Students

Below are some of the McGill-Kyoto students, illustrating the diverse research opportunities available. The order is by time of admission.

The myriad cells in our body realize their identities through various epigenetic markers dictating the activity of genes despite sharing the very same genetic blueprint. As meters of genetic material must be packed within micrometer-wide cells, the 3D conformation of DNA further contributes yet another layer of regulatory complexity. And while the 3D epigenome undergoes dramatic reorganization throughout development, they can experience similarly profound perturbations during tumorigenesis -- as developmental blockades emerge as a common thread tying together several malignancies. Capitalizing on the wealth of cancer biology resources at McGill University and the expertise in gametogenesis at Kyoto University, I aim to delineate 3D epigenome dynamics in germline development as well as brain tumours and other cancers towards uncovering fundamental mechanistic insights conducive to the development of targeted therapies.

I am one of the first cohort students enrolled in the Joint Degree from McGill. I am currently working on constructing an untargeted metabolome database with the Japanese Nagahama Cohort data to conduct multi-omics analysis with the available genetic and phenotypic information. From the aforementioned analysis, we aim to pinpoint potential phenotype-related biomarkers, identify novel metabolic quantitative trait loci, and uncover novel disease mechanisms.

During studying medicine, statistical genetics using NGS data interested me intensely. After being a junior resident in Japan, I have started this Ph.D. program. As the thesis project, I am working on two projects, multiple SNPs interaction and population-specific viruses identified from WGS data.

After finishing clinical training of respirology, Tomoko Nakanishi started her academic career in April 2018 as a graduate student in McGill - Kyoto Collaborative School in Genomic Medicine, co-supervised by Prof. Brent Richards and Prof. Toyohiro Hirai. Her thesis project is to investigate the genetic determinants of respiratory diseases and to seek their clinical implications. After COVID-19 crisis, she has also been dedicated to international collaborations in COVID-19 Host Genetic Initiatives.

I am interested in the exploration of intra-and inter-species regulatory maps using comparative epigenomics, focusing on sexual dimorphism in mice and epigenomic markers in closely related primates. My specific interests include regulatory mechanisms of non-coding regions and the roles Transposable Elements (TEs) playing in such complex regulatory system.

I am very interested in bioinformatics, though most of my previous research experiences came from the wet lab side of NGS. Thus, my current research projects are focusing on the analysis of pulmonary hypertension with whole-genome sequencing data. And with the help of WGS data and other bioinformatic methods, I hope I could investigate the genomic architecture of rare complex diseases more profoundly and improve the prognosis of these diseases.

I am developing an upgraded version of HLA-calling software which uses whole-genome sequencing data for HLA gene type inference. I am studying and applying NGS data analysis to understand Human genome and causal link between trial and common structural variants. Interest in quantum computing and its application on genetic data.

Human T lymphotropic virus type I (HTLV-I)-associated myelopathy/tropical spastic paraparesis (HAM/TSP) is a chronic progressive myelopathy characterized by bilateral pyramidal tract involvement. Less than 1% of HTLV-I careers develop a myelopathy, and its etiology is not fully understood. It is desired to establish diagnostic scheme and genetic prediction methodology of onset of HAM/TSP to prevent disease progression. Now I am trying to investigate association between host genotype and provirus genotype to catalog HAM/TSP-associated variants in human HLA region and HTLV-I genome using GWAS and WGS approach. By merging this information, I plan to construct onset risk model of the disease.

Satoshi Yoshiji has trained in the field of endocrinology and is currently a graduate student of the Kyoto-McGill joint PhD program. His research focuses on understanding the genetics of endocrine and metabolic disorders such as diabetes and translating the findings into clinical practice.

I am studying how evolution affected patterns of variation encoded in our genome and among populations. I am specifically intrigued by how these patterns affect the transferability of polygenic score among diverse groups

Melanoma poses a significant threat to individuals worldwide, with 97,610 new melanoma cases diagnosed in the United States in 2023 alone. To gain a more comprehensive understanding of the underlying mechanisms driving melanoma, my research focuses on the disease from an epigenetic perspective. This approach delves into DNA methylation and histone modifications to uncover how epigenetic factors influence melanoma growth and metastasis.

Moreover, recent advancements in immunotherapy have led to a rapid decline in mortality rates over the past decade. However, a substantial number of patients fail to respond to this promising therapy, and the factors influencing responsiveness remain unclear. To address this critical issue, I am employing cutting-edge techniques such as Single-cell Long-read Sequencing and Single Cell Multiome analysis. These methods enable the characterization of all cells within the tumor microenvironment, facilitating the identification of the most reliable markers for predicting an individual's response to immunotherapy.

I received my M.A in Clinical Medicine from Peking University in 2020. During my clinical work, I found genetics analysis interesting and want to study further into it. Here I'm working on mapping regulatory sequences that drive human & chimpanzee gene expression differences using lentiMPRA, which will generate the first human-specific cis-regulatory variants dictionary. I'm also interested in transposable elements (TEs), functional prediction of TEs with regulatory activity together with their target genes would be my next main project to focus on.

I transitioned from a wet-lab biochemist to a bioinformatician. My current project focuses on developing a new method for epigenetic analysis using pangenome to study transposable elements polymorphism especially on the younger families.

I graduated from McGill University with a Bachelor of Science in Neuroscience in 2023. My passion for bioinformatics began during an internship when I delved deep into studying neuroblastoma cell lines, employing long-read sequencing to investigate non-coding RNA. I’ve been hooked on the power and potential of third-generation sequencing technology ever since. Currently, I’m utilizing PacBio long-read sequencing to detect structural variants in challenging regions of the genome, such as the telomere, and I’m applying these methods to a discovery cohort. The complexity of the genome never ceases to amaze me, and I’m excited about the discoveries ahead.