Prakyat Prakash
Open to 2026 SWE & ML roles
Hi, I am Prakyat Prakash

I build systems that work
and models that learn.

Software engineer and pipelines architect by practice: data pipelines, full-stack systems, and ML models that go from notebook to production. I also do research, with a focus where computation meets biology.

Prakyat Prakash
Education
RIT

Rochester Institute of Technology

Aug 2024 – Dec 2026
Master 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. · bioRxiv, 2025
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 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%.
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

PTM Extraction dashboard, dataset summary

PTM Dataset Extraction Pipeline

Reconstructed phosphorylation and lysine-acetylation training datasets from 5 mass-spectrometry repositories, processing 24.4M peptide-spectrum matches into 361,789 tryptic-verified phosphosites. Replaced the field-standard "all non-positives are negatives" assumption with true experimentally-observed negatives via dual-pass FASTA verification across 35 parallel workers.

PandasNumPyUniProt
Dec 2025 – Mar 2026● Live
NYC Employee Time & Pay Dashboard, payroll rules engineIn progress

NYC Employee Time & Pay Dashboard

Built a serverless payroll system on AWS implementing a NY State labor-law rules engine with 8+ compliance rules spanning overtime, holiday pay, and spread-of-hours across 500+ shifts. Designed a REST API with 5 Lambda-backed endpoints delivering pay-stub generation in under 2 seconds, and integrated Spark to batch-process 10,000+ historical records, cutting weekly reporting time by 60%.

PythonAWS LambdaDynamoDBAPI GatewayS3
Ongoing2026
Get in touch
prakyat02@gmail.com
Open to software engineering and machine learning roles for 2026.
© 2026 Prakyat PrakashRochester, NY