Computational Biologist – Single-Cell Genomics

This is a fully remote position, open to applicants in New York.

📋 Description

• Create original graduate-level computational challenges in the fields of bioinformatics and single-cell genomics.

• Design tasks rooted in realistic research workflows and biological datasets.

• Develop multi-step problems that necessitate scientific interpretation and computational analysis.

• Generate reproducible tasks with clearly defined inputs, expected results, and criteria for validation.

• Adjust task difficulty based on testing outcomes and feedback received.

• Create problems related to single-cell RNA sequencing that involve preprocessing, quality control, dimensionality reduction, clustering, cell-type annotation, and subsequent analysis.

• Design problems focused on trajectory and dynamic analysis, encompassing pseudotime, cellular trajectory inference, scVelo, RNA velocity, and dynamic state analysis.

• Develop problems related to spatial transcriptomics that involve spatially resolved gene expression data, spatially variable genes, and neighborhood analysis.

• Construct workflows for multi-omic integration and evaluate batch effects, biological variation, and quality of integration.

• Create problems in topological data analysis using persistence-based workflows while interpreting topological structures in high-dimensional biological datasets.

• Write computational problem setups, oracle functions, and solution validators using Python.

• Ensure the numerical and biological accuracy of expected outputs.

• Identify limitations of software, computational edge cases, and potential analytical failure modes.

• Document key assumptions, dependencies, parameters, and validation logic.

• Test tasks against advanced systems and refine prompts, constraints, datasets, and expected outcomes.

• Assess whether problems necessitate authentic scientific reasoning rather than superficial pattern recognition.

⛳️ Requirements

• A Master's degree, PhD, or equivalent research experience in Bioinformatics, Computational Biology, Genomics, Systems Biology, or a closely related STEM field.

• Extensive hands-on experience with single-cell genomics and computational biological analysis.

• Demonstrated proficiency with specialized tools such as Scanpy, scVelo, Squidpy, GUDHI, or similar scientific software.

• Experience utilizing these tools in actual research or professional projects.

• Solid understanding of single-cell RNA-seq analysis, trajectory inference, spatial transcriptomics, or multi-omic integration.

• Strong programming skills in Python.

• Capability to design rigorous computational problems and independently verify solutions.

• Comfortable operating within Linux and terminal-based environments.

• All work must be performed without the use of confidential or proprietary information from any employer, client, institution, or other third party.

• H1-B and STEM OPT support is not available for this position.

🏝️ Benefits

• Flexible scheduling that aligns with project requirements.

• Fully remote working arrangement.

• Engagement as a part-time independent contractor.

• Possibility for project extensions depending on project needs and performance.