Stanford Center for Genomics and Personalized Medicine (SCGPM), situated in the heart of SF Bay Area, has an excellent opportunity available for a motivated junior bioinformatician. This position within our bioinformatics core team will support bioinformatics consulting services for faculty and researchers via the Genetics Bioinformatics Service Center (GBSC). For examples of the projects we support, please visit http://med.stanford.edu/gbsc/baas.html.
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).
We recommend that interested candidates explore the NIH RePORTER website (https://projectreporter.nih.gov/) to see the range of basic science research Stanford investigators are engaged in. Our bioinformatics service strives to support the entire range of research that is funded by NIH at Stanford.
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. Additional Information
Location: School of Medicine, Stanford, California, United States Schedule: Classification Level:
Stanford is an equal opportunity employer and all qualified applicants will receive consideration without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, veteran status, or any other characteristic protected by law.
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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 dedicated 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, 12000 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 is an equal empl...oyment 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. Stanford also welcomes applications from others who would bring additional dimensions to the University’s research, teaching and clinical missions.