Aghakhanian, F., Hoh, B.-P., Yew, C.-W., Kumar Subbiah, V., Xue, Y., Tyler-Smith, C., Ayub, Q. & Phipps, M.E. (2022) Sequence analyses of Malaysian Indigenous communities reveal historical admixture between Hoabinhian hunter-gatherers and Neolithic farmers. Scientific Reports. 12 (1), 13743. doi:10.1038/s41598-022-17884-8.​

After analyzing whole genomes of 15 individuals across five indigenous groups from Peninsular Malaysia and one from North Borneo, we propose that Orang Asli have more complex origins than initially thought, likely originating from at least three distinct ancestral populations related to the Hoabinhian hunter-gatherers, Neolithic farmers and Austronesian speakers.

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McColl, H., Racimo, F., Vinner, L., Demeter, F., Gakuhari, T., et al. (2018) The prehistoric peopling of Southeast Asia. Science (New York, N.Y.). 361 (6397), 88–92. doi:10.1126/science.aat3628.

The first transdisciplinary paper to comparatively analyse ancient human DNA samples with those from modern populations. It dispels 100 years of controversy about human habitation of Southeast Asia. Broadcast as news in mainstream media, BBC, ABC, Guardian and other websites.

Malaspinas, A.-S., Westaway, M.C., Muller, C., Sousa, V.C., Lao, O., et al. (2016) A genomic history of Aboriginal Australia. Nature. 538 (7624), 207–214. doi:10.1038/nature18299.

High impact publication and world's first to provide a comprehensive timeline of migration and genetic legacy of Aboriginal Australians publicised on BBC, ABC, The Guardian and other websites.
 

THE HUGO PAN-ASIAN SNP CONSORTIUM, Abdulla, M.A., Ahmed, I., Assawamakin, A., Bhak, J., et al. (2009) Mapping Human Genetic Diversity in Asia. Science. 326 (5959), 1541–1545. doi:10.1126/science.1177074.
A massive effort to catalog genetic variation among Asians has just weighed
in on the peopling of that vast continent. The work of a 40-institution consortium for Asians, by
Asians and of Asians has concluded that Asia was initially settled by a single wave of migration
out of Africa along the coastal routes.

Jinam, T.A., Hong, L.-C., Phipps, M.E., Stoneking, M., Ameen, M., Edo, J., HUGO Pan-Asian SNP Consortium & Saitou, N. (2012) Evolutionary History of Continental Southeast Asians: “Early Train” Hypothesis Based on Genetic Analysis of Mitochondrial and Autosomal DNA Data. Molecular Biology and Evolution. 29 (11), 3513–3527. doi:10.1093/molbev/mss169.
We demonstrate a more intricate migration history than that generally accepted of a two-wave hypothesis regarding the peopling of island Southeast Asia, after the initial Out of Africa migration. Specifically, 'early train' wave(s) of migration originating from South China or Indochina during late Pleistocene to early Holocene (30,000–10,000 YBP), predating the Neolithic expansion from Taiwan. 

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Reich, D., Patterson, N., Kircher, M., Delfin, F., Nandineni, M.R., Pugach, I., Ko, A.M.-S., Ko, Y.-C., Jinam, T.A., Phipps, M.E., Saitou, N., Wollstein, A., Kayser, M., Pääbo, S. & Stoneking, M. (2011) Denisova Admixture and the First Modern Human Dispersals into Southeast Asia and Oceania. The American Journal of Human Genetics. 89 (4), 516–528. doi:10.1016/j.ajhg.2011.09.005.

Genomic analyses suggests that Southeast Asia was settled by modern humans in multiple waves, consistent with an earlier archaeologically-motivated hypothesis of an early southern route migration. One wave contributed much of the ancestry of present-day East Asians and Indonesians. Another wave contributed the ancestors of present-day Onge, Jehai, Mamanwa, New Guineans, and Australians, some of whom interbred with Denisovans, an extinct group of hominids. 

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Phipps, M.E., Chan, K.K., Naidu, R., Mohamad, N.W., Hoh, B.-P., Quek, K.-F., Ahmad, B., Harnida, S.M., Zain, A.Z. & Kadir, K.A. (2015) Cardio-metabolic health risks in indigenous populations of Southeast Asia and the influence of urbanization. BMC Public Health. 15 (1), 47. doi:10.1186/s12889-015-1384-3. 

The first comprehensive description of cardio-metabolic risk factors of seven Orang Asli communities in Malaysia. We reported variable prevalence of obesity, cholesterol, hypertension and diabetes in the Orang Asli in contrast to the larger Malaysian ethnic groups (Malays, Chinese and Indians) and attribute this to socio-economic effects, lifestyle changes and in some sub-tribes, other factors including genetic predisposition. We expect these risk factors may worsen with further urbanization, increase the health burden of these communities and strain the government’s resources.

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Chai, H.C., Phipps, M.E. & Chua, K.H. (2011) Genetic Risk Factors of Systemic Lupus Erythematosus in the Malaysian Population: A Minireview. Clinical and Developmental Immunology. 2012, e963730. doi:10.1155/2012/963730.

SLE is an autoimmune disease that affects many populations worldwide, characterized by immunodeficiency, autoantibody production and failure of immune complex clearance. Out of the major ethnic populations of Malaysia, the Chinese seem to be most affected. Combining our own findings with previous reports, we summarized the association of several candidate genes with risk for SLE in Malaysians, revealing genetic heterogeneity that exists locally in Asians.

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Gan, G.G., Phipps, M.E., Lee, M.M.T., Lu, L.S., Subramaniam, R.Y., Bee, P.C. & Chang, S.H. (2011) Contribution of VKORC1 and CYP2C9 polymorphisms in the interethnic variability of warfarin dose in Malaysian populations. Annals of Hematology. 90 (6), 635–641. doi:10.1007/s00277-010-1119-6.

This paper was among the first in Malaysia demonstrating the importance of pharmacogenomics i.e. VKORC1 and CYP2C9 polymorphisms that contributed to the different warfarin dose requirements amongst Chinese, Malay and Indian patients treated for venous thromboembolic disease.

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Choy, M.-K. & Phipps, M.E. (2010) MICA polymorphism: biology and importance in immunity and disease. Trends in Molecular Medicine. 16 (3), 97–106. doi:10.1016/j.molmed.2010.01.002.

Major Histocompatibility Complex class I chain-related molecule A (MICA) is the most polymorphic member of the non-classical HLA class I gene family. Here we discussed the genetics and biology of the MICA gene and its products, as well as their emerging importance in disease, including but not limited to viral infection, cancer and allograft rejection or graft-versus-host disease.

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Yih, P.T., Phipps, M.E. and Bosco, J.J., 1999. Molecular HLA typing for bone marrow transplantation in Malaysia. Asia Pacific Journal of Molecular Biology and Biotechnology, 7(1), pp.29-38. 

This research project that was conducted on local patients and their families led me to establish the first molecular typing laboratory service in Malaysia. Our lab at University of Malaya Medical Centre had a turnaround time of 5 working days. Prior to that, adult and paediatric patients awaiting critical bone marrow/stem cell transplants had to wait up to 6 weeks to be matched using conventional immunological methods at a government facility.

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A comprehensive list of my publications is available on Google Scholar and in my CV .