Undergraduate research opportunities focusing on investigations of nuclear shape transitions

27 Feb 2025 by Christopher T. Lee

Positions for Undergraduate Research are available immediately in the ctleelab at the University of California San Diego. Details for the position follow.

Undergraduate Researcher

The ctleelab has openings for undergraduate researchers interested in developing methods for analyzing and running physical simulations from 3D fluorescence imaging datasets. In particular we hope to:

  • investigate pathways in the transition from monomorphonuclear to polymorphonuclear cells during differentiation using data-driven and biophysical models
  • enable exploration of the consequences of nuclear shape transitions by prototyping methods for generating geometric meshes from fluorescence data

Relevant Papers:

  • Biological context: Patta, I; et al.; Nuclear Morphology Is Shaped by Loop-Extrusion Programs. Nature 2024, 627 (8002), 196–203. https://doi.org/10.1038/s41586-024-07086-9.
  • Image processing using differentiable rendering: Ichbiah, S.; et al. Differentiable Rendering for 3D Fluorescence Microscopy. arXiv March 18, 2023. https://doi.org/10.48550/arXiv.2303.10440.
  • Mesh generation: Lee, CT; Laughlin, JG; et al. 3D Mesh Processing Using GAMer 2 to Enable Reaction-Diffusion Simulations in Realistic Cellular Geometries. PLOS Computational Biology 2020, 16 (4), e1007756. https://doi.org/10.1371/journal.pcbi.1007756.
  • Physical simulations: Francis, EA; Laughlin, JG; et al.; Spatial Modeling Algorithms for Reactions and Transport in Biological Cells. Nat Comput Sci 2024. https://doi.org/10.1038/s43588-024-00745-x.

Candidates should plan to commit to an initial 1 month trial period after which we will discuss research fit and options for course credit etc.

Responsibilities

This role advances the research aims of the ctleelab through supervised project development and individual exploration. Candidates can expect to:

  • Prototype analysis workflows for processing time-series of fluorescence micrographs
    • including mesh generation to support physical simulations
  • Explore conventional and AI/ML based methods for featurization of organelle shapes
  • Work closely with PI and supervising postdoctoral scholar or graduate student
  • Participate in group meetings and other activities
  • Read and discuss initially assigned primary literature leading to self-driven exploration
  • Commit >15 hours a week to research in the lab

Qualifications

Minimum Qualifications
  • Full-time student at UCSD pursuing an undergraduate degree in computer science, data science, mathematics, biology, chemistry or related studies
  • Experienced in at least one high-level programming language (e.g., Python)
  • Prior knowledge of calculus and linear algebra
  • Interest in methods and algorithms for analysis of image timeseries
  • Motivated to learn new skills and technologies and collaborate within an existing team’s practices
  • Excellent written and verbal communication skills
Preferred Qualifications
  • Background in basic concepts of biology
  • Experience with image processing libraries and tools (e.g., ImageJ, Pillow, OpenCV)
  • Experience in a low-level language (e.g., C++)
  • Familiarity with version control and other software development best practices

Application Requirements

Application will be reviewed on a rolling basis until the positions are filled with an initial screening by April 11, 2025. Informal inquiries are welcome. The ctleelab works on interdisciplinary topics and recognizes that complementary backgrounds facilitate our science and goals. As such, applicants with unique and complementary expertise to our ongoing team are particularly encouraged to apply.

Please contact Chris by email (ctleeobfuscate@ucsd.edu) with the following.

  1. statement of interest
    • Please highlight your relevant background and interest with respect to the roles and qualifications outlined above
    • (optional) include contact information for up to two references. Do not have letters sent
  2. a current CV/Resume
  3. a copy of your informal transcript or summary of relevant course work
  4. code samples or links to published/distributed code

To aid in applicant review, a coding sample is requested. We are happy to review whatever you are most proud of (in any programming language). If you do not have code that can be publicly shared, that is okay. Please apply anyway and just let us know that this is not available.

About UC San Diego

The University of California, San Diego is an Equal Opportunity/Affirmative Action Employer advancing inclusive excellence. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, age, covered veteran status, or other protected categories covered by the UC nondiscrimination policy.

For the University of California’s Affirmative Action Policy please visit: https://policy.ucop.edu/doc/4010393/PPSM-20.

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