Projects Portfolio
A comprehensive collection of my research projects, statistical tools, and computational applications in bioinformatics, genomics, and machine learning.
Major Research Projects
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 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.
Status: Manuscript in preparation. First and corresponding author.
TRIPinRNA
In silico platform that searches the human transcriptome for intramolecular RNA triple helices; its predictions include triplex-forming sequences in lncRNAs involved in X-chromosome inactivation, three of them validated in vitro.
DNA Repair Mechanisms Analysis
Single-cell RNA-seq analysis for a colleague's PhD study of how CRISPRi cells repair staggered versus blunt DNA ends: Seurat differential expression, gene-set comparisons and GO enrichment, with the heat map and volcano plots credited in her thesis.
Human 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.
Status: Research Square preprint; under revision at Stem Cell Reports.
G-Quadruplexes in CCN1 Regulation
Computational and proteomics analysis for a study of how IGF2BP1 regulates CCN1 expression by binding a G-quadruplex structure in its 3' UTR.
RNA 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.
Software & Tools
Confidence Intervals Explorer
Interactive educational application for understanding confidence intervals through visualizations, simulations, and practical applications.
StickForStats
An open-source web platform whose Guardian system runs the relevant subset of its eight assumption validators 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: Live (public beta). Preprint on bioRxiv (2026), DOI: 10.64898/2026.06.15.732278; in peer review at BMC Bioinformatics. First and corresponding author.
PCA Tool
Interactive web application for principal component analysis with customizable visualization options and detailed explanations.
Previous Projects
Ayurvedic Medicine Analysis for Osteoarthritis
Hybrid proteomics, cheminformatics and network-medicine analysis of Ashwagandha and Yograj Guggulu for osteoarthritis, with computational drug repurposing.
NMD Transcripts Analysis
Master's thesis project analyzing transcripts susceptible to Nonsense Mediated mRNA Decay (NMD) in UPF3b KO HEK293 Cells.
DNA Sequence Analysis and Protein Structure Visualization
Bachelor's thesis project creating a platform that integrates NCBI BLAST and PDB databases for protein image retrieval and detailed analysis.
Machine Learning Projects
Optimization Algorithms Comparison
Evaluated various optimization algorithms (SGD, Momentum, RMSProp, Adam) on a Saddle Point and MNIST dataset, comparing their efficacy and convergence properties.
DNA Sequence Classification using LSTM
Implemented recurrent neural networks to classify DNA sequences into categories based on intronic, exonic regions, and intron-exon boundaries.
N6-Methyladenine Sites Prediction
Developed models using CNN and LSTM for predicting N6-Methyladenine sites in the Rice Genome, comparing algorithmic performances and accuracies.
Research Output
Publications & Manuscripts
Peer-reviewed papers, preprints and submitted manuscripts, with summaries and citations, are on the Publications page.
Ongoing Development
Next steps for StickForStats, as outlined in the preprint:
StickForStats: planned extensions
Expanding the Bayesian analysis suite, adding dose-response modeling for pharmacological studies and CONSORT flow-diagram generation, and integrating with biological data repositories (GEO, ClinicalTrials.gov).
Outside the Lab
Two robots I build in my own time, both almost finished:
A walking TARS and a palm-sized quadrotor
A 3D-printed TARS from Interstellar and a quadrotor inspired by Vijay Kumar’s flying robots, each with its own CAD model and physics simulation. See them in motion.
Interested in Collaboration?
I'm always open to discussing new projects, research collaborations, and opportunities in bioinformatics and computational biology.