Stanford Center for Genomics and Personalized Medicine (SCGPM), situated in the heart of SF Bay Area, has an excellent new opportunity available for a motivated Bioinformatics Data Analyst. This is a key position with bioinformatics core team. As part of SCGPM core team, you will have access to other team members (http://stan.md/2nVyOTd). In terms of computational facility, the team has access to SCGPM bioinformatics facility which provides a best-in-class on-premise HPC cluster and fully integrated Google Cloud Platform.
Specifically, for this project, we are in the process of developing a scalable Cloud platform for genomic data augmentation, and annotation to aid experimental data interpretation. Currently, to interpret experiment specific data, a researcher spends significant time performing suitable data ETL (extract, transform, load) to available knowledge-bases (ENCODE, GTEx, GEO, KEGG, MSigDB, GWAS Catalog ClinVar, GO, pharmGKB). Due to potential scale of the data involved, we use Google Cloud for platform (http://stan.md/2eztPHE). We have completed POC implementation to import an existing knowledge base into Google Genomics as annotation sets in a scalable programmatic manner. Once the annotation sets are created and stored, they can be used to augment a user's genomic data stored as variant sets or in BigQuery. We have demonstrated use of BigQuery for real time variant exploration (http://biorxiv.org/content/early/2015/12/24/035295). In future, this platform will also support visualization and other user facing web services.
The Bioinformatics Data Analyst will need to bring various biological and genomic annotation sources on Google Platform to support scalable analysis. Understanding of biology and genomics is essential as well as ability to parse highly scientific literature – journals and public databases. An ideal analyst will have in depth knowledge of biology, informatics methods and a desire to learn new programming paradigms, analytical methods and scientific approaches.
Other responsibilities will include:
Staying abreast with best practices as well as cutting-edge data analysis from recent publications.
Conducting data transformation, quality analysis, scientific analysis and interpretation that meets quality needs of peer review publication.
Providing researchers and collaborators with data, analysis protocols, figures, method descriptions, code, documentation and anything else that might be needed.
Presenting the scientific content in a suitable internal or external forum. These may include presenting at internal meetings or conferences, posters or peer reviewed publications.
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.
Members of SCGPM team are expected to participate in activities that are important to the Center mission as well as collaborator's mission. This includes:
observing highest standards of customer interaction
following compliance requirements
participation in conferences, arranging seminars, attending annual retreats and other academic events as necessary
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.