Professor Mik Black

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

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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

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

Journal - Research Article

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

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

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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

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

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

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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

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

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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

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

Journal - Research Article

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 Article

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

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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

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

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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

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

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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 - Research Article

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

Journal - Research Article

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

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

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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

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

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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

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

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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

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

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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

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

Journal - Research Article

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

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

Journal - Research Article

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

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

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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.

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

Journal - Research Article

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

Journal - Research Article