About Me
I am a cross disciplinary researcher with expertise in single-cell and spatial genomics, stem cell biology, and machine learning. Broadly, the goal of my research has been to develop tools for analyzing and controlling biological systems, with applications in biomedicine. I pursued my Ph.D. at Washington University in the lab of Dr. Samantha Morris, where I developed a novel technology to pair lineage readout with single cell epigenomics, dubbed CellTag-multi. I used this to understand how clones from the same starting population go through distinct epigenetic and transcriptional changes over the course of reprogramming and differentiation, hence acquiring different cell fates.
Check out me Medium blog here.
Selected Research Projects
Gene Regulatory Network-based embedding of cells using Graph Neural Networks
Work in progress..
Dissecting the Role of Chromatin Remodeling in Direct Lineage Reprogramming
During my Ph.D I developed new molecular and computational tools to better study how cell state changes over time in the context of cellular reprogramming. A non-exhaustive list includes CellTag-multi, CellOracle, and other efforts in Adipocyte reprogramming, and Hirschprung’s disease. I will update this as more projects become available in the public domain.
My thesis can be found on ProQuest and an up-to-date list of my published works on Google Scholar.
CellTag-tools for atlas scale clonal analysis
Over the last few years, single-cell assays have rapidly expanded in scale and number of cells sequenced per run. This has also enabled atlas scale profiling of single cell clones and lineage. To rapidly process this data, we developed CellTag-tools, a highly scalable python-based software for clonal analysis.
Adversarial learning to simulate time course transcriotomic data
Piloted a novel Generative AI-based approach for Adversarial Data Augmentation to improve a Gene Regulatory Network classifier model.
Targeted in situ sequencing to spatially profile RNA and protein.
Developed and optimized library preparation method to profile a panel of RNA and protein molecules using in situ sequencing in cultured cells and tisses.
A Programmable ThermoFluidic Cycler for Automated FISSEQ
Developed an automated platform for thermal and microfluidic control during in situ sequencing library preparation.
Binding Site Analysis of an Acyl CoA Binding Protein
Investigated ligand-binding mechanics of ACBP16, a key metabolic regulator in Plasmodium falciparum, as an Indian Academy of Science Summer Research Fellow at the Centre for DNA Fingerprinting and Diagnostics. Findings aimed to inform targeted drug development for malaria. Report
A Novel Plug n Play MEMS-Based DNA Microarray
Designed a MEMS-based label-free DNA/RNA detection system to replace traditional microarray fluorophore-based readouts, integrating circuit design for digital signal conversion. Successfully simulated in COMSOL Multiphysics and LTSpice, and presented at the COMSOL Conference 2016, Boston. Details slides.