Scientist I/II, Bioinformatics

Your Impact at LILA 

Join us in shaping the future of science! We are seeking a bioinformaticist to join our data science team, where you’ll collaborate with software engineers, lab scientists, and machine learning engineers to build cutting-edge tools for automated scientific analysis and more. This role spans web services and data engineering, with a strong emphasis on Python development for scientific applications. If you thrive in a collaborative, fast-paced environment and bring best practices in git, development workflows, and user-centered design, we want to hear from you!

What You'll Be Building

• Design, develop, and maintain scalable NGS data processing pipelines (e.g., using Nextflow) for a variety of sequencing applications including whole-genome, RNA-seq, and targeted amplicon sequencing.
• Build and optimize single-cell RNA-seq (scRNA-seq) analysis workflows encompassing read alignment, quality control, doublet detection, normalization, dimensionality reduction, clustering, cell-type annotation, and differential gene expression analysis using tools such as Scanpy, Seurat, or CellRanger.
• Develop and maintain amplicon sequencing pipelines tailored to display technology platforms (e.g., phage display, yeast display, ribosome display), including variant calling, sequence enrichment analysis, clonal frequency tracking, and selection round-over-round comparisons.
• Perform downstream and integrative analyses such as gene set enrichment, trajectory/pseudotime inference, receptor-ligand interaction modeling, and multi-omic data integration as needed.Antibody domain knowledge (discoveryand/ordev of therapeutic antibodies)
• Align development with strategic goals, ensuring software supports broader organizational needs.
• Manage git repositories, team Jira board and Notion Hub, enforce best practices, assist lab scientists with use of new tools, and foster a collaborative development culture.
• Work directly with scientists to identify gaps and unmet needs, develop tailored software solutions for data management and automation.
• Support infrastructure as code and design efficient deployment strategies.
• Write clear, concise documentation for both engineers and end users.

What You’ll Need to Succeed

• Ph.D or Masters in bioinformatics or related field
• High-level proficiency in Python.
• Strong understanding of git best practices.
• Strong background in bioinformatics applications and common toolsets
• Acute listening skills and patience to deeply understand user challenges.
• Excellent problem-solving skills and team-first mentality.
• Strong communication skills to effectively collaborate with team members and stakeholders.
• Energetic self-starter and independent thinker, with strong attention to detail.
• Eager to work with highly skilled and dynamic teams in a fast-paced, entrepreneurial, and technical setting.

Bonus Points For

• Experience with workflow orchestration software (e.g. Flyte, NextFlow).
• Knowledge of modern developer tools (pydantic, pyright, uv).
• Understanding of Kubernetes, ArgoCD, and GitHub Actions.
• Familiarity with AWS fundamentals (e.g., RDS, EC2, S3, EKS).