Ahmed Hasan
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CV


Education

  • Ph.D. - University of Toronto Mississauga - 2017-2022

    • Computational & Evolutionary Genomics - Dept. of Cell and Systems Biology
    • Supervisor: Prof. Rob Ness

  • B.Sc. (Hons.) - University of Toronto - 2012-2016

    • Majors in Human Biology, Cell & Systems Biology
    • Thesis: Study of the endophytic bacterial and fungal communities inhabiting coconut palms infected by lethal yellowing-like phytoplasmas in Côte d’Ivoire.
    • Supervisors: Prof. Keiko Yoshioka & Dr. Yaima Arocha Rosete

Publications

Graduate Research

Hasan AR*, Lachapelle J*, El-Shawa SA, Potjewyd R, Ford SA, Ness RW (2022). Salt stress alters the spectrum of de novo mutation available to selection during experimental adaptation of Chlamydomonas reinhardtii. Evolution. doi:10.1111/evo.14604 Available online. (Preprint)

Craig RJ, Hasan AR, Ness RW, Keightley PD (2021). Comparative genomics of Chlamydomonas. The Plant Cell. 33(4), 1016-1041. doi:10.1093/plcell/koab026 Available online.

Hasan AR, Ness RW (2020). Recombination rate variation and infrequent sex influence genetic diversity in Chlamydomonas reinhardtii. Genome Biology and Evolution. 12(4), 370-380. doi:10.1093/gbe/evaa057. Available online. (Preprint)

Hasan AR, Duggal JK, Ness RW. (2019) Consequences of recombination for the evolution of the mating type locus in Chlamydomonas reinhardtii. New Phytologist. 224(3), 1339-1348. doi:10.1111/nph.16003. Available online. (Preprint)

Pedagogical Works

Johnston LW, Bonsma-Fisher M, Ostblom J, Hasan AR, Santangelo JS, Coome L, Tran L, Sales de Andrade E, Mahallati S. (2019) A graduate student-led participatory live-coding quantitative methods course in R: Experiences on initiating, developing, and teaching. Journal of Open Source Education. 2(16), 49. doi:10.21105/jose.00049. Available online.

Bonsma-Fisher M, Hasan AR (2018). Working with plant phenology data and fitting a nonlinear model using least squares in R. NEON Faculty Mentoring Network, QUBES Educational Resources. doi:10.25334/Q4Q73D. Available online.

Undergraduate Research

Morales-Lizcano NP, Hasan AR, To H, Lekadou TT, Copeland J, Wang PW, Diallo HA, Konan Konan JL, Yoshioka K, Moeder W, Scott J, Arocha Rosete Y (2017). Microbial diversity in leaves, trunk and rhizosphere of coconut palms (Cocos nucifera L.) associated with the coconut lethal yellowing phytoplasma in Grand-Lahou, Côte d’Ivoire. African Journal of Biotechnology. 16(27), 1534-1550. doi:10.5897/AJB2017.16006. Available online.

Arocha Rosete Y, Morales-Lizcano NP, Hasan AR, Yoshioka K, Moeder W, Michelutti R, Satta E, Bertaccini A, Scott J (2016). First report of the identification of a ‘Candidatus Phytoplasma pruni’-related strain in Trillium species in Canada. New Disease Reports, 34, 19. doi:10.5197/j.2044-0588.2016.034.019. Available online.

Oral Presentations

  • Hasan AR. How and why does recombination vary? UTM Biology Seminar Series, Department of Biology @ University of Toronto Mississauga, Mississauga, ON; 2022
  • Hasan AR*, Lachapelle J*, El-Shawa SA, Potjewyd R, Ford SA, Ness RW. Salt stress alters the spectrum of de novo mutation available to selection during experimental adaptation of Chlamydomonas reinhardtii. ASN Vice Presidential Symposium, Evolution 2022 @ Cleveland, OH, United States; 2022
  • Hasan AR, Craig RJ, Duggal JK, Keightley PD, Ness RW. Consequences of recombination for the evolution of the mating type locus in Chlamydomonas reinhardtii. Invited talk @ Botany 2020 Virtual Conference; 2020***
  • Hasan AR, Duggal JK, Ness RW. Consequences of recombination for the evolution of the mating type locus in Chlamydomonas reinhardtii. Evolution 2019 @ Providence, RI, United States; 2019
  • Hasan AR, Ness RW. Genomic correlates of recombination rate variation in Chlamydomonas reinhardtii. CSB Research Day, Dept of Cell and Systems Biology @ University of Toronto, Toronto, ON; 2018. Awarded Best Oral Presentation.
  • Hasan AR, Ness RW. Recombination rate variation in Chlamydomonas reinhardtii. Graduate Research Colloquium @ University of Toronto Mississauga, Mississauga, ON; 2018
  • Hasan AR, Ness RW. The landscape of recombination rate variation in Chlamydomonas reinhardtii. Dept of Cell and Systems Biology Seminar Series @ University of Toronto, Toronto, ON; 2017
  • Hasan AR, Ness RW. Recombination rate variation and leaky organelle inheritance in Chlamydomonas reinhardtii. Midwest PopGen 2017 @ Michigan State University, East Lansing, MI; 2017
  • Chan SSW, Hasan AR. Research: more than just a plan B. Operation Med School Toronto/STEM Fellowship; 2017
  • Noukhovitch A, Hasan AR. A new generation of data-native learners. Civic Tech Toronto; 2016. (Video)

*** Conference originally to be held in Anchorage, AK, but held virtually due to COVID-19 outbreak

Poster Presentations

  • Hasan AR, Ness RW. Recombination rate variation and infrequent sex influence genetic diversity in Chlamydomonas reinhardtii. SMBE 2020 @ Quebec City, QC, Canada; 2020***

  • Hasan AR, Duggal JK, Ness RW. Consequences of recombination for the evolution of the mating type locus in Chlamydomonas reinhardtii. SMBE 2020 @ Quebec City, QC, Canada; 2020***

  • Hasan AR, Ness RW. Recombination rate variation and linked selection in the Chlamydomonas reinhardtii genome. Joint Congress on Evolutionary Biology II @ Montpellier, France; 2018.

*** Abstract accepted, but conference cancelled due to COVID-19 outbreak

Software Packages

Liu J, Hasan AR, Ness RW. readcomb - fast detection of recombinant reads in BAM files. Currently in development: GitHub repo

Johnston LW, Ostblom J, Hasan AR. ROStools: Reproducible and open science toolkit. Currently in development: GitLab repo

Teaching, Mentoring, and Course Development

Course instructorships

  • Course Instructor, Quantitative Methods in R for Biology (EEB313), Department of Ecology and Evolutionary Biology, University of Toronto; 2018-2019
    • Responsible for teaching first quarter of course, grading relevant assignments, and assisting students with projects
    • Developed and taught module on Reproducible science with Git and GitHub
    • (2018) Responsible for course organization and course administration
    • Topics taught - introductory R, dplyr, tidyr, ggplot2, Git/GitHub

Teaching assistantships

  • Teaching Assistant, Bioinformatics (BIO362H5F), Department of Biology, University of Toronto Mississauga; Fall 2017, Spring 2019, Fall 2019 (marking only), Spring 2021
    • Assisted undergraduate students in learning Python for bioinformatics; graded labs; designed a lab introducing the pandas package.
    • Other packages taught: Bio.SeqIO, Bio.Phylo, re, pysam, numpy.
  • Teaching Assistant, Advanced Genetics (BIO341H1F), Department of Biology, University of Toronto Mississauga; Fall 2020
    • Ran weekly tutorials and assignments; graded term tests
  • Teaching Assistant, Genomics (BIO458H5S), Department of Biology, University of Toronto Mississauga; Spring 2018
    • Assisted graduate and undergraduate learners in navigating a Linux/Python environment for genomics analyses
    • Software taught: samtools, sickle, GATK, tophat, cufflinks, SPAdes

Course development

  • Quantitative Curriculum/Course Developer, Department of Biology, University of Toronto Mississauga; 2020
    • Designing introductory R material for first year labs at the University of Toronto Mississauga, as part of broader initiative to introduce quantitative and computational literacy skills into Biology’s undergraduate program
  • Course Developer, Genomics (BIO458H5S), Department of Biology, University of Toronto Mississauga; 2017
    • Designed course labs in JupyterHub environment alongside course instructor; topics included reference-based alignment, variant calling, transcriptomics, and de novo assembly

External teaching

  • President, University of Toronto Coders; 2019-present.
    • Overseeing the U of T Coders council and all organization activities.
    • Helped initiate a peer mentorship program (2020)
  • Instructor, Getting Started with Python, UTM Graduate Professional Development Conference; 2021
    • In association with the Robert Gillespie Academic Skills Centre, invited to develop and run a two-day workshop introducing graduate students to Python
    • Developed novel curriculum that focused on understanding Python library architecture so that researchers could more quickly incorporate field-specific libraries into their work (workshop material repo)
  • Co-instructor, Introduction to R and Graphics for Biology, International Exchange Program in Developmental and Perinatal Biology, University of Toronto Dept. of Physiology + Karolinska Institute; 2018
    • Topics - Introduction to R, plotting, compiling R markdown files, dplyr
  • Instructor/Contributor, Programming workshops + code-alongs, University of Toronto Coders; 2017-present.
    • Taught and designed various coding workshops (R, Python)
  • Helper, Software Carpentry workshops (Python). Event website; 2017

Workshops taught with the Carpentries

  • Instructor, Software Carpentry workshops (Python), University of Toronto. Event Website; 2020
    • Workshop taught in affiliation with U of T Libraries
    • Topics - The Unix Shell
  • Instructor, Data Carpentry workshops (R), University of Toronto. Event Website; 2020
    • Workshop taught in affiliation with U of T Libraries
    • Topics - data analysis and visualization with R using dplyr and ggplot2
  • Instructor, Data Carpentry workshops (Python), University of Toronto. Event Website; 2018
    • Topics - data analysis and visualization with matplotlib and seaborn
  • Instructor, Data Carpentry workshops (Genomics), Centre for Addiction and Mental Health (CAMH) Toronto. Event Website; 2018
    • Taught the Data Wrangling in Genomics session in a two-day workshop for researchers both at CAMH and around the GTA.
    • Topics - quality control of sequencing reads, FastQC, read trimming with trimmomatic, alignment with bwa, variant calling
  • Instructor, Software Carpentry workshops (R), University of Toronto. Event website; 2018
    • Taught the second R session in a two-day workshop for researchers and students at the University of Toronto.
    • Topics - loops, vectorization, dplyr, ggplot2

Mentoring

  • Jimmy Liu and Gabriel El-Haddad (2020). Detecting signatures of recombination in pooled next-generation sequencing reads.
  • Eniolaye Balogun (2018-2019). Is recombination mutagenic? Scanning for mutations in next-generation sequence data.

Awards

  • Roberta Bondar Graduate Student Excellence Award; Department of Biology, University of Toronto Mississauga; 2022
    • Value: $1,250. Award given on the basis of outstanding research excellence and positive contributions to extracurricular activities that enhance community life at UTM.
  • Black, Indigenous, and Racialized Graduate Research Fellowship; University of Toronto Mississauga; 2022
    • Value: $8,000.
  • NSERC Postgraduate Scholarship, Doctoral; Federal Award; 2021
    • Value: $63,000 over three years.
  • Ontario Graduate Scholarship; Provincial Award; 2020
    • Value: $15,000.
  • Duncan L. Gellatly Memorial Fellowship, Department of Cell and Systems Biology, University of Toronto; 2020
    • Value: $1,500. Award given on the basis of excellence in molecular biology research
  • Rustom H. Dastur Graduate Scholarship, Department of Cell and Systems Biology, University of Toronto; 2018
    • Value: $17,350. Award for graduate students in plant biology who successfully transfer into a PhD program, based on academic merit
  • Conference Travel Grant, School of Graduate Studies, University of Toronto; 2018
    • Value: $840. For attendance to the Joint Congress on Evolutionary Biology II, Montpellier, France
  • Best Oral Presentation, CSB Research Day 2018, Department of Cell and Systems Biology, University of Toronto; 2018
    • Value: $120.
  • Elizabeth Ann Wintercorbyn Award, Department of Cell and Systems Biology, University of Toronto; 2017
    • Value: $500. Research excellence award for a student in the department engaged in work with potential benefits for agriculture

Miscellaneous

Services

  • Vice-President, UTM Biology Graduate Student Society (2020-2021)
  • Co-President, UTM Biology Graduate Student Society (2019-2020)
  • Seminar Committee, UTM Biology (2019-2020)
  • Microbiology Faculty Search Graduate Student Representative, UTM Biology (2019-2020)
  • Secretary, University of Toronto Mississauga Association of Graduate Students (2018-2019)
  • UTM Representative, Cell and Systems Biology Graduate Union (2018-2019)
  • CSB Representative, UTM Biology Graduate Student Society (2018-2019)
  • Secretary, UTM Biology Graduate Student Society (2017-2018)

Programming languages/environments

  • Python
  • R (incl. tidyverse packages)
  • Bash/Unix shell
  • Jupyter (Notebook/Lab/Hub/nbgrader)
  • LaTeX
  • Git
  • JavaScript (familiarity)
  • ReactJS (familiarity)

More details regarding projects I’ve worked on are available on the Projects page.