Jinling Li
Tampa,FL
Summary
Ph.D. in Microbiology (Plant Pathology) with 7+ years of research in microbial genomics, comparative genomics, and host-pathogen interactions. Proven ability to design and implement bioinformatic frameworks for genomic screening (GWAS, QTL mapping) across 200+ isolates, including the analysis of core and lineage-specific (LS) effector catalogs. Deep expertise in developing and validating qPCR-based screening models and other molecular assays (NGS, transcriptomics) to assess microbial function and safety, including in BSL-3 containment. Seeking to apply this R&D and genomics skillset to build predictive safety and regulatory frameworks at Corteva Agriscience.
Overview
13
13
years of professional experience
Work History
Secondary Science Teacher
PACE Center for Girls
Lecanto, FL
02.2024 - Current
- Developed and implemented engaging science curriculum aligned with state standards.
- Fostered a positive learning environment through effective classroom management techniques.
- Utilized hands-on experiments to enhance students' understanding of scientific concepts.
- Collaborated with colleagues to design interdisciplinary projects promoting critical thinking skills.
Postdoctoral Research Fellow
North Dakota State University
01.2019 - 01.2023
- Genomic Discovery Lead (MPMI, 2024): Led a large-scale genomic study to design a bioinformatic framework to identify novel virulence loci in P. teres. This single project involved:
- QTL Mapping: Sequencing a 103-progeny bi-parental mapping population.
- GWAS: Sequencing a global 165-isolate natural population to conduct comparative genomics.
- Genome Assembly: Generating a reference-quality genome assembly for the virulent isolate (Mor40-3) using Oxford Nanopore and Illumina data.
- Transcriptomics: Managing deep transcriptome sequencing (RNA-seq) for annotation.
- Bioinformatics: Personally ran the full analysis using GATK, BWA-MEM, GAPIT, and QGene to identify two major QTLs (Ch1 and Ch8) associated with virulence.
- Functional Genomics Platform Lead: Led functional validation of genomic targets by developing and optimizing a transformation protocol for delivering CRISPR-Cas9-RNP complexes into protoplasts, boosting on-target editing efficiency from
- Expanded platform capabilities by optimizing Cas12a-RNP delivery, enabling editing of AT-rich genomic regions with a ~77% success rate.
- Y2H Screening Lead: Formulated, designed, and conducted a Yeast Two-Hybrid (Y2H) assay to detect novel protein-protein interactions. This included bait/prey vector construction and the generation of a high-capacity cDNA library (6 × 109 CFU/μg).
PhD Researcher
Wageningen University & Research
Netherlands
01.2013 - 01.2019
- Host-Pathogen Interaction (bioRxiv, 2022): Managed an end-to-end proteomics and functional genomics workflow to identify the in-planta targets of the Tom1 effector, a key component of host-pathogen interaction. This involved:
- Agrobacterium-mediated transient expression and protein expression in E. coli and Pichia systems.
- Performing protein isolation, Co-Immunopurification (Co-IP), and Western Blot analysis.
- Leading the preparation and analysis of over 30 protein samples for LC-MS/MS (TripleTOF5600+), successfully identifying Auxin Response Factors (ARFs) as the novel targets.
- Host-Pathogen Validation (VIGS/HIGS): Developed and validated multiple transient and stable RNA-based gene silencing assays to study pathogen effectors, demonstrating a "regulatory screening" approach.
- Viral Delivery (VIGS): Successfully used Tobacco Rattle Virus (TRV)-based VIGS to suppress the SlARF2a susceptibility target, resulting in an in-planta 50% reduction in pathogen colonization.
- RNAi (HIGS): Engineered stable transgenic Arabidopsis lines using hairpin RNAi constructs (pHellsgate/pFAST vectors) to achieve Host-Induced Gene Silencing.
- Comparative Genomics Lead (bioRxiv, 2019): Conducted a large-scale comparative genomics study of 21 V. dahliae strains to analyze "divergent effector catalogs." This involved whole-genome alignment (NUCmer), gene prediction (Maker2), effector profiling (EffectorP), and transcriptomic analysis (RNA-seq) to demonstrate differential core effector gene expression on different hosts.
- Molecular Analysis: Validated RNAi efficacy and quantified fungal biomass in planta via qPCR, demonstrating a strong background in molecular assay development.
Education
Ph.D. - Plant Biology & Molecular Biology (Microbiology focus)
Wageningen University & Research
The Netherlands01.2019
Master of Science - Plant Pathology
Northwest A&F University
Shaanxi, China01-2010
Skills
- Bioinformatics & Genomics
- Core Software: Geneious Prime, SnapGene, Benchling, Python, R, Bash, HPC environment
- Genomic Analysis: GWAS (GAPIT), QTL Mapping (MapDisto, QGene), Linkage Map Construction
- NGS Data Analysis (Illumina/Nanopore): Read alignment (BWA-MEM), variant calling (GATK HaplotypeCaller), trimming (Trimmomatic)
- Transcriptomics: RNA-seq alignment (Hisat2, STAR), transcript assembly (StringTie, RSEM)
- Genome Assembly & Annotation: De novo assembly (Canu), polishing (Pilon), annotation (funannotate)
- Cloud Platforms: Familiarity with AWS and Google Cloud for bioinformatics applications
- Molecular Assay Development & Validation
- Lab Safety: BSL-2 & BSL-3 containment and protocols
- Genomic Screening Models: qPCR & dPCR-based validation, transcriptomic analysis, LAMP
- Host-Pathogen Interaction Assays: in-planta functional and pathogenicity assays, VIGS/HIGS
- Protein Interaction Screening: Yeast Two-Hybrid (Y2H) cDNA library construction and screening
- Nucleic Acid Isolation & QC: High-throughput gDNA, total RNA, mRNA, and miRNA isolation; QC via qPCR, Agilent 2100 Bioanalyzer, and Qubit Fluorometry (RNA IQ Assay)
- Protein & DNA Analysis: Protein/DNA isolation, Southern Blot, Western Blot, Co-Immunopurification (Co-IP), LC-MS/MS
- Platform Development & Functional Validation
- CRISPR Editing: CRISPR-Cas9 & Cas12a RNP delivery platform optimization
- Viral Delivery: Virus-Induced Gene Silencing (VIGS)
- RNAi Platforms: Host-Induced Gene Silencing (HIGS)
- Cloning & Expression: Gateway, Gibson Assembly, Golden Gate, E coli & Agrobacterium transformation, Pichia protein expression
Selected Publications & Presentations
- Li, J., Wyatt, N.A., Skiba, R.M., et al. (2024). "Variability in Chromosome 1..." Molecular Plant-Microbe Interactions. (First Co-author: Led GWAS/QTL, comparative genomics, and NGS data analysis).
- Li, J., Faino, L., Fiorin, G.L., et al. (2022). "A single Verticillium dahliae effector..." bioRxiv. (First Co-author: Led VIGS, Co-IP, LC-MS/MS, and functional validation of host-pathogen targets).
- Gibriel, H.A.Y., Li, J., Zhu, L., et al. (2019). "Verticillium dahliae strains... highly divergent effector catalogs." bioRxiv. (First Co-author: Led comparative genomics and RNA-seq analysis).
- Invited Workshop Lead: "CRISPR-Cas9 Mediated Gene Editing" (2023). Led a technical training session for 23 graduate students at North Dakota State University.
Languages
English
Full Professional
Chinese (Mandarin)
Native or Bilingual
Timeline
Secondary Science Teacher
PACE Center for Girls
02.2024 - Current
Postdoctoral Research Fellow
North Dakota State University
01.2019 - 01.2023
PhD Researcher
Wageningen University & Research
01.2013 - 01.2019
Ph.D. - Plant Biology & Molecular Biology (Microbiology focus)
Wageningen University & Research
Master of Science - Plant Pathology
Northwest A&F University