Changyu (Joe) Yi
Bioinformatician
Melbourne,VIC
Summary
Computational biologist with Ph.D degree in biology and six-years experience analyzing high-throughput sequencing data including single-cell RNA sequencing (scRNA-seq), spatial transcriptomics and bulk RNA sequencing. Strong coding skills in R ,Python and Linux shell for data wrangling, normalization, analysis and visualization with solid background in biology and biostatistics principles. Looking for a bioinformatics analyst position to contribute my skills and expertise in molecular biology and computer science to cancer research.
Overview
3
3
years of professional experience
10
10
years of post-secondary education
1
1
Certification
Work History
Bioinformatician
La Trobe University
Bundoora, VIC
12.2019 - Current
- Developing and optimizing pipelines for processing and analyzing single-cell RNA sequencing and spatial transcriptomics data.
- Analyzing various type of high-throughput sequencing data (RNA-seq, ChIP-seq, WGS) by optimizing existing methods and pipelines.
- Developing and appling pipelines for analyzing long-read sequencing data.
- Building web-based tool (R/Shiny) for data visualization and mining in collaboration with IT department.
- Supervised one collaborative PhD student for RNA-seq data analysis.
- Working closely with bench-bashed biologists to design experimental plan and sequencing strategy.
- Carrying out statistical analyses, interpret analysis results within biological context and prepare manuscript for submission.
Education
Ph.D. - Plant Biology
La Trobe University
Melbourne, Australia 12.2015 - 12.2019
M.D. - Horticulture Science
Zhejiang University
Hangzhou, China 09.2012 - 03.2015
Bachelor - Horticulture Science
Jiangxi Agricultural University
Nanchang, China 09.2008 - 06.2012
Skills
Experience of high-throughput sequencing data analysis, including single-cell RNA-seq, spatial transcriptomics, RNA-seq, ChIP-seq, WGS
Proficient in Linux/UNIX systems, shell scripting and work with High-Performance Computing clusters
Strong coding skills in R and python including data analysis and visualization
Experience of developing data visualization and mining tool using Shiny
Experienced in GWAS analysis using TASSEL pipeline and GAPIT package
Familiarity with statistical methodologies such as ANOVA, generalized and/or linear mixed models, correlation analysis and principle component analysis (PCA)
Experienced in Git version control systems and container related tools (Docker)
Excellent communication skills and the ability to work constructively within a team environment
Microsoft Office Suite, Illustrator, Photoshop, Origin, Endnote
Genomic DNA/cDNA quantification with real-time PCR methods
Grants
Early Career Researcher Awards, La Trobe University, 2021.
Project title: Deciphering cell–cell communication during Arabidopsis seed development.
Project aims:This project aims to understand how cells communicate with each other to coordinate seed development by using scRNA-seq.
Invited talks
- Invited speaker, The 11th International Oat Conference, 2022, Perth, Australia.
- Invited speaker, International Horticultural Research Conference for The 120th Anniversary of NJAU, 2022, Online.
- Invited speaker, Australian Society of Plant Scientist (ASPS) annual meeting, 2019, Melbourne, Australia.
- Invited speaker, American Society of Plant Biologists (ASPB) annual meeting, 2017, Hawaii (because of the visa granted too late the talk had to be cancelled).
- Seminar, ARC Centre of Plant Energy Biology, 2019, Melbourne, Australia.
Publications
- Peirats-Llobet M, Yi C, Liew LC, Berkowitz O, Narsai R, Lewsey MG, Whelan J (2023) Spatially resolved transcriptomic analysis of the germinating barley grain. bioRxiv: 2023.2001.2024.525109. Co-first author.
- Lewsey MG, Yi C, Berkowitz O, Ayora F, Bernado M, Whelan J (2022) Sccloudmine: A cloud-based app for visualization, comparison, and exploration of single-cell transcriptomic data. Plant Communications 3: 100302.
- Meng X, Li L, Pascual J, Rahikainen M, Yi C, Jost R, He C, Fournier-Level A, Borevitz J, Kangasjärvi S, Whelan J, Berkowitz O (2022) Gwas on multiple traits identifies mitochondrial aconitase3 as important for acclimation to submergence stress. Plant Physiology 188: 2039-2058.
- Yi C, Wang X, Chen Q, Callahan DL, Fournier-Level A, Whelan J, Jost R (2021) Diverse phosphate and auxin transport loci distinguish phosphate tolerant from sensitive arabidopsis accessions. Plant Physiology 187: 2656-2673.
- Sun S, Yi C, Ma J, Wang S, Peirats-Llobet M, Lewsey MG, Whelan J, Shou H (2020) Analysis of spatio-temporal transcriptome profiles of soybean (glycine max) tissues during early seed development. International Journal of Molecular Sciences 21: 7603.
- Yi C, Yao K, Cai S, Li H, Zhou J, Xia X, Shi K, Yu J, Foyer CH, Zhou Y (2015) High atmospheric carbon dioxide-dependent alleviation of salt stress is linked to respiratory burst oxidase 1 (rboh1)-dependent h2o2 production in tomato (solanum lycopersicum). Journal of Experimental Botany 66: 7391-7404.
- Li H, Liu S, Yi C, Wang F, Zhou J, Xia X, Shi K, Zhou Y, Yu J (2014) Hydrogen peroxide mediates abscisic acid-induced hsp70 accumulation and heat tolerance in grafted cucumber plants. Plant, Cell & Environment 37: 2768-2780.
Awards
- Award for a La Trobe University Postgraduate Research Scholarship, 2015.
- Zhejiang university meritorious student Award in 2014, outstanding graduate student Award, 2014.
Certification
Certification of working with recombinant DNA
Reference
Professor Mathew Lewsey
AgriBio (L1Q4), ARC Research Hub for Medicinal Agriculture
La Trobe University
5 Ring Road, Bundoora VIC 3083, Australia
T: +61415921764
E: M.Lewsey@latrobe.edu.au
Timeline
Bioinformatician
La Trobe University
12.2019 - Current
Certification of working with recombinant DNA
01-2016
Ph.D. - Plant Biology
La Trobe University
12.2015 - 12.2019
M.D. - Horticulture Science
Zhejiang University
09.2012 - 03.2015
Bachelor - Horticulture Science
Jiangxi Agricultural University
09.2008 - 06.2012