Associate Professor Mik Black

Mik Black2
  • Biochemistry Department
  • School of Biomedical Sciences
  • University of Otago
  • P.O. Box 56
  • 710 Cumberland St
  • Dunedin 9054 , New Zealand
  • Tel.: 64 3 479-7831
  • Fax: 64 3 479-7866
  • Email:mik.black@otago.ac.nz

Assoc Prof Black joined the Department of Biochemistry as a Senior Lecturer in May 2006. He received a B.Sc.(Hons) in Statistics from the University of Canterbury in 1996, and M.S. and Ph.D. degrees in Mathematical Statistics and Statistics in 2000 and 2002 from Purdue University.

Research:

Assoc Prof Black's research interests include the analysis of data from gene expression microarray experiments, Bayesian statistical methods, and statistical computing.

Teaching:

Assoc Prof Black teaches a microarray module in BIOC 354 Bioinformatics and Functional Genomics, a statistics module in BIOC 452 Metabolism and Regulation, and a course (STAT435 Data Analysis for Bioinformatics ) on the use of statistical and bioinformatic methods for the analysis of data from microarray and second generation sequencing experiments.

Selected Publications

Eric A Ariazi, John C Taylor, Michael A Black, Emmanuelle Nicolas, Michael J Slifker, Diana J Azzam, and Jeff Boyd., A New Role for ERα: Silencing via DNA Methylation of Basal, Stem Cell, and EMT Genes., Mol Cancer Res 2016,15(2); 1-13., Link »

Murray Cadzow, Tony R Merriman, James Boocock, Nicola Dalbeth, Lisa K Stamp, Michael A Black, Peter M Visscher, and Phillip L Wilcox., Lack of direct evidence for natural selection at the candidate thrifty gene locus, PPARGC1A., BMC Med Genet 2016 vol. 17 (1) p. 80., Link »

Roberto Rangel, Song-Choon Lee, Kenneth Hon-Kim Ban, Liliana Guzman-Rojas, Michael B Mann, Justin Y Newberg, Takahiro Kodama, Leslie A McNoe, Luxmanan Selvanesan, Jerrold M Ward, Alistair G Rust, Kuan-Yew Chin, Michael A Black, Nancy A Jenkins, and Neal G Copeland., Transposon mutagenesis identifies genes that cooperate with mutant Pten in breast cancer progression., P Natl Acad Sci Usa 2016 p. 201613859., Link »

Edward S Taylor, John L McCall, Adam Girardin, Fran M Munro, Michael A Black, and Roslyn A. Kemp., Functional impairment of infiltrating T cells in human colorectal cancer., OncoImmunology 2016 p. e1234573., Link »

Anita Muthukaruppan, Annette Lasham, Kathryn J Woad, Michael A Black, Cherie Blenkiron, Lance D. Miller, Gavin Harris, Nicole McCarthy, Michael P Findlay, Andrew N. Shelling, and Cristin G. Print., Multimodal Assessment of Estrogen Receptor mRNA Profiles to Quantify Estrogen Pathway Activity in Breast Tumors., Clin Breast Cancer 2016., Link »

Karen M Mann, Justin Y Newberg, Michael A Black, Devin J Jones, Felipe Amaya-Manzanares, Liliana Guzman-Rojas, Takahiro Kodama, Jerrold M Ward, Alistair G Rust, Louise van der Weyden, Christopher Chin Kuan Yew, Jill L Waters, Marco L Leung, Keith Rogers, Susan M Rogers, Leslie A McNoe, Luxmanan Selvanesan, Nicholas Navin, Nancy A Jenkins, Neal G Copeland, and Michael B Mann., Analyzing tumor heterogeneity and driver genes in single myeloid leukemia cells with SBCapSeq., Nature Biotechnology 2016pp. 1-14., Link »

Gemma M Jenkins, Michael E Goddard, Michael A Black, Rudiger Brauning, Benoit Auvray, Ken G Dodds, James W Kijas, Noelle Cockett, and John C Mcewan., Copy number variants in the sheep genome detected using multiple approaches., BMC Genomics 2016 vol. 17 (1) p. 441., Link »

L M Smith, L C Parr-Brownlie, E J Duncan, M A Black, N J Gemmell, P K Dearden, and J N J Reynolds., Striatal mRNA expression patterns underlying peak dose l-DOPA-induced dyskinesia in the 6-OHDA hemiparkinsonian rat., Neuroscience 2016., Link »

Erica V Todd, Michael A Black, and Neil J Gemmell., The power and promise of RNA-seq in ecology and evolution., Mol Ecol 2016, Link »

James Boocock, David Chagné, Tony R Merriman, and Michael A Black., The distribution and impact of common copy-number variation in the genome of the domesticated apple, Malus x domestic Borkh., BMC Genomics 2015 vol. 16 (1) p. 848., Link »

R K Topless, T J Flynn, M Cadzow, L K Stamp, N Dalbeth, M A Black, and T R Merriman., Association of SLC2A9 genotype with phenotypic variability of serum urate in pre-menopausal women., Front Genet 2015 vol. 6 (OCT)., Link »

Sterling Sawaya, James Boocock, Michael A Black, and Neil J Gemmell. , Exploring possible DNA structures in real-time polymerase kinetics using Pacific Biosciences sequencer data., BMC Bioinformatics 2015 vol. 16 (1) p. 21., Link »

Michael B Mann, Michael A Black, Devin J Jones, Jerrold M Ward, Christopher Chin Kuan Yew, Justin Y Newberg, Adam J Dupuy, Alistair G Rust, Marcus W Bosenberg, Martin McMahon, Cristin G. Print, Neal G Copeland, and Nancy A Jenkins., Transposon mutagenesis identifies genetic drivers of Braf(V600E) melanoma., Nat Genet 2015., Link »

O Ahmadi, M D Stringer, M A Black, and J L McCall., 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 2015 vol. 111 (4) pp. 451-458., Link »

Louise C Kenny, Michael A Black, Lucilla Poston, Rennae Taylor, Jenny E Myers, Philip N Baker, Lesley M McCowan, Nigel A B Simpson, Gus A Dekker, Claire T Roberts, Kelline Rodems, Brian Noland, Michael Raymundo, James J Walker, and Robyn A North, Early Pregnancy Prediction of Preeclampsia in Nulliparous Women, Combining Clinical Risk and Biomarkers: The Screening for Pregnancy Endpoints (SCOPE) International Cohort Study., Hypertension 2014 vol. 64 (3) pp. 644-652, Link »

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

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

Augustine Chen, Henry Beetham, Michael A Black, Rashmi Priya, Bryony J Telford, Joanne Guest, George A R Wiggins, Tanis D Godwin, Alpha S Yap, and Parry J Guilford, E-cadherin loss alters cytoskeletal organization and adhesion in non-malignant breast cells but is insufficient to induce an epithelial-mesenchymal transition., BMC cancer 2014 vol. 14 p. 552, Link »

G. W. Tannock, C Taylor, B Lawley, D Loach, M Gould, A.C. Dunn, A.D. McLellan, M A Black, L McNoe, J Dekker, P Gopal, and M A Collett, Altered transcription of murine genes induced in the small bowel by administration of probiotic strain Lactobacillus rhamnosus HN001, Applied and environmental microbiology 2014 vol. 80 (9) pp. 2851-2859, Link »

Rebecca L Roberts, Mary C Wallace, Daniel F B Wright, Murray Cadzow, Nicola Dalbeth, Peter B Jones, Lisa K Stamp, Andrew A Harrison, Michael A Black, and Tony R Merriman, Frequency of CYP2C9 polymorphisms in polynesian people and potential relevance to management of gout with benzbromarone., Joint, bone, spine : revue du rhumatisme 2014 vol. 81 (2) pp. 160-163, Link »

Srikanth Nagalla, Jeff W. Chou, Mark C Willingham, Jimmy Ruiz, James P Vaughn, Purnima Dubey, Timothy L Lash, Stephen J Hamilton-Dutoit, Jonas Bergh, Christos Sotiriou, Michael A Black, and Lance D. Miller, Interactions between immunity, proliferation and molecular subtype in breast cancer prognosis, Genome Biology 2013 vol. 14 (4) p. , Link »

S Cappello, M J Gray, C Badouel, S Lange, M Einsiedler, M Srour, D Chitayat, F F Hamdan, Z A Jenkins, T Morgan, N Preitner, T Uster, J Thomas, P Shannon, V Morrison, N Di Donato, L Van Maldergem, T Neuhann, R Newbury-Ecob, M Swinkells, P Terhal, L C Wilson, P J G Zwijnenburg, A J Sutherland-Smith, M A Black, D Markie, J L Michaud, M A Simpson, S Mansour, H McNeill, M Götz, and S P Robertson, Mutations in genes encoding the cadherin receptor-ligand pair DCHS1 and FAT4 disrupt cerebral cortical development, Nature Genetics 2013, Link »

R L Roberts, M C Wallace, D F B Wright, M Cadzow, N Dalbeth, P B Jones, L K Stamp, A A Harrison, M A Black, and T R Merriman, Frequency of CYP2C9 polymorphisms in polynesian people and potential relevance to management of gout with benzbromarone, Joint Bone Spine 2013, Link »

Huiping Xu, Michael A Black, and Bruce A Craig, Evaluating accuracy of diagnostic tests with intermediate results in the absence of a gold standard, Statistics in Medicine 2013 vol. 32 (15) pp. 2571-2584, Link »

H T Nguyen, T R Merriman, and M A Black, CNVrd, a Read-Depth Algorithm for Assigning Copy-Number at the FCGR Locus: Population-Specific Tagging of Copy Number Variation at FCGR3B, PLoS ONE 2013 vol. 8 (4), Link »

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

Margi I Butler, Peter A Stockwell, Michael A Black, Robert C Day, Iain L Lamont, and Russell T M Poulter, Pseudomonas syringae pv. actinidiae from Recent Outbreaks of Kiwifruit Bacterial Canker Belong to Different Clones That Originated in China., PLoS ONE 2013 vol. 8 (2) p. e57464, Link »

S Sawaya, A Bagshaw, E Buschiazzo, P Kumar, S Chowdhury, M A Black, and N Gemmell, Microsatellite Tandem Repeats Are Abundant in Human Promoters and Are Associated with Regulatory Elements, PLoS ONE 2013 vol. 8 (2), Link »

R Debono, R Topless, D Markie, M A Black, and T R Merriman, Analysis of the DISC1 translocation partner (11q14.3) in genetic risk of schizophrenia, Genes, Brain and Behavior 2012 vol. 11 (7) pp. 859-863, Link »

C E Caldon, C M Sergio, J Kang, A Muthukaruppan, M N Boersma, A Stone, J Barraclough, C S Lee, M A Black, L.D. Miller, J M Gee, R I Nicholson, R L Sutherland, C.G. Print, and E A Musgrove, Cyclin E2 overexpression is associated with endocrine resistance but not insensitivity to CDK2 inhibition in human breast cancer cells, Molecular Cancer Therapeutics 2012 vol. 11 (7) pp. 1488-1499, Link »

S.H. Wu, M A Black, R.A. North, and A G Rodrigo, A Bayesian model for classifying all differentially expressed proteins simultaneously in 2D PAGE gels, BMC Bioinformatics 2012, 13:137,

Y.F. Lee, L.D. Miller, X.B. Chan, M A Black, B. Pang, C.W. Ong, M. Salto-Tellez, E.T. Liu, and K.V. Desai, JMJD6 is a driver of cellular proliferation and motility and a marker of poor prognosis in breast cancer, Breast Cancer Research 2012 vol. 14 (3), Link »

Annette Lasham, Weini Samuel, Helen Cao, Rachna Patel, Reena Mehta, J. Lewis Stern, Glen Reid, Adele G. Woolley, Lance D. Miller, Michael A Black, Andrew N. Shelling, Cristin G. Print, and Antony W. Braithwaite, YB-1, the E2F Pathway, and Regulation of Tumor Cell Growth, Journal of the National Cancer Institute 2012 vol. 104 (2) pp. 133-146, Link »

Kalamorz, F., Keis, S., McMillan, D.G., Olsson, K., Stanton, J.A., Stockwell, P., Black, M.A., Klingeman, D.M., Land, M.L., Han, C.S., Martin, S.L., Becher, S.A., Peddie, C.J., Morgan, H.W., Matthies, D., Preddie, L., Meier, T., Brown, S.D., Cook, G.M. (2011) Draft Genome Sequence of Thermoalkaliphilic Caldalkalibacillus thermarum strain TA2.A1.  Journal of Bacteriology. Jun 17, Epub ahead of print.[PubMed]

Soon, W.W., Miller, L.D., Black, M.A., Dalmasso, C., Chan, X.B., Pang, B., Ong, C.W., Salto-Tellez, M., Desai, K.V., 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, Jun 8, Epub ahead of print.[PubMed]

Linterman, K.S., Palmer, D.N., Kay, G.W., Barry, L.A., Mitchell, N.L., McFarlane, R.G., Black, M.A., Sands, M.S., Hughes, S.M. (2011) Lentiviral-mediated gene transfer to the sheep brain - implications for gene therapy in a neurodegenerative disease model. Human Gene Therapy, May 19, Epub ahead of print.[PubMed]

North, R.A., McCowan, L.M.E., Dekker, G.A., Poston, L., Chan, E.H.Y., Stewart, A.W., Black, M.A., Taylor, R.S., Walker, J.J., Baker, P.N., Kenny, L.C. (2011) Clinical risk prediction of pre-eclampsia in an international prospective cohort of nulliparous women. BMJ 2011; 342:d1875. [PubMed]

Nixon, G., Blattner, K., Dawson, J., Dovey, S., McLellan, A., Black, M.A., Wiklins, G., Dunn AC, McLellan AD. (2011) Streptokinase antibodies in patients presenting with acute coronary syndrome in three rural New Zealand populations. Journal of Clinical Pathology, Mar 11, Epub ahead of print.[PubMed]

Nasser, S., Cunliffe, H.E., Black, M.A., and Kim, S. (2011) Context-specific gene regulatory networks subdivide intrinsic subtypes of breast cancer.  BMC Bioinformatics, 12 (Suppl 2), S3. [PubMed]

Seed, P.T., Chappell, L., Black, M.A., Poppe, K., Hwang P.Y-C., Kasabov, N., McCowan, L., Shennan, A., Wu, S., Poston, L., North, R. (2011) Prediction of pre-eclampsia and delivery of small for gestational age babies based on a combination of clinical risk factors in high risk women. Hypertension in Pregnancy (2011) 30(1):58-73.[PubMed]

McCowan, L.M., Kho, E.M., Black, M.A., Chan, E., Dekker, G.A., Poston, L., Taylor, R.S., North, R.A., Roberts, C.T. (2010)   Paternal Contribution to Small for Gestational Age Babies: A Multicentre Prospective Study. Obesity, Dec 2, Epub ahead of print.[PubMed]

Nasri. S., Anjomshoaa, A., Song, S., Guilford, P., McNoe, L., Black, M., Phillips, V., Reeve, A., Humar, B. Oligonucleotide array outperforms SNP array on formalin-fixed paraffin-embedded clinical samples. Cancer Genetics and Cytogenetics (2010) vol. 198 (1) pp. 1-6.[PubMed]

Ariazi, E.A., Brailoiu E., Yerrum, S., Shupp, H.A., Slifker, M.J., Cunliffe, H.E., Black, M.A., Donato, A.L., Arterburn, J.B., Oprea, T.I., Prossnitz, E.R., Dun, N.J., Jordan, V.C. The G Protein-Coupled Receptor GPR30 Inhibits Proliferation of Estrogen Receptor-Positive Breast Cancer Cells. Cancer Research (2010) vol. 70 (3):1184-1194.[PubMed]