Associate Professor Chris Brown

2026

Journal - Research Article

Lim, C. S., & Brown, C. M. (2026). Decoding the interconnected splicing patterns of hepatitis B virus and host using large language and deep learning models. Microbial Genomics, 12(1), 001616. doi: 10.1099/mgen.0.001616

2025

Journal - Research Article

Lim, C. S., Gibbon, A. K., Nguyen, A. T. T., Chieng, G. S. W., & Brown, C. M. (2025). RIBOSS detects novel translational events by combining long- and short-read transcriptome and translatome profiling. Briefings in Bioinformatics, 26(2), bbaf164. doi: 10.1093/bib/bbaf164

Greenhough, H., Vignier, J., Smith, K. F., Brown, C. M., Kenny, N. J., & Rolton, A. (2025). Multi-stressor dynamics: Effects of marine heatwave stress and harmful algal blooms on juvenile mussel (Perna canaliculus) survival and physiology. Science of the Total Environment, 964, 178590. doi: 10.1016/j.scitotenv.2025.178590

2024

Journal - Research Article

Nilsen, A. R., Plett, J. M., May, T. W., Lebel, T., Brown, C. M., Catcheside, D. E. A., & Orlovich, D. A. (2024). Navigating the labyrinth: Searching for mechanistic clues to explain the evolution of sequestrate Agaricales with labyrinthine internal chambers. Fungal Biology Reviews, 49, 100380. doi: 10.1016/j.fbr.2024.100380

Moreira, S. M., Chyou, T.-y., Wade, J. T., & Brown, C. M. (2024). Diversification of the Rho transcription termination factor in bacteria. Nucleic Acids Research, 52, 8979-8997. doi: 10.1093/nar/gkae582

Achilleos, K., Smith, A. M., Kenny, N. J., & Brown, C. M. (2024). A new transcriptome resource for Cellaria immersa (Phylum: Bryozoa) reveals candidate genes and proteins related to biomineralization. Frontiers in Marine Science, 11, 1389708. doi: 10.3389/fmars.2024.1389708

Castañeda-Casasola, C. C., Nieto-Jacobo, M. F., Soares, A., Padilla-Padilla, E. A., Anducho-Reyes, M. A., Brown, C., … Mendoza-Mendoza, A. (2024). Unveiling a microexon switch: Novel regulation of the activities of sugar assimilation and plant-cell-wall-degrading xylanases and cellulases by Xlr2 in Trichoderma virens. International Journal of Molecular Sciences, 25, 5172. doi: 10.3390/ijms25105172

Schoch, K., Ruegg, M. S. G., Fellows, B. J., Cao, J., Uhrig, S., Einsele-Scholz, S., … Hawarden, S. R. A., … Brown, C. M., … Bicknell, L. S. (2024). A second hotspot for pathogenic exon-skipping variants in CDC45. European Journal of Human Genetics, 32, 786-794. doi: 10.1038/s41431-024-01583-1

Conference Contribution - Published proceedings: Abstract

Birkholz, N., Kamata, K., Feußner, M., Wilkinson, M. E., Samaniego, C. C., Migur, A., … Ceelen, M., … Brown, C. M., … Fagerlund, R. D., Jackson, S. A., & Fineran, P. C. (2024). Phage helix-turn-helix proteins bind RNA and DNA to control anti-CRISPR dynamics. Viruses of Microbes (VoM) Scientific Conference. Retrieved from https://www.vom2024.org/

Conference Contribution - Verbal presentation and other Conference outputs

Greenhough, H., Vignier, J., Smith, K. F., Brown, C., Rolton, A., & Kenny, N. J. (2024, August). The effects of harmful algal blooms and marine heatwaves on the early life stages of green-lipped mussels. Verbal presentation at the BMS Postgraduate Symposium, Dunedin, New Zealand.

Other Research Output

Lim, C. S., & Brown, C. (2024). Transcriptome, metaranscriptome, and translatome data for RIBOSS. doi: 10.5281/zenodo.13997374

2023

Chapter in Book - Research

Torbati, E., Stuart, G., Krause, K., Brown, C., & Wise, L. (2023). Methods to assess chemokine binding and anti-chemotactic activity of virus proteins. In A. R. Lucas (Ed.), Chemokine-glycosaminoglycan interactions: Methods and protocols: Methods in molecular biology (Vol. 2597). (pp. 217-234). New York, N Y: Humana Press. doi: 10.1007/978-1-0716-2835-5_16

Conference Contribution - Published proceedings: Abstract

Dobbie, F. L. W., Orlovich, D. A., & Brown, C. M. (2023). A genetic analysis of the causes of truffle-like morphology: What makes a fungus go round. Proceedings of the Genetics Otago (GO) Annual Symposium & Workshops. Retrieved from https://blogs.otago.ac.nz/go

Conference Contribution - Verbal presentation and other Conference outputs

Chyou, T., Fox, W., Padilla, E., Nilsen, A., Mendoza, A., Plett, J., Summerfield, T., Orlovich, D., & Brown, C. M. (2023, August). Detecting non-coding genes in mushroom and truffle-like fungal genomes. Verbal presentation at the Queenstown Molecular Biology (QMB) Genomics Satellite, Queenstown, New Zealand.

2022

Journal - Research Article

Shehreen, S., Birkholz, N., Fineran, P. C., & Brown, C. M. (2022). Widespread repression of anti-CRISPR production by anti-CRISPR-associated proteins. Nucleic Acids Research, 50(15), 8615-8625. doi: 10.1093/nar/gkac674

Conference Contribution - Published proceedings: Abstract

Achilleos, K., Smith, A. M., Kenny, N., & Brown, C. M. (2022). Transcriptome analysis of Cellaria immersa (Phylum: Bryozoa) provides insights into marine invertebrate biomineralizations and consequences of climatic changes. Proceedings of the Genetics Otago (GO) Annual Symposium. Retrieved from https://blogs.otago.ac.nz/go

Chyou, T.-y., Gavryushkina, A., & Brown, C. (2022). Fast and accurate prediction of protein thermal stability from gene sequences. Proceedings of the Genetics Otago (GO) Annual Symposium. Retrieved from https://blogs.otago.ac.nz/go

Conference Contribution - Poster Presentation (not in published proceedings)

Achilleos, K., Smith, A. M., Kenny, N., & Brown, C. M. (2022, August-September). Transcriptome analysis of Cellaria immersa (Phylum: Bryozoa) provides insights into marine invertebrate biomineralization and consequences of climatic changes. Poster session presented at the 31st Queenstown Molecular Biology Meeting (QMB), Queenstown, New Zealand.

Conference Contribution - Verbal presentation and other Conference outputs

Brown, C. (2022, November). Non-coding RNA genes from fungi. Verbal presentation at the Australasian Microbiology Society (ASM) Symposium at the NZ Microbiological Society Annual Conference: Microbes Rule! Wellington, New Zealand.

Nilsen, A. R., Chyou, D., Summerfield, T. C., Catcheside, D., Brown, C. M., & Orlovich, D. A. (2022, May). Molecular evolution of truffle like fungi in NZ: Clues from Leratiomyces. Verbal presentation at the Fungal Network of New Zealand 35th New Zealand 'Virtual' Fungal Foray including the 20th Mycology Colloquium, [Online].

2021

Journal - Research Article

Lim, C. S., Weinstein, B. N., Roy, S. W., & Brown, C. M. (2021). Analysis of fungal genomes reveals commonalities of intron gain or loss and functions in intron-poor species. Molecular Biology & Evolution, 38(10), 4166-4186. doi: 10.1093/molbev/msab094

Nilsen, A. R., Macrae, O. C., Andrew, K., Wang, X. Y., Te Tana, M. C., Soop, K., Brown, C. M., Summerfield, T. C., & Orlovich, D. A. (2021). Studies of New Zealand Cortinarius: Resolution of taxonomic conflicts in section Subcastanelli (Agaricales), new species and key to rozitoid species. New Zealand Journal of Botany, 59(4), 457-475. doi: 10.1080/0028825X.2021.1879877

Lim, C. S., Sozzi, V., Littlejohn, M., Yuen, L. K. W., Warner, N., Betz-Stablein, B., … Brown, C. M. (2021). Quantitative analysis of the splice variants expressed by the major hepatitis B virus genotypes. Microbial Genomics, 7, 000492. doi: 10.1099/mgen.0.000492

Schweiger, R., Padilla-Arizmendi, F., Nogueira-Lopez, G., Rostás, M., Lawry, R., Brown, C., … Mendoza-Mendoza, A. (2021). Insights into metabolic changes caused by the Trichoderma virens-maize root interaction. Molecular Plant-Microbe Interactions, 34(5), 524-537. doi: 10.1094/mpmi-04-20-0081-r

Conference Contribution - Published proceedings: Abstract

Nilsen, A., Chyou, D., Summerfield, T., Catcheside, D., Brown, C., & Orlovich, D. (2021). Molecular evolution of truffle like fungi in NZ: Clues from comparative genomics. Proceedings of the 16th Congress of the Federation of Asian & Oceanic Biochemists & Molecular Biologists (FAOBMB). (pp. 220). Retrieved from https://www.faobmb2021.org

Lim, C. S., Wardell, S., Kleffmann, T., Weinstein, B., Roy, S., & Brown, C. (2021). The evolution and function of introns. Proceedings of the 16th Congress of the Federation of Asian & Oceanic Biochemists & Molecular Biologists (FAOBMB). (pp. 161). Retrieved from https://www.faobmb2021.org

Chyou, T.-y., Biswas, A., Fineran, P., & Brown, C. (2021). Predicting hosts of nucleic acid sequences using CRISPR spacers. Proceedings of the 16th Congress of the Federation of Asian & Oceanic Biochemists & Molecular Biologists (FAOBMB). (pp. 121). Retrieved from https://www.faobmb2021.org

Orlovich, D. A., van Galen, L. G., Nilsen, A. R., Larcombe, M. J., Lord, J. M., Summerfield, T. C., & Brown, C. M. (2021). eDNA for detecting data-deficient fungi. Proceedings of the 16th Congress of the Federation of Asian & Oceanic Biochemists & Molecular Biologists (FAOBMB). (pp. 89). Retrieved from https://www.faobmb2021.org

Orlovich, D. A., Nilsen, A. R., McGovern, J., Lasham, S., Williams, D., van Galen, L. G., Summerfield, T. C., Larcombe, M. J., Lord, J. M., & Brown, C. M. (2021). Bush genomics: Using genetics and genomics tools to discover and understand New Zealand's truffle-like fungi [Invited]. Proceedings of the Genetics Otago (GO) Annual Symposium. Retrieved from https://blogs.otago.ac.nz/go

2020

Journal - Research Article

Pinilla-Redondo, R., Shehreen, S., Marino, N. D., Fagerlund, R. D., Brown, C. M., Sørensen, S. J., Fineran, P. C., & Bondy-Denomy, J. (2020). Discovery of multiple anti-CRISPRs highlights anti-defense gene clustering in mobile genetic elements. Nature Communications, 11(1), 5652. doi: 10.1038/s41467-020-19415-3

Nilsen, A. R., Wang, X. Y., Soop, K., Cooper, J. A., Ridley, G. S., Wallace, M., Summerfield, T. C., Brown, C. M., & Orlovich, D. A. (2020). Purple haze: Cryptic purple sequestrate Cortinarius in New Zealand. Mycologia, 112(3), 588-605. doi: 10.1080/00275514.2020.1730120

Rollie, C., Chevallereau, A., Watson, B. N. J., Chyou, T.-y., Fradet, O., McLeod, I., Fineran, P. C., Brown, C. M., … Westra, E. R. (2020). Targeting of temperate phages drives loss of type I CRISPR-Cas systems. Nature, 578, 149-153. doi: 10.1038/s41586-020-1936-2

Conference Contribution - Published proceedings: Abstract

Tan, Y. X., Brown, C. M., & Orlovich, D. (2020). Activity of Bacillus sp. as a biocontrol agent in controlling green mould disease in oyster mushrooms (Pleurotus sp.). Proceedings of the Genetics Otago (GO) Zoom Symposium. Retrieved from https://blogs.otago.ac.nz/go/2020-3/

2019

Journal - Research Article

Shehreen, S., Chyou, T.-y., Fineran, P. C., & Brown, C. M. (2019). Genome-wide correlation analysis suggests different roles of CRISPR-Cas systems in the acquisition of antibiotic resistance genes in diverse species. Philosophical Transactions of the Royal Society B, 374(1772), 20180384. doi: 10.1098/rstb.2018.0384

Nilsen, A. R., Brown, C. M., Summerfield, T. C., & Orlovich, D. A. (2019). Cortinarius atropileatus sp. nov. (Cortinariaceae) from New Zealand. New Zealand Journal of Botany, 57(1), 50-61. doi: 10.1080/0028825X.2018.1548493

Nicholson, T. J., Jackson, S. A., Croft, B. I., Staals, R. H. J., Fineran, P. C., & Brown, C. M. (2019). Bioinformatic evidence of widespread priming in type I and II CRISPR-Cas systems. RNA Biology, 16(4), 566-576. doi: 10.1080/15476286.2018.1509662

Chyou, T., & Brown, C. M. (2019). Prediction and diversity of tracrRNAs from type II CRISPR-Cas systems. RNA Biology, 16(4), 423-434. doi: 10.1080/15476286.2018.1498281

Conference Contribution - Published proceedings: Abstract

Orlovich, D. A., Nilsen, A. R., Summerfield, T. C., Brown, C. M., Ohlemüller, R., van Galen, L., Larcombe, M., & Lord, J. (2019). Using genomics tools to understand beech forests and their fungi. Proceedings of the Joint Conference of the Australasian Systematic Botany Society (ASBS) and the New Zealand Plant Conservation Network (NZPCN): Taxonomy for Plant Conservation: Ruia mai i Rangiātea. (pp. 38). Retrieved from https://systematics.ourplants.org

Achilleos, K., Brown, C., & Smith, A. M. (2019). Biochemical pathways involved in calcification of marine invertebrates: Focus on Cellaria immersa. Proceedings of the 18th International Bryozoology Association (IBA) Conference. (pp. 20). Retrieved from http://18iba.tul.cz

2018

Journal - Research Article

Lim, C. S., Wardell, S. J. T., Kleffmann, T., & Brown, C. M. (2018). The exon-intron gene structure upstream of the initiation codon predicts translation efficiency. Nucleic Acids Research, 46(9), 4575-4591. doi: 10.1093/nar/gky282

Journal - Research Other

Tate, W. P., Cridge, A. G., & Brown, C. M. (2018). 'Stop' in protein synthesis is modulated with exquisite subtlety by an extended RNA translation signal. Biochemical Society Transactions, 46(6), 1615-1625. doi: 10.1042/bst20180190

Lim, C. S., & Brown, C. M. (2018). Know your enemy: Successful bioinformatic approaches to predict functional RNA structures in viral RNAs. Frontiers in Microbiology, 8, 2582. doi: 10.3389/fmicb.2017.02582

Conference Contribution - Published proceedings: Abstract

Shehreen, S., Chyou, D., Fineran, P., & Brown, C. (2018). Horizontal transfer of antibiotic resistance genes: A CRISPR connection? Proceedings of the New Zealand Microbiological Society (NZMS) New Zealand Society for Biochemistry and Molecular Biology (NZSBMB) Joint Annual Conference: Microbes & Molecules. (pp. 81-82). Retrieved from https://www.nzmsconference.org.nz

Nilsen, A., Summerfield, T., Brown, C., & Orlovich, D. (2018). Evolution of sequestrate fungi in New Zealand, with emphasis on the genus Cortinarius. Proceedings of the New Zealand Microbiological Society (NZMS) New Zealand Society for Biochemistry and Molecular Biology (NZSBMB) Joint Annual Conference: Microbes & Molecules. (pp. 56). Retrieved from https://www.nzmsconference.org.nz

Brown, C., Chyou, T.-y., Lim, C. S., Padilla, E., Nilsen, A., Liu, S., … Summerfield, T., … Orlovich, D. (2018). The functions of non-coding RNAs and elements in fungal genomes: New roles in the regulation of gene expression. Proceedings of the New Zealand Microbiological Society (NZMS) New Zealand Society for Biochemistry and Molecular Biology (NZSBMB) Joint Annual Conference: Microbes & Molecules. (pp. 53). Retrieved from https://www.nzmsconference.org.nz

Shehreen, S., Chyou, T.-y., Fineran, P. C., & Brown, C. M. (2018). Horizontal transfer of antibiotic resistance genes: A CRISPR connection? Proceedings of the Otago Global Health Institute (OGHI) 11th Annual Conference. (pp. 23-24). Retrieved from https://www.otago.ac.nz/global-health/annual-conference

Conference Contribution - Poster Presentation (not in published proceedings)

Lim, C. S., & Brown, C. M. (2018, August). Analysis of transcript splicing. Poster session presented at the Queenstown Molecular Biology (QMB) Meetings, Queenstown, New Zealand.

Biggs, H., Brown, C., & Hughes, S. (2018, August). Meta-analysis of mRNAs loaded into exosomes suggests cell type specific RNA localisation elements. Poster session presented at the Queenstown Molecular Biology (QMB) Meetings, Queenstown, New Zealand.

Nicholson, T., & Brown, C. (2018, August). Prediction of the host domain for partial viral genomes from metagenomes. Poster session presented at the Queenstown Molecular Biology (QMB) Meetings, Queenstown, New Zealand.

2017

Journal - Research Other

Lim, C. S., & Brown, C. (2017). A new class of ribozyme from hepatitis B virus. FEBS Journal, 284(8), 1182-1183. doi: 10.1111/febs.14062

Conference Contribution - Published proceedings: Abstract

Lim, C. S., & Brown, C. (2017). Independent loss of introns during evolution across multiple fungal clades. Proceedings of the Annual Conference of the Genetics Society of Australasia (GSA) with the New Zealand Society for Biochemistry and Molecular Biology (NZSBMB). 680. Retrieved from http://gen2017.w.events4you.currinda.com

Brown, C., Chyou, D., Biswas, A., Baltazar, P., Nicholson, T., Croft, B., & Fineran, P. (2017). Bioinformatic discovery of noncoding RNA genes. Proceedings of the Annual Conference of the Genetics Society of Australasia (GSA) with the New Zealand Society for Biochemistry and Molecular Biology (NZSBMB). 655. Retrieved from http://gen2017.w.events4you.currinda.com

Ashby, R., Baird, H., Brauning, R., McCulloch, A., Brown, C., Clarke, S., & Gemmell, N. (2017). Genetic hitchhikers: What species are hiding in your sequence data? Proceedings of the Annual Conference of the Genetics Society of Australasia (GSA) with the New Zealand Society for Biochemistry and Molecular Biology (NZSBMB). 711. Retrieved from http://gen2017.w.events4you.currinda.com

Conference Contribution - Verbal presentation and other Conference outputs

Brown, C. M., Chyou, D., Biswas, A., Baltazar, P., Nicholson, T., Croft, B., & Fineran, P. (2017, September). Bioinformatic discovery of noncoding RNA genes. Verbal presentation at the Queenstown Molecular Biology (QMB) Meetings, Queenstown, New Zealand.

2016

Journal - Research Article

Bond, D. M., Albert, N. W., Lee, R. H., Gillard, G. B., Brown, C. M., Hellens, R. P., & Macknight, R. C. (2016). Infiltration-RNAseq: Transcriptome profiling of Agrobacterium-mediated infiltration of transcription factors to discover gene function and expression networks in plants. Plant Methods, 12, 41. doi: 10.1186/s13007-016-0141-7

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

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

Lim, C. S., & Brown, C. M. (2016). Hepatitis B virus nuclear export elements: RNA stem-loop α and β, key parts of the HBV post-transcriptional regulatory element. RNA Biology, 13(9), 743-747. doi: 10.1080/15476286.2016.1166330

Schmoll, M., Dattenböck, C., Carreras-Villaseñor, N., Mendoza-Mendoza, A., Tisch, D., Alemán, M. I., … Brown, C., … Herrara-Estrella, A. (2016). The genomes of three uneven siblings: Footprints of the lifestyles of three Trichoderma species. Microbiology & Molecular Biology Reviews, 80(1), 205-327. doi: 10.1128/mmbr.00040-15

Hellens, R. P., Brown, C. M., Chisnall, M. A. W., Waterhouse, P. M., & Macknight, R. C. (2016). The emerging world of small ORFs. Trends in Plant Science, 21(4), 317-328. doi: 10.1016/j.tplants.2015.11.005

Conference Contribution - Published proceedings: Abstract

Orlovich, D. A., Gillard, G., Wang, X., Nilsen, A. R., Brown, C. M., & Summerfield, T. C. (2016). Comparative genomics of a truffle-like fungus Cortinarius beeverorum and its close mushroom relative C. dulciolens. Proceedings of the Scientific Meeting of the Australasian Mycological Society (AMS) with the Fungal Network of New Zealand (FUNNZ). (pp. 14). Retrieved from https://www.australasianmycologicalsociety.com

Conference Contribution - Verbal presentation and other Conference outputs

Staals, R. H. J., Jackson, S. A., Biswas, A., Brouns, S. J. J., Brown, C. M., & Fineran, P. C. (2016, November). Interference-driven spacer acquisition is dominant over naive and primed adaptation in a native CRISPR-Cas system. Verbal presentation at the Joint Meeting of the New Zealand Microbiological Society (NZMS) and the New Zealand Society for Biochemistry and Molecular Biology (NZSBMB), Christchurch, New Zealand.

Ashby, R., Baird, H., Brauning, R., van Stijn, T., Anderson, R., Dodds, K., Rutherford, K., Brown, C., … Gemmell, N., & Clarke, S. (2016, August-September). Making a splash: Using genomics to aid the New Zealand aquaculture industry. Verbal presentation at the Queenstown Molecular Biology (QMB) Meetings, Nelson, New Zealand.

2015

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

Journal - Research Article

Davies, C., Brown, C. M., Westphal, D., Ward, J. M., & Ward, V. K. (2015). Murine norovirus replication induces a G₀/G₁ cell cycle arrest in asynchronous growing cells. Journal of Virology, 89(11), 6057-6066. doi: 10.1128/jvi.03673-14

Conference Contribution - Poster Presentation (not in published proceedings)

Ashby, R., Brauning, R., Rutherford, K., van Stijn, T., Baird, H., Brown, C., Gemmell, N., & Clarke, S. (2015, August-September). Utilisation of genomic tools and techniques to further understand the genetics of the New Zealand Greenshell^TM mussel, Perna canaliculus. Poster session presented at the Queenstown Molecular Biology (QMB) Meetings, Queenstown, New Zealand.

Torbati, E., Krause, K. L., & Brown, C. M. (2015, August-September). The evolution of poxvirus immuno-modulatory proteins. Poster session presented at the Queenstown Molecular Biology (QMB) Meetings, Queenstown, New Zealand.

Conference Contribution - Verbal presentation and other Conference outputs

Croft, B., Biswas, A., Fineran, P. C., & Brown, C. M. (2015, August). Analysis of rumen methanogens CRISPR-Cas systems. Verbal presentation at the 7th Annual New Zealand Next Generation Sequencing (NGS) Conference, Palmerston North, New Zealand.

Ashby, R., Brauning, R., van Stijn, T., Baird, H., Brown, C., Gemmell, N., & Clarke, S. (2015, August). Developing a pipeline for the Genotyping-by-sequencing (GBS) of the New Zealand Greenshell™ Mussel. Verbal presentation at the 7th Annual New Zealand Next Generation Sequencing (NGS) Conference, Palmerston North, New Zealand.

2014

Chapter in Book - Research

Stevens, S. G., & Brown, C. M. (2014). Bioinformatic methods to discover Cis-regulatory elements in mRNAs. In N. K. Kasabov (Ed.), Springer handbook of bio-/neuro-informatics. (pp. 151-169). Dordrecht, The Netherlands: Springer. doi: 10.1007/978-3-642-30574-0_10

Journal - Research Article

Chen, A., T-Thienprasert, N. P., & Brown, C. M. (2014). Prospects for inhibiting the post-transcriptional regulation of gene expression in hepatitis B virus. World Journal of Gastroenterology, 20(25), 7993-8004. doi: 10.3748/wjg.v20.i25.7993

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., 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

Gillard, G. B., Garama, D. J., & Brown, C. M. (2014). The transcriptome of the NZ endemic sea urchin Kina (Evechinus chloroticus). BMC Genomics, 15, 45. doi: 10.1186/1471-2164-15-45

Waugh, E., Chen, A., Baird, M. A., Brown, C. M., & Ward, V. K. (2014). Characterization of the chemokine response of RAW264.7 cells to infection by murine norovirus. Virus Research, 181, 27-34. doi: 10.1016/j.virusres.2013.12.025

2013

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

Stevens, S. G., & Brown, C. M. (2013). In silico estimation of translation efficiency in human cell lines: Potential evidence for widespread translational control. PLoS ONE, 8(2), e57625. doi: 10.1371/journal.pone.0057625

Conference Contribution - Published proceedings: Abstract

Waugh, E., Baird, M. A., Fleming, S. B., Brown, C. M., & Ward, V. K. (2013). Murine norovirus interaction with the host response. Proceedings of the Australasian Virology Society (AVS) Meeting. Retrieved from http://www.avs.org.au/scientific-program/

Conference Contribution - Verbal presentation and other Conference outputs

Garama, D., Stevens, S., Chen, X., Biswas, A., Sarman, A., Chen, A., & Brown, C. (2013, February). Translational control of gene expression by mRNA elements. Verbal presentation at the 38th Lorne Conference on Protein Structure and Function, Lorne, Australia.

2012

Journal - Research Article

Chen, X. S., & Brown, C. M. (2012). Computational identification of new structured cis-regulatory elements in the 3’-untranslated region of human protein coding genes. Nucleic Acids Research, 40(18), 8862-8873. doi: 10.1093/nar/gks684

Lange, S. J., Maticzka, D., Möhl, M., Gagnon, J. N., Brown, C. M., & Backofen, R. (2012). Global or local? Predicting secondary structure and accessibility in mRNAs. Nucleic Acids Research, 40(12), 5215-5226. doi: 10.1093/nar/gks181

Pilbrow, A. P., Folkersen, L., Pearson, J. F., Brown, C. M., McNoe, L., Wang, N. M., … Black, M. A., Troughton, R. W., Richards, A. M., … Cameron, V. A. (2012). The chromosome 9p21.3 coronary heart disease risk allele is associated with altered gene expression in normal heart and vascular tissues. PLoS ONE, 7(6), e39574. doi: 10.1371/journal.pone.0039574

Chen, A., & Brown, C. (2012). Distinct families of cis-acting RNA replication epsilon elements from hepatitis B viruses. RNA Biology, 9(2), 130-136. doi: 10.4161/rna.18649

2011

Journal - Research Article

Panjaworayan, N., & Brown, C. M. (2011). Effects of HBV genetic variability on RNAi strategies. Hepatitis Research & Treatment, 2011, 367908. doi: 10.1155/2011/367908

Stevens, S. G., Gardner, P. P., & Brown, C. (2011). Two covariance models for iron-responsive elements. RNA Biology, 8(5), 792-801. doi: 10.4161/rna.8.5.16037

Conference Contribution - Published proceedings: Abstract

Panjaworayan, N., Thongtae, N., & Brown, C. M. (2011). Analysis of functional regulatory elements within hepatitis B virus post-transcriptional regulatory element as new antiviral targets. Hepatology International. 5(1), (pp. 170). doi: 10.1007/s12072-010-9241-z

Conference Contribution - Poster Presentation (not in published proceedings)

Chen, A., Sarman, A., Riad, S., Stevens, S., & Brown, C. (2011, September). Changes in gene expression in a breast cancer cell line using RNA-Seq. Poster session presented at the Queenstown Molecular Biology (QMB) Meetings, Queenstown, New Zealand.

Biswas, A., & Brown, C. (2011, September). A web-based tool for analysis of regulatory elements in vertebrate 3’UTRs: Scan for motifs. Poster session presented at the Queenstown Molecular Biology (QMB) Meetings, Queenstown, New Zealand.

Conference Contribution - Verbal presentation and other Conference outputs

Stevens, S. G., Biswas, A., Gagnon, J., Wilkinson, T., Chen, A., Chen, S., & Brown, C. M. (2011, August). Bioinformatic approaches to the identification of localisation elements. Verbal presentation at the European Molecular Biology Organization (EMBO) Conference on Intracellular RNA Localization & Localized Translation, Tuscany, Italy.

Pilbrow, A. P., Pearson, J. F., Brown, C. M., McNoe, L., Sweet, W. E., Tang, W. H. W., Black, M. A., Troughton, R. W., Richards, A. M., … Cameron, V. A. (2011, September). Cardiac gene expression profiling. Verbal presentation at the Queenstown Molecular Biology (QMB) Meetings, Queenstown, New Zealand.

Brown, C. M., Das, A., Stevens, S., Biswas, A., Gagnon, J., McKinney, C., Chen, A., & Chen, S. (2011, September). Bioinformatic approaches to discover post-transcriptional regulatory elements in human mRNAs. Verbal presentation at the Queenstown Molecular Biology (QMB) Meetings, Queenstown, New Zealand.

2010

Journal - Research Article

Panjaworayan, N., Payungporn, S., Poovorawan, Y., & Brown, C. M. (2010). Identification of an effective siRNA target site and functional regulatory elements, within the hepatitis B virus posttranscriptional regulatory element. Virology Journal, 7, 216. doi: 10.1186/1743-422x-7-216

Milev, M. P., Brown, C. M., & Mouland, A. J. (2010). Live cell visualization of the interactions between HIV-1 Gag and the cellular RNA-binding protein Staufen1. Retrovirology, 7, 41. doi: 10.1186/1742-4690-7-41

Other Research Output

Brown, C. M. (2010, July). Analysis of nRNAs from eukaryotic cells: Bioinformatic and cell biology approaches. University of Otago Department of Biochemistry Seminar, Dunedin, New Zealand. [Department Seminar].

2009

Journal - Research Article

Jacobs, G. H., Chen, A., Stevens, S. G., Stockwell, P. A., Black, M. A., Tate, W. P., & Brown, C. M. (2009). Transterm: A database to aid the analysis of regulatory sequences in mRNAs. Nucleic Acids Research, 37(Database issue), D72-D76. doi: 10.1093/nar/gkn763

Conference Contribution - Published proceedings: Abstract

Pilbrow, A. P., Pearson, J., Brown, C. M., McNoe, L., Black, M. A., Sweet, W. E., … Troughton, R. W., Richards, A. M., … Cameron, V. A. (2009). Chromosome 6q25.1 and 2q36.3 coronary heart disease risk loci are associated with altered cardiac gene expression profiles in normal heart. Circulation, 120(18, Suppl.), (pp. S564). [Abstract]

Brown, C. M., Wilkinson, T., Panjaworayan, N., Firth, A. E., Chen, A., Stevens, S. G., Wong, A., Black, M., … Roessner, S. K. (2009). Analysis of virus and human genome sequences for RNA regulatory elements. Proceedings of the Webster Centre for Infectious Diseases Symposium. WCID. Retrieved from http://www.webstercentre.otago.ac.nz/WCIDSymposiumProgramme.pdf

2008

Conference Contribution - Poster Presentation (not in published proceedings)

Ballantine, S. T., Cheung, K.-C., O'Keefe, R., Stevens, S. G., & Brown, C. M. (2008, November-December). MicroRNA targets and other regulatory elements in conserved regions of the human genome. Poster session presented at the New Zealand Institute of Chemistry, New Zealand Society for Biochemistry and Molecular Biology and the New Zealand Society of Plant Biologists Combined Conference, Dunedin, New Zealand.

Conference Contribution - Verbal presentation and other Conference outputs

Brown, C., Chen, A., Ballantine, S., Black, M., Jacobs, G., & Stevens, S. (2008, November-December). Identification of post-transcriptional regulatory elements in mRNA sequences. Verbal presentation at the New Zealand Institute of Chemistry, New Zealand Society for Biochemistry and Molecular Biology and the New Zealand Society of Plant Biologists Combined Conference, Dunedin, New Zealand.

2007

Journal - Research Article

Panjaworayan, N., Roessner, S. K., Firth, A. E., & Brown, C. M. (2007). HBVRegDB: Annotation, comparison, detection and visualization of regulatory elements in hepatitis B virus sequences. Virology Journal, 4, 136. Retrieved from http://www.virologyj.com/content/4/1/136

Zadissa, A., McEwan, J. C., & Brown, C. M. (2007). Inference of transcriptional regulation using gene expression data from the bovine and human genomes. BMC Genomics, 8, 265. doi: 10.1186/1471-2164-8-265

2006

Journal - Research Article

Firth, A. E., & Brown, C. M. (2006). Detecting overlapping coding sequences in virus genomes. BMC Bioinformatics, 7, 75. doi: 10.1186/1471-2105-7-75

Chung, B. Y. W., Simons, C., Firth, A. E., Brown, C. M., & Hellens, R. P. (2006). Effect of 5'UTR introns on gene expression in Arabidopsis thaliana. BMC Genomics, 7, 120. doi: 10.1186/1471-2164-7-120

Jacobs, G. H., Stockwell, P. A., Tate, W. P., & Brown, C. M. (2006). Transterm: Extended search facilities and improved integration with other databases. Nucleic Acids Research, 34(Database), D37-D40.

2005

Journal - Research Article

Chen, A., Kao, Y. F., & Brown, C. M. (2005). Translation of the first upstream ORF in the hepatitis B virus pregenomic RNA modulates translation at the core and polymerase initiation codons. Nucleic Acids Research, 33(4), 1169-1181.

Firth, A. E., & Brown, C. M. (2005). Detecting overlapping coding sequences with pairwise alignments. Bioinformatics, 21(3), 282-292.

Conference Contribution - Published proceedings: Abstract

Panjaworayan, N., Rackham, O. R., & Brown, C. M. (2005). Visualizing RNA-protein interactions in living cells. Proceedings of the EMBO Conference on Protein Synthesis and Translational Control. (pp. 212). Heidelberg, Germany: EMBL. [Abstract]

Hellens, R. P., Simons, C., Chung, B., & Brown, C. (2005). Exploring the value of introns that reside within non-coding sequence. Proceedings of the Joint Annual Meeting of the International Society for Molecular Biology and Evolution and the Genetics Society of Australasia. Auckland, New Zealand: Bioinformatics Institute, University of Auckland. Retrieved from http://www.jevon.org/mbe/programme.php

Panjaworayan, N., Rackham, O., Chen, A., Kao, A. Y.-F., & Brown, C. M. (2005). Post-transcriptional regulation of gene expression in hepatitis B virus. Proceedings of the Meeting on the Molecular Biology of Hepatitis B Viruses. (pp. 30). Heidelberg, Germany. [Abstract]

2004

Journal - Research Article

Chapman, B., & Brown, C. (2004). Translation termination in Arabidopis thaliana: Characterisation of three versions of release factor 1. Gene, 341, 219-225.

Rackham, O., & Brown, C. M. (2004). Visualization of RNA-protein interactions in living cells: FMRP and IMP1 interact on mRNAs. EMBO Journal, 23(16), 3346-3355.

Conference Contribution - Published proceedings: Abstract

Zadissa, A., McEwan, J., & Brown, C. (2004). Detection of conserved cross-species regulatory elements in higher eukaryotes using motif detection algorithm. Proceedings of the 12th International Conference on Intelligent System for Molecular Biology and the 3rd European Conference on Computational Biology. (pp. 115). Glasgow, Scotland. [Abstract]

Firth, A. E., & Brown, C. M. (2004). Computational prediction of overlapping functional coding sequences. In A. Hinnebusch & T. Pestova (Eds.), Translational Control. Cold Spring Harbor, NY, USA: Cold Spring Harbor Laboratory Press. [Abstract]

Conference Contribution - Poster Presentation (not in published proceedings)

Firth, A. E., & Brown, C. M. (2004, September). Detecting overlapping coding sequences with pairwise alignments. Poster session presented at the International Conference on Bioinformatics, Auckland, New Zealand.

2003

Conference Contribution - Published proceedings: Full paper

Brown, C., Jacobs, G., Stockwell, P., & Schreiber, M. (2003). Detection of signals in mRNAs that influence translation. Applied Bioinformatics. 2(Suppl.3), (pp. S47-S51). [Full Paper]

Brown, C. M., Jacobs, G., & Schreiber, M. (2003). Signals in RNAs that influence the initiation of translation. In Y.-P. P. Chen (Ed.), Proceedings of the First Asia Pacific Bioinformatics Conference. 19. Australian Computer Society. [Full Paper]

2002

Journal - Research Article

Schreiber, M., & Brown, C. (2002). Compensation for nucleotide bias in a genome by representation as a discrete channel with noise. Bioinformatics, 18(4), 507-512.

Jacobs, G. H., Rackham, O., Stockwell, P. A., Tate, W. P., & Brown, C. M. (2002). Transterm: a database of mRNAs and translational control elements. Nucleic Acids Research, 30, 310-311.

2000

Chapter in Book - Research

Brown, C., Schreiber, M., Chapman, B., & Jacobs, G. (2000). Information Science and Bioinformatics. In N. Kasabov (Ed.), Future Directions for Intelligent Systems and Information Science. (pp. 251-287). Heidelberg, Germany: Springer.

Journal - Research Article

Jacobs, G. H., Stockwell, P. A., Schreiber, M. J., Tate, W. P., & Brown, C. M. (2000). Transterm: A database of messenger RNA components and signals. Nucleic Acids Research, 28, 293-295.

1999

Journal - Research Article

Dalphin, M. E., Stockwell, P. A., Tate, W. P., & Brown, C. M. (1999). TransTerm, the translational signal database, extended to include full coding sequences and untranslated regions. Nucleic Acids Research, 27, 293-294.

Brown, C. M., Jacobs, G. H., Schreiber, M. J., Magnum, J., McNaughton, J. C., Cambray, M., Futschik, M., Major, L. L., Rackham, O., Tate, W. P., … Stockwell, P. A., & Kasabov, N. K. (1999). Using bioinformatics to investigate post-transcriptional control of gene expression. New Zealand BioScience, 7, 11-12.

Conference Contribution - Published proceedings: Abstract

Futschik, M., Schreiber, M. J., Brown, C., & Kasabov, N. K. (1999). Comparative studies of neural network models for mRNA analysis. Abstracts of the International Conference on Intelligent Systems for Molecular Biology. (pp. 73). Heidelberg. [Abstract]

1998

Journal - Research Article

Dalphin, M. E., Brown, C. M., Stockwell, P. A., & Tate, W. P. (1998). The translational signal database, TransTerm, is now a relational database. Nucleic Acids Research, 26, 335-337.

1997

Journal - Research Article

Miller, W. A., Brown, C., & Wang, S. (1997). New punctuation for the genetic code: Luteovirus gene expression. Seminars in Virology, 8, 3-13.

Dalphin, M. E., Brown, C. M., Stockwell, P. A., & Tate, W. P. (1997). The translational signal database, TransTerm: more organisms, complete genomes. Nucleic Acids Research, 25, 246-247.

1996

Journal - Research Article

Dalphin, M. E., Brown, C., Stockwell, P. A., & Tate, W. P. (1996). TransTerm: a database of translational signals. Nucleic Acids Research, 24, 216-218.

Brown, C. M., Dinesh-Kumar, S. P., & Miller, W. A. (1996). Local and distant sequences are required for efficient readthrough of the barley yellow dwarf virus PAV coat protein gene stop codon. Journal of Virology, 70, 5884-5892.

1995

Journal - Research Article

Tate, W. P., Poole, E. S., Horsfield, J. A., Mannering, S. A., Brown, C. M., Moffat, J. G., Dalphin, M. E., … Major, L. L., & Wilson, D. N. (1995). Translational termination efficiency in both bacteria and mammals is regulated by the base following the stop codon. Biochemistry & Cell Biology, 73, 1095-1103. doi: 10.1139/o95-118