Molecular Biology Intern (High-Throughput Assays)

About the Role:

The intern will join the spatial proteomics R&D effort, focusing on building and optimizing high-throughput experimental workflows for screening custom proteins. They will work with display systems (e.g., yeast display) and surface-based assays to evaluate affinity, specificity, and performance of designed proteins across multiple formats.

On a day-to-day basis, the intern will design and clone constructs, develop and run high-throughput binding assays, establish and optimize conjugation strategies to link proteins to DNA or other reporters, and analyze large datasets from screening experiments to identify the most promising candidates. They will work closely with a cross-functional team spanning molecular biology, protein engineering, and computational design, and will regularly share results and recommendations with the broader program.

What you Will Be Doing:

Assay & Platform Development

• Develop, optimize, and execute high-throughput screening assays to evaluate custom proteins.
• Build and refine yeast surface display workflows (and/or related display platforms) for quantitative binder characterization using flow cytometry.
• Establish and compare surface-based screening formats, such as:
• Yeast display + FACS
• Surface-immobilized target assays (e.g., beads, chips, slides)
• Plate-based or bead-based binding and competition assays.
• Implement and benchmark conjugation strategies that link proteins to DNA or other reporter molecules for multiplexed assays and barcoded readouts.

Molecular Biology & Protein Engineering

• Design and execute cloning strategies for custom protein libraries and individual variants (PCR, Gibson/Golden Gate, site-directed mutagenesis).
• Construct and validate expression vectors for yeast and/or other systems, including QC of expression and display levels.
• Support expression and basic QC of selected binders (e.g., SDS-PAGE, Western blot, simple purification or lysate-based functional assays).

High-Throughput Screening & Data Analysis

• Plan and perform FACS-based and/or plate-based binder screening experiments, including appropriate controls, titrations, and replicates.
• Analyze high-dimensional assay data (e.g., from flow cytometry or barcoded readouts) to rank candidates based on affinity, specificity, and other performance metrics.
• Where applicable, prepare samples and data for sequencing-based readouts and collaborate with others to interpret sequence–function relationships.
• Summarize findings in clear figures, tables, and internal reports, and present progress in regular team meetings.

Collaboration & Documentation

• Work with computational design, protein production, and assay development teams to integrate experimental results into the design–build–test–learn cycle.
• Maintain detailed electronic lab notebook records, SOPs, and reagent documentation to ensure reproducibility and handoff.
• Contribute to a final internal report and presentation describing the developed workflows, experimental results, and recommendations for future development.

To Be Successful You Will Need:

• Current PhD candidate in Biochemistry, Biophysics, Molecular Biology, Bioengineering, Chemical Biology, or a closely related field.
• Ideally within the final 1–2 years of their PhD program, with substantial hands-on experimental training in protein or molecular biology.
• Proven ability to independently design, execute, and troubleshoot experiments.
• Strong quantitative and analytical mindset, including comfort with large datasets from high-throughput screens.
• Clear written and verbal communication skills, with the ability to present complex results across disciplines.
• Highly organized, collaborative, and comfortable working in a fast-paced, interdisciplinary R&D environment.

Core Technical Skills (Required):

• Strong molecular biology foundation:
• PCR, cloning (e.g., Gibson, Golden Gate), site-directed mutagenesis.
• Plasmid design, sequence verification, and basic construct troubleshooting.
• Experience with protein expression and characterization in at least one system (yeast, E. coli, or cell-free):
• Induction/optimization of expression, basic purification or lysate-based assays, SDS-PAGE/Western.
• Hands-on experience with high-throughput or quantitative assay formats, such as:
• Flow cytometry / FACS, plate-based binding assays (ELISA or similar), or cell-based functional assays.
• Comfort with data analysis and visualization:
• Experience with Python, R, or analysis tools such as GraphPad Prism is nice to have.
• General awareness and experience with AI data analysis

Preferred Experience (Nice to Have):

• Yeast surface display, phage display, ribosome/mRNA display, or other library-based screening technologies.
• Experience with conjugation and bioconjugation methods, for example:
• Cysteine-based conjugation (maleimide-thiol, halo tag, SNAP/CLIP, etc.).
• Click chemistry (e.g., azide–alkyne, DBCO, strain-promoted cycloaddition).
• DNA-barcoding of proteins, or other methods linking proteins to nucleic acids or reporters.
• Familiarity with translation-linked or puromycin-based conjugation methods, or related approaches that couple protein synthesis to covalent capture is highly desired.
• Background in protein engineering, antibody/nanobody development, or de novo mini-binder workflows.