Research
The thread through my work is whether a biological conclusion actually follows from the data that produced it. What I want to find out next is the repair-or-die decision: after a Cas9 break, whether a cell repairs or dies, whether the structure of the break and the manner of its delivery shape that commitment, and whether the decision is made cell by cell or coordinated across neighbours (more).
Research Overview
I am a bioinformatician specializing in computational genomics, RNA biology, and statistical tool development. As a Project Associate-II at the Institute of Genomics and Integrative Biology (CSIR-IGIB) under Dr. Debojyoti Chakraborty, I build computational and statistical methods for genome engineering and RNA biology, working on RNA structure analysis, DNA repair mechanisms, and tool development for researchers.
RNA Biology
G-quadruplexes
Triple Helices
Computational Genomics
Single-cell Analysis
Statistical Methods
Machine Learning
DNA Repair
Tool Development
Neurodevelopmental Disorders
Publications
The full list, with summaries, citations and the conference posters, is on the Publications page.
Selected
- TRIPinRNA: an in silico platform for the identification of RNA intramolecular triple helices. Biochemistry (ACS), 2025. Co-first author.
- StickForStats: automated statistical assumption validation for reproducible computational biology. bioRxiv, 2026; in peer review at BMC Bioinformatics. First and corresponding author.
- Checkability audit: most biomedical articles print no statistical result checkable by recomputation. In preparation; poster at ESTIC 2026, New Delhi. First and corresponding author.
Research Projects
TRIPinRNA: RNA Triple Helix Prediction
Co-developed (co-first author) an in silico platform that searches the human transcriptome for intramolecular RNA triple helices, and performed the bioinformatics analysis; its predictions include triplex-forming sequences in lncRNAs involved in X-chromosome inactivation.
View Project DetailsStickForStats Platform Development
An open-source React/Django web platform whose Guardian engine runs the relevant subset of its eight assumption validators before a test executes and, on critical violations, reroutes to an appropriate nonparametric alternative. MIT-licensed and validated against SciPy and R. It is live (public beta) at stickforstats.com.
bioRxiv preprint (DOI: 10.64898/2026.06.15.732278), in peer review at BMC Bioinformatics. First and corresponding author.
View Project DetailsCheckability Audit
A pre-registered audit of whether published biomedical statistics can be recomputed at all. With the protocol frozen before any data were fetched, 3,000 randomly sampled PubMed Central Open Access research articles (2020–2025) were checked for results whose p-value can be recomputed from the printed test statistic and degrees of freedom, and every frozen estimate was re-estimated out of sample on a further 20,000 articles. The measurement pipeline is deterministic, with no machine learning in it, so every number reproduces from committed code.
Manuscript in preparation. First and corresponding author.
In PublicationsDNA Repair Mechanisms Analysis
Analysed single-cell RNA-seq data for a colleague's PhD study of how CRISPRi cells repair staggered (en1FnCas9) versus blunt (SpCas9) DNA ends: Seurat QC, integration and differential expression, gene-set comparisons and GO enrichment, with the heat map and volcano plots credited in her thesis.
View Project DetailsHuman Forebrain Assembloids
Computational and statistical analysis for a study of interneuron migration in ERBB4-knockout human forebrain assembloids: RNA-seq with GO and pathway enrichment, a protein-interaction network, the pathway analysis of the sorted interneurons’ proteomics and, in the submitted manuscript, a pan-tissue correlation of the control assembloids.
View Project DetailsRNA Lab Navigator
Retrieval-augmented research assistant for internal lab documents and the primary literature: keyword (BM25) retrieval over a Weaviate index, with an LLM answering from the top passages; the source documents are listed under each answer. Deployed for the lab on the institute network in July 2025.
View Project DetailsG-Quadruplexes in Gene Regulation
Computational and proteomics analysis for a study of how IGF2BP1 regulates CCN1 expression by binding a G-quadruplex structure in its 3′ UTR (published in Biochemistry, ACS).
Research Methodology
Problem Identification
Working closely with experimental biologists to identify computational challenges in their research
Pipeline Development
Creating robust pipelines for processing and analyzing complex biological data
Statistical Rigor
Ensuring all analyses follow sound statistical principles and appropriate statistical tests
Tool Development
Developing user-friendly tools to make complex analyses accessible to non-computational researchers
Interdisciplinary Collaboration
Working across disciplines to integrate computational findings with experimental validation
Open Science Practices
Sharing code and methods to promote reproducibility and transparency
Research Journey
2023-Present
Project Associate-II at CSIR-IGIB
Co-developed TRIPinRNA (co-first author); did the downstream single-cell RNA-seq re-analysis for a colleague's CRISPRi DNA-repair PhD study (differential expression, gene-set comparisons, enrichment, and the heat-map and volcano figures credited in her thesis); built the StickForStats platform. Working under the supervision of Dr. Debojyoti Chakraborty.
2022
Senior Research Fellow at IIT Guwahati
Carried out a hybrid proteomics-cheminformatics-network-medicine analysis of Ashwagandha and Yograj Guggulu for osteoarthritis (protein-protein-interaction analysis and computational drug repurposing). Worked under the supervision of Dr. Vibin Ramakrishnan.
2021-2022
Master's Thesis at IIT Guwahati
Conducted RNA-seq analysis to classify transcripts susceptible to Nonsense Mediated mRNA Decay (NMD) and explored cellular behaviors in the absence of the UPF3B gene. Worked under the supervision of Dr. Kusum K. Singh.
2017-2018
Bachelor's Thesis at IEM Kolkata
Created a platform integrating NCBI BLAST and PDB databases for protein image retrieval and detailed analysis using Jupyter Notebook and API implementation. Worked under the supervision of Prof. Indranil Basu.
Research Collaborations
My research thrives on collaborations with talented scientists across disciplines. I have worked with researchers at several institutions on projects related to RNA biology, computational genomics, and tool development.
CSIR-IGIB
Working in Dr. Debojyoti Chakraborty's RNA Biology Group. The TRIPinRNA triple-helix work was co-supervised with Dr. Souvik Maiti, and the CCN1 G-quadruplex work with Dr. Mary K. Ekka.
University of California, Berkeley
Worked with a postdoctoral researcher at UC Berkeley to automate biological data-analysis pipelines in R and Python.
IIT Guwahati
Worked with researchers, as a Senior Research Fellow in 2022, on computational approaches for analyzing traditional medicine effects using network pharmacology.
I am always open to new collaborative opportunities, especially those that bridge computational approaches with experimental biology. If you're interested in potential collaborations, please get in touch.
Research Inquiries
If you're interested in my research, have questions about specific projects, or would like to discuss potential collaborations, I'd be happy to hear from you.