Dr Shalima Nair

Senior Research Officer

Conjoint/Adjunct Role(s)

Conjoint Lecturer, St Vincent's Clinical School, Faculty of Medicine, UNSW Australia

Shalima Nair completed her PhD from the National Center for Biological Sciences in Bangalore, India and moved to Australia, where she was initially working in Garvan's molecular genetics facility. In the facility, Shalima was instrumental in developing the mouse genotyping service, which currently caters to many research groups, both inside and outside Garvan. Shalima also initiated the development of Sequenom SNP genotyping and methylation analysis as a service in the facility.

Later she joined Prof Susan Clark’s lab as a Post-doctoral research officer. In this lab, Shalima has played a significant role in the successful completion of several projects that involved the use of Sequenom’s methylation detection technology and genome wide methylation profiling by next generation sequencing. Her experience and contributions in the field of epigenetics are recognised in her publications. Since 2012, Shalima has been actively involved in the SIEF project, a study advancing understanding of the epigenome of human visceral and subcutaneous adipocytes.

Shalima is also involved with the Garvan Research Foundation, presenting her work and Garvan’s research to prospective donors at external venues and also at Garvan. She is also a member of the Garvan WHS committee.

Research Interests

Understanding the epigenetic architecture of cells in normal and disease condition
DNA Methylation profiling technologies like whole genome bisulfite sequencing, Miseq bisulfite amplicon sequencing, Sequenom MassArray


2009 – PhD, National Centre for Biological Sciences (NCBS), Bangalore - India

Selected Publications

Clare Stirzaker*, Elena Zotenko*, Jenny Z. Song, Wenjia Qu, Shalima S Nair, Warwick Locke, Andrew Stone, Nicola Armstong, Mark D. Robinson, Alexander Dobrovic, Kelly A. Avery-Kiejda, Kate M. Peters, Juliet D. French, Sandra Stein, Matt Trau, John F. Forbes, Rodney Scott, Melissa A. Brown, Glenn Francis, Susan J. Clark. Methylome sequencing in triple negative breast cancer reveals distinct methylation clusters with prognostic value. Nature Communications, in press.

Kristina Warton, Vita Lin, Tina Navin, Nicola J. Armstrong, Warren Kaplan, Kevin Ying, Helena Mangs, Shalima S. Nair, Brian Gloss, Neville F. Hacker, Robert L. Sutherland, Susan J. Clark, Goli Samimi. Methylation-capture and Next-Generation Sequencing of free circulating DNA from human plasma. BMC Genomics 2014

Hulf T, Sibbritt T, Wiklund ED, Patterson K, Song JZ, Stirzaker C, Qu W, Nair S, Horvath LG, Armstrong NJ, Kench JG, Sutherland RL, Clark SJ. (2012) Epigenetic-induced repression of MicroRNA-205 is associated MED1 activation and a poorer prognosis in localized prostate cancer. Oncogene 2012

Peters KM, Edwards Stacey L, Nair SS, French JD, Bailey PJ, Salkield K, Stein S, Wagner, Francis GD, Clark SJ, Brown MA (2012) Androgen receptor expression predicts breast cancer survival: the role of genetic and epigenetic events. BMC Cancer Apr 2; 12:132

E J H Wee, K Peters, S S Nair, T Hulf, S Stein, S Wagner, P Bailey, S Y Lee, W J Qu, B Brewster, J D French, A Dobrovic, G D Francis, S J Clark, and M A Brown. Mapping the regulatory sequences controlling 93 breast cancer-associated miRNA genes leads to the identification of two functional promoters of the Hsa-mir-200b cluster, methylation of which is associated with metastasis or hormone receptor status in advanced breast cancer. Oncogene. 2012 September 20; 31(38): 4182–4195.

Valdés-Mora F, Song JZ, Statham AL, Strbenac D, Robinson MD, Nair SS, Patterson KI, Tremethick DJ, Stirzaker C, Clark SJ (2012) Acetylation of H2A.Z is a key epigenetic modification associated with gene deregulation and epigenetic remodeling in cancer. Genome Res. Feb; 22(2):307-21

Wiklund ED, Gao S, Hulf T, Sibbritt T, Nair S, Costea DE, Villadsen SB, Bakholdt V, Bramsen JB, Sørensen JA, Krogdahl A, Clark SJ, Kjems J. MicroRNA alterations and associated aberrant DNA methylation patterns across multiple sample types in oral squamous cell carcinoma. PLoS One 2011.

Nair SS, Coolen MW, Stirzaker C, Song JZ, Statham AL, Strbenac D, Robinson MD, Clark SJ (2011)  Comparison of methyl-DNA immunoprecipitation (MeDIP) and methyl-CpG binding domain (MBD) protein capture for genome-wide DNA methylation analysis reveal CpG sequence coverage bias. Epigenetics. 2011 Jan;6(1):34-44

Robinson MD, Stirzaker C, Statham AL, Coolen MW, Song JZ, Nair SS, Strbenac D, Speed TP, Clark SJ. Evaluation of affinity-based genome-wide DNA methylation data: effects of CpG density, amplification bias, and copy number variation. Genome Res. 2010, Dec;20(12):1719-29

Nair S, Agrawal N, Hasan G .Homeostasis of glutamate neurotransmission is altered in Drosophila Inositol 1,4,5-trisphosphate receptor mutants. Invert Neurosci. 2007 Sep; 7(3):137-47.

Srikanth S, Wang Z, Tu H, Nair S, Mathew MK, Hasan G, Bezprozvanny I . Functional properties of the Drosophila melanogaster inositol 1,4,5-trisphosphate receptor mutants. Biophys J. 2004 Jun;86(6):3634-46

Joshi R, Venkatesh K, Srinivas R, Nair S, Hasan G . Genetic dissection of itpr gene function reveals a vital requirement in aminergic cells of Drosophila larvae. Genetics. 2004 Jan;166(1):225-36

Dr Shalima Nair

Division Overview

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