Bioinformatics Engineer

OverviewStanford University is seeking a Bioinformatics Engineer to manage and analyze large amounts of information independently with minimal supervision.You will work with a leading-edge community of faculty and staff changing the world of health care and will have opportunities to influence and drive change with innovative ideas in a fast-paced, energetic environment.BenefitsEvents and programs for children, sports camps, and tuition optionsWorld-class learning and development opportunities, onsite conferences, and access to leading speakers and facultyWork/life and family-friendly policies and reimbursementParticipation in Stanford’s social responsibility and sustainable programsA vibrant university culture that values individual contributionsAbout the DepartmentThe Department of Pathology at Stanford School of Medicine is a leader among its peers. The department’s mission is to improve the diagnosis, treatment, and understanding of human disease through discovery, education, and clinical care. The department conducts clinical services across fields of anatomic and clinical pathology, molecular and genomic pathology, histocompatibility testing, and transfusion medicine, and supports research that advances precision medicine and health.For more information about the department, visit the Stanford pathology site. About GREGoR Stanford SiteGREGoR Stanford Site (GSS) is one of six NIH GREGoR consortium sites. The GSS mission is to provide a platform for functional genomics research and validation to improve diagnosis in Mendelian disease through integrated analysis of multi-omics data. The GSS is led by co-PIs from pathology, cardiovascular medicine, and medical genetics. The work includes exome sequencing, genome sequencing, transcriptomics, methylation assays, metabolomics, and lipidomics, analyzed with HIPAA-compliant cloud platforms and validated with advanced experimental approaches.PositionWe are seeking a highly talented Bioinformatics Engineer to support the GSS pipeline and data analysis team. Responsibilities include developing pipelines and tools for large-scale molecular data analysis (genomics, transcriptomics, metabolomics), and establishing and supporting cloud infrastructure for storage and computation. Strong understanding of biological experiments, large-scale data analysis, programming, and HPC or cloud environments is required.A complete application includes a CV and cover letter.Duties IncludeDevelop pipelines and tools for the analysis of large multi-omics data generated by GSSEstablish and maintain cloud infrastructure for GSS on AnVIL and GCPCollaborate with GREGoR team members and external tool developers to implement new tools and updatesDevelop intuitive reports for molecular pipelines to track progress and quality metricsMonitor pipeline analysis and data qualityExtract relevant data from various sources, including RESTful APIs, databases, and medical recordsServe as a resource for bioinformatics inquiries from clinical team membersModel metadata schemas by working with stakeholders across the consortiumMentor Junior Analysts on primary analysisDocument and report to fulfill grant and regulatory obligationsNote: This position will be fully onsiteOther duties may also be assignedDesired QualificationsGraduate degree (PhD or MS) in bio/medical informatics, engineering, computer science, or statistics preferredDomain expertise in at least one omics area (genomics, transcriptomics, metabolomics, ATAC-seq, proteomics)Proficiency in Python and/or R and Linux bash scriptingExperience with pipeline languages such as WDL, Snakemake, or NextflowExperience with HPC clusters or cloud platforms (GCP or AWS) and data/infrastructure managementExperience with container systems and setting up VMs and DockerExperience with code management (e.g., GitHub)Experience in systems biology data integration is a plusExperience developing tools and statistical methods for large-scale data analysis is a plusBiological domain knowledge in rare diseases is a plusExperience in bioinformatics or software development on team-based projectsAbility to work in a collaborative environment; NIH consortium experience a plusAbility to quickly learn new tools and skillsStrong communication skills and ability to prepare reports and presentationsAbility to work independently and reproduce results from methods and datasetsEducation & Experience (Required)Bachelor’s degree and three years of relevant experience, or combination of education and relevant experience. Experience in a quantitative discipline is preferred.Knowledge, Skills, and Abilities (Required)Substantial experience with MS Office and analytical programsExcellent writing and analytical skillsAbility to prioritize workloadPhysical RequirementsSitting at a computer for long periods with extensive keyboardingOccasionally use a telephoneRarely write by hand* The university provides reasonable accommodation to employees with a disability to perform essential functionsCompensation and BenefitsThe expected pay range for this position is $108,002 to $128,138 per annum. Stanford provides a pay range as a good faith estimate, with final offers based on factors including scope and responsibilities, qualifications, budget, and market conditions. The Cardinal at Work website provides details on Stanford’s benefits and rewards. Specifics about the rewards package may be discussed during the hiring process.Additional InformationWhy Stanford is for you: Stanford offers career development programs, tuition reimbursement, health and wellness resources, and a culture of discovery and support. We are an equal employment opportunity and affirmative action employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, protected veteran status, or any other characteristic protected by law. #J-18808-Ljbffr

Created: 2025-09-17