Research Scientist

Job Summary

This is a joint Research Scientist position appointed 50% to the Demirer Lab and 50% to the Nolan Lab at Caltech. The Research Scientist will lead two complementary frontier programs in plant synthetic biology and functional genomics. In the Demirer Lab, they will develop the next generation of plant genome-editing technologies, focusing on engineering the R2 non-LTR retrotransposon as a programmable platform for site-specific gene integration in plant genomes. In the Nolan Lab, they will establish a high-throughput CRISPR perturbation screening platform in plants, coupled with single-cell sequencing readouts, enabling functional dissection of gene regulatory networks that underlie root development and stress responses. The position requires a senior scientist who has built plant genome-editing tools from the ground up, translated those tools across model plants and multiple crop species, and led complex, multi-investigator genome-engineering programs in both academic and industry settings.

Essential Job Duties

Demirer Lab (50% effort)

• Design, construct, and optimize R2 retrotransposon-based tools for programmable, site-specific gene integration in plant genomes.
• Engineer modular DNA cassettes and protein-recruitment strategies that direct R2-mediated integration to user-defined loci in Arabidopsis and crop species.
• Benchmark R2-based integration against existing precision editing platforms (HDR enhancement, prime editing, CRISPR-associated transposons).
• Characterize off-target activity, cargo size limits, and chromatin-context dependence of R2-mediated integration.
• Generate stable transgenic lines, screen edited events, and contribute to invention disclosures, patent applications, and manuscripts arising from the platform.

Nolan Lab (50% effort)

• Establish a CRISPR perturbation screening pipeline in Arabidopsis compatible with single-cell or single-nucleus RNA-seq readouts.
• Design and clone pooled sgRNA libraries targeting developmental and stress-response gene networks, including barcoded perturbation constructs.
• Optimize protoplast isolation, single-cell capture, and direct sgRNA capture methods for plant Perturb-seq.
• Analyze multimodal single-cell datasets to infer gene function, regulatory relationships, and cell-type-specific responses.
• Coordinate with the Nolan Lab single-cell team and Caltech core facilities as needed.

Cross-cutting

• Mentor graduate students and postdocs across both labs in editing design, construct building, plant transformation, and NGS interpretation.
• Lead manuscripts, present at internal and external venues, and coordinate bi-weekly with both PIs.

Basic Qualifications

• PhD in Genetics and Genomics with a focus on plant genome and epigenome engineering.
• Minimum 5 years of post-PhD experience as a computational scientist.
• Minimum 5 years of post-PhD research experience developing site-specific genome and epigenome editing tools in plant systems.
• First-author authorship on at least one peer-reviewed publication.
• More than 5 years of experience in epigenome engineering.
• Prior experience leading a Precision Genome Engineering group at a commercial plant biotechnology or agricultural gene editing company, with direct responsibility for tool development, multiplexing strategies, and precise allele replacement.
• Programming proficiency in UNIX, MATLAB, R, and Python, with demonstrated experience analyzing single-cell RNA-seq, ChIP-seq, bisulfite sequencing, whole-genome sequencing, and amplicon sequencing data.
• Computational experience in the analysis of orthologues, whole-genome duplications, and synteny within and across species.
• Direct experience developing tools that enhance homology-directed repair, targeted integration, DNA methylation, and modifying chromatin marks.
• Experience coordinating genome engineering strategy across independent principal investigators at a multi-PI research institute.
• Experience supervising and mentoring a team on plant genome engineering projects.

Preferred Qualifications

• Experience executing large-scale targeted manipulations in plant genomes.
• Familiarity with single-cell or single-nucleus RNA-seq experimental design in plant tissues, including protoplast and nuclei isolation optimization.
• Familiarity with Perturb-seq, CROP-seq, or analogous pooled CRISPR screening platforms in any system.
• Working knowledge of non-LTR retrotransposon biology or transposon-based gene delivery.
• Background in root development, root system architecture, or root cell-type specification.
• Familiarity with carbon sequestration or sustainable agriculture research programs.
• Experience setting up new laboratory spaces, including equipment, growth chamber, and reagent specification.