Professor, Department of Human Genetics, McGill University
Director of Bioinformatics, McGill Genome Center
Detection of L1 insertion from long-read sequencing.
I apply pangenomic methods to study epigenomics and structural variation. Currently trying to use genome graphs for comparative genomics in primates.
Analyzing the relationship between transposable elements and the epigenome in order to develop new tools for their assessment.
Currently characterizing the Transposable element contents of the IHEC dataset.
Program-specific Assistant Professor
Developing new analytical methodologies to dissect the functional role of human non-coding DNA during evolution and human diseases development
Interaction of virus and human throughout whole-genome sequence data between two different populations.
Exploration of intra-and inter-species regulatory maps using comparative epigenomics, focusing on sexual dimorphism in mice and epigenomic markers in closely related primates.
Bioinformatic methods for mobile DNA annotation and analysis. Transposable Elements (TEs) insertion polymorphism and pangenomes. TE contribution to genome regulation and evolution
Enhancing our understanding of how epigenetic factors including Transposable Elements impact the growth, metastasis, and response to immunotherapy in melanomas.
Nicole (Yizhi) Yan
Mapping the regulatory sequences that underlie human and chimpanzee gene expression differences using lentiMPRA. Currently also working on computational functional prediction of transposable elements.
Nhi (Hoang) Nguyen
Developing a new method for epigenetic analysis using pangenome to study transposable elements polymorphism especially on the younger families.
Using PacBio long-read sequencing to detect structural variants in challenging regions of the genome, such as the telomere, and apply these methods to a discovery cohort
Bulk and single cell transcriptional heterogeneity in cancer.
Alexis Nolin Lapalme
Copy-Number Variant Detection in Low-Mappability Regions.
Currently studying the role of transposable elements in regulating the innate immune response to infection.
Working on comparative epigenomics to discover functional transposable elements.
Using bioinformatic tools to study allelic differences in STR sequences in twins compared to unrelated individuals as well as using data from an epilepsy cohort.
Post-Doc, MD and PhD in Medicine (Statistical Genetics) from Kyoto University, Japan.
Leeann joined the lab as an undergrad for a summer intership in 2012 and later continued for a Master. She has been looking at the expression of transposable elements in various cell types. She is now in working in France as a Ingénieur d’études at University de Bretagne Occidentale
Simon joined the group as a postdoctoral fellow in 2013. He looked at epigenetic changes across human tissues and across species. He is now a Professor at UQAC.
Bogdan joined the lab as an undergrad for a summer intership in 2015. He worked on a method for methylation calling from bisulfite sequencing.
Patrick Tran Van
Patrick joined as an undergrad for a summer internship in 2015. He integrated metagenomics analysis in our current pipeline. He is now a bioinformatics researcher and developer at the Universite de Lausanne (UNIL).
Eric joined the group as a postdoctoral fellow in 2012. He worked on de novo assembly methods to discover viral or transposon insertions. He is now a bioinformatician at IRIC (Université de Montréal).
Masoud joined the lab in 2011 as a research assistant. He looked at mappability of short reads across the human genome. He is now software developer.
Pierre-Etienne joined the lab as a Research Scientist in 2010. He has been working on a number of projects including a study of the contribution of transposable elements to primate-specific regulatory regions. He is now Assistant Professor at Sherbrooke University.
Xing Yi Woo
Xing Yi joined the group in 2007 as a postdoctoral fellow after obtaining my PhD in Chemical Engineering from University of Illinois and National University of Singapore. Previously, her research focused on multiscale modeling of pharmaceutical processes. She was working on making copy number predictions of cancer and normal genomes based on paired-end sequence data, and making comparisons with array-CGH and SNP-array data. She is now a consultant computational scientist at The Jackson Laboratory.
Justin joined the group in April 2008. Before he was working as a Research Assistant in Indian Institute of Science, India and NUS. He was involved in Prediction of Potential Repeat Associated Binding Sites for Transcription Factor with no genome-wide binding data in human and mouse and also analyzing potential motifs interaction in repeats. He is now a senior bioinformatics specialist at Genome Institute of Singapore.
Kelson joined the group in November of 2008. He was working on uncovering the architecture of rearranged genomes based on paired-end sequence data that has been mapped to a related reference genome.
Zhao joined GIS in 2005 as a postdoctoral fellow. His main research interest is on genome rearrangements. Specifically, identifying reliable ancestral rearrangement events and analyzing the underlining molecular mechanisms at the sequence level, as well as designing new algorithms to study the genomic distance between two genomes under the “fragile-breakage model”. He is now a Senior Computational Scientist at MD Anderson Cancer Center.
Chi-Ho joined the group as a Bioinformatics Specialist in 2005. Previously, he was actively looking at a specific bateria: Burkholderia Pseudomallei (Bp) which causes Meliodosis. Using Bp as a model system, he wanted to clarify at the relationship between large scale rearrangements and fine scale variations. Simultaneously, he was constructing a pan genome array for quick and easy detection of various Bp strains. He is now at the Centre for Genomic Sciences (University of Hong Kong).
Galih is a student in Duke-NUS Graduate Medical School Singapore, and when he’s not busy studying he’s busy taking care of his new baby.
His research interests include network and graph theory, high throughput genomics and proteomics, and sequence analyses. He is now Associate Professor at Tianjin University.