Research Interests
Single-Cell DNA Repair Biology
Developing computational pipelines to decipher repair mechanisms in CRISPR-edited cells using scRNA-seq data
CRISPR Repair Modeling
Multi-layer inference analysis for understanding HDR/NHEJ pathway selection in genome editing
RNA Structure & Function
Computational prediction of RNA triple helices and G-quadruplexes in gene regulation
Statistical Methods for Omics
Building user-friendly statistical tools for biological data analysis and experimental design
Research Software Development
Building open-source research software, validated against reference implementations
Publications
Peer-reviewed
Rakheja I.*, Bharti V.*, et al. (2024). Development of an in silico platform (TRIPinRNA) for the identification of novel RNA intramolecular triple helices and their validation using biophysical techniques. Biochemistry (ACS) 64(1):250-265. *Equal contribution. DOI: 10.1021/acs.biochem.4c00334
Sharma S., Bharti V., et al. (2026). MLC1 alteration in human iPSCs give rise to disease-like cellular vacuolation phenotype in the astrocyte lineage. Orphanet Journal of Rare Diseases 21:176. DOI: 10.1186/s13023-026-04316-3
Rakheja I., Bharti V., Singh V., Maiti S. (2026). Quercetin affects carcinogenic phenotype of breast and lung cancer cells differentially through sterol regulation mediated by MALAT1 perturbation. Chemistry - An Asian Journal 21(11):e70821. DOI: 10.1002/asia.70821
Das P.K., Aich M., Adu P., Bharti V., Maiti S., Chakraborty D. (2026). CRISPR-Cas diagnostics (CRISPR-Dx) of viral pathogens in low- and limited-resource areas. TrAC Trends in Analytical Chemistry 195:118590. DOI: 10.1016/j.trac.2025.118590
Rana P., Ujjainiya R., Bharti V., Maiti S., Ekka M.K. (2024). IGF2BP1-mediated regulation of CCN1 expression by specific binding to a G-quadruplex structure in its 3' UTR. Biochemistry (ACS) 63(17):2166-2182. DOI: 10.1021/acs.biochem.4c00172
Preprints and manuscripts
Bharti V., Chakraborty D. (2026). StickForStats: automated statistical assumption validation for reproducible computational biology. bioRxiv. DOI: 10.64898/2026.06.15.732278. First and corresponding author; in peer review at BMC Bioinformatics.
Bharti V., Chakraborty D. (2026). Most biomedical articles print no statistical result checkable by recomputation: a pre-registered audit with a 20,000-article out-of-sample replication. First and corresponding author; in preparation for submission to Nature Human Behaviour.
Rauthan R., Bharti V., et al. An interface of genetically engineered human forebrain assembloids and polymeric nanofiber scaffolds for multiscale profiling of interneuron-migration disorders. Research Square preprint, under revision at Stem Cell Reports. DOI: 10.21203/rs.3.rs-3831019/v1
Kochar M., Rao S., Bhattacharjee S., Goel P., Timsina H., Azhar M.K., Bharti V., et al. Folding on the way in: vectorial substrate recognition by human Hsp60. Submitted to Cell, 2026.
Azam T., Kumar A., Singh P., Bharti V., Ekka M.K. Structural and functional analysis of the Chast-NUCB1 interaction in cardiac hypertrophy. Submitted to the Journal of Biological Chemistry, 2026.
Awards
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2025
Best Poster Award, EMBO Conference 2025
CCMB Hyderabad, for StickForStats. Sole author and presenter.
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2020
GATE Biotechnology 2020, All-India Rank 127
Top ~1% in India's national postgraduate entrance examination.
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2020–22
Graduate Assistantship
Ministry of Education, Government of India, 2020 to 2022.
Projects
StickForStats
An open-source web platform whose Guardian system runs eight assumption validators (normality, variance homogeneity, independence, outliers, sample size, modality, linearity, homoscedasticity) before a test executes, and reroutes to an appropriate nonparametric alternative when a critical assumption fails. A companion module re-checks the statistical claims in manuscripts. Validated against SciPy and R. Best Poster Award, EMBO Conference 2025.
Status: Preprint on bioRxiv (2026); in peer review at BMC Bioinformatics. First and corresponding author.
Python Django React Statistics
Checkability 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 estimate was replicated 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.
Status: In preparation for submission to Nature Human Behaviour. First and corresponding author.
Python Meta-research Reproducibility PubMed Central
TRIPinRNA
In silico platform for predicting intramolecular RNA triple helix structures. Published in Biochemistry (2024), co-first author contribution. Applications in X chromosome inactivation and gene regulation mechanisms.
Python RNA Biology Bioinformatics
DNA Repair Analysis
Developed a three-layer computational pipeline to decipher repair factor requirements in staggered versus blunt-end DNA breaks using scRNA-seq data and advanced statistical methods.
R scRNA-seq Genomics
G-Quadruplexes in CCN1
Computational and proteomics analysis for a study of how IGF2BP1 regulates CCN1 expression by binding a G-quadruplex structure in its 3' UTR (Biochemistry, 2024).
Python Proteomics RNA Biology
Forebrain Assembloids
Computational analysis of RNA-seq data from human forebrain assembloids to understand interneuron migration disorders and their role in neurodevelopmental conditions.
RNA-seq Network Analysis Neuroscience
Confidence Intervals Explorer
Interactive educational tool for understanding statistical confidence intervals through visualizations and simulations, built during the early Streamlit prototype of StickForStats. Deployed on Streamlit Cloud with real-time parameter adjustment; it sleeps when idle, so the first load can take a minute.
Python Streamlit Plotly Statistics
RNA Lab Navigator
Retrieval-augmented research assistant over internal lab documents and the primary literature, for fast, grounded literature triage in a wet-dry lab. In routine use by about 21 researchers.
Django React PostgreSQL Docker RAG
About Me
Electronics-engineer-turned-bioinformatician, currently working as a Project Associate-II at CSIR-IGIB under Dr. Debojyoti Chakraborty. My work spans single-cell genomics, RNA structure analysis, CRISPR repair screens, and AI-driven statistical tools.
I hold an MTech in Biotechnology from IIT Guwahati and a BTech in Electronics and Communication from IEM Kolkata. GATE Biotechnology AIR 127 (2020). My research focuses on developing computational methods for analyzing complex biological data.
Research Focus
Computational Biology & Single-cell: I build statistical inference pipelines for single-cell data, most recently contrasting repair-factor requirements at staggered versus blunt CRISPR-induced DNA breaks.
Methods & Statistics: I build open-source statistical software that checks the assumptions behind a test before running it (StickForStats, validated against SciPy and R).
Path
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2014–2018B.Tech, Electronics & Communication Engineering
Institute of Engineering & Management, Kolkata
Photo: Pinakpani, Wikimedia Commons, CC BY-SA 4.0; cropped and rendered as characters -
2020–2022M.Tech, Biotechnology
Indian Institute of Technology Guwahati
Photo: Nilotpal Hazarika123, Wikimedia Commons, CC BY-SA 4.0; cropped and rendered as characters -
2023–RNA Biology Group (Dr. Debojyoti Chakraborty)
CSIR-Institute of Genomics and Integrative Biology, New Delhi
Photo: Singhprtk, Wikimedia Commons, CC BY-SA 4.0; cropped and rendered as characters
Technical Proficiencies
Programming & Software
Bioinformatics & Genomics
Machine Learning & AI
Computational Resources
Future Research Interests
The repair-or-die decision
SpCas9 leaves blunt DNA ends. FnCas9 leaves a staggered overhang of two to five bases. That difference is small, and it is enough to change which repair pathway a cell commits to. I want to understand the decision one level above pathway choice: whether a cell repairs at all, or dies, and whether the structure of a break and the manner of its delivery propagate upward into that commitment. In our single-cell data we recovered pathway-specific signatures and no death signature at all, and that absence is what I want to work on.
The second half of the question is whether that decision is made cell by cell or coordinated across neighbours. Dissociation destroys the information needed to answer it, so this requires reading perturbation and outcome in the same tissue section rather than building a better model of dissociated data.
Adjacent interests
Systems Biology & Network Medicine
Understanding disease mechanisms through network analysis of multi-omics data, developing computational models of cellular systems, and identifying biomarkers through integrative analysis of genomic, transcriptomic, and proteomic data.
RNA Biology & Therapeutics
Continuing my work on RNA structural elements (G-quadruplexes, triple helices) and their regulatory roles, developing computational tools for RNA drug design, and exploring RNA-based therapeutic interventions for genetic disorders.
Let's Collaborate
I'm open to research collaborations, consulting opportunities, and discussions about bioinformatics, statistical tools, and computational biology.
© 2026 Vishal Bharti. All rights reserved.