PhD candidate in Bioinformatics at UBC and BC Cancer’s Genome Sciences Centre, applying machine learning to genome assembly, nanopore signal analysis, and methylation profiling. Strong programming skills in Python and C++, with experience in developing high-performance bioinformatics tools. Passionate about computational biology, deep learning, and contributing to translational research in multidisciplinary teams.

SKILLS

Bioinformatics & Genomics — Genome Assembly, Variant Calling, Sequence Alignment, Nanopore Sequencing, Methylation Analysis, Single Cell Sequencing

Machine Learning & AI — Deep Learning, Reinforcement Learning, Signal Processing, Natural Language Processing

Programming & Development — Python, C++, Java, Django, REST APIs, Git, PostgreSQL

Visualization & Reporting — Matplotlib, Seaborn, Pandas, Plotly

EXPERIENCE

Graduate Research Assistant - BC Cancer’s Genome Sciences Centre 2021 - Present

• Member of the Bioinformatics Technology Lab (birollab.ca)
• Worked in a multidisciplinary research environment, collaborating with genomics scientists and software engineers
• Developed tools in C++ and Python for genomics analysis
• Used machine learning and deep learning for assembly polishing and nanopore signal analysis

Backend Developer and System Administrator - University of Isfahan 2018 - 2021

• Lead developer of the University of Isfahan’s Alumni Social Website
• Deployed and maintained as a Django app on a Linux server with nginx and uwsgi

Teaching Assistant - University of Isfahan 2016 - 2020

• Fundamentals of Computer Programming (C++) and Advanced Programming (Java/C++)
• Data Structures and Algorithm Design
• Artificial Intelligence (developed a game environment for evaluating final projects)
• Technical English for Computer Engineering

EDUCATION

PhD Candidate in Bioinformatics - University of British Columbia 2021 - Present

• 1 first-author publication, 4 paper collaborations

MSc in Computer Engineering (AI) - University of Isfahan 2019 - 2021

• Thesis: Deep Reinforcement Learning for Training Intelligent Agents in Natural Language Environments
• GPA: 18.42/20
• 1 first-author publication

BSc in Computer Engineering (Software) - University of Isfahan 2015 - 2019

• Thesis: Predicting Persian Twitter Users’ MBTI Personality Using Text Mining Methods
• GPA: 18.25/20 (highest in cohort)
• Attended ICPC West Asia Regionals 2016 and 2017
• Competed in Robocup IranOpen 2D Soccer Simulation League 2017
• Finalist at the National Computer Engineering Olympiad 2019

VOLUNTARY AND 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. (2024). Human ancestry inference at scale, from genomic data. bioRxiv, 2024-03.

Coombe, L., Kazemi, P., Wong, J., Birol, I., & Warren, R. L. (2024). Multi-genome synteny detection using minimizer graph mappings. bioRxiv, 2024-02.

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.org/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.org/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.org/10.1109/tfuzz.2021.3133905

PRESENTATIONS

Kazemi, P., Coombe, L., Warren, R. L., & Birol, I. (2024). AIEdit: Genome Assembly Polishing using Machine Learning and Spaced Seeds. Poster in BIG Research Day 24 (Vancouver, Canada)

Kazemi, P., Mohamadi, H., Chu, J., Coombe, L., Warren, R. L., & Birol, I. (2023). 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, Turkey)

Kazemi, P. (2020). Natural language processing: what, how, and why. Presentation at the University of Isfahan’s Annual Research Week (Esfahan, Iran)