The ideal person for this position is a bioinformatician who lives and breathes NGS data analysis and is passionate about learning. The successful candidate will have deep knowledge of NGS technologies, quality analysis for read alignment and variant calling (secondary analysis), and a large suite of analytical methods for discovering genetic components of human diseases (tertiary analysis).
Responsibilities will include:
- Meeting faculty members and researchers to evaluate their bioinformatics needs.
- Conducting data analysis that meets quality standards of major peer-reviewed publications.
- Providing faculty members and researchers with data, analysis protocols, figures, method descriptions, code, documentation, support, and anything else that might be needed to meet project goals.
- Managing time and projects efficiently to support the analysis needs of multiple labs simultaneously.
- Establishing, refining, and standardizing the process for bioinformatics analysis and validation. Benchmark-driven development is expected, e.g., use of PrecisionFDA/Genome-in-a-Bottle for DNASeq analysis, or the use of well-characterized data or simulated data where commonly-used reference datasets do not exist.
- Presenting bioinformatics efforts and best-practices at conferences and symposia. Writing peer-reviewed publications with and outside of client laboratories are strongly encouraged as a part of this position.
- Delivering quick proof-of-concept feedback on new methods and protocols.
- Providing training to researchers to allow them to learn and use new techniques for analysis.
- Staying abreast with bioinformatics best-practices (e.g., large consortium Data Coordination Centers like ENCODE and HMP) as well as cutting-edge data analysis methods from recent publications.
- Meeting 3rd party developers, service providers, and consortium members to stay on top of development of new tools, solutions, and practices in the field.
- Observing the highest standards of customer interaction, including maintaining confidentiality when required.
- - Other duties may also be assigned.
This position will take direction from and collaborate with senior bioinformatics team members, who will manage the interactions between team members and the members of the client lab.
The GBSC bioinformatics service team is supported by a group of expert software developers and biomedical engineers who are proficient in a variety of development environments, including large HPC clusters and multiple cloud platforms (e.g., DNAnexus, Google Cloud Platform).
- While a wide background in NGS bioinformatics will be useful, deep experience with DNA-seq and/or RNA-seq data is strongly preferred, including whole genome, whole exome, SNP-array, tumor/normal.
- Strong background in one or more of the following: pedigree analysis, machine learning, statistical methods, variant annotation and interpretation, Genome Wide Association Studies (GWAS).
- Knowledge of general principles for regulatory compliance, including understanding of the NIH Security Best Practices for Controlled Access Data Subject to the NIH Genomic Data Sharing (GDS) Policy (aka dbGaP compliance).
- Experience working in academic environments.
- Experience with mentorship or project management.
EDUCATION & EXPERIENCE (REQUIRED):
- Bachelor's degree and three years of relevant experience or a combination of education and relevant experience.
KNOWLEDGE, SKILLS AND ABILITIES (REQUIRED):
- Current knowledge of latest software and design standards.
- Ability to define and solve logical problems for technical applications.
- Knowledge of and ability to select, adapt, and effectively use a variety of programming methods.
- Ability to recognize and recommend needed changes in user and/or operations procedures.
- Basic knowledge of software engineering principles.
- Strong knowledge of at least one programming language.
- Ability to define and solve logical problems for highly technical applications.
- Deep understanding of next¬-generation sequencing data and bioinformatics algorithms. While Illumina sequencers are the most common data source, it is not unusual to see 10xGenomics or PacBio data.
- Provide best-¬practices data analysis, including QC and visualization, employing common NGS pipelines such as RNAseq, ChIP-seq, ATAC-seq, Methyl-seq, DNA-seq, and Microbiome Sequencing. Multiomics analysis is often needed.
- Proven experience working in a Linux cluster environment. Experience in cloud environments is also a plus.
- Ability to select, adapt, and effectively use a variety of programming methods. Strong programming skills in Python and R are expected. Familiarity with C, C++, Java. and Perl are useful. Best practices in coding, including techniques of reproducible and transparent science (github, DockerHub, markdown documentation) will be required.
- The core team has developed extensive set of data analysis pipelines on the local cluster and the cloud. We expect reuse of these pipelines. The candidate is also expected to add to this analysis library by developing custom/novel pipelines.
- Excellent verbal and written communication skills with both technical and non-technical clients.
- Stanford offers a supporting learning environment and ability to learn rapidly is a critical need. Our service supports a large and growing customer base and Stanford researchers are engaged in innovative basic science research. We expect our team members to ramp up rapidly to support this level of innovation.
- Strong work ethics are critical in this role, since the individual will be responsible for the highest quality scientific data analysis.
- Constantly perform desk-based computer tasks.
- Frequently sit, grasp lightly/fine manipulation.
- Occasionally stand/walk, writing by hand.
- Rarely use a telephone, lift/carry/push/pull objects that weigh up to 10 pounds
- - Consistent with its obligations under the law, the University will provide reasonable accommodation to any employee with a disability who requires accommodation to perform the essential functions of his or her job.
- May work extended hours, evening and weekends.
- Interpersonal Skills: Demonstrates the ability to work well with Stanford colleagues and clients and with external organizations.
- Promote Culture of Safety: Demonstrates commitment to personal responsibility and value for safety; communicates safety concerns; uses and promotes safe behaviors based on training and lessons learned.
- Subject to and expected to comply with all applicable University policies and procedures, including but not limited to the personnel policies and other policies found in the University's Administrative Guide, http://adminguide.stanford.edu.