Strand Life Sciences, Bangalore
April, 2022 -- Present
Multi Cancer Early Detection
Machine learning on the whole genome, targeted methylSeq and fragmentomics datasets along with data exploration and visualisation.
Developing novel algorithms which are used to generate sample cohort specific signatures from liquid biopsies which in turn can be readily utilised in an ML centric operation.
Analysis and curation of biomarkers from public methylation datasets which includes TCGA and multiple datasets sourced from public NGS repositories.
AWS EC2, S3 and HealthOmics based optimization of multi-omics bioinformatics pipelines and designing strategies to pair concurrent bioinformatics exploration in parallel to design of experimental assays, by providing feedback to the lab on signal variation across diverse protocols.
Client Project: Automation and QC for CNV Algorithms
Conducted copy number analysis on FFPE and fresh frozen tissue samples, performed concordance analysis across different versions of CNV algorithms and checks for cross-contamination between samples.
Client Project: B-Cell Depletion Therapies
Multiomics analysis of targets, genes and pathways perturbed by different B-cell depletion mechanisms.
Repurposing of different B-cell therapies for other diseases.
Miscellaneous
Deep learning algorithms for classification of digital histopathology images.
Experienced in building documentation for filing IPR applications on genomic workflows paired with experimental protocols as a cumulative kit for novel NGS testing strategies.
COVID-19 Response Group at Centre for Networked Intelligence, IISc.
March, 2020 -- March, 2022
City Scale Agent-Based Simulator (With TIFR, Mumbai)
Developed an agent based simulator from scratch using JavaScript that can simulate around 100K agents and runs natively in the browser (One of three members who coded up the simulator engine).
Provided support in translating the simulator from JavaScript to C++ for higher performance and scalability. Added new feature like age-based interaction rates in the C++ simulator. The C++ simulator can simulate around 2M agents.
Co-wrote Python wrappers and calibration scripts for the simulator. Ran the calibrations in a supercomputing facility at IISc. This was used for running epidemic simulation to predict disease progression at city scale.
Softwares: C++, Python, JavaScript, Supercomputing
Simulator: https://cni-iisc.github.io/epidemic-simulator/
Code: https://github.com/cni-iisc/epidemic-simulator
Mobility Data Analysis
Analysis of mobility patterns to understand travel behavior at large scale using various mobility data sources like Google, Facebook, etc.
Designed a local database to store these large datasets (Millions of rows and 10s of GBs in size) and provided access to the rest of the group for ease of information retrieval and computations.
Contributed insights from the mobility data. These served as a proxy of interaction rates among communities and/or between different administrative regions.
Softwares: Python, PostgreSQL with PostGIS extension
Workplace Readiness Indicator
Designed the score computing algorithm that provides not only a quantitative readiness score but also suggestions on measures to improve the safety of office space so that they could relaunch economic activities in a safe manner.
Designed the website and deployed it on an AWS instance.
Softwares: JavaScript, HTML, Python, MongoDB, Nginx, Gunicorn
Website: https://covid.readiness.in/
Swabs2Labs and Optimal Serosurvey Design
Developed interactive maps that visualises transport routes from the sample collection centres to the testing labs in Karnataka state. The routes are colour coded based on the number of sample travelling on that route.
Deployed both of these tools on the websites, hosted on AWS instances.
Softwares: Python, KeplerGL, Nginx, Gunicorn
Website: https://swabs2labs.readiness.in/bengaluru
https://optimaldesign.readiness.in/
COVID-19 Forecast Dashboard
A website that displays predicted daily number of cases from different models for all the states in India.
Deployed website and setup automatic pipeline for fetching predictions from different models.
Softwares: Python, Dash, Plotly
Website: https://www.isibang.ac.in/ incovid19/dash.php
Netradyne Technology India Pvt. Ltd.
November, 2019 -- March, 2020
Data Science Intern (Part Time)
GeoSpatio-Temporal analysis for finding hidden patterns in driving behaviour.
Database management for archiving, handling, and exchange of large data sets.
Softwares: Python, PostgreSQL, KeplerGL