Stanford Center for Genomics and Personalized Medicine (SCGPM), situated in the heart of SF Bay Area, has an excellent opportunity available for a motivated bioinformatician. This is a key position with bioinformatics core team that will support bioinformatics services via Genetics Bioinformatics Service Center (GBSC, details at http://med.stanford.edu/gbsc.html). For example projects, please visit http://med.stanford.edu/gbsc/baas.html. This position is 1 year, fixed-term, renewable based on funding.
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, various library preparation protocols, quality analysis, and a suite of analytical methods.
Responsibilities will include:
Meeting faculty members and researchers to evaluate their bioinformatics needs.
Conducting data analysis that meets quality needs of peer review publication.
Providing customers with data, analysis protocols, figures, method descriptions, code, documentation and anything else that might be needed to meet project goals.
Staying abreast with best practices (e.g. large consortium Data Coordination Centers like ENCODE and HMP) as well as cutting-edge data analysis methods from recent publications.
Providing quick proof-of-concept of new methods and protocols.
Establishing and refining the process for bioinformatics analysis and validation. Benchmark driven development is expected, e.g., use of precisionFDA/Genome-in-a-Bottle for DNA-Seq analysis, using well characterized data or simulated data where reference datasets do not exist.
Presenting the bioinformatics efforts and best practices at conferences. Peer reviewed publications are encouraged.
Managing time and projects efficiently to support analysis needs of multiple labs.
Provide training to researchers so they can become proficient in analysis.
Meeting 3rd party developers, service providers and consortium members to stay abreast of new tools, solutions and practices in the field and bring suitable ones in-house.
Observing highest standards of customer interaction including maintaining confidentiality where needed.
Members of SCGPM team are expected to participate in activities that are important to the Center mission including participation in conferences, arranging seminars, attending annual retreats and other academic events as necessary.
The bioinformatics service team is supported by a group of expert software developers and biomedical engineers who are proficient in a variety of development environment including large HPC cluster and multiple Clouds (DNAnexus, Google Cloud Platform).
We recommend that interested candidates further explore NIH RePORTER https://projectreporter.nih.gov/reporter.cfm (search for organization Stanford, text search Sequencing) to see the range of basic science research Stanford investigators are engaged in. Our bioinformatics service strives to support the entire range.
PhD in Bioinformatics, Computational Biology, Physics, Computer Science or related field.
Ability to define and solve logical problems for highly technical applications.
Proven experience working in a Linux cluster environment. Some solutions may need to be Cloud based.
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. Follow best practices in coding including reproducible and transparent science (github, dockerhub, markdown documentation).
Deep understanding of next-generation sequencing data and bioinformatics algorithms. While Illumina data is most common data type, 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 RNA-Seq, ChIP-Seq, ATAC-Seq, Methyl-Seq, DNA-Seq, and Microbiome Sequencing. Multi-omics analysis is often needed.
The core team has developed extensive set of data analysis pipelines on the local cluster and Cloud. We expect reuse of these pipelines. Candidate is also expected to develop 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 innovation.
Strong work ethics are critical in this role since the individual will be responsible for highest quality scientific data analysis.
While a wide background in NGS bioinformatics will be useful, deep experience with DNA-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 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.
Mentorship or project management experience.
What to expect during the interview process:
Candidates must apply through Stanford career site. Applications can not proceed unless you apply directly via Stanford career site. SCGPM Bioinformatics team follows SF Bay Area industry standards when conducting interviews. A typical interview process consists of resume screening, phone screenings, coding challenge, on-site visit, reference and background checks.
SCGPM Bioinformatics Core team members are dedicated and respectful individuals and will make their best effort to process your application in time. It is not unusual for the process to take 3 months and we appreciate your patience. We encourage candidates to explore Stanford benefits on the web and if you have specific constraints or questions, please make sure that you mention those in your cover letter.
Stanford may be able to process a H1-B visa for qualified candidates. We expect the candidate to be able to start on OPT while the visa is in process. H1-B visas can take 3 or more months to process.
Affirmative Action statement: Stanford University is an equal opportunity employer and is committed to increasing the diversity of its faculty and academic staff. It welcomes nominations of and applications from women and members of minority groups, as well as others who would bring additional dimensions to the Universitys research, teaching and clinical missions."
Located between San Francisco and San Jose in the heart of Silicon Valley, Stanford University is recognized as one of the world's leading research and teaching institutions. Leland and Jane Stanford founded the University to "promote the public welfare by exercising an influence on behalf of humanity and civilization." Stanford opened its doors in 1891, and more than a century later, it remains d...edicated to finding solutions to the great challenges of the day and to preparing students for leadership in a complex world. The University's thriving diverse community is comprised of nearly 7000 undergraduate students, 9000 graduate students, 2000 faculty members, 1900 postdoctoral scholars, and over 11,000 academic and administrative staff in seven schools including several interdisciplinary research centers and institutes. The campus spreads over 8000 contiguous acres and nearly all undergraduates live on campus. Stanford offers bachelor's and master's degrees in addition to doctoral degrees (PhD, MD, DMA and JD) plus a number of professional and continuing education programs and certifications. More at http://facts.stanford.edu and http://www.stanford.edu.
Stanford University is an equal opportunity employer and is committed to increasing the diversity of its faculty. It welcomes nominations of and applications from women, members of minority groups, protected veterans and individuals with disabilities, as well as from others who would bring additional dimensions to the university’s research, teaching and clinical missions.