Scientist I/II, Bioinformatics

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!

• 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.

• 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.

• 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).

Lila Sciences is committed to equal employment opportunity regardless of race, color, ancestry, religion, sex, national origin, sexual orientation, age, citizenship, marital status, disability, gender identity or Veteran status.

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