Positions

Cancer Variant Curator

We are currently seeking to hire a Cancer Variant Curator. If you are interested to learn more please contact us for details or follow the Application Link

The position’s primary task will be assisting in the editorial maintenance and evolution of the Clinical Interpretations of Variants in Cancer knowledgebase (civicdb.org). The position will involve review of genomic findings to assist in the curation of the biomedical literature and use of basic bioinformatics skills and resources. Initially, most effort will involve mining the literature and creating summaries of known clinically actionable genomic alterations. The applicant will ultimately be expected to help produce educational materials and training of other CIViC curators as part of their role on the project. Individuals in this role will be expected to support planned Hackathon and Curation Workshops (at national and international venues), providing training and organizational / planning support alongside other CIViC team members. Prior events can be found here. Collaboration with developers, clinicians and researchers is a routine portion of this position.

Role requirements: Strong oral and written communication skills Extensive experience in variant interpretation and/or cancer research Candidates can demonstrate significant independence and drive Bioinformatic or programming experience is preferred

Learning expectations: The position will involve review of cancer genomic literature and will greatly increase the applicants knowledge of this field with a specific focus on the well-characterized recurrent genomic aberrations that currently have clinical implications as predictive, diagnostic, predictive, or prognostic markers as well as functional characterization of variants. Use of common informatics tools (Biomart, genome browsers, etc) will be necessary. Some amount of basic programming may be learned but this is not the main focus.

Position highlights: CIViC has gained international recognition, with routine conference calls with clinical directors, bioinformaticians and researchers from around the globe. Ample connections to ABMGG certified individuals and clinical labs are provided. Attendance of at least 1 conference per year will be supported. Co-authorship and potentially lead authorship on future publications is anticipated. Driven candidates have the opportunity for international exposure, research inquiries, bioinformatic experience and collaboration with organizations driving international standards and guidelines. The prior candidate in this position went on to a laboratory genetics and genomics fellowship.

Supervision: The initial phase of training will involve one on one instruction from postdoctoral fellows or faculty with the expectation of self-directed work. Weekly meetings with the CIViC team and Griffith Lab will be expected. Additional formal meetings will be conducted as needed.

Read more about CIViC:

• Initial publication in Nature Genetics
• ClinGen Collaboration
• CIViC Curation Standard Operating Procedures

Related publications:

• CIViCpy - CIViC analysis toolkit (in review)
• CIViCmine - Text mining clinical relevant biomarkers (in review)
• GA4GH Variant Interpretation for Cancer Consortium - (in review)

Bioinformatics staff

We are currently seeking to hire at least one bioinformatician. If you are interested to learn more please contact us for details or follow the Application Link.

Position summary Assists in developing and conducting research projects, including experimental design, data analysis, and documentation of experiment results. The primary focus of this position will be the analysis of genomic and transcriptomic data from patients with various types of cancer, the creation of new computational approaches for cancer genomics and immunogenomics, and the development of tools to support these activities. Responsibilities include use of existing bioinformatics tools to process sequence data (alignment, variant calling, etc.), producing visualizations that aid interpretation of large data sets, working with software developers to release open access bioinformatics tools, and contributing to publications and educational workshops.

Primary duties and responsibilities

1. Designs, develops, and implements:
   • Algorithms and computer software for analyzing high-throughput, massively parallel genomic data sets;
   • Relational databases to store, disseminate and analyze data, including verification of data submitted and recommendations for analyses;
   • Web interfaces and queries to access relational databases; maintains web server;
   • Independent research projects, including design of research protocols and development of procedures for the collection, verification, and management of data.
2. Performs complex systems analysis of data and writes interpretative reports.
3. Evaluates commercial and academic bioinformatics software.
4. Trains other researchers on the everyday use of analysis software and research databases.
5. Assists with grant preparation and reporting of methods, data, and results.
6. Solves practical problems relating to difficulties with equipment or test subjects; suggests technical or procedural improvements in testing methods.

Computer scientist and engineering staff

While we do not currently have official positions open for software engineers, we are often aware of such positions. Please feel free to contact us if you are a computer scientist or engineer with a strong interest in application of these skills to basic and translational cancer research.