Education

Ph.D. - University of Toronto Mississauga - 2017-present
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, Duggal JK, Ness RW. (2019) Consequences of recombination in the mating type locus of Chlamydomonas reinhardtii. bioRxiv. doi:/10.1101/565275. Available online.

Hasan AR, Ness RW (2018). The genomic landscape of recombination rate variation in Chlamydomonas reinhardtii reveals effects of linked selection. bioRxiv. doi:10.1101/340992. Available online.

Pedagogical Works

Johnston LW, Bonsma-Fisher M, Ostblom J, Hasan AR, Santangelo JS, Coome L, Tran L, Sales de Andrade E, Mahallati S. 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 A, 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 A, 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 A, 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 A, Ness RW. Recombination rate variation in Chlamydomonas reinhardtii. Graduate Research Colloquium @ University of Toronto Mississauga, Mississauga, ON; 2018
  • Hasan A, 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 A, 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 A. Research: more than just a plan B. Operation Med School Toronto/STEM Fellowship; 2017
  • Noukhovitch A, Hasan A. A new generation of data-native learners. Civic Tech Toronto; 2016. (Video)

Poster Presentations

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

Teaching

  • President, University of Toronto Coders; 2019-present.
    • Overseeing the U of T Coders council and all organization activities.
  • Instructor/Contributor, Programming workshops + code-alongs, University of Toronto Coders; 2017-present.
    • Taught and designed various coding workshops (R, Python)
  • Teaching Assistant, Bioinformatics (BIO362H5F), Department of Biology, University of Toronto Mississauga; Fall 2017, Spring 2019
    • Assisted undergraduate students in learning Python for bioinformatics; designed a lab introducing the pandas package.
    • Other packages taught: Bio.SeqIO, Bio.Phylo, re, pysam, numpy.
  • Course Coordinator/Instructor, Quantitative Methods in R for Biology (EEB313), Department of Ecology and Evolutionary Biology, University of Toronto; 2018
    • Responsible for course organization, course administration, and teaching four introductory R lectures
    • Topics taught - introductory R, dplyr, tidyr, ggplot2
  • Instructor, Data Carpentry workshops (Python), University of Toronto. Event Website; 2018
    • Topics - data analysis and visualization with matplotlib and seaborn
  • 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, 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
  • Teaching Assistant, Genomics (BIO458H5S), Department of Biology, University of Toronto Mississauga; 2018
    • Assisted graduate and undergraduate learners in navigating a Linux/Python environment for genomics analyses
    • Software taught: samtools, sickle, GATK, tophat, cufflinks, SPAdes
  • 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 assembly, variant calling, transcriptomics, and de novo assembly
  • Helper, Software Carpentry workshops (Python). Event website; 2017

Awards

  • 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
  • Conference Travel Grant, Department of Biology, University of Toronto Mississauga; 2018
    • Value: $900. 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
  • Conference Travel Grant, Department of Biology, University of Toronto Mississauga; 2017
    • Value: $250. For attendance to the Midwest Population Genetics 2017 conference, Michigan State University, East Lansing, MI

Miscellaneous

Programming languages/environments

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

Genomics software

  • GATK
  • plink
  • bwa
  • samtools
  • vcftools
  • LDhelmet
  • tophat
  • cufflinks
  • FastQC
  • Trimmomatic
  • SPAdes

Some more details regarding projects I’ve worked on are available on the About page.