Publications
My research contributions to the field of bioinformatics and computational biology, featuring peer-reviewed articles, preprints, and manuscripts in review or in preparation.
Peer-reviewed
Development of an in silico platform (TRIPinRNA) for the identification of novel RNA intramolecular triple helices and their validation using biophysical techniques
Summary
TRIPinRNA is a Python tool that scans human long noncoding and protein-coding transcripts for sequence patterns that could fold into intramolecular RNA triple helices. With it, the study predicts both canonical (homopyrimidine) and noncanonical (heteropurine-pyrimidine) triplexes, shows with biophysical tests on selected candidates that both kinds form in vitro, and reports a strong correlation between triplex occurrence and local GC content. The tool can be applied to any organism with an annotated transcriptome.
MLC1 alteration in human iPSCs give rise to disease-like cellular vacuolation phenotype in the astrocyte lineage
Summary
This study models Megalencephalic Leukoencephalopathy with subcortical Cysts (MLC) in human iPSCs: lines reprogrammed from a patient carrying the MLC1 132dupC variant, and CRISPR MLC1-knockout lines with isogenic controls, differentiated into neural stem cells and astrocytes. I did the study’s computational analysis and prepared the related figures: the RNA-seq analysis of MLC1-knockout against control neural stem cells (differential expression, functional, pathway and disease enrichment, and a protein-interaction analysis of the differentially expressed genes linked to epilepsy), and the mapping of those genes’ proteins to approved, investigational and experimental drugs in DrugBank. I also did the image analysis and the statistical analysis. The study shows that MLC1 alteration in human iPSCs gives rise to a disease-like cellular vacuolation phenotype in the astrocyte lineage.
Quercetin affects carcinogenic phenotype of breast and lung cancer cells differentially through sterol regulation mediated by MALAT1 perturbation
CRISPR-Cas diagnostics (CRISPR-Dx) of viral pathogens in low- and limited-resource areas
IGF2BP1-mediated regulation of CCN1 expression by specific binding to a G-quadruplex structure in its 3' UTR
Summary
This study elucidates how G-quadruplex structures in the 3'UTR of CCN1 mRNA regulate gene expression through specific binding by IGF2BP1. Using a combination of computational predictions, biophysical characterization, and proteomics analysis, we demonstrate that IGF2BP1 recognizes and stabilizes G-quadruplex structures, leading to enhanced CCN1 expression. Our findings reveal a mechanism of post-transcriptional regulation where RNA secondary structures serve as binding platforms for regulatory proteins, with implications for understanding cellular proliferation and wound healing processes.
Preprints and manuscripts
StickForStats: automated statistical assumption validation for reproducible computational biology
Most biomedical articles print no statistical result checkable by recomputation: a pre-registered audit with a 20,000-article out-of-sample replication
Summary
Can a reader check a paper’s statistics by recomputing a printed p-value from its test statistic and degrees of freedom? This pre-registered audit measures how often biomedical articles allow that check, and how often the results that can be checked are consistent as printed. With the protocol frozen before any data were fetched, 3,000 randomly sampled PubMed Central Open Access research articles (2020–2025) were scored by a deterministic extractor, flagged results were classified by fixed adjudication rules, and every frozen estimate was re-estimated, unchanged, on a further 20,000 articles. My roles (CRediT): conceptualization, methodology, software, investigation, formal analysis, data curation and writing of the original draft; Dr. Debojyoti Chakraborty: supervision, and writing (review and editing). Poster selected for presentation at ESTIC 2026, Bharat Mandapam, New Delhi, 27 to 29 Oct 2026. Poster session: 28 Oct, afternoon.
An interface of genetically engineered human forebrain assembloids and polymeric nanofiber scaffolds for multiscale profiling of interneuron-migration disorders
Summary
The study knocks out ERBB4 in human iPSCs that carry an interneuron reporter, fuses dorsal and ventral forebrain organoids into assembloids, and follows interneuron migration in the assembloids and on polymeric nanofiber scaffolds. I did the study’s computational and statistical analysis: the RNA-seq analysis of knockout against control assembloids (differential expression, GO and pathway enrichment, and the overlap with epilepsy and intellectual-disability genes), a protein-interaction network of the neuron-migration genes, the pathway analysis of the sorted interneurons’ proteomics, the statistical tests on the imaging and migration measurements and, in the submitted manuscript, a pan-tissue correlation of the control assembloids.
Folding on the way in: vectorial substrate recognition by human Hsp60
Structural and functional analysis of the Chast-NUCB1 interaction in cardiac hypertrophy
Conferences, Talks & Posters
Most biomedical articles print no statistical result a reader can recompute
Summary
The poster is on the pre-registered checkability audit (manuscript in preparation), listed under Preprints and manuscripts.
StickForStats: Publish Research with Confidence
43rd Mahabaleshwar Seminar: Molecules, Membranes and Organelles (TIFR)
Summary
Built and presented a simulation of organelles interacting with motor proteins under varying levels of molecular crowding in a breakout session.
Boundary Without Fence
Summary
A concept poster on liquid–liquid phase separation in membraneless condensates: how condensates behave (droplets fuse and recover after photobleaching), how they form through protein–protein, protein–RNA and RNA–RNA interactions (with the Flory–Huggins interaction parameter), and why they matter as reaction crucibles and for sequestering molecules. It then asks whether synthetic organelles, engineered condensates such as the light-inducible CasDrop droplets, could carry CRISPR to its target with more precision than viral vectors (adeno-associated virus, lentivirus, adenovirus), which can induce immune reactions. The figures are adapted from the cited studies.
Academic Profiles
Collaboration & Inquiries
I'm always interested in discussing research collaborations, sharing data and code, or answering questions about my publications. Feel free to reach out!