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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

Wang, X., Reilly, K., Heathcott, R., Biswas, A., Johnson, L. J., Teasdale, S., … Morales, S. E. (2022). Soil nitrogen treatment alters microbiome networks across farm niches. Frontiers in Microbiology, 12, 786156. doi: 10.3389/fmicb.2021.786156

Meaden, S., Biswas, A., Arkhipova, K., Morales, S. E., Dutilh, B. E., . . ., & Fineran, P. C. (2022). High viral abundance and low diversity are associated with increased CRISPR-Cas prevalence across microbial ecosystems. Current Biology. Advance online publication. doi: 10.1016/j.cub.2021.10.038

Hapuarachchi, I. U., Hannaway, R. F., Roman, T., Biswas, A., Dyet, K., Morgan, X., & Ussher, J. E. (2021). Genetic evaluation of ESBL-producing Escherichia coli urinary isolates in Otago, New Zealand. JAC: Antimicrobial Resistance. Advance online publication. doi: 10.1093/jacamr/dlab147

Meaden, S., Capria, L., Alseth, E., Gandon, S., Biswas, A., Lenzi, L., … Westra, E. R. (2021). Phage gene expression and host responses lead to infection-dependent costs of CRISPR immunity. ISME Journal, 15, 534-544. doi: 10.1038/s41396-020-00794-w

Centanni, M., Sims, I. M., Bell, T. J., Biswas, A., & Tannock, G. W. (2020). Sharing a β-glucan meal: Transcriptomic eavesdropping on a Bacteroides ovatus-Subdoligranulum variabile-Hungatella hathewayi consortium. Applied & Environmental Microbiology, 86(20), e01651-20. doi: 10.1128/aem.01651-20

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

Chapter in Book - Research

Wang, X., Reilly, K., Heathcott, R., Biswas, A., Johnson, L. J., Teasdale, S., … Morales, S. E. (2022). Soil nitrogen treatment alters microbiome networks across farm niches. Frontiers in Microbiology, 12, 786156. doi: 10.3389/fmicb.2021.786156

Journal - Research Article

Hapuarachchi, I. U., Hannaway, R. F., Roman, T., Biswas, A., Dyet, K., Morgan, X., & Ussher, J. E. (2021). Genetic evaluation of ESBL-producing Escherichia coli urinary isolates in Otago, New Zealand. JAC: Antimicrobial Resistance. Advance online publication. doi: 10.1093/jacamr/dlab147

Journal - Research Article

Meaden, S., Capria, L., Alseth, E., Gandon, S., Biswas, A., Lenzi, L., … Westra, E. R. (2021). Phage gene expression and host responses lead to infection-dependent costs of CRISPR immunity. ISME Journal, 15, 534-544. doi: 10.1038/s41396-020-00794-w

Journal - Research Article

Centanni, M., Sims, I. M., Bell, T. J., Biswas, A., & Tannock, G. W. (2020). Sharing a β-glucan meal: Transcriptomic eavesdropping on a Bacteroides ovatus-Subdoligranulum variabile-Hungatella hathewayi consortium. Applied & Environmental Microbiology, 86(20), e01651-20. doi: 10.1128/aem.01651-20

Journal - Research Article

Chevallereau, A., Meaden, S., Fradet, O., Landsberger, M., Maestri, A., Biswas, A., … Westra, E. R. (2020). Exploitation of the cooperative behaviors of anti-CRISPR phages. Cell Host & Microbe, 27, 189-198. doi: 10.1016/j.chom.2019.12.004

Journal - Research Article

Myat, T. O., Oo, K. M., Mone, H. K., Htike, W. W., & Biswas, A. (2020). A prospective study of bloodstream infections among febrile adolescents and adults attending Yangon General Hospital, Yangon, Myanmar. PLoS Neglected Tropical Diseases, 14(4), e0008268. doi: 10.1371/journal.pntd.0008268

Journal - Research Article

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, 85(7), e02783-18. doi: 10.1128/aem.02783-18

Journal - Research Article

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

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, 113, 641-648. doi: 10.1093/trstmh/trz053

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

Meaden, S., Biswas, A., Arkhipova, K., Morales, S. E., Dutilh, B. E., . . ., & Fineran, P. C. (2022). High viral abundance and low diversity are associated with increased CRISPR-Cas prevalence across microbial ecosystems. Current Biology. Advance online publication. doi: 10.1016/j.cub.2021.10.038

Journal - Research Other

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