PROGRAM DESCRIPTION

KEY ROLES & RESPONSIBILITIES

• Function as a scientific thought leader within the CGR bioinformatics group and the CGR leadership team, and manage collaborative analytical efforts with DCEG investigators with an eye towards scientific productivity and reproducibility
• Provide technical expertise within a highly collaborative environment and support and establish a culture of engagement, innovation, and continuous improvement
• Collaborate closely with DCEG PIs on scientific manuscript development, submission, and revision activities with significant co-authorship and potentially first authorship opportunities
• Guide the development, execution, and continual improvement of robust, tested pipelines for a wide variety of computational genomics applications, with an emphasis on scalability, portability, and thorough documentation
• Utilize computational biology methods to integrate, analyze and visualize results with data sets obtained from a wide variety of genotyping platforms including whole-genome, methylation and targeted genotyping data generated by multiple applications, including Illumina Infinium, Illumina EPIC, TaqMan, qPCR and others
• Utilize computational biology methods to integrate, analyze and visualize results with data sets obtained from a wide variety of sequencing platforms including whole-genome, exome, transcriptome, methylome, microbiome, and targeted sequencing data generated by multiple technologies, including Illumina, Pacific Biosciences, Ion Torrent, Oxford Nanopore and others
• Manage the dissemination of data to DCEG investigators and other collaborators, including adequate technical and scientific annotation required for interpretation. Support posting of data sets to public data repositories (dbGaP/SRA/GDC) as required based on NIH genomic data sharing policies and in concert with existing ontologies and FAIR principles
• Develop and lead strategic approaches for IT infrastructure support, including management of on-prem resources, archiving strategies for all data streams with CGR and NCI staff utilizing FAIR data principles, implementation of appropriate cloud resources, software install support and data migration support
• Manage and coordinate with additional resources throughout DCEG, including fellows, post-docs, other contract resources to support an integrative, collaborative, collegial environment

BASIC QUALIFICATIONS

• Possession of a Bachelor's degree from an accredited college/university according to the Council for Higher Education Accreditation (CHEA) in computer science, software engineering, bioinformatics, statistics, or related field or four (4) years relevant experience in lieu of degree. Foreign degrees must be evaluated for U.S. equivalency
• In addition to educational requirements, a minimum of eight (8) years progressively responsible scientific software engineering and/or complex system management/bioinformatics experience, including six (6) years of experience supervising or leading teams or projects
• Team-oriented with excellent written and verbal communication skills, organizational skills, and attention to detail; ability to organize and execute multiple projects in parallel both independently and as part of working groups, interact effectively with cross-functional teams, including laboratory, LIMS, project management, data scientists, epidemiologists and biostatisticians
• Demonstrated experience in successfully managing bioinformaticians and serving as a mentor for other bioinformatics and/or software developer staff members on analysis approaches and best practices
• Proven ability and demonstrated strategies to stay current with new bioinformatics analysis tools and software technologies
• Experience managing complex pipelines, including support of best-practice full lifecycle software development experience and source code management (Git, SVN, unit testing) is required
• Proven experience and ability to benchmark tools and compare performance to existing pipelines
• Familiarity with workflow management systems and environment/dependency management tools
• Experience managing large computational tasks in a Linux-based high-performance computing environment
• Experience with a variety of programming languages and environments such as C/C++, Java, or Rust, and at least one scripting language such as Bash, Python, Perl, or R
• Ability to obtain and maintain a security clearance

PREFERRED QUALIFICATIONS

• Masters or PhD strongly preferred
• Familiarity with diverse primary sequencing tools (e.g. BWA/Novoalign, tophat/star/bowtie, bedtools, GATK suite, SV/CNV detection, somatic/low AF mutation detection, IGV, Samtools), Long reads (e.g. PacBio, Oxford Nanopore) based analysis (repeat analysis, assembly, large mutation detection, phasing), Microbiome analysis tools (e.g. QIIME II, DADA2, MetaPhlAn), GWAS QC and analysis tools (e.g. KING, GRAF, EAGLE, minimac, plink, Michigan Imputation Server, SNPtest, SAIGE, BOLT-LMM, VCFtools), and annotation tools (e.g. snpEff, Annovar, SIFT, PolyPhen)
• Experience with Google Cloud, AWS, or managed cloud environments
• Experience with CI/CD (GitLab CI/CD, GitHub Actions, Travis CI, CircleCI, etc.)
• Experience in using project management approaches for documentation and communication (Fogbugz, JIRA, Teams, Slack) to document/summarize project status and development activities
• Knowledge of various DevOps tools and technologies, such as Docker/Singularity, Kubernetes, Ansible/Terraform
• Familiarity with relational and NoSQL databases design, data warehousing, and data modeling (e.g. MySQL, Amazon Redshift, MongoDB, Elasticsearch, FileMaker)
• Hands-on experience with commercial and open-source bioinformatics and genomics analysis software (IVA, GoldenHelix, Sentieon)
• Ability to incorporate multiple data sources for use in downstream analysis, including microarray genotype data, epidemiological data, publicly available data sources (e.g. TCGA, ENCODE, 1000 Genomes, COSMIC, TopMed, gnomAD, ESP) and diverse genomic annotations.
• Experience with prioritization in a high-pressure environment

TERMS

LOCATION

HOW TO APPLY