Garth Kong
Bioinformatic Scientist
Email: kongga2017@gmail.com
Website: http://gartician.github.io
Linkedin: http://linkedin.com/garth-kong
Bioinformatic Skills
| Proficient Languages | Proficient with | Familiar with | Experience in |
|---|---|---|---|
| Bash Python R |
Snake Make Anaconda TIdyverse ggplot2 + plotly Pandas |
Seurat SLURM Jupyter RShiny + Dash GNU Parallel |
ATAC-Seq ChIP-Seq CITE-Seq CUT&TAG RNA/DNA-Seq |
Education
Master in Bioinformatics and Genomics
University of Oregon, Jun 2018 - Dec 2019
H. Bachelor in Biochemistry and Biophysics
Oregon State University, Oct 2013 - Apr 2018
Minor in Chemistry
Work
Computational Biologist | Jun 2019 - Present
Dr. Julia Maxson Lab
- Provide generic and project-specific analyses to 5 bench scientists to drive projects forward.
- Develop, re-purpose, maintain, and test pipelines to analyze sequencing data like ATAC-Seq, ChIP-Seq, CITE-Seq, CUT&TAG, and RNA-Seq.
- Modify, adapt, and improve open-source bioinformatics tools to fit project objectives.
- Write the bioinformatic analysis methods for 2 upcoming papers and 2 conference papers.
Graduate Researcher | Apr 2019 - Apr 2020
Dr. Rohner Lab
- Refined an analysis pipeline to identify genetic variants that leads to phenotypic differences in mexican cavefish Astyanax Mexicanus using bash, python, R, and GATK (40+ samples, 3 conditions, > 500 FASTQ files).
- Discovered 2+ genetic variants (SNPs and indels) in blind, eye-less cavefish Astyanax Mexicanus that leads to abnormal lens development.
- Frequently tailored complex concepts of variant-calling algorithms to an interdisciplinary team of 3 scientists; drafted the computational section for the upcoming manuscript.
Dr. Alvarado Sanchez
- Developed a pipeline using bash, python, and R, to quantify transcript levels in RNA-Seq dataset (7 time points, 4 replicates, 2 conditions).
- Results were packaged into an R Shiny app for 10+ lab members to view gene expression over time and condition.
Graduate Student Researcher | Oct 2018 - Apr 2019
Dr. Karen Guillemin Lab
- Developed an analysis pipeline using Seurat to process single-cell RNA-Seq data (40K cells, 2 conditions) in R.
- Investigated single-cell transcriptomic differences in zebrafish raised in either germ-free (sterile) or conventional (with bacteria) environments to infer the effects of the microbiota on host development.
- Discovered a family of 50+ genes that may be involved in abnormal development in germ-free fish.
General Chemistry Lab TA | Sept 2018 – Dec 2018
Taught two sections of General Chemistry lab (30 total students) at University of Oregon, helped students one-on-one during office hours, and resolved grading conflicts with students and head professors.
Waiter | Oct 2018 – Jun 2019
Worked in a team at Thai Chili to help serve customers in the storefront, reported daily revenue, trained 5 employees, and frequently communicated with 70+ customers per shift.
TRiO Tutor | 2014 – 2018
As a TRiO tutor at Oregon State University, I participated in team-building activities between tutors, assessed teaching performance with an advisor 2 times per term, and tutored 20+ students in math and science classes throughout my three years of experience. Classes I’ve tutored included general biology and chemistry, algebra to vector calculus, and scientific writing.
Programming Projects
Publications
- Olson B, Zhu X, Norgard MA, Diba P, Levasseur PR, Buenafe AC, Huisman C, Burfeind KG, Michaelis KA, Kong G, Braun T, Marks DL. Chronic cerebral lipocalin 2 exposure elicits hippocampal neuronal dysfunction and cognitive impairment. Brain Behav Immun. 2021 Jul 8:S0889-1591(21)00266-X. doi: 10.1016/j.bbi.2021.07.002. Epub ahead of print. PMID: 34245812.
Volunteer
Computational biology mentor | Apr 2020 – Sep 2020
- Lead a team of 2 high school and 1 undergraduate students to detect genetic mutations in Acinetobacter baumannii that may confer antibiotic resistance to the drug rifabutin.
- Consistent communication and incorporation of feedback with program manager to adjust program timeline and material.
- Lead weekly student-mentor meetings to go over project progress and research direction.
Accolades
- SURE Summer Research Grants
- McDonald Dunn Scholarship
- Wei Family Foundation Scholarship
- OSU Honors College Grandma Honors Scholarship
- Knowledge Advancement Research Experience Grant