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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. 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.

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

Requirements

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

Skills

Single-cell RNA sequencing
Perturb-seq
CRISPR-based perturbation screen data
Nextflow
Docker
AWS
Python
numpy
pandas
scanpy
scikit-learn
Unix
GitHub
Statistical methods
Machine learning methods

Location

South San Francisco

Work Type

On-site

Experience Level

Senior Scientist
5+ years of relevant industry and/or applied research experience

Education Level

Ph.D. in Computational Biology, Bioinformatics, Genomics, or a related quantitative field

Salary/Compensations

$136,000 - $170,000 annually

Benefits

Competitive compensation and benefits package
Open, flexible, and friendly work environment
Platform to develop long-term careers
Base salary, bonus, and equity

About the Company

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.

Equal Opportunity

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.