targets. RNA Biology, 10(5), 817-827. doi: 10.4161/rna.24046

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