I am currently working as a Staff Bioinformatics Scientist at Illumina. The most intriguing questions occupying my research mind are related to structural variants in the human genome: more precise identification, better ways to represent and compare them, etc.
In line with my background in Stringology, I stay updated with new research related to kmers, seeding-chaining, alignments, polishing, indexing, assembling, and related areas. Many thanks to Academic Twitter and Bluesky for the valuable insights!
Being a mother of two young children is another role I lovingly embrace. My family and my work are what motivate me to keep improving and striving to do my best.
Skills
My routine work and hobby projects involve data analysis (scripting and plotting with Python, Pandas, NumPy, Bash, Awk, etc.), method development (C++ for implementation, and I'm also learning Rust), and building pipelines (Nextflow, Snakemake, etc.). A combination of Git, JIRA, and Confluence is the usual framework I rely on to keep everything organized.
PostDoc
I was a post-doctoral research fellow at the National University of Singapore (School of Computing), under the mentorship of Prof. Wing-Kin Sung. I worked on several projects related to genomic analysis of Singaporean population and the development of long reads/hybrid assemblers. We developed a polisher and scaffolder (HyPo) that uses Illumina short reads to improve ONT-based draft assemblies. This work was published in Nature Methods
PhD
I completed my PhD at King’s College London (Department of Informatics) and was the recipient of the 2019 King’s Outstanding PhD Thesis Prize (sponsored by Elsevier)[link].
Title: Algorithmic Advances in Handling Uncertainty and Regularity in Strings [Thesis] [Slides]
Mentors: Dr. Toktam Mahmoodi and Dr. Solon Pissis
Timeline: Started in October 2015; Thesis-submission in July 2018; Defence in January 2019.
Examiners: Prof. Thomas Erlebach (University of Leicester) and Prof Leszek Gąsieniec (University of Liverpool)
Research Interests
- Algorithms in Bioinformatics; particularly for assembly, alignment, and analysis of the third generation sequencing data
- Algorithms and data structures for sequences in pattern matching, indexing, text-compression etc.
- Algorithmic Engineering
Other Interests
Currently, I have two toddlers, so I don’t have much bandwidth for other pursuits. However, I still try to return to these interests when I can.
- Programming: I love programming! “Correct” (read efficient) implementation of an algorithm is as important as the algorithm itself. These days, I have a few classical algorithms by Prof. Maxime Crochemore on my to-implement list. Apart from software-tools, I occasionally indulge in programming robotic kits.
- Teaching: In my opinion, nothing clarifies your own concepts and foundations better than trying to explain them to non-experts. Whenever possible, I try to get involved in academic teaching. I've also started publishing online tutorials on String algorithms.
- Health and Nutrition: Over the years, I've realized how misguided conventional wisdom can be regarding what is healthy for us. I regularly read blogs and research articles to update my knowledge on healthy living. Two of my favorite sources are the blogs, articles, and podcasts of Dr. Ray Peat and P. D. Mangan.
- Indic culture and history: I am trying to learn Sanskrit (albeit at a snail's pace) to be able to read ancient Indic texts and scriptures. Currently, I'm focusing on understanding the fundamentals of Ayurveda and Yoga, primarily through the works of Dr. David Frawley.