My research contributions to the field of bioinformatics and computational biology, featuring peer-reviewed articles and manuscripts under review.
We present TRIPinRNA, a computational platform designed to predict intramolecular RNA triple helix structures with high accuracy. Using a combination of thermodynamic calculations and structural constraints, our algorithm identifies potential triple helix forming regions in RNA sequences. We validated our predictions using biophysical techniques including circular dichroism spectroscopy and thermal denaturation studies. Our analysis reveals that triple helices are more prevalent in the human transcriptome than previously recognized, with significant enrichment in long non-coding RNAs involved in gene regulation and chromatin organization.
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 novel 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.
We present a novel platform combining human forebrain organoids with polymeric nanofiber scaffolds to study interneuron migration disorders. Through comprehensive computational analyses including RNA-seq, protein-protein interaction networks, and pan-tissue expression analysis, we identified key molecular pathways disrupted in neurodevelopmental disorders. Our multiscale approach reveals how physical scaffolds can rescue migration defects, providing insights into potential therapeutic strategies for conditions like autism spectrum disorder and epilepsy.
This study investigates the cellular and molecular mechanisms underlying Megalencephalic Leukoencephalopathy with subcortical Cysts (MLC) using patient-derived iPSCs. I led the RNA-seq data analysis and developed a diagnostic platform to identify the 132dupC MLC1 gene mutation. Our findings reveal how MLC1 mutations lead to astrocyte dysfunction and characteristic vacuolation phenotypes, providing insights into disease pathogenesis and potential therapeutic targets for this rare neurological disorder.
This poster presented our work on understanding how chromatin boundaries are established and maintained without physical barriers. Using computational approaches to analyze CTCF binding sites and chromatin accessibility data, we demonstrated how dynamic interactions between architectural proteins create functional boundaries in the genome. The work has implications for understanding gene regulation and chromatin organization in health and disease.
Growing Impact
Recent publications gaining recognition in the scientific community
30+ Co-authors
Working with researchers across multiple institutions
4 Major Domains
RNA Biology, Genomics, Neuroscience, Bioinformatics Tools
100% Open Access
All publications freely available to the research community
I'm always interested in discussing research collaborations, sharing data and code, or answering questions about my publications. Feel free to reach out!