Karsan Lab Interview
Talk, Dr. Aly Karsan Lab, BC Cancer Research Institute, Canada's Michael Smith Genome Sciences Centre
Click here to see the slides presented at my interview for the Karsan Lab.
Presentations
MSc Thesis Defence: High throughput in silico discovery of antimicrobial peptides in amphibian and insect transcriptomes
Talk, MSc Thesis Committee, University of British Columbia
Click here to see the slides presented at my MSc thesis defence.
rAMPage: Rapid Antimicrobial Peptide Annotation and Gene Estimation
Poster, Intelligent Systems For Molecular Biology (ISMB)/European Conference On Computational Biology (ECCB), Virtual
Abstract: Antimicrobial peptides (AMPs) are a family of short defence proteins produced naturally by all organisms. Since AMPs do not confer resistance as easily as antibiotics, they are a potential alternative to antibiotics. Past research has shown that amphibians have the richest known AMP diversity, specifically the North American bullfrog has demonstrated potential in aiding the discovery of novel putative AMPs. Antibiotic resistance is becoming more prevalent each day, requiring agricultural practices to reduce the use of antibiotics to protect human health, animal health, and food safety. rAMPage is a scalable bioinformatics-based discovery platform for mining AMP sequences in publicly available genomic resources. RNA-seq amphibian and insect reads from the Sequence Read Archive (SRA) are used. After trimming, reads are assembled with RNA-Bloom into transcripts, filtered, and translated in silico. Then, the translated protein sequences are compared to known AMP sequences from the NCBI protein database and specific AMP databases, via homology search. These sequences are cleaved into their mature/bioactive form. Next, machine learning algorithm AMPlify, is employed to classify and prioritize the candidate AMPs based on their AMP probability score. Finally, these candidate AMPs are annotated and characterized. Across 84 datasets, rAMPage detected >1000 putative AMPs for downstream validation.
Discovering antimicrobial peptides in amphibians and insect transcriptomes
Talk, GSC Bioinformatics Weekly Seminar, Canada's Michael Smith Genome Sciences Centre
Click here to see the slides presented at the GSC Bioinformatics Weekly Seminar in 2021. This seminar doubled as an exit seminar for the Bioinformatics Graduate Program.
MSc Thesis Committee Meeting #2
Talk, MSc Thesis Committee, University of British Columbia
Click here to see the slides presented at my second committee meeting.
rAMPage: Rapid Antimicrobial Peptide Annotation and Gene Estimation
Poster, Bioinformatics | Indisciplinary Oncology | Genome Sciences and Technology (BIG) Research Day, University of British Columbia
Click here to view the poster presented at BIG Research Day 2021.
Mining Amphibian and Insect Transcriptomes for Antimicrobial Peptides
Poster, BC Cancer Research Day, BC Cancer Research Institute
Click here to view the poster presented at BC Cancer Research Day 2020.
Mining amphibian and insect transcriptomes for antimicrobial peptides
Talk, GSC Bioinformatics Weekly Seminar, Canada's Michael Smith Genome Sciences Centre
Click here to see the slides presented at the GSC Bioinformatics Weekly Seminar in 2020.
MSc Thesis Committee Meeting #1
Talk, MSc Thesis Committee, University of British Columbia
Click here to see the slides presented at my first committee meeting.
Data Visualization Lessons from Hackseq
Workshop, RLadies Vancouver, Dialpad Canada Inc.
Click here to view the Eventbrite event.