Bioinformatics Engineer

Description

Arcus is seeking a Bioinformatics Engineer that will work in a highly embedded, collaborative model with colleagues across the organization.

The engineer will join highly technical, interdisciplinary teams and bring a creative, problem-solving mindset to challenging work. The successful applicant will help improve and harmonize bioinformatics processes, as well as take lead in augmenting a growing internal database of multimodal, high-dimensional datasets to enable critical bioinformatics functions. They will use their expertise to build infrastructure, develop pipelines and frameworks, optimize algorithms, and process harmonized high-dimensional molecular datasets.

The individual may also support cross-departmental infrastructure developments to enable effective inter-departmental information exchange and develop LLM systems (e.g., literature review agents, retrieval-augmented knowledge systems) to enable bioinformatics and drug development discoveries.

Responsibilities

• Process and QC high-dimensional datasets to expand internal databases (e.g., RNA-seq, scRNA-seq, spatial transcriptomics, proteomics, etc.).
• Maintain and improve internal pipelines for data processing, including RNA-seq and WES.
• Develop standardized internal pipelines for processing of additional data types such as scRNA-seq and spatial transcriptomics.
• Work closely with Bioinformatics Scientists on improving internal processes and databases to enable efficient data extraction and transformation for rapid bioinformatics analysis and visualization.
• Collaborate with constituencies in IT and Scientific Computing to improve on-prem and cloud-based infrastructures to support bioinformatics functions.
• Serve as the technical resource for optimizing pipelines, benchmarking algorithms, developing reproducible frameworks, and updating SOP documentation & internal knowledge base.

Qualifications

• Master's in Bioinformatics, Computational Biology, Data Science, Computer Science, or similar field, with 5+ years of experience.
• Strong understanding of data structures and transformations to enable efficient modeling.
• Proven coding expertise in Unix and SQL for systems and database query and development.
• Proficiency in R and/or Python for bioinformatics pipelines and analysis.
• Experience with a workflow language such as Snakemake or Nextflow.
• Adept at building reproducible computing environments using tools such as Docker, Singularity/Apptainer, uv, or conda.
• Ability to work with on-prem and cloud-based systems including HPC clusters (e.g., SLURM) and AWS.
• Fluent with version control using Git/GitHub and collaborating with other bioinformatics scientists/engineers.
• Comfortable working in a cross-functional environment and handling several concurrent fast paced projects.

Preferred Experience

• Understanding of high-dimensional molecular data types, such as RNA-seq, scRNA-seq, etc.
• Familiarity with best coding practices such as unit testing, CI/CD, reproducible code, and modular pipeline design.
• Experience developing pipelines and general frameworks for data analysis.
• Ability to write concise technical documentation.
• Familiarity with LLM-based tools, including LLM-assisted and agentic programming.

This hybrid role will be based at our Hayward, CA location. The anticipated salary range for fully qualified candidates applying for this position is $120,000 - $155,000 USD annually. This salary range is an estimate of what we reasonably expect to pay for this posted position. The actual salary may vary based on various factors including, without limitation, individual education, experience, tenure, skills and abilities, internal equity and alignment with market data. In addition to a competitive market-based salary, Arcus offers the opportunity to participate in stock programs, a performance-based bonus, and a comprehensive benefits package. Additional information about our total rewards program can be found here: https://arcusbio.com/careers.

Arcus Biosciences is an Equal Opportunity Employer and prohibits discrimination and harassment of any kind. Arcus is committed to the principle of equal employment opportunity for all employees and does not discriminate based on race, religion, color, sex, gender identify, sexual orientation, age, non-disqualifying physical or mental disability, national origin, veteran status or any other legally protected status. EOE/AA/Vets

PHYSICAL REQUIREMENTS: • Frequently stand, walk, twist, bend, stoop, squat, grasp lightly, use fine manipulation, grasp forcefully, perform desk-based computer tasks, use telephone, write by hand, lift, carry, push and pull objects weighing over 40 pounds. • Occasionally sit, kneel, crawl, reach and work above shoulders, sort and file paperwork or parts. • Rarely climb, scrub, sweep, mop, chop and mix or operate hand and foot controls. • Must have correctible vision to perform duties of the job. • Ability to bend, squat, kneel, stand, reach above shoulder level, and move on hard surfaces for up to eight hours. • Ability to lift heavy objects, possibly weighing up to 50 pounds. • Position may require repetitive motion. WORKING CONDITIONS: • May require working near blood borne pathogens. • May require work in an environment where animals are used for teaching and research. • Position may at times require the employee to work with or be in areas where hazardous materials and/or infectious diseases are present. • Employee must perform tasks that require the use of personal protective equipment, such as safety glasses and shoes, protective clothing and gloves, and possibly a respirator. • May require extended or unusual work hours based on research requirements and business needs. *Consistent with its obligations under the law, the company will provide reasonable accommodation to any employee with a disability who requires accommodation to perform the essential functions of their job.

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