Prakyat Prakash
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Education
RIT
Rochester Institute of Technology
Aug 2024 – Dec 2026Master of Science, Computer Science · Rochester, NY
Relevant coursework
Data Structures & AlgorithmsComputer ArchitectureMachine LearningFoundations of AIBig DataAdvanced Computer Vision
Research
Where computation meets biology
My research sits at the intersection of machine learning and molecular biology, specifically how computational methods can extract signal from messy, large-scale biological data. I work in the Cui Lab at RIT, where the problems range from proteomics data engineering to understanding how the genome regulates itself.
Right now I'm focused on two things: building rigorous PTM extraction pipelines for post-translational modification data, fixing assumptions the field has accepted for years, and studying genomics and 3D chromatin organization through deep learning models. The thread connecting all of it is the same: biology generates enormous, noisy datasets, and good software and good models are what turn that noise into biology.
Published work
Machine learning-based determination of sex-related bladder cancer biomarkers
Pizzi, J.R., Adhikari, I., Prakash, P., Miyamoto, H., & Cui, F. · Frontiers in Bioinformatics, 2026
Intrinsic DNA codes govern distinct modes of nucleosome–transcription factor interactions
Carson, C.W., Nagalakshmi, S.U., Adhikari, I., Freewoman, J.M., Pizzi, J.R., Prakash, P., & Cui, F. · Nature Communications, 2026
Experience
Where I've been building
May 2025 – Present
Rochester, NY
Graduate Research Assistant · Machine Learning
Rochester Institute of Technology
- ▶Co-authored 2 research papers in computational genomics: a peer-reviewed publication in Frontiers in Bioinformatics on ML-based bladder cancer biomarker discovery, and a paper in Nature Communications on nucleosome–transcription factor interactions.
- ▶Engineered an end-to-end PTM verified-negatives extraction pipeline processing 24.4M raw peptide-spectrum matches into 361,789 verified phosphosites across 35 parallel workers.
- ▶Built a dual-pass FASTA verification pipeline with tryptic-context filtering, correcting trypsin-cleavage bias and reducing terminal-K over-representation from 33.2% to 3.6%.
Jan 2025 – Apr 2025
Remote, NY
AI Engineer
Handshake AI
- ▶Architected an LLM-based RAG pipeline for Python automation tasks, improving code generation accuracy by 25% through targeted retrieval optimization and prompt engineering.
- ▶Built a systematic LLM evaluation and debugging workflow using LangChain tooling, cutting output error rates by 30% and enabling faster root-cause diagnosis of model failures.
- ▶Standardized response generation frameworks for chat-based LLM interactions, driving consistent, production-grade execution across automated workflows.
Mar 2024 – Jun 2024
Bengaluru, India
AI Intern
Acinonyx Technologies Pvt. Ltd.
- ▶Built an AI-driven backend service with Flask and REST APIs to automate license management, cutting manual oversight by 30% and streamlining renewals for 500+ users.
- ▶Developed an ML model to predict license-expiration patterns, enabling real-time tracking and cutting unexpected service downtime by 40%.
- ▶Applied AI-powered analytics on transactional data to trigger automated payment reminders, improving processing efficiency and driving sales growth.
Projects
Things I've built
© 2026 Prakyat PrakashRochester, NY