Senior Research Bioinformatician – SSDA PhD Student
Pan Hong is the senior researcher bioinformatician in Joanna’s Lab, SICS working for epigenetics and the epigenome-wide association studies (EWAS) and modelling. Before joining SICS, she has worked for ten years in computational biology and knowledge discovery in Institute for Informcomm Research, Genome Institute of Singapore, Lilly Centre for Drug Discovery with track record of awards, patents, publications and products. She has good experiences in large-scaled Illunima450k array data analysis, high performance computing, EWAS study and system biology. With Scientific Staff Development Award from A*STAR, she started part-time phd study in School of Computer Engineering, Nanyang Technological University in 2013.
Epigenetics methodologies are being increasingly applied to assess the associations between epigenetic variants, environmental influences and disease risks. GUSTO cohort provides the opportunities of research on the effect of genotype and in utero environment on inter-individual variants in neonate mathylomes. We are also interested in how the interaction effects between genes and environment (GxE) could associate the changes of DNA methylation and further to imply the phenotype changes. The environment factors of early developmental stage include mother’s depression level, folate intake, gestational diabetes status, and baby’s clinical data includes birth weight, gestational age and etc. With the complexity of environment factors, genetic information and epigenetic changes, modelling the EWAS study can help us the landscape of neonate methylomes with the evidence for genomic moderation of environment effects.
Advanced in Illumina450k array and Next Generation Sequence (NGS) technologies, genome-wide and single nucleic acid based DNA methylation and genetic variants can be measured, which also bring in the computational challenges in handling “Big Data”. We also work out high performance computing to facilitate genome wide research on large sample cohort.
Kim SY, Sim CK, Zhang Q, Tang H, Brunmeir R, Pan H, Karnani N, Han W, Zhang K, Xu F. ''An Alternative Strategy for Pan-acetyl-lysine Antibody Generation''. PLoS One. 08 Sep 2016. 11(9):e0162528. doi: 10.1371/journal.pone.0162528.
Pan H, Holbrook JD, Karnani N, Kwoh CK. ''Gene, Environment and Methylation (GEM): a tool suite to efficiently navigate large scale epigenome wide association studies and integrate genotype and interaction between genotype and environment''. BMC Bioinformatics. 02 Aug 2016. 17:299. doi: 10.1186/s12859-016-1161-z.
Teh AL, Pan H, Lin X, Lim YI, Patro CP, Cheong CY, Gong M, MacIsaac JL, Kwoh CK, Meaney MJ, Kobor MS, Chong YS, Gluckman PD, Holbrook JD, Karnani N. ''Comparison of Methyl-capture Sequencing vs. Infinium 450K methylation array for methylome analysis in clinical samples''. Epigenetics. 19 Jan 2016. 11(1):36-48. doi: 10.1080/15592294.2015.1132136.
Huang RC, Garratt ES, Pan H, Wu Y, Davis EA, Barton SJ, Burdge GC, Godfrey KM, Holbrook JD, Lillycrop KA. ''Genome-wide methylation analysis identifies differentially methylated CpG loci associated with severe obesity in childhood''. Epigenetics. 02 Nov 2015. 10(11):995-1005. doi: 10.1080/15592294.2015.1080411.
Unternaehrer E, O'Donnell K, Bouvette-Turcot AA, Gaudreau H, Cost K, Fleming A, Steiner M, MacIsaac J, Mah S, McEwen L, Kobor M, Chen L, Pan H, Hui WY, Holbrook J, Meaney M. ''Maternal early life adversities and the offspring's epigenome: A M.A.V.A.N. project''. Psychoneuroendocrinology. 08 Aug 2015. 61:32. doi: 101016/jpsyneuen201507477.
Pan H, Lin X, Wu Y, Chen L, Teh AL, Soh SE, Lee YS, Tint MT, MacIsaac JL, Morin AM, Tan KH, Yap F, Saw SM, Kobor MS, Meaney MJ, Godfrey KM, Chong YS, Gluckman P, Karnani N, Holbrook JD. ''HIF3A association with adiposity: the story begins before birth''. Epigenomics. 26 May 2015. 7(6):937-50. doi: 102217/epi1545.
Chen L, Pan H, Tuan TA, Teh AL, MacIsaac JL, Mah SM, McEwen LM, Li Y, Chen H, Broekman BF, Buschdorf JP, Chong YS, Kwek K, Saw SM, Gluckman P, Fortier MV, Rifkin-Graboi A, Kobor MS, Qiu A, Meaney MJ, Holbrook JD. ''Brain-derived neurotrophic factor (BDNF) Val66Met polymorphism influences the association of the methylome with maternal anxiety and neonatal brain volumes''. Dev Psychopathol. 02 Feb 2015. 27(1):137-150. doi: 101017/S0954579414001357.
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