Parham Kazemi

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PARHAM KAZEMI

pkazemi3@gmail.com parham-k.github.io github.com/parham-k linkedin.com/in/p-kazemi

PhD Candidate in Bioinformatics at UBC and Canada’s Michael Smith Genome Sciences Centre with expertise in high-performance software development and deep learning (C++/Python). Specialized in creating tools for genomic sequence analysis and analyzing Oxford Nanopore signal data.

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 & 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.org/10.1093/bioadv/vbaf287

  • 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.org/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 & 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)