Ambuj Kumar

About Ambuj Kumar

Bioinformatics scientist with experience in adapting to fast-paced, dynamic and…

Experience

1. Bioinformatics Scientist

   Nationwide Children's Hospital

   Oct 2023 — Present · Columbus, OH, US

   Built LightRAG and GraphRag based knowledge graph to add long term memory to AI Agents. • Implemented large language model quantization, testing, and fine tuning for efficient AI Agent design. • Full-Stack Web development using Django, and Next.js, with JWT Authentication. Experienced in designing scalable API for efficient and developer-friendly integration.• Constructed Retrieval-augmented generation (RAG) AI framework and vector database to assist in Pediatric cancer research.• Conducted comprehensive whole genome sequencing analyses to accurately pinpoint gene insertion sites.• Performed single-cell data analyses to uncover and validate critical biomarkers, enhancing the understanding of cellular heterogeneity and disease mechanisms.• Executed differential gene expression and pathway enrichment analyses to elucidate the systemic effects of gene knockout, providing insights into the resultant pathway-level alterations.• Analyzed ChIP-seq, ATAC-seq, and RNA-seq datasets to investigate the regulatory influence of transcription factor binding on pathway modulation, contributing to the understanding of gene regulatory networks.• Analyzed long-read sequencing data to identify and characterize alternate transcripts induced by gene knockout.• Applied protein modeling, docking, molecular dynamics simulations, and machine learning to study protein-receptor binding and allosteric mechanisms, providing insights into protein function and its potential therapeutic targets.

Education

• University of Florida

  Master's Degree, Zoology/Animal Biology

  2013 — 2016

• Vellore Institute of Technology

  B.Tech, Bioinformatics

  2008 — 2012

• Iowa State University

  Doctor of Philosophy (Ph.D.), Bioinformatics

  2016

Skills

• Bioinformatics
• Computational Biology
• Molecular Biology
• Genomics
• Biochemistry
• Sequence Analysis
• Comparative Genomics
• Structural Bioinformatics
• Molecular Modeling
• Dna Sequencing
• Python
• R
• Prolog
• Genetics