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Updated as of Jan 23, 2024! :)

Basics

Name Rana A. Barghout
Label PhD student
Email rana.barghout@mail.utoronto.ca
Url https://ranaabarghout.github.io
Summary A passionate PhD student studying metabolic engineering through the lense of AI

Volunteer

  • 2023.09 - curent
    HR/Recruitment Team Member
    BridgeTO Youth
    Work on streamlining the volunteer recruitment process as well as other HR tasks revolving around programs for underrepresented & underserved youth.
  • 2023.07 - curent
    VP Info
    Graduate Society of Women Engineers
    Assisted president with administrative tasks, planned events, and built connections across Toronto revolving around entrepeneurship, charity, and other PD topics
  • 2022.07 - 2023.09
    Graduate Student Mentorship Program Coordinator
    Chemical Engineering Graduate Student Association
    Coordinated mentorship groups for incoming graduate students in the department and paired them with senior graduate students. Organized events to facilitate community building and mentorship for both undergraduate and graduate students.

Education

  • 2021.09 - current

    Toronto, ON

    PhD
    University of Toronto, St. George
    Metabolic engineering and ML
  • 2016.09 - 2021.05

    Vancouver, BC

    Bachelor of Applied Science
    University of British Columbia
    Chemical and Biological Engineering

Awards

  • 2022 & 2023
    Rein Otson Memorial Graduate Scholarship
    Department of Chemical Engineering & Applied Chemistry
    Awarded to outstanding international students in the Chemical Engineering & Applied Chemistry department on the basis of academic merit.
  • 2022.08.01
    MAX Scholarship in Science and Engineering
    MAX
    Awarded to science & engineering students in post-secondary schooling demonstrating high academic achievement and contribution.
  • 2021.03.01
    CHBE Undergraduate 3MT First Place Winner
    Department of Chemical and Biological Engineering
    Awarded to the first-place winner at the Department of Chemical and Biological Engineering's (UBC) Research Day 3-minute thesis competition.
  • 2021.03.01
    CHBE Short Research Presentation First Place Winner
    Department of Chemical and Biological Engineering
    Awarded to the first-place winner at the Department of Chemical and Biological Engineering's (UBC) Research Day short research poster presentation competition.
  • 2021.03.01
    Thomas Bennett Scholarship
    Department of Chemical and Biological Engineering
    Awarded to students demonstrating high academic achievement, leadership, and social and environmental concern in the Department of Chemical and Biological Engineering.
  • 2020.12
    UBC International Community Achievement Award
    UBC
    Awarded to students demonstrating leadership in community service, international engagement, intercultural understanding, promotion of diversity, and intellectual pursuits.
  • 2020.11
    Faculty of Applied Science International Student Scholarship
    Faculty of Applied Science, UBC
    Awarded to students demonstrating strong academic achievement, engagement in the Faculty, and the potential to make a scholarly contribution within their chosen field of study. The scholarships are made on the recommendation of the Faculty of Applied Science.
  • 2020.10
    Trek Excellence Scholarsihp for International Students
    UBC
    Awarded to top 10% of international students in the Faculty of Applied Science at UBC.

Publications

  • 2023.11.04
    Advances in Generative Modeling Methods and Datasets to Design Novel Enzymes for Renewable Chemicals & Fuels
    Current Opinion in Biotechnology
    This review paper aims to summarize the state of the art in generative models for protein design and how they can be applied to bioenergy applications, including the underlying architectures and training strategies. Additionally, it highlights the importance of high-quality datasets for training and evaluating generative models, organizes available datasets for generative protein design, and discusses the potential of applying generative models to strain design for bioenergy production.
  • 2022.10.12
    KinMod database: a tool for investigating metabolic regulation
    Database
    In this paper, we introduce the KinMod database that encompasses more than 2 million data points on the metabolism and metabolic regulation network of 9814 organisms KinMod database employs a hierarchical data structure to: (i) signify relationships between kinetic information obtained through in-vitro experiments and proteins, with an emphasis on SMRN, (ii) provide a thorough insight into available kinetic parameters and missing experimental measurements of this regulatory network and (iii) facilitate machine learning approaches for parameter estimation and accurate kinetic model construction by providing a homogeneous list of linked omics data.
  • 2020.08.16
    Foundations of Chemical and Biological Engineering I
    Pressbooks -BCcampus
    This open-source textbook was published as a resource for early career engineering students to learn foundational topics pertaining to chemical and biological engineering.

Skills

Deep learning - Pytorch/Tensorflow
In-silico protein engineering
Protein language models
Molecule encoding
Protein property prediction
Compound-protein interactions
Computational Biology - Python
Strain engineering
Genome-scale modeling
Genome-scale biological optimization
Sequence alignment

Languages

English
Fluent
Arabic
Fluent

Interests

Computational Biology
Protein Engineering
Strain Engineering
Deep Learning
Protein Language Models
Generative Models

Projects

  • 2022.01 - ongoing
    Deep Learning for Genome-scale Models
    Deep learning has proven to be a powerful tool for extracting and learning information from large datasets. In my work, we leverage deep learning to fill gaps in genome-scale models, make them more representative, and apply new methods to strain design.
    • Genome scale models (GEMs)
    • Compound-protein interaction prediction
    • Strain Design