Inside Higher Ed
Bioinformatics Engineer II (18 Month Fixed-Term) (Hybrid Opportunity)
Inside Higher Ed, Stanford, California, United States, 94305
Overview
Join to apply for the
Bioinformatics Engineer II (18 Month Fixed-Term) (Hybrid Opportunity)
role at
Inside Higher Ed . The Department of Medicine, Division of Cardiovascular Medicine at Stanford University is seeking a Bioinformatics Engineer II to join the Bioinformatics Core (BIC) of the Molecular Transducers of Physical Activity Consortium (MoTrPAC). You will help unravel the molecular mechanisms underlying the benefits of physical activity, working under the supervision of co-PIs Dr. Euan Ashley and Dr. Matthew Wheeler to support personalized exercise science and public health. Your work will focus on genome, epigenome, and transcriptome analyses (GET) using WGS, ATAC-seq, and RNA-seq, developing scalable workflows, and delivering analysis-ready results and visualizations to the consortium. This is an 18-month fixed-term, hybrid-eligible position. Responsibilities
Architect and operate scalable workflows for GET analyses (WGS variant calling and joint genotyping, RNA-seq quantification and differential expression, ATAC-seq peak calling and differential accessibility). Adapt rigorous QC frameworks across modalities and deliver integrated multi-omics analyses (eQTL/caQTL/colocalization) with clear visualizations, genome browser tracks, and interactive dashboards. Build reproducible pipelines with Nextflow and/or WDL/Cromwell (or Snakemake), containerize and test for cloud and HPC deployment; leverage GCP services (Cloud Storage, BigQuery). Design robust schemas for omics metadata and results; apply software engineering best practices (version control, code reviews, automated testing, documentation) and data governance aligned with FAIR principles and secure handling of controlled-access genomic data. Collaborate with wet-lab scientists, clinicians, and data engineers to translate biological questions into robust computational analyses and communicate findings in reports, presentations, and publications. Qualifications
Comprehensive RNA-seq workflows (read alignment, quantification, QC, differential expression; isoform and fusion analyses as a plus). Extensive experience with WGS data from raw reads to variant calling and interpretation; proficiency with BWA, GATK Best Practices, DeepVariant, bcftools, and scalable VCF/BCF handling. Experience with SV/CNV calling and QC (e.g., Manta, Delly, LUMPY) and cohort metrics. ATAC-seq processing and analysis (alignment, peak calling, QC metrics, differential accessibility, footprinting, motif enrichment); regulatory element annotation. Multi-omics data integration (eQTL/caQTL/colocalization) and linking chromatin accessibility to gene expression. Advanced Python and R (Bioconductor) for genomics; strong statistical and reproducible analysis skills. Experience designing, testing, and deploying workflows in cloud/HPC with containerization and CI/CD; familiarity with Nextflow and/or WDL/Cromwell. Experience with GCP (Cloud Storage, BigQuery) and genomics platforms (Terra, AnVIL); SQL and omics metadata schema design; knowledge of gnomAD, ClinVar, Ensembl/RefSeq, dbSNP. Genome browser expertise and ability to create publication-quality visualizations and dashboards. Software engineering practices: version control, code review, testing, and documentation; data governance and FAIR compliance; HIPAA/IRB awareness for controlled-access data. Strong collaboration and communication skills to work with cross-functional teams. Education & Experience (required)
Bachelor’s degree and three years of relevant experience, or equivalent combination of education and experience. Experience in a quantitative discipline is preferred. Knowledge, Skills And Abilities (required)
Substantial experience with MS Office and analytical software; excellent writing and analytical skills; ability to prioritize workload. Certifications & Licenses
None Physical Requirements
Sitting at a computer for long periods; keyboarding/dexterity; occasional telephone use; light writing by hand. Working Conditions
Work may be performed in a laboratory or field setting. Working Standards
Interpersonal skills to work with Stanford colleagues and external partners; commitment to safety; adherence to University policies and procedures. The expected pay range for this position is $108,002 to $128,138 per annum. Stanford University provides pay ranges representing its good faith estimate of compensation. Details about rewards and benefits are discussed during the hiring process. Why Stanford is for You
Benefits
Stanford offers a comprehensive rewards package with opportunities for growth, a caring culture, health benefits, retirement plans, and resources to support work-life balance. Equal Opportunity
Stanford 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. Additional information: Schedule: Full-time; Job Code: 4752; Employee Status: Fixed-Term; Requisition ID: 107526; Work Arrangement: Hybrid Eligible.
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Join to apply for the
Bioinformatics Engineer II (18 Month Fixed-Term) (Hybrid Opportunity)
role at
Inside Higher Ed . The Department of Medicine, Division of Cardiovascular Medicine at Stanford University is seeking a Bioinformatics Engineer II to join the Bioinformatics Core (BIC) of the Molecular Transducers of Physical Activity Consortium (MoTrPAC). You will help unravel the molecular mechanisms underlying the benefits of physical activity, working under the supervision of co-PIs Dr. Euan Ashley and Dr. Matthew Wheeler to support personalized exercise science and public health. Your work will focus on genome, epigenome, and transcriptome analyses (GET) using WGS, ATAC-seq, and RNA-seq, developing scalable workflows, and delivering analysis-ready results and visualizations to the consortium. This is an 18-month fixed-term, hybrid-eligible position. Responsibilities
Architect and operate scalable workflows for GET analyses (WGS variant calling and joint genotyping, RNA-seq quantification and differential expression, ATAC-seq peak calling and differential accessibility). Adapt rigorous QC frameworks across modalities and deliver integrated multi-omics analyses (eQTL/caQTL/colocalization) with clear visualizations, genome browser tracks, and interactive dashboards. Build reproducible pipelines with Nextflow and/or WDL/Cromwell (or Snakemake), containerize and test for cloud and HPC deployment; leverage GCP services (Cloud Storage, BigQuery). Design robust schemas for omics metadata and results; apply software engineering best practices (version control, code reviews, automated testing, documentation) and data governance aligned with FAIR principles and secure handling of controlled-access genomic data. Collaborate with wet-lab scientists, clinicians, and data engineers to translate biological questions into robust computational analyses and communicate findings in reports, presentations, and publications. Qualifications
Comprehensive RNA-seq workflows (read alignment, quantification, QC, differential expression; isoform and fusion analyses as a plus). Extensive experience with WGS data from raw reads to variant calling and interpretation; proficiency with BWA, GATK Best Practices, DeepVariant, bcftools, and scalable VCF/BCF handling. Experience with SV/CNV calling and QC (e.g., Manta, Delly, LUMPY) and cohort metrics. ATAC-seq processing and analysis (alignment, peak calling, QC metrics, differential accessibility, footprinting, motif enrichment); regulatory element annotation. Multi-omics data integration (eQTL/caQTL/colocalization) and linking chromatin accessibility to gene expression. Advanced Python and R (Bioconductor) for genomics; strong statistical and reproducible analysis skills. Experience designing, testing, and deploying workflows in cloud/HPC with containerization and CI/CD; familiarity with Nextflow and/or WDL/Cromwell. Experience with GCP (Cloud Storage, BigQuery) and genomics platforms (Terra, AnVIL); SQL and omics metadata schema design; knowledge of gnomAD, ClinVar, Ensembl/RefSeq, dbSNP. Genome browser expertise and ability to create publication-quality visualizations and dashboards. Software engineering practices: version control, code review, testing, and documentation; data governance and FAIR compliance; HIPAA/IRB awareness for controlled-access data. Strong collaboration and communication skills to work with cross-functional teams. Education & Experience (required)
Bachelor’s degree and three years of relevant experience, or equivalent combination of education and experience. Experience in a quantitative discipline is preferred. Knowledge, Skills And Abilities (required)
Substantial experience with MS Office and analytical software; excellent writing and analytical skills; ability to prioritize workload. Certifications & Licenses
None Physical Requirements
Sitting at a computer for long periods; keyboarding/dexterity; occasional telephone use; light writing by hand. Working Conditions
Work may be performed in a laboratory or field setting. Working Standards
Interpersonal skills to work with Stanford colleagues and external partners; commitment to safety; adherence to University policies and procedures. The expected pay range for this position is $108,002 to $128,138 per annum. Stanford University provides pay ranges representing its good faith estimate of compensation. Details about rewards and benefits are discussed during the hiring process. Why Stanford is for You
Benefits
Stanford offers a comprehensive rewards package with opportunities for growth, a caring culture, health benefits, retirement plans, and resources to support work-life balance. Equal Opportunity
Stanford 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. Additional information: Schedule: Full-time; Job Code: 4752; Employee Status: Fixed-Term; Requisition ID: 107526; Work Arrangement: Hybrid Eligible.
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