The Institute for Systems Biology (ISB) is a leading research institution in the fields of computational and systems biology, with a focus on issues in human health. The Shmulevich lab is looking for a Bioinformatics Scientist to take part in a multiyear, National Cancer Institute (NCI) funded Cancer Moonshot effort to support the development of the Human Tumor Atlas Network (HTAN, humantumoratlas.org). The network is using transformative technologies and computational approaches to develop a comprehensive view of cancer. Related projects in which the lab plays a key role are the ISB Cancer Genomics Cloud (isb-cgc.org), the CRI iAtlas interactive portal for immuno-oncology research (cri-iatlas.org), and NCI's Imaging Data Commons (imaging.datacommons.cancer.gov). We are looking for someone with a high-level of self-motivation and a strong work ethic. Excellent analytical, programming, and communication skills are essential - as is careful attention to detail.

The candidate will work with software engineers, bioinformaticians and scientists in our lab, as well as with our HTAN collaborators to develop and implement software to enable data sharing both within the network and with the scientific community. Accomplishing this will involve solving a variety of technical challenges ranging from setting up mechanisms for managing and curating large heterogeneous data sets to enabling data access to researchers with varying levels of computational experience through cloud technologies.

This position will provide an excellent opportunity to work and train as part of a highly motivated interdisciplinary team in the rapidly developing areas of cancer genomics, biomolecular imaging and precision cancer care. HTAN includes a wide variety of data types, ranging from clinical and phenotypic information, sequence data, single-cell gene expression and methylation data as well as imaging data from multiple platforms.

Typical job responsibilities will include:

• Collaborating with biologists and software engineers on the development of data models and workflows to support the variety of data types
• Employing a variety of scripting languages and tools that bridge across disparate systems
• Learning about, understanding, evaluating, and incorporating new cloud tools and technologies
• Rapidly translating concepts to prototypes for user interfaces
• Understanding an existing codebase, and learning how to interact with a variety of other tools, data resources, APIs, etc.
• Working with workflow languages and batch computing tools to support data processing workflows
• Enabling sharing of HTAN data through NCI's Cancer Research Data Commons
• Working with HTAN data contributors to enable and facilitate data transfer and annotation
• Authoring computational notebooks, documentation, and other resources that inform researchers about HTAN data and capabilities

Required education, skills, and experience:

• MS in Bioinformatics, Data Science, Computer Science or related discipline
• Hands-on development experience; coding samples are highly desired
• Proficiency in Python/Jupyter and/or R/RStudio
• Experience with version control systems (e.g. Git/GitHub)
• Strong analytical, programming, and communication skills
• Motivation to explore data and code with careful attention to detail
• Experience with common bioinformatics methods, tools, and data resources, e.g.:
  • high-throughput data processing tools and techniques
  • exploratory data analysis, statistical analysis and visualization
  • genome sequence analysis, retrieving, manipulating and managing data from public data repositories such as GDC, TCGA, ENCODE, NCBI and Ensembl

Desirable skills and experience:

• Cloud computing infrastructures (Google Cloud Platform and AWS)
• Relational or NoSQL databases (eg MySQL, Postgres, BigQuery, MongoDB)
• Knowledge of workflow systems such as Nextflow, Common Workflow Language

Applicants should include a brief statement summarizing their relevant experience, personal goals, and reasons for interest in the position.

Physical Demands:

Position is in a typical office environment with no adverse environmental conditions expected. Regularly requires sitting for extended periods. Regularly required to lift and/or move up to 10 pounds. Frequently required to communicate with others using voice and hearing to exchange information. Regularly requires repeating motions that may include hands, wrist, or fingers (e.g. using a computer keyboard and mouse). Specific vision abilities required by this job include close vision, color vision, peripheral vision and ability to adjust focus.

ISB is an affirmative action and equal opportunity employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, sexual orientation, gender identity, gender expression, national origin, age, protected veteran or disabled status, or genetic information.

Pay Range: $67,725 - 104,680 annually

Benefits: https://isbscience.org/careers/benefits/