Senior Scientist, Computational Biology

Xaira Therapeutics; South San Francisco (CA); On-site; USD 136,000 - 170,000; Full time

Benefits offered by this job

Competitive compensation package

Equity options

Flexible work environment

Job summary

Xaira Therapeutics, located in South San Francisco, is seeking a Senior Scientist for their Computational Biology team. The role focuses on supporting large-scale single-cell perturbation screens, utilizing expertise in RNA sequencing and bioinformatics. You'll collaborate with researchers and develop innovative workflows, contributing to a dynamic and innovative environment.

The position requires a Ph.D. and offers a base salary range of $136,000 to $170,000, along with a comprehensive benefits package including bonuses and equity options.

Qualifications

• 5+ years of industry and/or applied research experience in computational biology.
• Experience with Perturb-seq or CRISPR-based perturbation screen data.
• Ability to integrate heterogeneous datasets from multiple sources.

Responsibilities

• Own computational analysis of Perturb-seq datasets for therapeutic discovery.
• Design analytical frameworks for integrating Perturb-seq data.
• Build and maintain bioinformatics pipelines for large-scale data.

Skills

Single-cell RNA sequencing analysis

Bioinformatics workflows

Python programming

Machine learning methods

Education

Ph.D. in Computational Biology or related field

Tools

Nextflow

Docker

AWS

Job description

About Xaira Therapeutics

Xaira is an innovative biotech startup focused on leveraging AI to transform drug discovery and development. The company is leading the development of generative AI models to design protein and antibody therapeutics, enabling the creation of medicines against historically hard‑to‑drug molecular targets. It is also developing foundation models for biology and disease to enable better target elucidation and patient stratification. Collectively, these technologies aim to continually enable the identification of novel therapies and to improve success in drug development. Xaira is headquartered in the San Francisco Bay Area, Seattle, and London.

About the Role

We are 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

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. The package includes base salary, bonus, and equity. The base pay range for this position is expected to be $136,000 – $170,000 annually; however, the amount offered may vary depending on the market, knowledge, skills, and experience.

Xaira Therapeutics is 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.