My Interests

I am passionate about applying genomics to medicine. In my early work, I analyzed whole exome and whole genome sequencing data to identify variants associated with diseases such as diabetes, cardiomyopathy, and others.

I am proud to have contributed to early work understanding the utility of whole genome sequencing in a clinical environment.

Clinical genome sequencing requires medical-grade variant discovery pipelines. Towards this goal, I developed a genome simulation and evaluation framework to evaluate current variant discovery pipelines. I used this framework to evaluate several state-of-the-art INDEL detection approaches, and found that current tools are insufficient, particularly for larger INDELs. To address this issue, I developed a novel method for INDEL detection that leverages machine learning approaches and signatures of poor alignment to accurately detect larger INDELs. I also employed my evaluation framework to determine the effect of lossy compression or denoising of base quality scores on variant discovery.

At The Jackson Laboratory for Genomic Medicine, my main research focus was creating new computational pipelines to analyze epigenomic patterns (with a focus on 5hmC) from low coverage oxidative bisulfite sequencing of tumor, normal, and cell-free DNA samples. The goal of this work is to further characterize epigenomic patterns in cancer to enable liquid biopsy diagnostics.

Quality control and regulatory science efforts are required to ensure that we obtain accurate and actionable information from the genome. For instance, I developed an approach to determine sample identity from individual lanes of a sequencing flowcell and a metric for assessing sequencing coverage of key disease genes. I’ve also studied the medical implications of incomplete coverage or inaccurate variant calls, which was written up in Nature Reviews Genetics and several popular press articles (e.g. here and here); you can see my blog post on the topic here.

More recently, as a Computational Scientist at The Jackson Laboratory, my research focused on bioinformatic analyses of data from long-read sequencing technologies. For example, I created quality control methods to evaluate PacBio targeted RNA sequencing. Additionally, I recently compared and evaluated Oxford Nanopore’s three RNA Sequencing approaches in terms of their yield, read length, transcripts covered, transcript definition accuracy, and isoform quantification accuracy to determine which approach is best for specific applications.

Over the years, some of my most rewarding experiences have come from training the next generation of scientists. For example, I co-developed and co-taught a Stanford Biosciences introductory course on Personalized Genomic Medicine with Dr. Dennis Wall and was a Teaching Assistant for a Stanford Genetics course on Genomics and Personalized Medicine with Dr. Stuart Kim where students had the opportunity to browse their own genomic data.

I truly enjoy mentoring others. A few highlights include summer students in the Stanford Summer Research Program, graduate rotation students, and an undergraduate intern.

To facilitate scientific communication, I co-chaired the 2015 Biomedical Computation at Stanford Symposium, where students, postdocs, and faculty shared their work related to bioinformatics, genomics, and structural biology. I also co-chaired a workshop on Harnessing Big Data for Precision Medicine at the 2017 Pacific Symposium on Biocomputing.

Most recently, I coordinated The Jackson Laboratory’s 2018 - 2022 Workshops on Long-Read Sequencing for over 200 internal and external attendees.

I also have extensive experience in leadership, collaboration, and developing and implementing large-scale coordination projects. Recently, I was the Project Manager for The Jackson Laboratory’s COVID-19 Testing efforts. This role required managing interdisciplinary teams, establishing timelines, tracking action items, and clearly communicating with internal and external stakeholders to ensure complex logistics were well-executed.

I recently co-founded a web development company, Wingfully. We’d love to develop your next conference, meeting, or event website! We offer great discounts for academics, non-profits, and other do-gooders.