😇About Me

Something about me :)

During my years as a student of Science and Mathematics during my High School years back in India, Biology interested me apart from Computers. The first aspect of Biology that interested me was Genetics. It was all so interesting and fascinating at that point in time, and I never knew that this fascination of mine with both biology and computers will drive me toward Bioinformatics, the supposed jargon at that time. It was through the internet that I got to know about Bioinformatics and its application. Those made me pretty much sure about my future path. I started reading about the Human Genome Project, genes, and genomes and it all started attracting me.

What better platform would I have got at that time than pursuing a Bachelor’s degree in Bioinformatics at D Y Patil University, which not only made me aware of different facets of bioinformatics but also strengthened my Mathematics and Computer Science skills. The first computer language I learned was C as well as C++ and it really changed my approach to programming. Though a newbie at programming at that time, I always had friends with whom I would discuss better programming practices.

It was during the sophomore year we went for my first curriculum training at the Institute of Bioinformatics and Applied Biotechnology, Bengaluru, India on GENES to DRUGS: In-Silico Drug Discovery, It was 25 days of training where we had a hands-on experience on SGI machines using IRIX with different tools related to bioinformatics such as GCG, Insight II, Cerius 2 and Catalyst all part of the Accelrys suite for molecular modeling. Here we came face to face with computational biology an aspect of bioinformatics that we thought was all limited to Rasmol, Blast, Fasta, Homology modeling, searching Protein Data Bank, Pfam, etc. Later during the same, we wrote Perl programs, accessed Biological Databases, worked on various bioinformatics tools, and developed small applications using Perl. We learned MS Access through a project for our course on Airline Reservation Systems. It was all exciting, not only developing my skills in wet-lab techniques like DNA extraction, developing cell media, cell plating, and many more but also sharpening my programming skills.

While doing my senior design project at Bhabha Atomic Research Center (BARC), Mumbai, India, we had an opportunity to work with a senior scientist who explained to me the very importance of understanding the basics for whatever you learn, at BARC we did a wet lab project on Characterization of Fusarium Monoliforme, which we combined with bioinformatics by developing C++ program to identify optimal fungal growth determined by the data obtained from the experimental results. By then, I had decided that I want to learn more in this field and, that this is just the start. I started looking for graduate courses in India but could find no satisfactory courses at all and I decided to fly to the United States of America for my higher studies.

Important attributes of a successful data scientist include the ability to advance human knowledge, and understanding by providing meaningful insights from the coarse data available at hand. I was fortunate to imbibe these traits in the department of Bioinformatics and Computational Biology at George Mason University. My Master’s program was a great learning curve. Not only did I expand my interests in computational biology but also in the software engineering component of the field. From being involved in projects for building a database of Human Genes with HUGO Gene Nomenclature using MySQL and providing it a web interface for searching it using Perl and CGI. Doing protein-protein structure alignment using Python and doing a survey of different available short read sequence assemblers with respect to the data produced by the sequencing technology at that time which was from Solexa. We worked on SVM based method (kernel) to assess the reliability of protein-protein interactions. We learned R for statistics through our course Research Methods. We also worked on the Bovine dataset to understand the variation within a given species and analyzed using SNP Genotypes for determining the linkage disequilibrium, haplotypes, and signatures of selection. We helped to design the database for Bovine Hapmap Project and created a web-based program for displaying various data types by querying the database. For our master’s project, I worked on evolutionary analysis of dopamine d2 receptors, particularly looking at the intracellular loop via multiple sequence alignment and creating and comparing phylogenetic trees for the differences in evolution using TOPD/FMTS and Rate4Site.

After my Master’s in Bioinformatics and Computational Biology, I identified my research interest in the broad field of Genomics. First working as a contractor for Monsanto Co, I helped develop frameworks to analyze sequencing data generated from different sequencing technologies, performing genome assembly, working towards making draft genomes, then working as a Computational Biologist for Memorial Sloan Kettering Cancer Center, doing analysis of cancer specific sequencing data to gain meaningful insight in patients tumor molecular profile. As an independent researcher for the past five years, much of my focus has been to do develop, automate and improve the framework to do in depth analysis of the targeted sequencing data produced by Illumina based machines for clinical as well as research projects, leading to publications (Google Scholar) in various aspect of Cancer Genomics research. In addition to a background in research, I have sought out leadership and management experience. For the past two years I have grown to appreciate my role both as mentor and collaborator while advising high school students through their summer internship projects.

In my role as Director of Bioinformatics at Northwell Health (NH) working at Feinstein Institute for Medical Research (FIMR), I helped them evaluate their current infrastructure shortcomings w.r.t to doing large-scale genomics projects. Helped them develop and deploy a small cluster to analyze genomics data until we were able to build a large hybrid system.

As a Sr. Manager and Lead Scientist at MSKCC, I lead a team of computational biologists and bioinformatics software engineers at the Center for Molecular Oncology that develops, maintains, and operates bioinformatics pipelines and databases. Furthermore, I perform collaborative research with other labs and clinicians both within MSKCC and beyond. Each day, I and my team examine blood samples from patients with tissue-based cancer, profiling the circulating tumor DNA extracted from blood to avoid the need for tumor biopsies. In particular, I and my group are responsible for designing, developing, and implementing software for processing, analyzing, and interpreting high throughput, next-generation sequencing data, especially for liquid biopsy applications (MSK-ACCESS& Clonal Hematopoiesis Panel). During his time at MSK, he developed and validated a workflow for the analysis of MSK-IMACT data, both for clinical analysis and for research.