Kevin Shen

Kevin Shen

University of Waterloo

Researcher, Project Co-lead

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ScienceReview92
Published on Dec 28, 2024

Status update (December 2024)

The following is a status update of the project as of December 2024. The project officially started in spring 2024 after we received enough funding and is still ongoing. This lab note is a rough su...

Group 6 Copy 20
Published on Oct 31, 2023

Bioinformatics Plan

This lab note will elaborate in detail the bioinformatics portion of our project and how it will help us with our goals. We are flexible on the configurations/software/tools we use and will most li...

Group 6 Copy 101
Published on Oct 25, 2023

Climate Impact Justification

Details for additional info points 2 and 3 from the Problem Statement.Point #2Step 1: Total carbon emissions from fisheries and aquacultureCarbon emissions will mainly come from two sources - fishe...

Group 6 Copy 50
Published on Oct 16, 2023

Bioinformatics Plan

This lab note will elaborate in detail the bioinformatics portion of our project and how it will help us with our goals. We are flexible on the configurations/software/tools we use and will most li...

Group 6 Copy 180
Published on Oct 16, 2023

Project Budget (Detailed)

Detailed Project BudgetAll monetary values are by default in CAD unless stated otherwise. Stage 1 - Cell CulturingKillifish Growth MediumBase medium taken from: https://doi.org/10.1016/j.cbpa.2014....

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Published on Oct 25, 2023

Solution Statement

GoalsOne of our advisors, Tobias Messmer, has executed the only related work (https://doi.org/10.26481/dis.20230421tm) we could find, in bovine satellite cells. Our project is inspired by his proje...

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ScienceReview92
Group 6 Copy 124
Reply to:Erin WilsonErin Wilson
They are related because of scATAC-seq. Please feel free to refer to the comment in the solution statement.
Nov 14, 2023
Project: Cultivated Seafood: Single-Cell Multiomic Analysis of Killifish for...
Reply to:Erin WilsonErin Wilson
It would be more of the latter - identifying functions/processes of cell types. The clustering of cell types could be done without GO terms, so we won’t need to feed these GO terms back into cell type classification, though they can serve as a useful sanity check in that analysis! The GO term fun...more
Nov 14, 2023
Project: Cultivated Seafood: Single-Cell Multiomic Analysis of Killifish for...
Reply to:Erin WilsonErin Wilson
Feel free to check the reply in the solution statement for the answer to this question.
Nov 14, 2023
Project: Cultivated Seafood: Single-Cell Multiomic Analysis of Killifish for...
Reply to:Erin WilsonErin Wilson
We think so too! The scGPT model we found was trained on a combined/integrated dataset of 33 million human cells. The only two existing papers we have found that have generated single cell data in a cultivated meat context total ~50k cells (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE21...more
Nov 14, 2023
Project: Cultivated Seafood: Single-Cell Multiomic Analysis of Killifish for...
Reply to:Breanna DuffyBreanna Duffy
Yup! There are reference genomes available for our next three species. 1) Cyprinus carpio (Common Carp): https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_018340385.1/ Killifish is similar to carp, and as such carp is the species we expect to gain the most translatable insights from through our in...more
Nov 14, 2023
Project: Cultivated Seafood: Single-Cell Multiomic Analysis of Killifish for...