Seminar: Combinatorial algorithms to study development and disease evolution
Palash Sashittal
Assistant Professor, Computer Science
Virginia Tech
Friday, September 27, 2024
2:30 - 3:45PM
3100 Torgersen Hall
Abstract
Rapid advancements in sequencing technologies are revolutionizing the field of modern medicine. In recent years, several groundbreaking techniques such as CRISPR-Cas9 genome editing and barcoding of biomolecules from individual cells have emerged. These breakthroughs, coupled with the decreasing costs of genomic sequencing, have resulted in the development of various “*-Seq” protocols for measuring DNA, RNA, and proteins at unprecedented throughput and resolution. The diverse characteristics of these sequencing methods have created a pressing need for specialized algorithms capable of effectively interpreting the vast amounts of sequencing data.
In this talk, I will summarize my contributions in three research areas: cancer genomics, developmental genomics and infection genomics. First, I will introduce ConDoR, an algorithm to infer the evolutionary history of a cancer tumor using targeted single-cell DNA sequencing (scDNA-seq) data. Second, I will discuss combinatorial algorithms for cell fate mapping using recently developed single-cell lineage tracing technologies. Lastly, I will present algorithms to sample, count and summarize parsimonious transmission histories of infectious disease outbreaks using genomic and epidemiological data. Overall, my talk will underscore the crucial role of specialized models and algorithms in studying biological systems using genomics data.
Biography
Dr. Palash Sashittal is an Assistant Professor of Computer Science at Virginia Tech. Prior to joining Virginia Tech, he was a Postdoctoral Research Associate with Prof. Ben Raphael in the Computer Science Department at Princeton University. He received a Ph.D. in Aerospace Engineering and M.S. in Computer Science from the University of Illinois Urbana-Champaign (UIUC), and B.Tech. in Aerospace Engineering from Indian Institute of Technology Bombay (IIT Bombay).
His research focuses on the design of combinatorial and statistical algorithms to analyze and interpret sequencing data. Recent areas of emphasis include infectious disease evolution and transmission, cancer genome evolution, and cell fate mapping of developmental systems. Palash’s work has been recognized by multiple awards and honors, including Mistletoe Research Fellowship, Best Paper Award at RECOMB CCB, Cornell Future Faculty Fellowship and Mavis Future Faculty Fellowship (UIUC). Palash is firmly committed to enhancing diversity, equity, and inclusion in STEM through mentoring, outreach, and service activities.