My research focuses on the intersection of bioinformatics, RNA biology, and computational methods, with a particular emphasis on understanding RNA structures and their roles in gene regulation.
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 lead several research projects focusing on RNA structure analysis, DNA repair mechanisms, and tool development for researchers.
Biochemistry (2024)
Presented TRIPinRNA, a computational platform for predicting intramolecular RNA triple helix structures and validated the predictions using biophysical techniques. The research revealed that triple helices are more prevalent in the human transcriptome than previously recognized.
Biochemistry (2024)
Investigated how G-quadruplex structures regulate CCN1 gene expression through IGF2BP1 binding. Conducted comprehensive computational analyses and analyzed proteomics data to understand the mechanisms of post-transcriptional regulation.
Under revision @ Stem Cell Reports
Conducted comprehensive computational analyses, including RNA-seq, PPI network, and pan-tissue analysis, to elucidate interneuron migration disorders in human forebrain organoids. This research contributes to understanding neurodevelopmental disorders.
bioRxiv
Led RNA-seq data analysis and developed a diagnostic platform to identify the 132dupC MLC1 gene mutation, enhancing understanding of MLC disease and brain development. This work has implications for understanding neurological disorders.
Vishal Bharti, Debojyoti Chakraborty
Poster presentation at the international conference "Frontiers in Genome Engineering 2023," BITS Pilani Goa Campus.
Developing and refining an in silico platform for predicting intramolecular RNA triple helix structures with applications in understanding X chromosome inactivation and gene regulation mechanisms.
View Project DetailsCreating an advanced statistical toolkit that bridges complex inference with an intuitive interface, designed for researchers with limited statistical backgrounds. The platform includes modules for confidence intervals, PCA, and statistical quality control.
View Project DetailsDeveloping 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.
View Project DetailsConducting computational analyses of RNA-seq data from human forebrain organoids to understand interneuron migration disorders and their implications for neurodevelopmental conditions.
AI-powered RAG assistant transforming laboratory knowledge management with intelligent question-answering, enterprise security, and sub-5-second response times. Successfully deployed on institute network for lab-wide use.
View Project DetailsInvestigating how G-quadruplex structures influence gene expression through interactions with RNA-binding proteins, with a focus on CCN1 regulation by IGF2BP1.
Working closely with experimental biologists to identify computational challenges in their research
Creating robust pipelines for processing and analyzing complex biological data
Ensuring all analyses follow sound statistical principles and appropriate statistical tests
Developing user-friendly tools to make complex analyses accessible to non-computational researchers
Working across disciplines to integrate computational findings with experimental validation
Sharing code and methods to promote reproducibility and transparency
Leading multiple computational biology projects, including TRIPinRNA development, DNA repair mechanism analysis, and StickForStats platform development. Working under the supervision of Dr. Debojyoti Chakraborty.
Led computational analysis for investigating the efficacy of Ashwagandha and Yogaraj Guggulu for osteoarthritis treatment using a hybrid Proteomics-Cheminformatics-Network medicine approach. Worked under the supervision of Dr. Vibin Ramakrishnan.
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.
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.
My research thrives on collaborations with talented scientists across disciplines. I am currently collaborating with researchers from various institutions on projects related to RNA biology, computational genomics, and tool development.
Collaborating with Dr. Debojyoti Chakraborty and Dr. Souvik Maiti on RNA structure analysis and tool development for predicting triple helices and G-quadruplexes.
Working with postdoctoral researchers on automating biological data pipelines using R and Python for high-throughput analysis of genomic data.
Continuing collaboration with researchers 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.
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.