CORE SKILLS

Software Engineering: Agile/Scrum, Clean Code, CI/CD & DevOps, Docker, Unit Testing, Git, Documentation

High-Performance Computing: C++, Parallelism, SIMD/Vectorization, Memory Optimization, Performance Profiling

Backend & System Design: Django, REST APIs, Microservices, Distributed Systems, SQL, NoSQL, SysAdmin

AI & Data Engineering: Deep Learning (PyTorch, libtorch), NLP, Signal Processing, pybind11, Terabyte-scale

Bioinformatics: DNA Sequence Analysis, Genome Assembly, Nanopore Signal, Algorithm Design

EXPERIENCE

Graduate Research Assistant

BC Cancer Research Institute 2021 - Present

• Intellectual Property: Filed a provisional patent for thesis-derived technology (2026).
• Software Engineering: Lead developer for open-source projects; implemented pybind11 interfaces and CI/CD and published on Bioconda.
• High-Performance Computing: Optimized C++ libraries (ntHash2, ntStat) for 100GB-scale genomic datasets. Focused on parallelism and custom memory management to maximize throughput.
• Machine Learning: Developed AIEdit, an ML-based genome assembly polisher. Managed the full engineering lifecycle from PyTorch modeling to high-performance libtorch/C++ deployment.
• Deep Learning: Utilized Transformers to analyze and basecall terabyte-scale raw nanopore signal data; orchestrated large-scale training and inference workloads using SLURM on high-performance clusters.
• Applied Research & Development: Authored and reviewed high-impact research in Bioinformatics and PLOS CB; presented at international venues.

Backend Developer and System Administrator

University of Isfahan 2018 - 2021

• Backend Development: Engineered a Django-based Alumni Social platform; integrated legacy university systems to automate real-time data synchronization and alumni profile provisioning. Implemented a verification engine that cross-referenced credentials against institutional records to enable instant, automated social network registration.
• Database design: Managed PostgreSQL relational models for the university-wide alumni database, optimizing schemas for high-concurrency retrieval and data integrity.
• Infrastructure: Administered the full production stack on Linux (Nginx/uWSGI) to maintain high availability for the institution’s core networking platform

Teaching Assistant

University of Isfahan 2016 - 2020

• Technical mentorship: Taught Advanced Programming in Java and C++, focusing on Object-Oriented Design (OOD), data structures, and algorithm efficiency
• AI & Automation: Developed a custom game environment to provide a standardized, automated platform for testing and grading student AI project submissions.

EDUCATION

PhD in Bioinformatics - University of British Columbia 2021 - 2026

• Focus: High-performance software for genomic sequence analysis and Oxford Nanopore signal data.

MSc in Computer Engineering - University of Isfahan 2019 - 2021

• Thesis: Deep Reinforcement Learning for Training Intelligent Agents in Natural Language Environments
• GPA: 18.42/20 (highest in cohort)

BSc in Computer Engineering - University of Isfahan 2015 - 2019

• Thesis: Predicting Persian Twitter Users’ MBTI Personality Using Text Mining Methods
• GPA: 18.25/20 (highest in cohort)

HONOURS AND AWARDS

• Finalist: National Computer Engineering Olympiad (2019)
• Competitive Programming: ACM-ICPC West Asia Regional Contest participant (2016, 2017)
• Robotics: Robocup IranOpen 2D Soccer Simulation League competitor (2017)

VOLUNTARY & EXTRACURRICULAR WORK

Student Mentor - Undergraduate Research Opportunities (UBC URO) 2024 - 2025

• Mentored 5 students from computer science, biochemistry, and medical school backgrounds
• Supervised a mini-review project on nanopore sequencing and its applications in understanding cancer therapy resistance

Conference Adjudicator - Multidisciplinary Undergraduate Research Conference (UBC MURC) 2024

• Reviewed and adjudicated undergraduate posters related to bioinformatics and genome sequencing

Volunteer Organizer - Vancouver Bioinformatics User Group (vanbug.org) 2023 - 2024

• Responsible for promoting monthly bioinformatics seminars by local and international speakers

ACM Students Chapter Member - University of Isfahan 2017 - 2019

• Coached 2 university teams at ICPC West Asia Regionals 2020
• Instructed Python and Django courses
• Assisted in technical setup for high school and undergraduate programming contests and AI challenges

PUBLICATIONS

• Warren, R. L., Coombe, L., Wong, J., Kazemi, P., & Birol, I. (2025). ntRoot: computational inference of human ancestry at scale from genomic data. Bioinformatics Advances, vbaf287. doi:10.1093/bioadv/vbaf287

• Coombe, L., Kazemi, P., Wong, J., Birol, I., & Warren, R. L. (2025). ntSynt: multi-genome synteny detection using minimizer graph mappings. BMC biology, 23(1), 367. doi:10.1186/s12915-025-02455-w

• Wong, J., Kazemi, P., Coombe, L., Warren, R. L., & Birol, I. (11 2023). aaHash: recursive amino acid sequence hashing. Bioinformatics Advances, vbad162. doi:10.1093/bioadv/vbad162

• Nikolić, V., Kazemi, P., Coombe, L., Wong, J., Afshinfard, A., Chu, J., Warren, R. L., & Birol, I. (2022). btllib: A C++ library with Python interface for efficient genomic sequence processing. Journal of Open Source Software, 7(79), 4720. doi:10.21105/joss.04720

• Kazemi, P., Wong, J., Nikolić, V., Mohamadi, H., Warren, R. L., & Birol, I. (2022). ntHash2: recursive spaced seed hashing for nucleotide sequences. Bioinformatics, 38(20), 4812–4813. doi:10.1093/bioinformatics/btac564

• Kazemi, P., & Karshenas, H. (2021). Fuzzy Word Sense Induction and Disambiguation. IEEE Transactions on Fuzzy Systems, 30(9), 3918–3927. doi:10.1109/tfuzz.2021.3133905

PRESENTATIONS & TALKS

• Modelling k-mer profiles of sequencing data with evolutionary algorithms (Vancouver Bioinformatics User Group, 2025)

• AIEdit: Genome Assembly Polishing using Machine Learning and Spaced Seeds (Poster in BIG Research Day 2024, UBC)

• ntHits: streaming through raw sequencing data to profile and filter k-mers with selected multiplicities (Poster in the 13th RECOMB Satellite Conference on Biological Sequence Analysis, Istanbul, 2023)

• Not so artificial intelligence (TEDx University Of Isfahan, 2021)

• Natural language processing: what, how, and why (Presentation at the University of Isfahan’s Research Week, 2020)