Nuclear positioning and its translation dynamics is regulated by cell geometry
Poster presentaton at a Conference at Biophysical Society-MBI Thematic Meeting: Mechanobiology of Disease, Singapore
PDF version is also available here
EDUCATION
- B.Tech in Biotechnology(with Distinction), SASTRA University, India, 2015
- Ph.D in Mechanobiology, National University of Singapore, Singapore (2021 Expected)
WORK EXPERIENCE
- Visiting Researcher, Paul Scherrer Institute & ETH Z ̈urich
- Consultant, Computer Vision, Qritive
- Research Assistant, NUS
SKILLS
- Statistics: Linear algebra,Multivariate analysis,Machine Learning, Clustering,Pattern recognition, Diffusion maps and Psuedotime analysis
- Computer Vision: Segmentation, Feature generation and Particle tracking
- Computational Biology: Next Gen-Sequencing analysis of Microarray, RNA-Seq including single cell RNA-Seq and HiC data
- Experimental Skills: Microscopy, Tissue engineering and mechanical manipulation of cells
SELECTED RESEARCH PROJECTS
Automated feature generator for 3D images
- Built an automatic image processing pipelines for segmentation and feature generation that reduced the processing time by 60%.
- Engineered features for morphology, textural and spatial distribution of objects in images.
- Integrated multi-domain features such as protein expression, RNA seq and image features to enable deduction of functional links.
Digital pathology platform for grading breast cancer stages at single cell resolution
- Performed instance segmentation of singe nuclei from patient tissue biopsies using U-Net based CNN and extracted geometric and textural features of nuclei.
- Built machine learning models to diagnose breast cancer stages at single cell resolution from patient breast tissue biopsies with 80\% accuracy.
- Developed a single cell tumorigenesis score that varies with tumor progression.
Deconvolving cell variability in cancer
- Developed a 3D in-vitro tissue model to study cancer progression amenable to high resolution imaging.
- Implemented a classifier to predict cell shape with an accuracy of 95\% and used the latent feature vectors along with regression models to show that cell shape is coupled to its function.
- Demonstrated a causal relationship between cell shape and activation by cancer cells using multimodal-multivariate analysis.
- Established the use of the 3D tissue model to assay the treatment efficacy of radiotherapy.
Trajectory inference to accelerate reprogramming of skin cells to stem cells.
- Developed a novel technique to reprogram skin cells to stem cells with high efficiency.
- Performed statistical tests and pathway analysis on RNA seq data to characterize the temporal changes in the transcription profile during reprogramming.
- Modeled trajectories of reprogramming cells using clustering and diffusion models of single cell image features.
- Identified sources of low efficiency in large noisy image data which were experimentally validated to accelerate stem cell generation.
CONFERENCE: TALKS AND POSTERS
Role of 3D chromatin architecture in differential genome regulation
Conference talk at 3rd International Symposium on Mechanobiology, Singapore
Role of cell geometry and 3D chromatin structure in differential genome regulation
Conference Talk at EMBO Workshop: Nuclear Mechanogenomics, Singapore
Heterogeneity in cell geometric states regulate the selective activation of fibroblasts in engineered 3D tumor microenvironment
Poster presentaton at a conference at Mechanobiology after 10 Years: The Promise of Mechanomedicine, Singapore
Multivariate analysis of fibroblast activation in engineered 3D tumor microenvironments
Conference talks at International Conference on Genomes and AI: From Packing to Regulation, Singapore
Mechano-Genomics: from Cell-Fate Decisions to Biomarkers
Conference talks at Drug Discovery 2019 – Looking Back To The Future, Liverpool, UK
Cell geometry modulates the activation of fibroblasts in 3D tumor microenvironments
Conference talks at 64th Annual Meeting of the Biophysical Society, San Diego, USA
AWARDS AND HONOURS
- Dean’s Merit list of the top 2-10% in the University (2014-2015)
- Inspirational Mentorship Award, NUS High School(2017)
- Best Oral Presentation Award, International Conference on Genomes and AI (2019)