Bioinformatics Engineer

OverviewStanford University is seeking a Bioinformatics Engineer to support the GREGoR Stanford Site (GSS) pipeline and data analysis team. The role focuses on development of pipelines and tools for comprehensive analysis of large multi-omics datasets (genomics, transcriptomics, metabolomics) and establishing cloud infrastructure for storage and computation. The work is onsite and requires collaboration with a multidisciplinary team to enable diagnosis and discovery of disease-gene associations.ResponsibilitiesDevelop pipelines and tools for the analysis of large multi-omics data generated by the GREGoR Stanford Site.Establish and maintain cloud infrastructure for GSS on AnVIL and Google Cloud Platform (GCP).Interact with GREGoR team members and external tool developers to implement new tools, algorithms, and updates.Develop intuitive reports for molecular pipelines to track progress and quality metrics.Monitor and report issues with pipeline analysis and underlying data.Extract relevant data from diverse sources, including RESTful APIs, databases, and medical records.Serve as a resource for bioinformatics inquiries from clinical team members.Collaborate with stakeholders across the consortium to understand data structures and model metadata schemas.Mentor Junior Analysts on primary analysis.Document and report as needed to fulfill grant and regulatory obligations.Note: This position is fully onsite.Other duties may be assigned.QualificationsGraduate degree (Ph.D. or M.S.) in bio/medical informatics, engineering, computer science, statistics, or related field.Domain expertise in analysis and running pipelines for at least one of: genomics, transcriptomics, metabolomics, ATAC-seq, proteomics.Proficiency in Python and/or R and Linux shell scripting.Experience with pipeline languages such as WDL, Snakemake, or Nextflow.Experience with data and infrastructure management in HPC clusters or cloud (e.g., GCP, AWS).Experience with container systems and deploying virtual machines or Docker instances.Experience with code management (e.g., GitHub).Knowledge of systems biology approaches for data integration is a plus.Experience in developing tools and statistical methods for large-scale data analysis is a plus.Biological domain knowledge (rare disease) is a plus.Experience in bioinformatics or software development in team settings; willingness to work in a collaborative NIH consortium environment.Ability to quickly learn new tools and skills and strong communication skills for reporting results.Ability to work independently to locate papers, assess methods, implement approaches, and apply them to datasets.Education & Experience (Required)Bachelor’s degree and three years of relevant experience, or an equivalent combination of education and experience. Experience in a quantitative discipline (e.g., economics, finance, statistics, engineering).Knowledge, Skills, and Abilities (Required)Substantial experience with MS Office and analytical software.Excellent writing and analytical skills.Ability to prioritize workload.Physical RequirementsProlonged sitting and keyboarding with dexterity.Occasional telephone use.Limited handwriting.Reasonable accommodations available for employees with disabilities as required by pensationThe expected pay range for this position is $108,002 to $128,138 per annum. Stanford provides pay ranges as a good faith estimate, with final pay determined by factors including scope and responsibilities, qualifications, budget, internal equity, geographic location, and market comparisons.Benefits and Workplace CultureStanford provides a comprehensive rewards package. Details are available at Cardinal at Work. Benefits may be discussed during the hiring process.Equal OpportunityStanford is 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