CV

Education

• M.Sc. in Bioinformatics, University of British Columbia, 2021
  • British Columbia Graduate Scholarship: $15,000
• B.Sc. in Physiology, McGill University, 2014
  • J. W. McConnell Scholarship: $3,000

Research Experience

• 2022 - Present: Research Programmer - Data Scientist
  • Canada’s Michael Smith Genome Sciences Centre
  • BC Cancer Resarch Institute
  • Supervisor: Dr. Joshua Bridgers
  • Principal Investigator: Dr. Aly Karsan
• 2019 - 2021: Graduate Student
  • University of British Columbia
  • Supervisor: Dr. Inanc Birol
  • Principal Investigator: Dr. Inanc Birol
• 2018 - 2019: Student Intern
  • Canada’s Michael Smith Genome Sciences Centre
  • Supervisor: René Warren
  • Principal Investigator: Dr. Inanc Birol

Publications

Mining the UniProtKB/Swiss-Prot database for antimicrobial peptides

Li, C., Sutherland, D., Salehi, A., Richter, A., Lin, D., Aninta, S.I., Ebrahimikondori, H., Yanai, A., Coombe, L., Warren, R.L., Kotkoff, M., Hoang, L.M.N., Helbing, C.C., & Birol, I. (2025). "Mining the UniProtKB/Swiss-Prot database for antimicrobial peptides." Protein Science 34(4):e70083.

Associating Biological Activity and Predicted Structure of Antimicrobial Peptides from Amphibians and Insects

Richter, A., Sutherland, D., Ebrahimikondori, H., Babock, A., Louie, N., Li, C., Coombe, L., Lin, D., Warren, R.L., Yanai, A., Kotkoff, M., Helbing, C.C., Hof, F., Hoang, L.M.N., & Birol, I. (2022). "Associating Biological Activity and Predicted Structure of Antimicrobial Peptides from Amphibians and Insects." Antibiotics 11(12):1710.

Mining Amphibian and Insect Transcriptomes for Antimicrobial Peptide Sequences with rAMPage

Lin, D., Sutherland, D., Aninta, S.I., Louie, N., Nip, K.M., Li, C., Yanai, A., Coombe, L., Warren, R.L., Helbing, C.C., Hoang, L.M.N., & Birol, I. (2022). "Mining Amphibian and Insect Transcriptomes for Antimicrobial Peptide Sequences with rAMPage." Antibiotics 11(7):952.

The genome of the forest insect pest Pissodes strobi reveals genome expansion and evidence of a Wolbachia endosymbiont

Gagalova, K. K., Whitehill, J. G. A., Culibrk, L., Lin, D., Levesque-Tremblay, V., Keeling, C. I., Coombe, L., Birol, I., Bohlmann, J., Jones, S. J. M. (2022). "The genome of the forest insect pest Pissodes strobi reveals genome expansion and evidence of a Wolbachia endosymbiont." G3 Genes|Genomes|Genetics, jkac038.

Pissodes strobi mitochondrion, partial genome

Lin, D., Coombe, L., Jackman, S. D., & Birol, I. (2021). "Pissodes strobi mitochondrion, partial genome." NCBI GenBank.

High throughput in silico discovery of antimicrobial peptides in amphibian and insect transcriptomes

Lin, D. (2021). "High throughput in silico discovery of antimicrobial peptides in amphibian and insect transcriptomes." University of British Columbia.

Complete Chloroplast Genome Sequence of a Black Spruce (Picea mariana) from Eastern Canada

Lo, T., Coombe, L., Lin, D., Warren, R. L., Kirk, H., Pandoh, P., Zhao, Y., Moore, R. A., Mungall, A. J., Ritland, C., Bousquet, J., Jones, S. J. M., Bohlmann, J., Thomson, A., & Birol, I. (2020). "Complete Chloroplast Genome Sequence of a Black Spruce (Picea mariana) from Eastern Canada." Microbiology Resource Announcements, 9(39).

Picea mariana isolate 40-10-1 chloroplast, complete genome

Lo, T., Coombe, L., Lin, D., Warren, R. L., & Birol, I. (2020). "Picea mariana isolate 40-10-1 chloroplast, complete genome." NCBI GenBank.

Genome Skimming

Lin, D. & Khan, A. (2020). "Genome skimming." Wikipedia, The Free Encyclopedia.

Complete Chloroplast Genome Sequence of an Engelmann Spruce (Picea engelmannii, Genotype Se404-851) from Western Canada

Lin, D., Coombe, L., Jackman, S. D., Gagalova, K. K., Warren, R. L., Hammond, S. A., McDonald, H., Kirk, H., Pandoh, P., Zhao, Y., Moore, R. A., Mungall, A. J., Ritland, C., Doerksen, T., Jaquish, B., Bousquet, J., Jones, S. J. M., Bohlmann, J., & Birol, I. (2019). "Complete Chloroplast Genome Sequence of an Engelmann Spruce (Picea engelmannii, Genotype Se404-851) from Western Canada." Microbiology Resource Announcements, 8(24).

Complete Chloroplast Genome Sequence of a White Spruce (Picea glauca, Genotype WS77111) from Eastern Canada

Lin, D., Coombe, L., Jackman, S. D., Gagalova, K. K., Warren, R. L., Hammond, S. A., Kirk, H., Pandoh, P., Zhao, Y., Moore, R. A., Mungall, A. J., Ritland, C., Jaquish, B., Isabel, N., Bousquet, J., Jones, S. J. M., Bohlmann, J., & Birol, I. (2019). "Complete Chloroplast Genome Sequence of a White Spruce (Picea glauca, Genotype WS77111) from Eastern Canada." Microbiology Resource Announcements, 8(23).

Picea glauca isolate WS77111 chloroplast, complete genome

Coombe, L., Lin, D., Warren, R. L., Jackman, S. D., & Birol, I. (2019). "Picea glauca isolate WS77111 chloroplast, complete genome." NCBI GenBank.

Picea engelmannii isolate Se404-851 chloroplast, complete genome

Lin, D., Coombe, L., Warren, R. L., Jackman, S. D., & Birol, I. (2019). "Picea engelmannii isolate Se404-851 chloroplast, complete genome." NCBI GenBank.

Presentations

Karsan Lab Interview

MSc Thesis Defence: High throughput in silico discovery of antimicrobial peptides in amphibian and insect transcriptomes

rAMPage: Rapid Antimicrobial Peptide Annotation and Gene Estimation

Discovering antimicrobial peptides in amphibians and insect transcriptomes

MSc Thesis Committee Meeting #2

rAMPage: Rapid Antimicrobial Peptide Annotation and Gene Estimation

Mining Amphibian and Insect Transcriptomes for Antimicrobial Peptides

Mining amphibian and insect transcriptomes for antimicrobial peptides

MSc Thesis Committee Meeting #1

Data Visualization Lessons from Hackseq

Teaching

STAT545B: Exploratory Data Analysis II

STAT545A: Exploratory Data Analysis I

Mentorship

• 2022 - 2024: Co-op Supervisor
  • Dr. Aly Karsan Lab
  • University of British Columbia
• 2019 - 2021: Bioinformatics Mentor
  • Bioinformatics Graduate Program
  • Univeristy of British Columbia
• 2017 - 2018: Synapse Mentor
  • Physiology Undergraduate League of Students (PULS)
  • McGill University
• 2015 - 2018: Student Ambassador
  • Campus Life & Engagement
  • McGill University

Skills

• De novo genome assembly and annotation
• De novo transcriptome assembly and annotation
• Next-generation sequencing technology pipeline development and sequence analysis workflows inlucding but not limited to:
  • scATAC-seq (single cell chromatic accessibility)
  • scRNA-seq (single cell gene expression)
  • CITE-seq (single cell gene expression and surface proteine xpression)
  • DOGMA-seq (single cell chromatin accessibility, gene expression, surface protein expression, and mitochondrial genomic capture
  • scWGBS (single cell whole genome bisulfite sequencing)
• Phylogenetic tree construction
• Differential expression analysis of RNA-seq data
• Familiarity with the Unix environment and command-line tools
• Familiarity with workflow languages:
  • snakemake
  • Nextflow
  • make
• Familiarity with high performance computing clusters and job schedulers:
  • SLURM
• Experience in programming (in order of decreasing familiarity):
  • R
  • Shell (bash)
  • Python
  • Java
  • C
  • C++

Service

• Present: Social Committee Member
  • Dr. Aly Karsan Lab
• 2023: Team Mentor
  • Vancouver DataJam 2023
• 2021: Webmaster & Social Media Coordinator
  • BC Cancer Graduate Student and Postdoctoral Fellow Society (GrasPods)
• 2020 - 2021: Seminar Organizer
  • Bioinformatics Technology Lab
• 2020 - 2021: Social Committee Leader
  • Bioinformatics Technology Lab
• 2019 - 2020: Workshop Leader
  • Geneskool, Genome BC
• 2017 - 2018: Computer Director
  • Physiology Undergraduate League of Students (PULS)
  • McGill University
• 2015 - 2018: Webmaster
  • World Vision Student Committee