BIOINFORMATICIAN II

This Position is Fully Grant Funded

School of Medicine

Established in 1930, Duke University School of Medicine is the youngest of the nation's top medical schools. Ranked sixth among medical schools in the nation, the School takes pride in being an inclusive community of outstanding learners, investigators, clinicians, and staff where interdisciplinary collaboration is embraced and great ideas accelerate translation of fundamental scientific discoveries to improve human health locally and around the globe. Composed of more than 2,600 faculty physicians and researchers, nearly 2,000 students, and more than 6,200 staff, the Duke University School of Medicine along with the Duke University School of Nursing, and Duke University Health System comprise Duke Health, a world-class academic medical center. The Health System encompasses Duke University Hospital, Duke Regional Hospital, Duke Raleigh Hospital, Duke Health Integrated Practice, Duke Primary Care, Duke Home Care and Hospice, Duke Health and Wellness, and multiple affiliations.

Bioinformatician II

Summary

We are looking for a talented and motivated individual to work with teams of Researchers and Scientists providing bioinformatics expertise, consulting, application development, and support as part of the Duke Predictive Modeling Center (PMC), an NHGRI-funded center with the Impact of Genomic Variation on Function (IGVF) Consortium.

Work performed

• Contribute to the design, development, adaptation, implementation, and testing of neural networks that are used for predictive modeling of genomic data. Work involved with require increased independence of identifying and implementing solutions with some leadership and supervisory activities.  (30%)
• Train predictive models using machine learning approaches and technologies. This might include not only writing new code but repackaging and documenting existing scripts to make them reusable and easy to maintain. Work will include training increasingly complex models and will require navigating dynamic computing environments. (25%)
• Collaborate and consult with researchers individually or in small groups to analyze problems, recommend technology-based solutions, and design computational strategies for a wide range of biological research. Initiate interdisciplinary collaborations with other centers or departments within the Duke PMC and in collaboration with other research teams with the IGVF consortium. (20%)
• Recommend new methods, strategies, and improvements to incorporate into existing models. Try latest tools and analysis methods for new non-conventional genomic data (e.g. CRISPR screens), evaluating their fit and gradually incorporating them into existing analysis pipelines. (15%)
• Provide training on bioinformatics-related concepts, applications, and tools to researchers across the PMC and relevant teams within the IGVF. Design and participate in hands-on workshops to teach scientists how to use predictive models and associated neural networks so that these resources are accessible to other groups. (10%)

Skills

• Experience working with high throughput sequencing datasets (e.g. RNA-seq, ChIP-seq, ATAC-seq, etc.).
• Strong and demonstrable programming skills in Python, Tensorflow, and/or R.
• Experience with independently identifying solutions and ability to investigate and learn new approaches necessary to adapt existing or new models.
• Experience with collaborative development environments, including management of shared repositories (github).
• Good communication skills; run and deliver results in a clear and precise way.
• Familiarity with High Performance Computing clusters (e.g. SLURM, PBS), including computing environments constructed with CPUs and GPUs.
• Familiarity with workflow languages (e.g. CWL, WDL).

Education

Work requires a M.S. in Bioinformatics or the biological sciences with demonstrable computational skills or a M.S. in computer science with a strong interest in biology/genomics. PhD preferred.

Experience

Strong expertise with programming required.

Work requires a M.S. in Bioinformatics or the biological sciences with demonstrable computational skills or a M.S. in computer science with a strong interest in biology/genomics. PhD preferred.

Work requires at least 2 years of experience in bioinformatics. OR AN EQUIVALENT COMBINATION OF RELEVANT EDUCATION AND/OR EXPERIENCE Experience with web-based bioinformatics tools, public domain biological databases and software tools for sequence, domain and structural analysis. Extensive familiarity with and development of computational tools in biology that use genomic data to generate biological hypotheses. Experience with a procedural language, proficient in Java, Perl, 'C', web design, DNA genome informatics, proteomics informatics, statistics, and computer science. Experience with relational databases and SQL helpful.

Duke is an Affirmative Action/Equal Opportunity Employer committed to providing employment opportunity without regard to an individual's age, color, disability, gender, gender expression, gender identity, genetic information, national origin, race, religion, sex, sexual orientation, or veteran status.

Duke aspires to create a community built on collaboration, innovation, creativity, and belonging. Our collective success depends on the robust exchange of ideas—an exchange that is best when the rich diversity of our perspectives, backgrounds, and experiences flourishes. To achieve this exchange, it is essential that all members of the community feel secure and welcome, that the contributions of all individuals are respected, and that all voices are heard. All members of our community have a responsibility to uphold these values.

Essential Physical Job Functions: Certain jobs at Duke University and Duke University Health System may include essentialjob functions that require specific physical and/or mental abilities. Additional information and provision for requests for reasonable accommodation will be provided by each hiring department.