Senior Scientist, Computational Biology

ABOUT THE ROLE

Xaira is seeking a highly motivated and experienced Senior Scientist to join our Computational Biology team with a focus on supporting large-scale single-cell perturbation screens. The ideal candidate will bring deep expertise in single-cell RNA sequencing, Perturb-seq, and a proven track record of processing and integrating large-scale datasets from multiple experimental sources.

This position offers the opportunity to contribute to cutting-edge efforts at the intersection of functional genomics, machine learning, and disease biology. You will work closely with wet-lab scientists, AI/ML scientists, automation engineers, and disease biology teams to develop scalable perturbation workflows, implement new technologies, and drive high-quality data generation and experimental innovation across multiple therapeutic areas.

This will be an on-site role in South San Francisco.

KEY RESPONSIBILITIES

• Own end-to-end computational analysis of Perturb-seq datasets, spanning quality control, biological interpretation, and translation of large-scale single-cell data into actionable insights for therapeutic discovery and AI/ML modeling
• Design and implement standardized analytical frameworks for integrating Perturb-seq data across diverse experimental contexts, such as cell types, library designs, and sequencing platforms, to enable reliable cross-source analysis
• Build and maintain scalable, production-grade bioinformatics pipelines, with an emphasis on reproducibility, modularity, and performance at the scale of large perturbation screens
• Integrate Perturb-seq data with complementary omics modalities, including CITE-seq, ATAC-seq, spatial transcriptomics, as well as external reference datasets, to enrich biological context and support multi-modal analyses
• Partner closely with AI/ML scientists to ensure data products meet modeling requirements, and collaborate with wet-lab scientists to translate experimental design into optimal computational workflows
• Manage code repositories, maintain versioned and documented workflows, and uphold computational environment standards that ensure long-term pipeline reliability
• Contribute to scientific strategy, publications, and patents while mentoring and providing scientific guidance to researchers within the organization

QUALIFICATIONS

• Ph.D. in Computational Biology, Bioinformatics, Genomics, or a related quantitative field, with 5+ years of relevant industry and/or applied research experience (candidates with fewer years are also encouraged to apply and job level can be adjusted as appropriate)
• Deep expertise in single-cell RNA sequencing analysis with substantial hands-on experience in Perturb-seq or CRISPR-based perturbation screen data, including thorough familiarity with the full processing stack from raw reads to interpretable outputs
• Demonstrated ability to integrate heterogeneous datasets from multiple sources, with a strong command of batch correction, normalization, and quality control strategies tailored to large-scale perturbation experiments
• Experience building and maintaining production bioinformatics workflows (e.g. Nextflow), comfort with containerized environments (Docker) and cloud computing platforms (AWS)
• Strong software engineering fundamentals: proficiency in Python (numpy, pandas, scanpy, scikit-learn), fluency in Unix environments, and experience with version control and collaborative software development via GitHub. 
• Working knowledge of statistical and machine learning methods applied to biological data, with the ability to critically evaluate analytical choices and collaborate effectively with AI/ML teammates
• Demonstrated ability to independently lead scientific initiatives, drive cross-functional collaboration, and communicate quantitative results to both wet lab and computational audiences
• Excellent analytical, organizational, written, and verbal communication skills, with the ability to thrive in fast-paced, highly collaborative environments focused on scientific innovation

Compensation

We offer a competitive compensation and benefits package, seeking to provide an open, flexible, and friendly work environment to empower employees and provide them with a platform to develop their long-term careers. A Summary of Benefits is available for all applicants. We offer a competitive package that includes base salary, bonus, and equity.  The base pay range for this position is expected to be $136,000 - $170,000 annually; however, the base pay offered may vary depending on the market, job-related knowledge, skills and capabilities, and experience.

Xaira Therapeutics an equal-opportunity employer. We believe that our strength is in our differences. Our goal to build a diverse and inclusive team began on day one, and it will never end.

TO ALL RECRUITMENT AGENCIES: Xaira Therapeutics does not accept agency resumes. Please do not forward resumes to our jobs alias or employees. Xaira Therapeutics is not responsible for any fees related to unsolicited resumes.