Chun Su, Ph.D
Jersey City,NJ
Summary
Plant systematics, plant taxonomy, and bioinformatics expert specializing in researching the systematics, taxonomy, and biogeography of flowering plants in the eastern Asian flora. Proficient in performing bioinformatics and phylogenomic analyses using high-throughput Next-Generation Sequencing (NGS) data.
Overview
3
3
years of professional experience
Work History
Postdoctoral Fellow
Dr. Joyce Onyenedum Lab, New York University
09.2023 - 09.2024
- Conducted bioinformatics research titled “Phylogenetics and Evolution of the Tribe Paullinieae (Sapindaceae)” using Next Generation Sequencing (NGS) with the Angiosperm 353 target enrichment technique.
- Setup the data analysis pipeline for Environmental Studies department at NYU. This pipeline has been successfully used for end-to-end analysis of 800 genomic samples.
- Created the HPC environment for gene analysis with necessary software installed from source
- Authored customized batch scripts for raw data quality assessment (FastQC), data cleaning (Trimmomatic), gene assembly (Novoplasty, HybPiper, Easy353 etc.), and final phylogenetic tree construction (ASTRAL, IQ-TREE, MrBayes, RAxML, iTOL)
- Established data storage and backup systems for the large data (cloud based and hardware based)
- One paper is currently in progress.
Research Assistant
Canopy Ecology Group, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences
07.2021 - 06.2022
- Project Assistance & Manuscript Preparation: Assisted the Canopy Ecology Group (XTBG) with creating proposals for National Natural Science Foundation of China (NSFC) and other grants
- Worked with research groups on manuscript preparation, evaluation, translation into Mandarin, and submitting the proposals to RFPs.
- Responsible for successfully securing grant awards for seven different proposals from four Principal Investigators.
- Troubleshooting & Team Management: Managed group operations, including troubleshooting, recruiting postdocs and students, and media promotion.
- Assisted in hiring one postdoc and one assistant professor, facilitated the graduation of one master’s and one bachelor’s student, and participated in two documentary productions and one promotional event.
- Organized an international online conference with over 100 participants over three days.
Education
Ph.D. (Botany) -
Northwest A&F University
Shaanxi, China07.2021
Visiting Graduate Student - Botany
Department of Botany, National Museum of Natural History, Smithsonian Institution
Washington, DC10.2020
B.S. (Biosciences) -
Northwest A&F University
Shaanxi, China07.2017
Skills
- Quality control of NGS data
- Nuclear gene and chloroplast genome assembly
- Phylogenetic and biogeography analysis (ENM)
- Proficiency with bioinformatics tools (NCBI, EBI, CNGB, SRA, Geneious)
- Sample preparation and nucleic acid isolation
- Quality control methods (Qubit, Tapestation, gel electrophoresis)
- PCR amplification, library prep, bead-based clean-up, fragment analysis
- NGS platform operations (NovaSeq) and sequencing technologies (Genome skimming, Hyb-seq, RNAseq)
- Biological microscopy (Light Microscope, SEM) and karyotype analysis (plants)
NGS Analysis
Laboratory Skills
- Specimen collection, identification, and herbarium management
- Photomicrography
- Software: MS Office, bash/shell scripting, Singularity, Nextflow
- Programming: R, Python
- High-Performance Computing (slurm, PBS)
- Experimental design and project coordination
- Manuscript preparation and statistical modeling
- Lab management and research protocol development
Plant Taxonomy
Computational Proficiency
Research Skills
Publications
https://www.researchgate.net/profile/Chun-Su-6, https://scholar.google.com/citations?user=KYb0rcsAAAAJ&hl=en
Timeline
Postdoctoral Fellow
Dr. Joyce Onyenedum Lab, New York University
09.2023 - 09.2024
Research Assistant
Canopy Ecology Group, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences
07.2021 - 06.2022
Ph.D. (Botany) -
Northwest A&F University
Visiting Graduate Student - Botany
Department of Botany, National Museum of Natural History, Smithsonian Institution
B.S. (Biosciences) -
Northwest A&F University
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