About Me

I am currently a Principal Bioinformatics Scientist at Achilles Therapeutics. My primary focus has been to develop an industry-grade immunotherapy/immunogenomics pipeline (based on the TRACERx pipeline pioneered from Charles Swanton’s lab) that identifies clonal neo-antigens that can elicit antitumor responses. In particular, I am spearheading the research and improvements on copy number profiling, clonal mutation detection, and neoantigen generation.

I completed my Bioinformatics PhD in 2017 under the co-supervision of Dr. Sohrab Shah and Dr. Christian Steidl studying tumour heterogeneity and its implications on disease progression in B-cell lymphomas. In particular, how tumour evolution plays a role in treatment resistance and how understanding this process may aid in the determination of relevant and precise therapeutic approaches for each cancer patient. Throughout my PhD and industry experience, I have acquired experience/skills in the following specific areas:

• Cancer genomic analyses that include prediction of somatic single nucleotide variants, small insertions/deletions, genomic breakpoints, gene-fusions, and copy number calling.
• Cancer evolution analyses that include the deconvolution of clonal composition, both at the single region and multi-regional level, and tracking of tumor evolution over time through serial sampling (e.g. primary vs. relapse)
• Prognostic biomarker discovery and modeling (e.g. multi-variate elastic-net Cox regression)
• Immunogenomics analyses that include HLA typing, and neo-antigen predictions

I have a passion for applying statistical and machine learning approaches to big data, in particular genomics data (e.g. sequencing data). In terms of technical skills:

• I have expertise in dealing with big data in the R programming language (e.g. data.table, tidyr, dplyr) and a thorough understanding of the core principles around R
• I have extensive experience in doing reproducible research through interactive applications and D3 web reporting (e.g. Rmarkdown, knitr, pandoc, git, shiny)
• I have expertise in developing/managing big data processing pipelines through the Make engine with experience in using ruffus, bpipe, snakemake, and nextflow.
• I have experience in continuous integration/unit testing in production based workflows.

Selected Publications [Google Scholar]