Scientist II, Genomic Core

Xaira Therapeutics; South San Francisco (CA); On-site; USD 124,000 - 155,000; Full time

Job summary

Xaira Therapeutics is seeking an experienced Scientist II for its Genomics Core to lead high-throughput sequencing workflows on Illumina platforms (MiSeq, NextSeq, NovaSeq). You will design and optimize sequencing strategies for CRISPR-based perturbation studies, single-cell and bulk RNA-seq, and collaborate across biology, automation, and computational teams.

The role emphasizes hands-on leadership, independent experimental design, and ongoing optimization of genomics workflows within a startup

Qualifications

• Ph.D. or MS/BS with equivalent industry experience in a relevant field.
• Hands-on experience operating Illumina sequencing platforms (MiSeq/NextSeq/NovaSeq).
• Strong experience with 10x Genomics workflows (3’, 5’, ATAC, Multiome, Flex).
• Expertise in NGS library preparation for single-cell and bulk RNA-seq; CRISPR-based sequencing assays.

Responsibilities

• Perform high-quality sequencing on Illumina platforms (MiSeq, NextSeq, NovaSeq).
• Design, optimize, validate, and troubleshoot sequencing workflows to improve data quality and throughput.
• Prepare and QC sequencing libraries for 10x Genomics single-cell RNA-seq, bulk RNA-seq, and CRISPR-based assays.
• Guide cross-functional teams on sequencing strategy to address biological and computational goals.
• Support Perturb-seq and pooled CRISPR screens; collaborate with automation and computational biology groups.
• Scale automated library preparation and sequencing workflows with automation engineers.
• Ensure data meet quality standards for downstream AI/ML analyses.
• Serve as SME for sequencing technologies and troubleshoot technical challenges.
• Maintain sequencing instruments and lab equipment; manage samples and ELN/LIMS records.
• Evaluate emerging sequencing tech and library prep methods; present updates to teams.

Skills

NGS library preparation

Illumina sequencing

10x Genomics workflows

CRISPR-based sequencing

Experiment design

Cross-functional collaboration

Technical leadership

Education

PhD in Functional Genomics or related field

MS/BS with equivalent industry experience

Tools

MiSeq

NextSeq

NovaSeq

10x Genomics

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

As a Scientist II on Xaira's Genomics Core team within the High Throughput Biology organization, you will play a key role in generating high-quality sequencing data that powers our discovery platform and AI-driven research. You will serve as a technical leader responsible for designing, developing, optimizing, and executing next-generation sequencing (NGS) workflows, with a primary focus on Illumina sequencing platforms, including MiSeq, NextSeq, and NovaSeq. You will partner closely with Functional Genomics, Disease Biology, Automation, and Computational Biology teams to develop scalable sequencing strategies that support CRISPR-based perturbation studies, single-cell genomics, and other high-throughput discovery efforts.

The ideal candidate is an experienced experimental scientist with deep expertise in NGS library preparation, Illumina sequencing operations, and 10x Genomics workflows. This is a highly collaborative, hands-on laboratory role that requires independent scientific thinking, experimental design, and technical leadership to implement new technologies and continuously improve genomics workflows across the organization.

Responsibilities

• Perform high-quality next-generation sequencing operations across Illumina platforms, including MiSeq, NextSeq, and NovaSeq.
• Independently design, develop, optimize, validate, and troubleshoot sequencing workflows to improve data quality, throughput, scalability, and reproducibility.
• Prepare and QC sequencing libraries for a variety of applications, including 10x Genomics single-cell RNA sequencing, bulk RNA sequencing, CRISPR-based sequencing assays, and targeted sequencing workflows.
• Design sequencing strategies and provide technical guidance to cross-functional project teams to ensure generation of high-quality datasets that address biological and computational objectives.
• Partner with Functional Genomics scientists to support Perturb-seq, pooled CRISPR screening, guide sequencing, and other genomics-based discovery programs.
• Collaborate with Automation Engineers to develop, implement, and scale automated library preparation and sequencing workflows.
• Work closely with Computational Biology teams to ensure sequencing data meets quality standards for downstream analysis and AI/ML applications.
• Serve as a technical subject matter expert for sequencing technologies by evaluating new methodologies, identifying experimental risks, troubleshooting complex technical challenges, and recommending scientifically sound solutions.
• Perform routine maintenance, calibration, and troubleshooting of sequencing instrumentation and associated laboratory equipment.
• Manage sequencing sample intake, experimental tracking, reagent inventory, and laboratory documentation.
• Maintain accurate experimental records using electronic laboratory notebooks (ELN) and laboratory information management systems (LIMS).
• Evaluate and implement emerging sequencing technologies, library preparation methods, and genomics workflows to expand core capabilities.
• Present technical updates, experimental findings, and workflow improvements to cross-functional project teams.
• Contribute to laboratory operations while ensuring compliance with safety and quality standards.

Qualifications

• Ph.D. in Functional Genomics, Molecular Biology, Genetics, Genomics, or a related discipline with 2+ years of industry experience, or M.S./B.S. with equivalent industry experience.
• Extensive hands‑on experience operating Illumina sequencing platforms, including MiSeq, NextSeq, and NovaSeq.
• Extensive hands‑on experience with 10x Genomics workflows: 3’, 5’, ATAC, Multiome, Flex, etc.
• Strong expertise in next-generation sequencing library preparation, including single-cell RNA‑seq, bulk RNA‑seq, CRISPR-based sequencing assays, and targeted sequencing workflows.
• Demonstrated experience supporting CRISPR-based genomics workflows, including Perturb‑seq, pooled CRISPR screens, guide sequencing, or related functional genomics applications.
• Demonstrated ability to independently design, optimize, troubleshoot, and execute complex genomics experiments with minimal supervision.
• Proven experience developing, validating, and implementing new NGS workflows while driving improvements in data quality, throughput, and reproducibility.
• Strong understanding of sequencing quality control methods, library characterization techniques, and experimental troubleshooting.
• Experience collaborating with multidisciplinary teams, including molecular biologists, automation engineers, and computational scientists.
• Ability to independently prioritize multiple projects while providing scientific and technical leadership within cross‑functional teams.
• Excellent written and verbal communication skills, including the ability to present technical findings to diverse scientific audiences.
• A proactive, collaborative mindset with strong troubleshooting and problem-solving abilities.
• Enthusiasm for working in a highly interdisciplinary startup environment.

Preferred Qualifications

• Experience working in a genomics core facility or high-throughput sequencing laboratory.
• Experience developing or supporting automated library preparation workflows.
• Experience with additional 10x Genomics applications such as ATAC, Immune Profiling, Multiome, etc.
• Experience with molecular cloning, cell engineering, lentiviral workflows, or other functional genomics techniques.
• Basic familiarity with bioinformatics tools, NGS data quality assessment, and sequencing data analysis pipelines.
• Experience evaluating and implementing emerging sequencing technologies.
• Experience supporting AI/ML‑driven biological research through generation of high-quality genomic datasets.

Compensation

Annual

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 $124,000 to $155,000 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.

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