Professor Mik Black

2024

Journal - Research Article

Bilton, T. P., Sharma, S. K., Schofield, M. R., Black, M. A., Jacobs, J. M. E., Bryan, G. J., & Dodds, K. G. (2024). Construction of relatedness matrices in autopolyploid populations using low-depth high-throughput sequencing data. Theoretical & Applied Genetics, 137, 64. doi: 10.1007/s00122-024-04568-2

2023

Journal - Research Article

Maurin, M., Ranjouri, M., Megino-Luque, C., Newberg, J. Y., Du, D., Martin, K., … Black, M. A., & Mann, K. M. (2023). RBFOX2 deregulation promotes pancreatic cancer progression and metastasis through alternative splicing. Nature Communications, 14, 8444. doi: 10.1038/s41467-023-44126-w

McGuinness, C. F., Black, M. A., & Dunbier, A. K. (2023). Restriction site associated DNA sequencing for tumour mutation burden estimation and mutation signature analysis. Cancer Medicine. Advance online publication. doi: 10.1002/cam4.6711

Te Aika, B., Liggins, L., Rye, C., Perkins, E. O., Huh, J., Brauning, R., Godfery, T., & Black, M. A. (2023). Aotearoa genomic data repository: An āhuru mōwai for taonga species sequencing data. Molecular Ecology Resources, 13866. Advance online publication. doi: 10.1111/1755-0998.13866

Yang, Z., Guarracino, A., Biggs, P. J., Black, M. A., Ismail, N., Wold, J. R., Merriman, T. R., … de Ligt, J. (2023). Pangenome graphs in infectious disease: A comprehensive genetic variation analysis of Neisseria meningitidis leveraging Oxford Nanopore long reads. Frontiers in Genetics, 14, 1225248. doi: 10.3389/fgene.2023.1225248

Taylor, M. F., Black, M. A., Hampton, M. B., & Ledgerwood, E. C. (2023). Insights into H₂O₂-induced signaling in Jurkat cells from analysis of gene expression. Free Radical Research. Advance online publication. doi: 10.1080/10715762.2023.2165073

Conference Contribution - Published proceedings: Abstract

Hughes, M., Brew, T., Godwin, T., Black, M., & Guilford, P. (2023). Single-cell RNA sequencing reveals synthetic lethal targets for chemoprevention of hereditary diffuse gastric cancer. Proceedings of the Genetics Otago (GO) Annual Symposium & Workshops. Retrieved from https://blogs.otago.ac.nz/go

Nielsen Dandoroff, E., Bicknell, L., & Black, M. (2023). Genetic protection against cancer informed by Mendelian conditions. Proceedings of the Genetics Otago (GO) Annual Symposium & Workshops. Retrieved from https://blogs.otago.ac.nz/go

Redpath, K., Vaessen, C., Decourtye-Espiard, L., Schulpen, E., Godwin, T., Bougen-Zhukov, N., McElroy, K., Black, M., & Guilford, P. (2023). Single-cell RNA-Seq reveals candidate synergistic treatments for the chemoprevention of hereditary diffuse gastric cancer. Proceedings of the Genetics Otago (GO) Annual Symposium & Workshops. Retrieved from https://blogs.otago.ac.nz/go

Black, M. (2023). Genomics Aotearoa: Past, present and future [Invited]. Proceedings of the Genetics Otago (GO) Annual Symposium & Workshops. Retrieved from https://blogs.otago.ac.nz/go

Black, M., Liggins, L., Huh, J. W., Rye, C., & Perkins, E. (2023). Building a taonga species data repository for Aotearoa New Zealand. Proceedings of the eResearch NZ Conference. (pp. 74). Retrieved from www.eresearchnz2023.org.nz

Yang, Z., Ren, U., de Ligt, J., Prins, P., Garrison, E., & Black, M. (2023). Pangenome graph: Towards a “reference freer future”. Proceedings of the eResearch NZ Conference. (pp. 44). Retrieved from www.eresearchnz2023.org.nz

Halliday, B. J., Markie, D., Goodin, E., Black, M., Sporle, A., Watson, H., Wilcox, P., & Robertson, S. P. (2023). Detection and mitigation of microbiome DNA presence in saliva-derived whole genome sequence data. Proceedings of the eResearch NZ Conference. (pp. 43). Retrieved from www.eresearchnz2023.org.nz

Conference Contribution - Verbal presentation and other Conference outputs

Lamont, A., Wilcox, P., & Black, M. (2023, November-December). Development of a population simulator to optimise study designs and estimate polygenic disease risk/resilience in Aotearoa New Zealand Māori populations. Verbal presentation at the International Biometric Society Australasian Region (IBS-AR) and the Statistical Ecology and Environmental Monitoring (SEEM) Joint Conference, Waitangi, New Zealand.

Yang, Z., Guarracino, A., Biggs, P. J., Black, M. A., Ismail, N., Wold, J. R., Merriman, T. R., … de Ligt, J. (2023, August). Pangenome graphs in infectious disease: A promising and practical implementation for comprehensive genetic variation analysis. Verbal presentation at the Queenstown Molecular Biology (QMB) Genomics Satellite, Queenstown, New Zealand.

Halliday, B. J., Markie, D., Goodin, E., Black, M., Sporle, A., Watson, H., Wilcox, P., & Robertson, S. P. (2023, August). Detection and mitigation of microbiome DNA presence in saliva-derived whole genome sequence data. Verbal presentation at the Queenstown Molecular Biology (QMB) Genomics Satellite, Queenstown, New Zealand.

2022

Journal - Research Article

Mehta, S., Wright, D., Black, M. A., Merrie, A., Anjomshoaa, A., Munro, F., Reeve, A., McCall, J., & Print, C. (2022). Impact of clinical data veracity on cancer genomic research. JNCI Cancer Spectrum. doi: 10.1093/jncics/pkac070

Bougen-Zhukov, N., Decourtye-Espiard, L., Mitchell, W., Redpath, K., Perkinson, J., Godwin, T., Black, M. A., & Guilford, P. (2022). E-cadherin-deficient cells are sensitive to the multikinase inhibitor dasatinib. Cancers, 14, 1609. doi: 10.3390/cancers14071609

Gardner, P. P., Paterson, J. M., McGimpsey, S., Ashari-Ghomi, F., Umu, S. U., Pawlik, A., Gavryushkin, A., & Black, M. A. (2022). Sustained software development, not number of citations or journal choice, is indicative of accurate bioinformatic software. Genome Biology, 23, 56. doi: 10.1186/s13059-022-02625-x

Conference Contribution - Published proceedings: Abstract

Hannah, S. J., Chen, A., Day, R. C., & Black, M. A. (2022). Improvising read accuracy for ctDNA diagnostics. Proceedings of the Genetics Otago (GO) Annual Symposium. Retrieved from https://blogs.otago.ac.nz/go

Hughes, M., Brew, T., Black, M., & Guilford, P. (2022). Single-cell RNA sequencing reveals potential synthetic lethal targets for chemoprevention of hereditary diffuse gastric cancer. Proceedings of the Genetics Otago (GO) Annual Symposium. Retrieved from https://blogs.otago.ac.nz/go

Redpath, K. J., Bougen-Zhukov, N., Black, M. A., & Guilford, P. J. (2022). Identification and development of novel drug combinations for diffuse gastric cancer. Proceedings of the Genetics Otago (GO) Annual Symposium. Retrieved from https://blogs.otago.ac.nz/go

Ismail, L., Black, M., Williams, M., Coassin, S., Forer, L., Kronenberg, F., & McCormick, S. (2022). Variants in solute cation transporters 3 associate with high Lp(a) levels independent of apo(a) isoform size. Circulation, 146(Suppl. 1), 12528. doi: 10.1161/circ.146.suppl_1.13062

McGuinness, C. F., Black, M., & Dunbier, A. K. (2022). RADseq for tumour mutation burden estimation and mutation signature analysis. Annals of Oncology, 33(Suppl. 8), (pp. S1415). doi: 10.1016/j.annonc.2022.09.106

Ismail, L., Black, M., Cadzow, M., Merriman, T., Williams, M., & McCormick, S. (2022). Two variants are associated with high lipoprotein (a) levels independent of apolipoprotein (a) isoform size. Proceedings of the ComBio Conference. (pp. 169). Retrieved from https://combio.org.au/combio2022/

Conference Contribution - Verbal presentation and other Conference outputs

McGuinness, C., Black, M. A., & Dunbier, A. K. (2022, August). A novel mechanism for APOBEC mutagenesis in carriers of the APOBEC3B deletion polymorphism. Verbal presentation at the Cancer Satellite Meeting: Queenstown Research Week, Queenstown, New Zealand.

Moloney-Geany, K., Slatter, T., Black, M., & Guilford, P. (2022, August). Characterisation of single cell transcriptomics in urinary cells for the detection of bladder cancer. Verbal presentation at the Cancer Satellite Meeting: Queenstown Research Week, Queenstown, New Zealand.

Other Research Output

Black, M. (2022, September). Genomics by the numbers: Adventures in the data-verse. University of Otago, Dunedin, New Zealand. [Inaugural Professorial Lecture].

2021

Journal - Research Article

Decourtye-Espiard, L., Bougen-Zhukov, N., Godwin, T., Brew, T., Schulpen, E., Black, M. A., & Guilford, P. (2021). E-cadherin-deficient epithelial cells are sensitive to HDAC inhibitors. Cancers, 14(1), 175. doi: 10.3390/ cancers14010102

Pullikuth, A. K., Routh, E. D., Zimmermann, K. D., Chifman, J., Chou, J. W., Soike, M. H., … Black, M. A., … Miller, L. D. (2021). Bulk and single-cell profiling of breast tumors identifies TREM-1 as a dominant immune suppressive marker associated with poor outcomes. Frontiers in Oncology, 11, 734959. doi: 10.3389/fonc.2021.734959

Pinkney, H. R., Black, M. A., & Diermeier, S. D. (2021). Single-cell RNA-seq reveals heterogeneous lncRNA expression in xenografted triple-negative breast cancer cells. Biology, 10(10), 987. doi: 10.3390/biology10100987

Aiderus, A., Newberg, J. Y., Guzman-Rojas, L., Contreras-Sandoval, A. M., Meshey, A. L., Jones, D. J., … Black, M. A., … Mann, M. B. (2021). Transposon mutagenesis identifies cooperating genetic drivers during keratinocyte transformation and cutaneous squamous cell carcinoma progression. PLoS Genetics, 17(8), e1009094. doi: 10.1371/journal.pgen.1009094

Wiggins, G. A. R., Black, M. A., Dunbier, A., Morley-Bunker, A. E., kConFab Investigators, Pearson, J. F., & Walker, L. C. (2021). Increased gene expression variability in BRCA1-associated and basal-like breast tumours. Breast Cancer Research & Treatment, 189, 363-375. doi: 10.1007/s10549-021-06328-y

Wiggins, G. A. R., Black, M. A., Dunbier, A., Merriman, T. R., Pearson, J. F., & Walker, L. C. (2021). Variable expression quantitative trait loci analysis of breast cancer risk variants. Scientific Reports, 11(1), 7192. doi: 10.1038/s41598-021-86690-5

Muradova, E., Patel, N., Sell, B., Bittencourt, B. B., Ojeda, S. S., Adelmann, C. H., … Black, M. A., … Tsai, K. Y. (2021). Non-invasive assessment of epidermal genomic markers of UV exposure in skin. Journal of Investigative Dermatology, 141(1), 124-131.e2. doi: 10.1016/j.jid.2020.05.093

Conference Contribution - Published proceedings: Abstract

Platt, R., McCormick, S., Black, M., & Ismail, L. (2021). Sequencing of lipoprotein(a) null individuals to determine mutations causing phenotype. Proceedings of the 16th Congress of the Federation of Asian & Oceanic Biochemists & Molecular Biologists (FAOBMB). (pp. 60). Retrieved from https://www.faobmb2021.org

Ismail, L., Black, M., Jones, G., Williams, M., & McCormick, S. (2021). Identifying functional variants associated with high lipoprotein (a) phenotypes. Proceedings of the 16th Congress of the Federation of Asian & Oceanic Biochemists & Molecular Biologists (FAOBMB). (pp. 55). Retrieved from https://www.faobmb2021.org

Taylor, M., Black, M., Hampton, M., & Ledgerwood, L. (2021). Transcriptional response of Jurkat T lymphoma cells to hydrogen peroxide. Proceedings of the 16th Congress of the Federation of Asian & Oceanic Biochemists & Molecular Biologists (FAOBMB). (pp. 276). Retrieved from https://www.faobmb2021.org

Russell, N., Black, M., Larsen, P., & Benton, M. (2021). Deep learning in a clinical context: The big picture from "big data". Proceedings of the eResearch NZ Conference. (pp. 103). Retrieved from https://www.eresearchnz2021.org.nz

Black, M. (2021). Building a(n) (almost) sustainable institutional training culture. Proceedings of the eResearch NZ Conference. (pp. 15-16). Retrieved from https://www.eresearchnz2021.org.nz

Conference Contribution - Poster Presentation (not in published proceedings)

McAtamney, A., Black, M., & Guilford, P. (2021, September). Early detection of colorectal cancer through analysis of ctDNA fragment sizes. Poster session presented at the Achieving Health Equity from Research Conference [Otago Spotlight Series], Wellington, New Zealand.

Conference Contribution - Verbal presentation and other Conference outputs

Kang, J., Dodds, K., Black, M., Byrne, S., Milbourne, D., Faville, M., … Wilcox, P. (2021, February). Can short haplotypes improve genomic prediction? Verbal presentation at the Quantitative Genetics Symposium, Dunedin, New Zealand.

Bilton, T. P., Bryan, G. J., Schofield, M. R., Black, M. A., Jacobs, J. M. E., Sharma, S. K., & Dodds, K. G. (2021, February). Relatedness estimation in autopolyploid species using low-depth high-throughput sequencing data. Verbal presentation at the Quantitative Genetics Symposium, Dunedin, New Zealand.

Wilcox, P. L., Lee, M., & Black, M. (2021, February). More than just numbers: 21st century quantitative genetics education in Otago. Verbal presentation at the Quantitative Genetics Symposium, Dunedin, New Zealand.

Black, M. (2021, February). Bioinformatics and infrastructure. Verbal presentation at the Quantitative Genetics Symposium, Dunedin, New Zealand.

2020

Journal - Research Article

Zou, D., Day, R., Cocadiz, J. A., Parackal, S., Mitchell, W., Black, M. A., … Jackson, C., & Guilford, P. (2020). Circulating tumor DNA is a sensitive marker for routine monitoring of treatment response in advanced colorectal cancer. Carcinogenesis, 41(11), 1507-1517. doi: 10.1093/carcin/bgaa102

Eom, J., Park, S. M., Feisst, V., Chen, C.-J. J., Mathy, J. E., McIntosh, J. D., … Black, M. A., … Dunbar, P. R. (2020). Distinctive subpopulations of stromal cells are present in human lymph nodes infiltrated with melanoma. Cancer Immunology Research, 8(8), 1-14. doi: 10.1158/2326-6066.Cir-19-0796

Lasham, A., Fitzgerald, S. J., Knowlton, N., Robb, T., Tsai, P., Black, M. A., … Mehta, S. Y., Harris, G., … Print, C. G. (2020). A predictor of early disease recurrence in patients with breast cancer using a cell-free RNA and protein liquid biopsy. Clinical Breast Cancer, 20(2), 108-116. doi: 10.1016/j.clbc.2019.07.003

Conference Contribution - Published proceedings: Abstract

Lucere, K. M., Frewen, A. J., Black, M. A., Schmeier, S., & Diermeier, S. D. (2020). Targeting long non-coding RNAs to inhibit tumour progression and metastasis in colorectal cancer. Proceedings of the Genetics Otago (GO) Epigenetics User Group (EUG) Symposium. Retrieved from https://blogs.otago.ac.nz/go/2020-3/

Santana, A. F., Benton, M. C., Macartney-Coxson, D., & Black, M. A. (2020). Per-sample pathway analysis tool for DNA methylation data. Proceedings of the Genetics Otago (GO) Epigenetics User Group (EUG) Symposium. Retrieved from https://blogs.otago.ac.nz/go/2020-3/

Black, M. (2020). Epigenetics research in Genomics Aotearoa [Invited]. Proceedings of the Genetics Otago (GO) Epigenetics User Group (EUG) Symposium. Retrieved from https://blogs.otago.ac.nz/go/2020-3/

Wiggins, G., Pearson, J., Black, M., Dunbier, A., Merriman, T., & Walker, L. (2020). Variable expression quantitative trait loci analysis of breast cancer risk variants. New Zealand Medical Journal, 133(1524), (pp. 145). Retrieved from https://www.nzma.org.nz/journal

2019

Journal - Research Article

Bougen-Zhukov, N., Nouri, Y., Godwin, T., Taylor, M., Hakkaart, C., Single, A., Brew, T., Permina, E., Chen, A., Black, M. A., & Guilford, P. (2019). Allosteric AKT inhibitors target synthetic lethal vulnerabilities in E-cadherin-deficient cells. Cancers, 11(9), 1359. doi: 10.3390/cancers11091359

Todd, E. V., Ortega-Recalde, O., Liu, H., Lamm, M. S., Rutherford, K. M., Cross, H., Black, M. A., Kardailsky, O., … Hore, T. A., … Gemmell, N. J. (2019). Stress, novel sex genes, and epigenetic reprogramming orchestrate socially controlled sex change. Science Advances, 5(7), eaaw7006. doi: 10.1126/sciadv.aaw7006

Parackal, S., Zou, D., Day, R., Black, M., & Guilford, P. (2019). Comparison of Roche Cell-Free DNA collection Tubes^® to Streck Cell-Free DNA BCT^®s for sample stability using healthy volunteers. Practical Laboratory Medicine, 16, e00125. doi: 10.1016/j.plabm.2019.e00125

Norton, S. E., Ward-Hartstonge, K. A., McCall, J. L., Leman, J. K. H., Taylor, E. S., Munro, F., Black, M. A., … Kemp, R. A. (2019). High-dimensional mass cytometric analysis reveals an increase in effector regulatory T cells as a distinguishing feature of colorectal tumors. Journal of Immunology, 202, 1871-1884. doi: 10.4049/jimmunol.1801368

Godwin, T. D., Kelly, S. T., Brew, T. P., Bougen-Zhukov, N. M., Single, A. B., Chen, A., Stylianou, C. E., … Currie, S. K., Telford, B. J., Beetham, H. G., … Black, M. A., & Guilford, P. J. (2019). E-cadherin-deficient cells have synthetic lethal vulnerabilities in plasma membrane organisation, dynamics and function. Gastric Cancer, 22(2), 273-286. doi: 10.1007/s10120-018-0859-1

Conference Contribution - Published proceedings: Abstract

Doudney, K., Lacey, C. J., Bridgman, P. G., Mulder, R. T., Zarifeh, J. J., Kimber, B., Cadzow, M., Black, M. A., Merriman, T. R., … Pearson, J. F., Cameron, V. A., & Kennedy, M. A. (2019). Rare copy number variants involving cardiac function and development genes detected in earthquake induced takotsubo cardiomyopathy patients. European Journal of Human Genetics, 27(Suppl. 1), (pp. 160). doi: 10.1038/s41431-019-0407-4

Croft, S., & Black, M. (2019). Modelling social dilemmas and treatment scheduling in tumours using evolutionary game theory. Proceedings of the New Zealand Statistical Association Conference. (pp. 44). Retrieved from https://www.otago.ac.nz/nzsa/programme-and-speakers/

Kang, J., Wilcox, P., Black, M., Milbourne, D., Byrne, S., & Dodds, K. (2019). Construction of multi-allelic genomic relationship matrices using Genotyping-by-Sequencing (GBS) data. Proceedings of the New Zealand Statistical Association Conference. (pp. 26). Retrieved from https://www.otago.ac.nz/nzsa/programme-and-speakers/

Millar, T., Thomson, S., McCallum, J., Baldwin, S., Wilcox, P., & Black, M. (2019). Local haplotype assembly in autopolyploid Actinidia. Proceedings of the MapNet Meeting. (pp. 24). Retrieved from http://mapnet2019.nz/

Conference Contribution - Verbal presentation and other Conference outputs

Santana, A. F., Benton, M. C., Macartney-Coxson, D., & Black, M. A. (2019, August-September). A per-sample pathway analysis tool for DNA methylation data. Verbal presentation at the Queenstown Molecular Biology (QMB) Meetings, Queenstown, New Zealand.

Santana, A. F., Benton, M. C., Merriman, T. R., Black, M. A., & Macartney-Coxson, D. (2019, August-September). Hypomethylation of TXNIP in type-two diabetes female case with Māori ancestry: A sex difference reported. Verbal presentation at the Queenstown Molecular Biology (QMB) Meetings, Queenstown, New Zealand.

Benton, M., Clapham, J., Stubbs, R., Black, M., & Macartney-Coxson, D. (2019, August-September). The jejunal methylome differs in individuals with and without type-two diabetes. Verbal presentation at the Queenstown Molecular Biology (QMB) Meetings, Queenstown, New Zealand.

2018

Journal - Research Article

Tomek, P., Gore, S. K., Potts, C. L., Print, C. G., Black, M. A., Hallermayr, A., … Ching, L.-M. (2018). Imprinted and ancient gene: A potential mediator of cancer cell survival during tryptophan deprivation. Cell Communication & Signaling, 16, 88. doi: 10.1186/s12964-018-0301-7

Craig, H. J. B., Stachowicz, K., Black, M., Parry, M., Burke, C. R., Meier, S., & Amer, P. R. (2018). Genotype by environment interactions in fertility traits in New Zealand dairy cows. Journal of Dairy Science, 101, 10991-11003. doi: 10.3168/jds.2017-14195

Aiderus, A., Black, M. A., & Dunbier, A. K. (2018). Fatty acid oxidation is associated with proliferation and prognosis in breast and other cancers. BMC Cancer, 18, 805. doi: 10.1186/s12885-018-4626-9

Thomas, A., Routh, E. D., Pullikuth, A., Jin, G., Su, J., Chou, J. W., … Black, M. A., … Miller, L. D. (2018). Tumor mutational burden is a determinant of immune-mediated survival in breast cancer. OncoImmunology, 7(10), e1490854. doi: 10.1080/2162402X.2018.1490854

Lawrence, B., Blenkiron, C., Parker, K., Tsai, P., Fitzgerald, S., Shields, P., … Black, M., … Robinson, B., … Carroll, R., … Morrin, H., … Jackson, C., … Print, C. (2018). Recurrent loss of heterozygosity correlates with clinical outcome in pancreatic neuroendocrine cancer. npj Genomic Medicine, 3, 18. doi: 10.1038/s41525-018-0058-3

Newberg, J. Y., Black, M. A., Jenkins, N. A., Copeland, N. G., Mann, K. M., & Mann, M. B. (2018). SB Driver Analysis: A Sleeping Beauty cancer driver analysis framework for identifying and prioritizing experimentally actionable oncogenes and tumor suppressors. Nucleic Acids Research, 45(16), e94. doi: 10.1093/nar/gky450

Lacey, C. J., Doudney, K., Bridgman, P. G., George, P. M., Mulder, R. T., Zarifeh, J. J., Kimber, B., Cadzow, M. J., Black, M. A., Merriman, T. R., … Pearson, J. F., Cameron, V. A., & Kennedy, M. A. (2018). Copy number variants implicate cardiac function and development pathways in earthquake-induced stress cardiomyopathy. Scientific Reports, 8, 7548. doi: 10.1038/s41598-018-25827-5

Taylor, E. S., McCall, J. L., Shen, S., Girardin, A., Munro, F. M., Black, M. A., Ward-Hartstonge, K. A., & Kemp, R. A. (2018). Prognostic roles for IL-2-producing and CD69⁺ T cell subsets in colorectal cancer patients. International Journal of Cancer, 143(8), 2008-2016. doi: 10.1002/ijc.31598

Bilton, T. P., Schofield, M. R., Black, M. A., Chagné, D., Wilcox, P. L., & Dodds, K. G. (2018). Accounting for errors in low coverage high-throughput sequencing data when constructing genetic maps using biparental outcrossed populations. Genetics, 209(1), 65-76. doi: 10.1534/genetics.117.300627

Stovall, W. R., Taylor, H. R., Black, M., Grosser, S., Rutherford, K., & Gemmell, N. J. (2018). Genetic sex assignment in wild populations using genotyping‐by‐sequencing data: A statistical threshold approach. Molecular Ecology Resources, 18(2), 179-190. doi: 10.1111/1755-0998.12767

Campbell, H., Fleming, N., Roth, I., Mehta, S., Wiles, A., Williams, G., … Munro, F., McNoe, L., Black, M., McCall, J., Slatter, T. L., … Braithwaite, A. W. (2018). Δ133p53 isoform promotes tumour invasion and metastasis via interleukin-6 activation of JAK-STAT and RhoA-ROCK signalling. Nature Communications, 9(1), 254. doi: 10.1038/s41467-017-02408-0

Lee, S. L. J., Horsfield, J. A., Black, M. A., Rutherford, K., & Gemmell, N. J. (2018). Identification of sex differences in zebrafish (Danio rerio) brains during early sexual differentiation and masculinisation using 17α-methyltestoterone. Biology of Reproduction, 99(2), 446-460. doi: 10.1093/biolre/iox175

Conference Contribution - Published proceedings: Abstract

Pullikuth, A. K., Chifman, J., Routh, E. D., Chou, J., Jin, G., Black, M. A., & Miller, L. D. (2018). Triggering receptor expressed in myeloid cells 1 (TREM1) is a predictive marker for breast cancer therapeutics. Cancer Research, 78(13, Suppl.), 3791. doi: 10.1158/1538-7445.Am2018-3791

Maurin, M. M., Newberg, J. Y., Black, M. A., Jones, D. J., Jenkins, N. A., Copeland, N. G., & Mann, K. M. (2018). TCF12 regulates metastasis-promoting genes in pancreatic cancer. Cancer Research, 78(13, Suppl.), 1081. doi: 10.1158/1538-7445.Am2018-1081

Robb, T., Blenkiron, C., Tsai, P., Parker, K., Drummond, A., Black, M., Gavryushkin, A., … Print, C. (2018). Investigating tumour evolution in a single patient with disseminated cancer. Annals of Oncology, 29(Suppl. 9), (pp. ix156). doi: 10.1093/annonc/mdy425.018

Rhodes, J., McCall, J., Pattison, S., Ward-Hartstonge, K., Sandford, S., Munro, F., Black, M., & Kemp, R. (2018). Refining multiplex immunohistochemistry to quantify in situ immune infiltrate: Improving survival of colorectal cancer patients. Proceedings of the New Zealand Society for Oncology (NZSO) Conference. Retrieved from http://www.nzsoncology.org.nz/

Tomek, P., Print, C., Black, M., & Ching, L.-M. (2018). Imprinted and ancient gene: A potential mediator of cancer cell resistance to tryptophan catabolism induced by IDO1. Proceedings of the New Zealand Society for Oncology (NZSO) Conference. Retrieved from http://www.nzsoncology.org.nz/

Wiggins, G., Pearson, J., Black, M., Dunbier, A., & Walker, L. (2018). Expression variability is associated with breast tumour subtype. Proceedings of the New Zealand Society for Oncology (NZSO) Conference. Retrieved from http://www.nzsoncology.org.nz/

Harris, J., Black, M., Miller, L., & Cunliffe, H. (2018). Investigating the clinical significance of Fibroblast Growth Factor Inducible 14 in breast cancer. Proceedings of the New Zealand Society for Oncology (NZSO) Conference. Retrieved from http://www.nzsoncology.org.nz/

Norton, S., Ward-Hartstonge, K., McCall, J., Leman, J., Shen, S., Taylor, E., Munro, F., Black, M., … Kemp, R. (2018). An increase in effector Tregs is a classifying feature of the immune landscape in colorectal tumours. Proceedings of the New Zealand Society for Oncology (NZSO) Conference. Retrieved from http://www.nzsoncology.org.nz/

Robb, T., Blenkiron, C., Tsai, P., Parker, K., Drummond, A., Black, M., Gavryushkin, A., … Print, C. (2018). Investigating tumour evolution in a single patient with disseminated cancer. Proceedings of the New Zealand Society for Oncology (NZSO) Conference. Retrieved from http://www.nzsoncology.org.nz/

Klück, V., Crisan, T., Cleophas, M., Keating, S., Novakovic, B., Dalbeth, N., Stamp, L., Phipps-Green, A., Black, M., … Merriman, T., & Joosten, L. (2018). DNA methylation of SOCS3 as a possible mechanism for persistent urate induced inflammation. Annals of the Rheumatic Diseases, 77(Suppl. 2), (pp. 887-888). doi: 10.1136/annrheumdis-2018-eular.6281

Conference Contribution - Poster Presentation (not in published proceedings)

Santana, A. F., Macartney-Coxson, D., Benton, M. C., & Black, M. A. (2018, August). Differentially methylated genes and pathway perturbation in adipose tissues from gastric bypass intervention. Poster session presented at the Queenstown Molecular Biology (QMB) Meetings, Queenstown, New Zealand.

Robb, T., Blenkiron, C., Tsai, P., Parker, K., Drummond, A., Black, M., Gavryushkin, A., … Print, C. (2018, August). Investigating tumour evolution in a single patient with disseminated cancer. Poster session presented at the Queenstown Molecular Biology (QMB) Meetings, Queenstown, New Zealand.

Harris, J. J., Black, M. A., Miller, L. D., & Cunliffe, H. E. (2018, August). Investigating the clinical significance of Fibroblast Growth Factor Inducible 14 in breast cancer. Poster session presented at the Queenstown Molecular Biology (QMB) Meetings, Queenstown, New Zealand.

Wiggins, G., Pearson, J., Black, M., Dunbier, A., & Walker, L. (2018, August). Expression variability is associated with breast tumour subtype. Poster session presented at the Queenstown Molecular Biology (QMB) Meetings, Queenstown, New Zealand.

Conference Contribution - Verbal presentation and other Conference outputs

Black, M. A. (2018, August). Genomics Aotearoa: Bioinformatics as underpinning infrastructure for genomics research in New Zealand. Verbal presentation at the Queenstown Molecular Biology (QMB) Meetings, Queenstown, New Zealand.

Tomek, P., Potts, C. L., Print, C. G., Black, M. A., Gore, S. K., & Ching, L. (2018, August). A role for the imprinted and ancient gene in survival of cancer cells during tryptophan deprivation. Verbal presentation at the Queenstown Molecular Biology (QMB) Meetings, Queenstown, New Zealand.

Rhodes, J. L., McCall, J. L., Pattison, S. T., Ward-Hartstonge, K. A., Sandford, S. K., Munro, F. M., Black, M. A., & Kemp, R. A. (2018, August). Refining multiplex immunohistochemistry to quantify in situ immune infiltrate: Improving survival of colorectal cancer patients. Verbal presentation at the Queenstown Molecular Biology (QMB) and Australasian Society for Immunology New Zealand Branch (ASI-NZ) Joint Meeting, Queenstown, New Zealand.

2017

Journal - Research Article

Muthukaruppan, A., Lasham, A., Blenkiron, C., Woad, K. J., Black, M. A., Knowlton, N., … Shelling, A. N. (2017). Gene expression profling of breast tumours from New Zealand patients. New Zealand Medical Journal, 130(1464), 40-56. Retrieved from http://www.nzma.org.nz/journal

Lee, S. L. J., Horsfield, J. A., Black, M. A., Rutherford, K., Fisher, A., & Gemmell, N. J. (2017). Histological and transcriptomic effects of 17α-methyltestosterone on zebrafish gonad development. BMC Genomics, 18, 557. doi: 10.1186/s12864-017-3915-z

McInnes, T., Zou, D., Rao, D. S., Munro, F. M., Phillips, V. L., McCall, J. L., Black, M. A., Reeve, A. E., & Guilford, P. J. (2017). Genome-wide methylation analysis identifies a core set of hypermethylated genes in CIMP-H colorectal cancer. BMC Cancer, 17, 228. doi: 10.1186/s12885-017-3226-4

Ariazi, E. A., Taylor, J. C., Black, M. A., Nicolas, E., Slifker, M. J., Azzam, D. J., & Boyd, J. (2017). A new role for ERα: Silencing via DNA methylation of basal, stem cell, and EMT genes. Molecular Cancer Research, 15(2). doi: 10.1158/1541-7786.mcr-16-0283

Muthukaruppan, A., Lasham, A., Woad, K. J., Black, M. A., Blenkiron, C., Miller, L. D., Harris, G., … Findlay, M. P., … Print, C. G. (2017). Multimodal assessment of estrogen receptor mRNA profiles to quantify estrogen pathway activity in breast tumors. Clinical Breast Cancer, 17(2), 139-153. doi: 10.1016/j.clbc.2016.09.001

Journal - Research Other

Roelands, J., Decock, J., Boughorbel, S., Rinchai, D., Maccalli, C., Ceccarelli, M., Black, M., … Hendrickx, W. (2017). A collection of annotated and harmonized human breast cancer transcriptome datasets, including immunologic classification [Data note]. F1000Research, 6, 296. doi: 10.12688/f1000research.10960.1

Conference Contribution - Published proceedings: Abstract

Liu, H., Lamm, M. S., Rutherford, K., Todd, E. V., Black, M. A., Godwin, J. R., & Gemmell, N. J. (2017). New insights into sexual plasticity in fish using RNA-Seq. Proceedings of the Annual Conference of the Genetics Society of Australasia (GSA) with the New Zealand Society for Biochemistry and Molecular Biology (NZSBMB). 551. Retrieved from http://gen2017.w.events4you.currinda.com

Bilton, T. P., Schofield, M. R., Black, M. A., Chagne, D., Wilcox, P., & Dodds, K. G. (2017). Constructing linkage maps using low coverage sequencing data for multi-family full-sib populations. Proceedings of the MapNet Conference. Retrieved from http://scienceevents.co.nz/mapnet/

Print, C., Lasham, A., Knowlton, N., Trevarton, A., Jebb, A., Blenkiron, C., … Harris, G., … Braithwaite, A., & Black, M. (2017). Bioinformatic prospecting for breast cancer drivers. In A. Blackman, L. Gillman, C. Oliver & D. Dantzic (Eds.), Proceedings of the Inaugural New Zealand Breast Cancer Symposium (NZBCS): United for a Cure through Research. (pp. 60). Auckland, New Zealand: Auckland University of Technology. [Abstract]

Muthukaruppan, A., Lasham, A., Blenkiron, C., Woad, K. J., Black, M. A., Knowlton, N., … Shelling, A. N. (2017). Gene expression profiling of breast tumours from New Zealand patients. In A. Blackman, L. Gillman, C. Oliver & D. Dantzic (Eds.), Proceedings of the Inaugural New Zealand Breast Cancer Symposium (NZBCS): United for a Cure through Research. (pp. 48). Auckland, New Zealand: Auckland University of Technology. [Abstract]

Pearson, J. F., Wiggins, G. A. R., Black, M., Dunbier, A., & Walker, L. C. (2017). Expression variability is associated with breast cancer tumour subtype. Proceedings of the American Society of Human Genetics (ASHG) Annual Meeting. 746. Retrieved from http://www.ashg.org/2017meeting/

Conference Contribution - Verbal presentation and other Conference outputs

Blenkiron, C., Parker, K., Tsai, P., Fitzgerald, S., Shields, P., Yeong, M. L., … Black, M., … Robinson, B., … Connor, S., Morrin, H., … Lawrence, B. (2017, October). Three distinct genomic landscapes define clinical outcome of pancreatic neuroendocrine tumours (pNETs). Verbal presentation at the 19th Annual Scientific Meeting of the Australasian Gastro-Intestinal Trials Group (AGITG): Trials in Action, Cairns, Australia.

Aiderus, A., Black, M., & Dunbier, A. (2017, September). Insights into the prognostic association of fatty acid oxidation in cancer. Verbal presentation at the Queenstown Molecular Biology (QMB) Meetings, Queenstown, New Zealand.

Kelly, S. T., Stylianou, C., Chen, A., Guilford, P. J., & Black, M. A. (2017, September). In silico detection of candidate synthetic lethal gene pairs using cancer genomics data. Verbal presentation at the Queenstown Molecular Biology (QMB) Meetings, Queenstown, New Zealand.

Working Paper; Discussion Paper; Technical Report

Lacey, C. J., Doudney, K., Bridgman, P. G., George, P. M., Mulder, R. T., Zarifeh, J. A., Kimber, B., Cadzow, M. J., Black, M. A., Merriman, T. R., … Pearson, J. F., Cameron, V. A., & Kennedy, M. A. (2017). Copy number variants implicate cardiac function and development pathways in earthquake-induced stress cardiomyopathy. bioRxiv. doi: 10.1101/144675

2016

Journal - Research Article

Nguyen, H. T., Boocock, J., Merriman, T. R., & Black, M. A. (2016). SRBreak: A read-depth and split-read framework to identify breakpoints of different events inside simple copy-number variable regions. Frontiers in Genetics, 7, 160. doi: 10.3389/fgene.2016.00160

Cadzow, M., Merriman, T. R., Boocock, J., Dalbeth, N., Stamp, L. K., Black, M. A., … Wilcox, P. L. (2016). Lack of direct evidence for natural selection at the candidate thrifty gene locus, PPARGC1A. BMC Medical Genetics, 17, 80. doi: 10.1186/s12881-016-0341-z

Rangel, R., Lee, S.-C., Ban, K. H.-K., Guzman-Rojas, L., Mann, M. B., Newberg, J. Y., … McNoe, L. A., Selvanesan, L., … Black, M. A., … Copeland, N. G. (2016). Transposon mutagenesis identifies genes that cooperate with mutant Pten in breast cancer progression. PNAS, 113(48), E7749-E7758. doi: 10.1073/pnas.1613859113

Taylor, E. S., McCall, J. L., Girardin, A., Munro, F. M., Black, M. A., & Kemp, R. A. (2016). Functional impairment of infiltrating T cells in human colorectal cancer. OncoImmunology, 5(11), e1234573. doi: 10.1080/2162402X.2016.1234573

Mann, K. M., Newberg, J. Y., Black, M. A., Jones, D. J., Amaya-Manzanares, F., Guzman-Rojas, L., … McNoe, L. A., Selvanesan, L., … Mann, M. B. (2016). Analyzing tumor heterogeneity and driver genes in single myeloid leukemia cells with SBCapSeq. Nature Biotechnology, 34(9), 962-972. doi: 10.1038/nbt.3637

Jenkins, G. M., Goddard, M. E., Black, M. A., Brauning, R., Auvray, B., Dodds, K. G., … McEwan, J. C. (2016). Copy number variants in the sheep genome detected using multiple approaches. BMC Genomics, 17, 441. doi: 10.1186/s12864-016-2754-7

Miller, L. D., Chou, J. A., Black, M. A., Print, C., Chifman, J., Alistar, A., … Marincola, F. M. (2016). Immunogenic subtypes of breast cancer delineated by gene classifiers of immune responsiveness. Cancer Immunology Research, 4(7). doi: 10.1158/2326-6066.cir-15-0149

Smith, L. M., Parr-Brownlie, L. C., Duncan, E. J., Black, M. A., Gemmell, N. J., Dearden, P. K., & Reynolds, J. N. J. (2016). Striatal mRNA expression patterns underlying peak dose L-DOPA-induced dyskinesia in the 6-OHDA hemiparkinsonian rat. Neuroscience, 324, 238-251. doi: 10.1016/j.neuroscience.2016.03.012

Todd, E. V., Black, M. A., & Gemmell, N. J. (2016). The power and promise of RNA-seq in ecology and evolution. Molecular Ecology, 25(6), 1224-1241. doi: 10.1111/mec.13526

Conference Contribution - Published proceedings: Abstract

Norton, S., Taylor, E., Dunn, E., Munro, F., Black, M., McCall, J., & Kemp, R. (2016). Tumours from patients with colorectal cancer may dysregulate gut macrophage function and phenotype. European Journal of Immunology, 46(Suppl. 1), (pp. 439). doi: 10.1002/eji.201670200

Bin Aiderus, A. A., Black, M. A., & Dunbier, A. K. (2016). Expression of metabolic genes is associated with prognosis in breast cancer. Molecular Cancer Research, 14(1, Suppl.), A44. doi: 10.1158/1557-3125.metca15-a44

Conference Contribution - Verbal presentation and other Conference outputs

Todd, E. V., Liu, H., Lamm, M. S., Rutherford, K., Black, M. A., Godwin, J. R., & Gemmell, N. J. (2016, November). Genomic basis of sex change in fish. Verbal presentation at the 5th Australian Sex Summit, Lancefield, Australia.

Black, M. (2016, March). Genomic data visualisation: Making it fun for everyone. Verbal presentation at the Genetics Otago Symposium, Dunedin, New Zealand.

Black, M. (2016, October). How to train your bioinformatician (and yourself). Invited presentation at the New Zealand Society for Oncology Conference, Palmerston North, New Zealand.

Black, M. (2016, October). Investigating the association between patient body mass index and tumour molecular characteristics using the NZ breast cancer registers. Verbal presentation at the New Zealand Society for Oncology Conference, Palmerston North, New Zealand.

Burns, N., Topless, R., Boocock, J., Black, M. A., & Merriman, T. (2016, August-September). Interactive exploration of genome-scale datasets. Verbal presentation at the Queenstown Molecular Biology (QMB) Meetings, Nelson, New Zealand.

Wiggins, G. A. R., Pearson, J., Dunbier, A., Black, M., & Walker, L. (2016, August-September). Gene expression variability in breast tumours. Verbal presentation at the Queenstown Molecular Biology (QMB) Meetings, Nelson, New Zealand.

Black, M. (2016, August-September). Bioinformatic analysis of insertional mutagenesis data from Sleeping Beauty mouse models of cancer. Verbal presentation at the Queenstown Molecular Biology (QMB) Meetings, Nelson, New Zealand.

Gemmell, N. J., Todd, E. V., Liu, H., Lee, S., Lamm, M. S., Rutherford, K., Horsfield, J. A., Black, M. A., & Godwin, J. R. (2016, August-September). Fishing for answers with RNA-seq. Keynote presentation at the Queenstown Molecular Biology (QMB) Meetings, Nelson, New Zealand.

2015

Journal - Research Article

Liu, H., Lamm, M. S., Rutherford, K., Black, M. A., Godwin, J. R., & Gemmell, N. J. (2015). Large-scale transcriptome sequencing reveals novel expression patterns for key sex-related genes in a sex-changing fish. Biology of Sex Differences, 6, 26. doi: 10.1186/s13293-015-0044-8

Topless, R. K., Flynn, T. J., Cadzow, M., Stamp, L. K., Dalbeth, N., Black, M. A., & Merriman, T. R. (2015). Association of SLC2A9 genotype with phenotypic variability of serum urate in pre-menopausal women. Frontiers in Genetics, 6, 313. doi: 10.3389/fgene.2015.00313

Boocock, J., Chagné, D., Merriman, T. R., & Black, M. A. (2015). The distribution and impact of common copy-number variation in the genome of the domesticated apple, Malus x domestica Borkh. BMC Genomics, 16(1), 848. doi: 10.1186/s12864-015-2096-x

Sawaya, S., Boocock, J., Black, M. A., & Gemmell, N. J. (2015). Exploring possible DNA structures in real-time polymerase kinetics using Pacific Biosciences sequencer data. BMC Bioinformatics, 16, 21. doi: 10.1186/s12859-014-0449-0

Mann, M. B., Black, M. A., Jones, D. J., Ward, J. M., Yew, C. C. K., Newberg, J. Y., … Jenkins, N. A. (2015). Transposon mutagenesis identifies genetic drivers of Braf^V600E melanoma. Nature Genetics, 47(5), 486-495. doi: 10.1038/ng.3275

Ahmadi, O., Stringer, M. D., Black, M. A., & McCall, J. L. (2015). Clinico-pathological factors influencing lymph node yield in colorectal cancer and impact on survival: Analysis of New Zealand Cancer Registry data. Journal of Surgical Oncology, 11(4), 451-458. doi: 10.1002/jso.23848

Conference Contribution - Published proceedings: Abstract

Kemp, R., Norton, S., Taylor, E., Dunn, E., Munro, F., Black, M., & McCall, J. (2015). Colorectal tumour associated macrophages are more pro-inflammatory than adjacent control bowel tissue macrophage populations. Journal of Immunology, 194(1, Suppl.), TUM6P.1003. [Abstract]

Conference Contribution - Poster Presentation (not in published proceedings)

Muthukaruppan, A., Lasham, A., Woad, K. J., Black, M. A., Blenkiron, C., Miller, L. D., Harris, G., … Print, C. G. (2015, August-September). Multimodal assessment of oestrogen receptor status, expression and signalling activity in breast tumours. Poster session presented at the Queenstown Molecular Biology (QMB) Meetings, Queenstown, New Zealand.

McInnes, T., Zou, D., Black, M. A., Reeve, A. E., & Guilford, P. J. (2015, August-September). Genome-wide methylation analysis identifies a core set of hypermethylated CpG islands in CIMP-H colorectal cancer. Poster session presented at the Queenstown Molecular Biology (QMB) Meetings, Queenstown, New Zealand.

Munro, F. M., McCall, J. L., & Black, M. A. (2015, August-September). The effect of vitamin D on gene expression in colorectal cancer and normal colon. Poster session presented at the Queenstown Molecular Biology (QMB) Meetings, Queenstown, New Zealand.

Todd, E. V., Black, M., & Gemmell, N. J. (2015, August-September). Designing powerful RNA-seq experiments. Poster session presented at the Queenstown Molecular Biology (QMB) Meetings, Queenstown, New Zealand.

Conference Contribution - Verbal presentation and other Conference outputs

Muthukaruppan, A., Lasham, A., Woad, K. J., Black, M. A., Blenkiron, C., Miller, L. D., Harris, G., … Print, C. G. (2015, August-September). Multimodal assessment of oestrogen receptor status, expression and signalling activity in breast tumours. Verbal presentation at the Medical Sciences Congress (MedSci), Queenstown, New Zealand.

Kennedy, M., Doudney, K., Bickley, V., Bridgman, P., Cameron, V., Cadzow, M., Black, M., Merriman, T., … Miller, A., Zarifeh, J., Kimber, B., George, P., & Lacey, C. (2015, August-September). Genomes, earthquakes and broken hearts. Verbal presentation at the Queenstown Molecular Biology (QMB) Meetings, Queenstown, New Zealand.

2014

Journal - Research Article

Dubouzet, J. G., Donaldson, L., Black, M. A., McNoe, L., Liu, V., & Lloyd-Jones, G. (2014). Heterologous hybridisation to a Pinus microarray: Profiling of gene expression in Pinus radiata saplings exposed to ethephon. New Zealand Journal of Forestry Science, 44, 21. doi: 10.1186/s40490-014-0021-8

Alistar, A., Chou, J. W., Nagalla, S., Black, M. A., D'Agostino, R., & Miller, L. (2014). Dual roles for immune metagenes in breast cancer prognosis and therapy prediction. Genome Medicine, 6(10), 80. doi: 10.1186/s13073-014-0080-8

Kenny, L. C., Black, M. A., Poston, L., Taylor, R., Myers, J. E., Baker, P. N., … North, R. A. (2014). Early pregnancy prediction of preeclampsia in nulliparous women, combining clinical risk and biomarkers: The Screening for Pregnancy Endpoints (SCOPE) international cohort study. Hypertension, 64(3), 644-652. doi: 10.1161/hypertensionaha.114.03578

Cadzow, M., Boocock, J., Nguyen, H. T., Wilcox, P., Merriman, T. R., & Black, M. A. (2014). A bioinformatics workflow for detecting signatures of selection in genomic data. Frontiers in Genetics, 5, 293. doi: 10.3389/fgene.2014.00293

Chen, A., Beetham, H., Black, M. A., Priya, R., Telford, B. J., Guest, J., Wiggins, G. A. R., Godwin, T. D., … Guilford, P. J. (2014). E-cadherin loss alters cytoskeletal organization and adhesion in non-malignant breast cells but is insufficient to induce an epithelial-mesenchymal transition. BMC Cancer, 14, 552. doi: 10.1186/1471-2407-14-552

Nguyen, H. T., Merriman, T. R., & Black, M. A. (2014). The CNVrd2 package: Measurement of copy number at complex loci using high-throughput sequencing data. Frontiers in Genetics, 5, 248. doi: 10.3389/fgene.2014.00248

Ahmadi, O., Stringer, M. D., Black, M. A., & McCall, J. L. (2014). Influence of age and site of disease on lymph node yield in colorectal cancer. New Zealand Medical Journal, 127(1395). Retrieved from http://www.nzma.org.nz/journal

Tannock, G. W., Taylor, C., Lawley, B., Loach, D., Gould, M., Dunn, A. C., McLellan, A. D., Black, M. A., McNoe, L., Dekker, J., … Collett, M. A. (2014). Altered transcription of murine genes induced in the small bowel by administration of probiotic strain Lactobacillus rhamnosus HN001. Applied & Environmental Microbiology, 80(9), 2851-2859. doi: 10.1128/aem.00336-14

Roberts, R. L., Wallace, M. C., Wright, D. F. B., Cadzow, M., Dalbeth, N., Jones, P. B., Stamp, L. K., Harrison, A. A., Black, M. A., & Merriman, T. R. (2014). Frequency of CYP2C9 polymorphisms in Polynesian people and potential relevance to management of gout with benzbromarone. Joint Bone Spine, 81(2), 160-163. doi: 10.1016/j.jbspin.2013.07.006

Batt, C., Phipps-Green, A. J., Black, M. A., Cadzow, M., Merriman, M. E., Topless, R., … Harrison, A., Highton, J., … Stamp, L., … Merriman, T. R. (2014). Sugar-sweetened beverage consumption: A risk factor for prevalent gout with SLC2A9 genotype-specific effects on serum urate and risk of gout. Annals of the Rheumatic Diseases, 73(12), 2101-2106. doi: 10.1136/annrheumdis-2013-203600

Journal - Professional & Other Non-Research Articles

Roberts, R. L., Wallace, M. C., Wright, D. F. B., Cadzow, M., Dalbeth, N., Jones, P. B., Stamp, L. K., Harrison, A. A., Black, M. A., & Merriman, T. R. (2014). Fréquence des polymorphismes du CYP2C9 chez les Polynésiens et pertinence potentielle concernant le traitement de la goutte par benzbromarone. Revue du Rhumatisme, 81(2), 159-163. doi: 10.1016/j.rhum.2013.08.005

Conference Contribution - Published proceedings: Full paper

Jenkins, G., McEwan, J. C., Black, M. A., Goddard, M. E., Auvray, B., & Dodds, K. G. (2014). Association between raw SNP data and growth and meat yield traits in sheep. Proceedings of the 10th World Congress of Genetics Applied to Livestock Production. doi: 10.13140/2.1.2129.8564

Conference Contribution - Published proceedings: Abstract

Norton, S., Taylor, E., Dunn, E., Munro, F., & Black, M. (2014). Colorectal tumour associated macrophages are more pro-inflammatory than adjacent control bowel tissue macrophage populations. New Zealand Medical Journal, 127(1404). Retrieved from http://www.nzma.org.nz/journal

Ahmadi, O., McCall, J. L., Stringer, M. D., & Black, M. A. (2014). Clinico-pathological factors influencing lymph node yield in colorectal cancer and impact on survival: Analysis of New Zealand Cancer Registry database. ANZ Journal of Surgery, 84(Suppl. 1), (pp. 40). doi: 10.1111/ans.12609

Conference Contribution - Poster Presentation (not in published proceedings)

Muthukaruppan, A., Woad, K. J., Findlay, M. P., Black, M. A., Miller, L. D., Harris, G., … Print, C. G. (2014, August). Multimodal assessment of oestrogen receptor status, expression and signalling activity in breast tumours. Poster session presented at the Queenstown Molecular Biology (QMB) Meetings, Queenstown, New Zealand.

Kelly, S. T., Guilford, P. J., & Black, M. A. (2014, August). Bioinformatic prioritisation of synthetic lethal drug targets against E-cadherin deficient cancers. Poster session presented at the Queenstown Molecular Biology (QMB) Meetings, Queenstown, New Zealand.

Conference Contribution - Verbal presentation and other Conference outputs

Black, M., & Biggs, P. (2014, November). Introduction to visualising genomic data. Workshop presentation at the Genetics Otago Annual Symposium & Workshop, Dunedin, New Zealand.

Black, M. (2014, November). Free lunch? Analysis and visualisation of publicly accessible genomic data. Verbal presentation at the Genetics Otago Annual Symposium & Workshop, Dunedin, New Zealand.

Black, M. (2014, August). Detection of genome-wide copy number variation in apple. Verbal presentation at the Queenstown Molecular Biology (QMB) Meetings, Queenstown, New Zealand.

2013

Journal - Research Article

Trevarton, A. J., Mann, M. B., Knapp, C., Araki, H., Wren, J. D., Stones-Havas, S., Black, M. A., & Print, C. G. (2013). MelanomaDB: A web tool for integrative analysis of melanoma genomic information to identify disease-associated molecular pathways. Frontiers in Oncology, 3, 184. doi: 10.3389/fonc.2013.00184

Cappello, S., Gray, M. J., Badouel, C., Lange, S., Einsiedler, M., Srour, M., … Jenkins, Z. A., Morgan, T., Preitner, N., … Black, M. A., Markie, D., … Robertson, S. P. (2013). Mutations in genes encoding the cadherin receptor-ligand pair DCHS1 and FAT4 disrupt cerebral cortical development. Nature Genetics, 45(11), 1300-1308. doi: 10.1038/ng.2765

Nagalla, S., Chou, J. W., Willingham, M. C., Ruiz, J., Vaughn, J. P., Dubey, P., … Black, M. A., & Miller, L. D. (2013). Interactions between immunity, proliferation and molecular subtype in breast cancer prognosis. Genome Biology, 14, R34. doi: 10.1186/gb-2013-14-4-r34

tan Nguyen, H., Merriman, T. R., & Black, M. A. (2013). CNVrd, a read-depth algorithm for assigning copy-number at the FCGR Locus: Population-specific tagging of copy number variation at FCGR3B. PLoS ONE, 8(4), e63219. doi: 10.1371/journal.pone.0063219

Butler, M. I., Stockwell, P. A., Black, M. A., Day, R. C., Lamont, I. L., & Poulter, R. T. M. (2013). Pseudomonas syringae pv. actinidiae from recent outbreaks of kiwifruit bacterial canker belong to different clones that originated in China. PLoS ONE, 8(2), e57464. doi: 10.1371/journal.pone.0057464

Sawaya, S., Bagshaw, A., Buschiazzo, E., Kumar, P., Chowdhury, S., Black, M. A., & Gemmell, N. (2013). Microsatellite tandem repeats are abundant in human promoters and are associated with regulatory elements. PLoS ONE, 8(2), e54710. doi: 10.1371/journal.pone.0054710

Xu, H., Black, M. A., & Craig, B. A. (2013). Evaluating accuracy of diagnostic tests with intermediate results in the absence of a gold standard. Statistics in Medicine, 32(15), 2571-2584. doi: 10.1002/sim.5695

Girardin, A., McCall, J., Black, M. A., Edwards, F., Phillips, V., Taylor, E. S., Reeve, A. E., & Kemp, R. A. (2013). Inflammatory and regulatory T cells contribute to a unique immune microenvironment in tumor tissue of colorectal cancer patients. International Journal of Cancer, 132(8), 1842-1850. doi: 10.1002/ijc.27855

Conference Contribution - Published proceedings: Abstract

Kemp, R., Taylor, E., Girardin, A., Munro, F., Black, M., & McCall, J. (2013). Inflammatory and regulatory T cells contribute to a unique immune microenvironment in tumor tissue of colorectal cancer patients. Journal of Immunology, 190(1, Suppl.), 170.29. [Abstract]

Taylor, E., Girardin, A., Dunn, E., Munro, F., Black, M., McCall, J., & Kemp, R. (2013). Analysis of T cell subsets in colorectal cancer patients. Proceedings of the 43rd Australasian Society for Immunology (ASI) Annual Scientific Meeting. (pp. 102). Retrieved from http://www.asi2013.org/

Black, M. (2013). Identification of synthetic lethal gene pairs for targeted cancer therapies. Proceedings of the Joint New Zealand Statistical Association (NZSA) and Operations Research Society of New Zealand (ORSNZ) Conference: Analytics for a Changing World: From Data to Decisions. (pp. 61). Retrieved from https://secure.orsnz.org.nz/conf47/index.php

Batt, C., Phipps-Green, A. J., Black, M. A., Cadzow, M., Merriman, M. E., Topless, R., … Harrison, A., Highton, J., … Stamp, L., … Merriman, T. R. (2013). Sugary drinks and the risk of gout: Evidence for SLC2A9 gene interaction. New Zealand Medical Journal, 126(1384). Retrieved from http://www.nzma.org.nz/journal

Merriman, T., Phipps-Green, A., Black, M., Cadzow, M., Merriman, M., Topless, R., … Harrison, A., Highton, J., … Stamp, L., … Batt, C. (2013). Sugar-sweetened beverage consumption: A risk factor for prevalent gout that interacts with SLC2A9 genotype in a non-additive fashion. Internal Medicine Journal, 43(Suppl. 2), (pp. 2). doi: 10.1111/imj.12139

Conference Contribution - Verbal presentation and other Conference outputs

Black, M. (2013, September). Big data: Genomic number crunching. Verbal presentation at the Inaugural Genetics Week, Dunedin, New Zealand.

Black, M. (2013, August). From data to decisions: The bioinformatician’s role in genomic-enabled medicine. Verbal presentation at the Queenstown Molecular Biology (QMB) Meetings, Queenstown, New Zealand.

2012

Journal - Research Article

Wu, S. H., Black, M. A., North, R. A., & Rodrigo, A. G. (2012). A Bayesian model for classifying all differentially expressed proteins simultaneously in 2D PAGE gels. BMC Bioinformatics, 13, 137. doi: 10.1186/1471-2105-13-137

Lee, Y. F., Miller, L. D., Chan, X. B., Black, M. A., Pang, B., Ong, C. W., … Desai, K. V. (2012). JMJD6 is a driver of cellular proliferation and motility and a marker of poor prognosis in breast cancer. Breast Cancer Research, 14(3), R85. doi: 10.1186/bcr3200

Debono, R., Topless, R., Markie, D., Black, M. A., & Merriman, T. R. (2012). Analysis of the DISC1 translocation partner (11q14.3) in genetic risk of schizophrenia. Genes, Brain & Behavior, 11(7), 859-963. doi: 10.1111/j.1601-183X.2012.00832.x

Caldon, C. E., Sergio, C. M., Kang, J., Muthukaruppan, A., Boersma, M. N., Stone, A., … Black, M. A., … Musgrove, E. A. (2012). Cyclin E2 overexpression is associated with endocrine resistance but not insensitivity to CDK2 inhibition in human breast cancer cells. Molecular Cancer Therapeutics, 11(7), 1488-1499. doi: 10.1158/1535-7163.mct-11-0963

Mann, K. M., Ward, J. M., Yew, C. C. K., Kovochich, A., Dawson, D. W., Black, M. A., … Copeland, N. G. (2012). Sleeping Beauty mutagenesis reveals cooperating mutations and pathways in pancreatic adenocarcinoma. PNAS, 109(16), 5934-5941. doi: 10.1073/pnas.1202490109

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

Lasham, A., Samuel, W., Cao, H., Patel, R., Mehta, R., Stern, J. L., … Woolley, A. G., … Black, M. A., Shelling, A. N., Print, C. G., & Braithwaite, A. W. (2012). YB-1, the E2F Pathway, and regulation of tumor cell growth. Journal of the National Cancer Institute, 104(2), 133-146. doi: 10.1093/jnci/djr512

Conference Contribution - Published proceedings: Abstract

Merriman, T. R., Dalbeth, N., Gow, P. J., Harrison, A., Highton, J., Jones, P. B. B., Stamp, L. K., Cadzow, M., Merriman, M. E., Topless, R., Black, M. A., Phipps-Green, A., & Batt, C. M. (2012). Epistatic interaction between solute carrier 2A9 genotype and sugar-sweetened beverage consumption in the determination of gout risk. Arthritis & Rheumatism, 64(10, Suppl.), (pp. S696). doi: 10.1002/art.37735

Smith, L. M., Duncan, E. J., Parr-Brownlie, L. C., Black, M. A., Dearden, P. K., & Reynolds, J. N. J. (2012). Transcriptome analysis of levodopa-induced dyskinesias in the 6-hydroxydopamine hemiparkinsonian rat. Proceedings of the Society for Neuroscience 42nd Annual Meeting. SfN. Retrieved from http://www.sfn.org/index.aspx?pagename=abstracts_am2012

Smith, L., Duncan, E., Parr-Brownlie, L., Black, M., Dearden, P., & Reynolds, J. (2012). Understanding the mechanisms behind levodopa-induced dyskinesias. New Zealand Medical Journal, 125(1364). Retrieved from http://www.nzma.org.nz/journal

Conference Contribution - Poster Presentation (not in published proceedings)

Taylor, E., Girardin, A., Dunn, E., Munro, F., Black, M., McCall, J., & Kemp, R. (2012, September). T cell subset analysis in human colorectal cancer patients. Poster session presented at the Division of Health Sciences Research Forum: Health Matters: Research Excellence at Otago, Dunedin, New Zealand.

Nguyen, T. H., Merriman, T. R., & Black, M. A. (2012, August). CCL3L1 copy number and tag SNPs in European populations. Poster session presented at the Queenstown Molecular Biology (QMB) Meetings, Queenstown, New Zealand.

Debono, R., Topless, R., Markie, D., Black, M. A., & Merriman, T. R. (2012, August). Assessment of genetic association of the DISC1 translocation partner 11q14.3 with schizophrenia. Poster session presented at the Queenstown Molecular Biology (QMB) Meetings, Queenstown, New Zealand.

Dasari, S., Black, M., McNoe, L., McCall, J., & Reeve, A. (2012, August). Determining the molecular mechanisms in triple negative colorectal cancer. Poster session presented at the Queenstown Molecular Biology (QMB) Meetings, Queenstown, New Zealand.

Conference Contribution - Verbal presentation and other Conference outputs

Mehta, S., Lasham, A., Wright, D., Black, M. A., Reeve, A., Guilford, P., McCall, J., … Print, C. (2012, August). Towards improving clinical decisions for colon cancer patients: A step closer to personalised medicine. Verbal presentation at the Queenstown Molecular Biology (QMB) Meetings, Queenstown, New Zealand.

Guilford, P., Telford, B., Black, M., & Chen, A. (2012, August). Synthetic lethal targeting of the tumour suppressor gene CDH1 in common cancers. Invited presentation at the Queenstown Molecular Biology (QMB) Meetings, Queenstown, New Zealand.

2011

Journal - Research Article

Miller, L. D., Coffman, L. G., Chou, J. W., Black, M. A., Bergh, J., Agostino, Jr, R. D., … Torti, F. M. (2011). An iron regulatory gene signature predicts outcome in breast cancer. Cancer Research, 71(21), 6728-6737. doi: 10.1158/0008-5472.can-11-1870

Kemp, R. A., Black, M. A., McCall, J., Yoon, H.-S., Phillips, V., Anjomshoaa, A., & Reeve, A. E. (2011). T cell subpopulations in lymph nodes may not be predictive of patient outcome in colorectal cancer. Journal of Experimental & Clinical Cancer Research, 30, 78. doi: 10.1186/1756-9966-30-78

Linterman, K. S., Palmer, D. N., Kay, G. W., Barry, L. A., Mitchell, N. L., McFarlane, R. G., Black, M. A., … Hughes, S. M. (2011). Lentiviral-mediated gene transfer to the sheep brain: Implications for gene therapy in Batten disease. Human Gene Therapy, 22(8), 1011-1020. doi: 10.1089/hum.2011.026

Soon, W. W., Miller, L. D., Black, M. A., Dalmasso, C., Chan, X. B., Pang, B., … Liu, E. T. (2011). Combined genomic and phenotype screening reveals secretory factor SPINK1 as an invasion and survival factor associated with patient prognosis in breast cancer. EMBO Molecular Medicine, 3(8), 451-464. doi: 10.1002/emmm.201100150

Kalamorz, F., Keis, S., McMillan, D. G. G., Olsson, K., Stanton, J.-A., Stockwell, P., Black, M. A., … Cook, G. M. (2011). Draft genome sequence of the thermoalkaliphilic Caldalkalibacillus thermarum strain TA2.A1. Journal of Bacteriology, 193(16), 4290-4291. doi: 10.1128/jb.05035-11

Nixon, G., Blattner, K., Dawson, J., Dovey, S., Black, M. A., Wilkins, G., Dunn, A. C., & McLellan, A. D. (2011). Streptokinase antibodies in patients presenting with acute coronary syndrome in three rural New Zealand populations. Journal of Clinical Pathology, 64, 426-429. doi: 10.1136/jcp.2010.085837

McCowan, L. M. E., North, R. A., Kho, E. M., Black, M. A., Chan, E. H. Y., & Dekker, G. A. (2011). Paternal contribution to small for gestational age babies: A multicenter prospective study. Obesity, 19(5), 1035-1039. doi: 10.1038/oby.2010.279

North, R. A., McCowan, L. M. E., Dekker, G. A., Poston, L., Chan, E. H. Y., Stewart, A. W., Black, M. A., … Kenny, L. C. (2011). Clinical risk prediction for pre-eclampsia in nulliparous women: Development of model in international prospective cohort. BMJ, 342, d1875. doi: 10.1136/bmj.d1875

Seed, P. T., Chappell, L. C., Black, M. A., Poppe, K. K., Hwang, Y.-C., Kasabov, N., … North, R. A. (2011). Prediction of preeclampsia and delivery of small for gestational age babies based on a combination of clinical risk factors in high-risk women. Hypertension in Pregnancy, 30(1), 58-73. doi: 10.3109/10641955.2010.486460

Conference Contribution - Published proceedings: Full paper

Payne, G. M., Goddard, M. E., McEwan, J. C., Black, M. A., & Dodds, K. G. (2011). Association between SNP intensity data and growth and meat yield traits in sheep. In P. Vercoe (Ed.), Proceedings of the Nineteenth Association for the Advancement of Animal Breeding and Genetics (AAABG) Conference: Breeding Objectives: A New Paradigm. 19, (pp. 387-390). Perth, Australia: Association for the Advancement of Animal Breeding and Genetics. [Full Paper]

Nasser, S., Cunliffe, H. E., Black, M. A., & Kim, S. (2011). Context-specific gene regulatory networks subdivide intrinsic subtypes of breast cancer. BMC Bioinformatics. 12(Suppl. 2), S3. doi: 10.1186/1471-2105-12-S2-S3

Conference Contribution - Published proceedings: Abstract

Black, M., Laurie, R., McNoe, L., & Merriman, T. (2011). The resequencing coverage limbo: How low can you go? Proceedings of the 3rd Next Generation Sequencing Conference. Retrieved from http://www.nzconferences.org.nz/NGS%20Conferences/NGS2011/abstracts.html

Pilbrow, A. P., Pearson, J. F., McNoe, L., Ellis, K. L., Black, M. A., Sweet, W. E., … Troughton, R. W., Richards, A. M., … Cameron, V. A. (2011). Chromosome 1q41 and 3q22.3 coronary artery disease risk loci are associated with altered cardiac gene expression profiles in normal and diseased heart. Circulation, 124, A12170. [Abstract]

Peacock, H. E., Black, M. A., Empson, R. M., & Hughes, S. M. (2011). FEZF2 regulates projection maintenance in postnatal neurons in vitro. In B. Leitch (Ed.), Proceedings of the 29th International Australasian Winter Conference on Brain Research. 29, 1.2. AWCBR. Retrieved from http://psy.otago.ac.nz/awcbr/abstracts/abstracts2011.html

Harley, J. A., Kennedy, M. A., Doudney, K., Allington, M., Pearson, J., Black, M., & Joyce, P. R. (2011). Antidepressants cause specific changes in the rat peripheral blood transcriptome. Biological Psychiatry. 69(9, Suppl. 1), (pp. 89S). [Abstract]

Black, M., Anjomshoaa, A., Print, C., McCall, J., & Reeve, A. (2011). Bioinformatic approaches in colorectal cancer. Proceedings of the Inaugural International Cancer Symposium. Retrieved from http://www.wnmeds.ac.nz/cancersymposium/programme.html

Conference Contribution - Poster Presentation (not in published proceedings)

Cadzow, M., Black, M., & Merriman, T. (2011, September). Investigation of copy number variation at the ABCG2 locus. Poster session presented at the Queenstown Molecular Biology (QMB) Meetings, Queenstown, New Zealand.

Print, C., Muthukaruppan, A., Hurley, D., Black, M., & Shelling, A. (2011, September). Bioinformatics of estrogen responsiveness in breast cancer. Poster session presented at the Queenstown Molecular Biology (QMB) Meetings, Queenstown, New Zealand.

Conference Contribution - Verbal presentation and other Conference outputs

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.

Black, M. (2011, June-July). BeSTGRID basics. Verbal presentation at the New Zealand eResearch Symposium, Dunedin, New Zealand.

Black, M. (2011, December). Molecular signatures for prognosis prediction in colorectal cancer. Verbal presentation at the Maurice Wilkins Centre for Molecular Biodiscovery Workshop: Celebrating Collaboration in Biomedical Research, Dunedin, New Zealand.

Allen, T., Black, M., Blenkiron, C., Crampin, E., Hurley, D., Lasham, A., … Print, C. (2011, February). Translating the molecular signatures of tumours into clinically and biologically useful information. Verbal presentation at the Inaugural International Cancer Symposium, Wellington, New Zealand.

Intellectual Property

Anjomshoaa, A., Reeve, A. E., Lin, Y.-H., & Black, M. A. (2011). Proliferation signature and prognosis for gastrointestinal cancer. (562237).

2010

Journal - Research Article

Nasri, S., Anjomshoaa, A., Song, S., Guilford, P., McNoe, L., Black, M., Phillips, V., Reeve, A., & Humar, B. (2010). Oligonucleotide array outperforms SNP array on formalin-fixed paraffin-embedded clinical samples. Cancer Genetics & Cytogenetics, 198(1), 1-6. doi: 10.1016/j.cancergencyto.2009.12.002

Ariazi, E. A., Brailoiu, E., Yerrum, S., Shupp, H. A., Slifker, M. J., Cunliffe, H. E., Black, M. A., … Jordan, V. C. (2010). The G protein-coupled receptor GPR30 inhibits proliferation of estrogen receptor-positive breast cancer cells. Cancer Research, 70(3), 1184-1194. doi: 10.1158/0008-5472.CAN-09-3068

Conference Contribution - Published proceedings: Abstract

Black, M. A. (2010). Pharmacogenomics of breast cancer treatment. Proceedings of the Australasian Society of Clinical and Experimental Pharmacologists and Toxicologists New Zealand Annual Scientific Meeting and the 6th Annual Carney Pharmacogenomics Symposium. ASCEPT. Retrieved from http://www.ascept.org.nz/

Harley, J. A., Doudney, K., Allington, M. A., McNoe, L., Pearson, J., Black, M., Joyce, P. R., & Kennedy, M. A. (2010). Antidepressant specific changes in rat whole blood gene expression identified by gene-chip analysis. Proceedings of the Australasian Society of Clinical and Experimental Pharmacologists and Toxicologists New Zealand Annual Scientific Meeting and the 6th Annual Carney Pharmacogenomics Symposium. ASCEPT. Retrieved from http://www.ascept.org.nz/

Getz, J. E., Anderson, E. M., Black, M. A., Hedenfalk, I. A., Balagurunathan, Y., Willis, A. L., & et al (2010). Loss of VAV3 expression as a novel biomarker and indicator of chemosensitivity in basal-like breast cancer. Proceedings of the American Association for Cancer Research (AACR) 101st Annual Meeting. Retrieved from http://www.aacrmeetingabstracts.org/

Conference Contribution - Verbal presentation and other Conference outputs

Black, M. (2010, August). Investigating copy number variation at the FCGR3B locus. Verbal presentation at the Second Annual Next Generation Sequencing Conference, Dunedin, New Zealand.

Black, M. (2010, May). Collaborative initiatives that are changing the face of cancer research. Verbal presentation at the New Zealand Society for Oncology (NZSO) Annual Meeting, Auckland, New Zealand.

Linterman, K., Mitchell, N. L., Barry, L. A., Jay, N. P., McFarlane, R. G., Black, M. A., … Hughes, S. M. (2010, February). Viral therapy for batten disease in sheep. Verbal presentation at the New Zealand Chapter of the Controlled Release Society 12th Conference on Formulation and Delivery of Bioactives, Dunedin, New Zealand.

2009

Journal - Research Article

Atkinson, K. R., Blumenstein, M., Black, M. A., Wu, S. H., Kasabov, N., Taylor, R. S., … on behalf of the SCOPE Consortium. (2009). An altered pattern of circulating apolipoprotein E3 isoforms is implicated in preeclampsia. Journal of Lipid Research, 50, 71-80. doi: 10.1194/jlr.M800296-JLR200

Blumenstein, M., McMaster, M. T., Black, M. A., Wu, S., Prakash, R., Cooney, J., … North, R. A. (2009). A proteomic approach identifies early pregnancy biomarkers for preeclampsia: Novel linkages between a predispositon to preeclampsia and cardiovascular disease. Proteomics, 9(11), 2929-2945. doi: 10.1002/pmic.200800625

Wu, S. H., Black, M. A., North, R. A., Atkinson, K. R., & Rodrigo, A. G. (2009). A statistical model to identify differentially expressed proteins in 2D PAGE gels. PLoS Computational Biology, 5(9), e1000509. doi: 10.1371/journal.pcbi.1000509

Kho, E. M., McCowan, L. M. E., North, R. A., Roberts, C. T., Chan, E., Black, M. A., … on behalf of the SCOPE Consortium. (2009). Duration of sexual relationship and its effect on preeclampsia and small for gestational age perinatal outcome. Journal of Reproductive Immunology, 82(1), 66-73. doi: 10.1016/j.jri.2009.04.011

Anjomshoaa, A., Nasri, S., Humar, B., McCall, J. L., Chatterjee, A., Yoon, H.-S., McNoe, L., Black, M. A., & Reeve, A. E. (2009). Slow proliferation as a biological feature of colorectal cancer metastasis. British Journal of Cancer, 101(5), 822-828. doi: 10.1038/sj.bjc.6605229

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

Black, M. (2009). Copy number variation and oncogenic pathway activation in cancer. Proceedings of the 5th New Zealand Molecular Mapping Workshop. (pp. 22). Retrieved from https://mapnet.agresearch.co.nz/mediawiki/images/2/29/MapNet_Workshop_BOOKLET_2009.pdf

Black, M. (2009). eResearch resources for VISG. Proceedings of the 5th New Zealand Molecular Mapping Workshop. (pp. 13). Retrieved from https://mapnet.agresearch.co.nz/mediawiki/images/2/29/MapNet_Workshop_BOOKLET_2009.pdf

Harley, J. A., Doudney, K., Allington, M., Pearson, J., Black, M., Joyce, P. R., & Kennedy, M. A. (2009). Blood mRNA changes induced by antidepressants. Proceedings of the 5th Annual Carney Pharmacogenomics Symposium. Retrieved from http://www.otago.ac.nz/christchurch/otago019049.pdf

Black, M. (2009). Genomic data analysis with GenePattern. Proceedings of the eResearch@Otago Bi-annual Conference. Retrieved from http://extreme.otago.ac.nz/ocs/index.php/eResearch/er09/

Anderson, E. M., Getz, J. E., Balagurunathan, Y., Black, M. A., Willis, A. L., Hyder, P., … Cunliffe, H. E. (2009). Investigation of VAV3 as a novel biomarker and indicator of chemosensitivity in basal-like breast cancer. Proceedings of the American Association for Cancer Research (AACR) 100th Annual Meeting. Retrieved from http://www.aacrmeetingabstracts.org/

Harley, J. A., Doudney, K., Allington, M., Pearson, J., Black, M., Joyce, P. R., & Kennedy, M. A. (2009). Blood mRNA changes induced by antidepressants: Future biomarkers to tailor depression treatment? Proceedings of the ComBio2009 Conference. [CD-ROM] [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

Intellectual Property

Reeve, A. E., Black, M. A., McCall, J. L., Nekarda, H., Rosenberg, R., Friederichs, J., … Lin, Y.-H., & Pollock, R. C. (2009). Prognosis prediction for colorectal cancer. (544432).

Other Research Output

Black, M. (2009, September). Cancer genomics: A number cruncher's perspective. Otago Institute Lecture Series. Dunedin, New Zealand. [Public Seminar].

2008

Journal - Research Article

Pilbrow, A. P., Ellmers, L. J., Black, M. A., Moravec, C. S., Sweet, W. E., Troughton, R. W., Richards, A. M., Frampton, C. M., & Cameron, V. A. (2008). Genomic selection of reference genes for real-time PCR in human myocardium. BMC Medical Genomics, 1, 64. doi: 10.1186/1755-8794-1-64

John, T., Black, M. A., Toro, T. T., Leader, D., Gedye, C. A., Davis, I. D., Guilford, P. J., & Cebon, J. S. (2008). Predicting clinical outcome through molecular profiling in stage III melanoma. Clinical Cancer Research, 14(16), 5173-5180.

Anjomshoaa, A., Lin, Y.-H., Black, M. A., McCall, J. L., Humar, B., Song, S., Fukuzawa, R., Yoon, H.-S., … van Rij, A., Thompson-Fawcett, M., & Reeve, A. E. (2008). Reduced expression of a gene proliferation signature is associated with enhanced malignancy in colon cancer. British Journal of Cancer, 99, 966-973. doi: 10.1038/sj.bjc.6604560

Song, S., & Black, M. A. (2008). Microarray-based gene set analysis: A comparison of current methods. BMC Bioinformatics, 9, 502. doi: 10.1186/1471-2105-9-502

Willis, A. L., Tran, N. L., Chatigny, J. M., Charlton, N., Vu, H., Brown, S. A. N., Black, M. A., … Cunliffe, H. E. (2008). The fibroblast growth factor-inducible 14 receptor is highly expressed in HER2-positive breast tumors and regulates breast cancer cell invasive capacity. Molecular Cancer Research, 6(5), 725-734. doi: 10.1158/1541-7786.MCR-08-0005

Conference Contribution - Published proceedings: Abstract

Black, M. (2008). GenePattern@Otago: Local tools for the analysis of microarray data. Proceedings of the 8th Annual Australasian Microarray and Associated Technologies (AMATA) Conference. Retrieved from http://www.amata.org.au/index.php/resources/2008-conference-abstracts

Black, M. A., Song, S., Anjomshoaa, A., & Reeve, A. E. (2008). Gene set meta-analysis: Application to breast cancer microarray data. Proceedings of the American Association for Cancer Research (AACR) 99th Annual Meeting. Retrieved from http://www.aacrmeetingabstracts.org/

Pilbrow, A., Pearson, J., McNoe, L., Black, M., Moravec, C., Sweet, W., … Troughton, R., Richards, M., & Cameron, V. (2008). The chromosome 9p21.3 coronary artery disease risk locus is associated with altered cardiac gene expression in individuals without overt cardiac abnormality. Circulation, 118(18, Suppl.), (pp. S_390-S_391). [Abstract]

Conference Contribution - Verbal presentation and other Conference outputs

Smyth, G., Black, M., & Robinson, M. (2008, November). Differential expression analysis of microarray data: Bioconductor and limma software [Workshop]. Verbal presentation at the 8th Annual Australasian Microarray and Associated Technologies (AMATA) Conference, Dunedin, New Zealand.

Allen, T., & Black, M. (2008, November). Using reconstructed gene networks to assist with prognosis prediction in breast cancer. Verbal presentation at the 8th Annual Australasian Microarray and Associated Technologies (AMATA) Conference, Dunedin, New Zealand.

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

Naot, D., Bava, U., Matthews, B., Callon, K. E., Gamble, G. D., Black, M., … Reid, I. R. (2007). Differential gene expression in cultured osteoblasts and bone marrow stromal cells from patients with Paget's disease of bone. Journal of Bone & Mineral Research, 22(2), 298-309. doi: 10.1359/JBMR.061108

Lin, Y.-H., Friederichs, J., Black, M. A., Mages, J., Rosenberg, R., Guilford, P. J., Phillips, V., Thompson-Fawcett, M., … van Rij, A., Yoon, H.-S., McCall, J. L., … Reeve, A. E. (2007). Multiple gene expression classifiers from different array platforms predict poor prognosis of colorectal cancer. Clinical Cancer Research, 13(2), 498-507. doi: 10.1158/1078-0432.CCR-05-2734

Conference Contribution - Published proceedings: Abstract

Wu, S., Black, M., North, R., & Rodrigo, A. (2007). A novel statistical model to identify biomarkers in 2D proteomic gels. Proceedings of the New Zealand Statistical Association Annual Conference. NZSA. Retrieved from http://www.math.canterbury.ac.nz/nzsa2007/presentations.shtml

Lin, Y.-H., Anjomshoaa, A., Song, S., Black, M. A., McCall, J. L., & Reeve, A. E. (2007). A proliferation gene signature can predict clinical outcome of multiple cancers. Proceedings of the American Association for Cancer Research (AACR) 98th Annual Meeting. Retrieved from http://www.aacrmeetingabstracts.org/

Conference Contribution - Verbal presentation and other Conference outputs

Pilbrow, A. P., Ellmers, L. J., Black, M., Sweet, W. E., Moravec, C. S., Troughton, R. W., Richards, A. M., & Cameron, V. A. (2007, November). Multiple reference genes are required for accurate normalisation of gene expression levels in human heart. Verbal presentation at the Medical Sciences Congress, Queenstown, New Zealand.

2006

Conference Contribution - Published proceedings: Full paper

Guindon, S., Black, M., & Rodrigo, A. (2006). Control of the false discovery rate applied to the detection of positively selected amino acid sites. Molecular Biology & Evolution, 23(5), (pp. 919-926). doi: 10.1093/molbev/msj095

Conference Contribution - Published proceedings: Abstract

Matthews, B., Naot, D., Bava, U., Callon, K., Black, M., Cornish, J., & Reid, I. (2006). Evidence for osteoblast involvement in Paget's disease of bone. Proceedings of the New Zealand Society of Endocrinology Annual Meeting. NZSE. Retrieved from http://nzse.rsnz.org/NZSE%20Abstracts%202006.pdf

Anjomshoaa, A., Lin, Y., Chatterjee, A., Lin, H., McCall, J., Black, M., & Reeve, A. E. (2006). Low proliferation is an indicator of poor outcome in colorectal cancer. New Zealand Medical Journal, 119(1237). Retrieved from http://journal.nzma.org.nz/journal/119-1237/2062/content.pdf

2000

Journal - Research Article

Black, M. A., Jones, R. D., Carroll, G. J., Dingle, A. A., Donaldson, I. M., & Parkin, P. J. (2000). Real-time detection of epileptiform activity in the EEG: A blinded clinical trial. Clinical Electroencephalography, 31, 122-130.

1999

Conference Contribution - Published proceedings: Abstract

Black, M. A., Jones, R. D., Carroll, G. J., & Craig, B. A. (1999). A Bayesian approach to the assessment of diagnostic test accuracy in the absence of a gold standard. Proceeding of 20th Conference of American Statistical Association. Baltimore. [Abstract]

1998

Journal - Research Article

Black, M. A., & Jones, R. D. (1998). Sensitivity and selectivity for continuous perception values - a comment. Electroencephalography & Clinical Neurophysiology, 106(5), 457-459.

1997

Conference Contribution - Published proceedings: Abstract

Black, M. A., Jones, R. D., Carroll, G. J., & Smith, M. (1997). Bayesian evaluation of automated EEG analysis system in the absence of a gold standard. New Zealand Medical Journal. 110(1054), (pp. 444). [Abstract]

Conference Contribution - Verbal presentation and other Conference outputs

Black, M. A., Jones, R. D., Carroll, G. J., & Smith, M. (1997). Bayesian evaluation of automoated EEG analysis system in the absence of a gold standard. Verbal presentation at the Christchurch Medical Research Society, Christchurch.

1996

Conference Contribution - Published proceedings: Full paper

Jones, R. D., Dingle, A. A., Carroll, G. J., Green, R. D., Black, M. A., Donaldson, I. M. A., … Burgess, K. L. (1996). A system for detecting epileptiform discharges in the EEG: realtime operation and clinical trial. Proceedings of the 18th Annual International Conference of the IEEE Engineering in Medicine and Biology Society. Amsterdam, Holland: IEEE. [Full Paper]