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AI in Bioinformatics
I am a bioinformatics professional pursuing an M.S. in Bioinformatics at Indiana University, with a B.E. in Biomedical Engineering from Mumbai University. My expertise spans NGS data analysis, variant calling, RNA-seq, workflow automation (Snakemake, Nextflow), and cloud computing (AWS, GCP).
I am passionate about the intersection of AI and bioinformatics, particularly in machine learning-driven genomics. Currently, I am working on gene prediction using BERT NLP models and experimenting with AI integration in bioinformatics workflows. I enjoy exploring and implementing AI-driven solutions using ChatGPT, DeepSeek, and Gemini APIs to enhance genomic data interpretation and automation.
ai
AI in Bioinformatics
I am a bioinformatics professional pursuing an M.S. in Bioinformatics at Indiana University, with a B.E. in Biomedical Engineering from Mumbai University. My expertise spans NGS data analysis, variant calling, RNA-seq, workflow automation (Snakemake, Nextflow), and cloud computing (AWS, GCP).
I am passionate about the intersection of AI and bioinformatics, particularly in machine learning-driven genomics. Currently, I am working on gene prediction using BERT NLP models and experimenting with AI integration in bioinformatics workflows. I enjoy exploring and implementing AI-driven solutions using ChatGPT, DeepSeek, and Gemini APIs to enhance genomic data interpretation and automation.
Projects
Bulk RNA-Seq Analysis
Analyzed bulk RNA-seq data to identify differentially expressed genes (DEGs), enriched pathways, and key biomarkers using DESeq2, KEGG, and Reactome. Applied NGS pipelines for gene expression profiling, enabling insights into disease mechanisms and therapeutic targets.
Single-Cell RNA-Seq
Developed single-cell RNA-seq pipelines using Seurat and Scanpy to explore cellular heterogeneity and immune responses. Applied clustering, normalization, and differential analysis to uncover key insights in tumor microenvironments, immunotherapy, and disease progression.
Variant Calling & Annotation
Designed variant calling pipelines (BWA, GATK, VEP) for detecting clinically significant mutations and novel variants. Automated workflows to enhance genomic data interpretation, supporting applications in precision medicine, rare disease research, and population genetics.
ATAC-Seq & Epigenomics
Performed chromatin accessibility analysis using ATAC-Seq and MACS2 to map open chromatin regions and regulatory elements. Integrated data with RNA-seq and ChIP-seq to investigate gene regulation, epigenetic modifications, and transcription factor binding sites.
Machine Learning
Applied machine learning models for drug discovery, bioactivity prediction, and genomic analysis. Built Random Forest models (R² = 0.65) for compound bioactivity and performed EDA to identify key molecular features, aiding in lead identification and precision medicine.
Deep Learning
Leveraged deep learning (BERT NLP models) for gene function prediction, automating gene identification and characterization. Explored biological sequence tokenization and embeddings, enhancing genomic annotation, functional analysis, and AI-driven bioinformatics applications.
Professional Experience
Genomics Analyst
Genomics Analyst Intern at Karyosoft Inc., building scalable variant analysis pipelines for long- and short-read sequencing. Automating workflows with Snakemake and AWS Batch. Enhancing genomic interpretation with NLP, troubleshooting workflows, supporting clients, and maintaining documentation for transparency and best practices.
Research Assistant
Conducting genetic language modeling using BERT transformers to predict gene functions with 89.5% accuracy. Developing single-cell RNA-seq pipelines for tumor analysis. Presenting research findings, coordinating lab discussions, and contributing to a book chapter on RNA modifications under faculty supervision.
Teaching Assistant
Supporting students in Introduction to bioinformatics course by grading assignments, evaluating project reports, and resolving coding queries in Python and R. Coordinating guest lectures and assisting in course management. Facilitating discussions on computational tools and workflows to enhance student understanding of bioinformatics analysis.
Active Leadership & Academic Involvement
Graduate Ambassador
Facilitating student engagement by mentoring prospective students, coordinating with university departments, and organizing events like orientations and workshops. Leading outreach initiatives through virtual events and social media. Representing the university at recruitment events, open days, and campus tours to promote academic programs.
President Luddy Journal Club
Leading the Luddy Journal Club to foster academic discussions and knowledge-sharing. Organizing events, inviting speakers, and facilitating Q&A sessions. Advocating for funding at ICSC meetings. Enhancing networking, communication, and event management skills while engaging with emerging topics in biomedical informatics.
Co-Director Graphic Design (SAPB)
Designing visual materials to promote campus events as part of Student Activities Programming Board (SAPB). Collaborating on marketing strategies to boost student engagement. Aligning designs with event goals, assisting in event management, and enhancing branding to create a dynamic and connected student community at Indiana University.