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
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
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