BIOINFORMATICIAN I

Location
Durham, NC
Posted
Jun 21, 2017
Institution Type
Four-Year Institution

diversity employer



BIOINFORMATICIAN I
STATISTICAL CENTER


Applications will not be reviewed unless accompanied by a proper cover letter containing a statement of purpose for the application along with a summary of the candidate's technical and educational credentials relevant to the position

**This is a 100% sponsored funded position.**

Occupational Summary
This position is a key member of the Duke Cancer Institute (DCI) Bioinformatics team. Provide support for the statistical and computational considerations of research projects led by basic, translational, and clinical scientists from the DCI. These projects aim to address key questions in cancer biology, pharmacology, pharmacogenomics, and immunology on the basis of data generated from high-throughput genomic sequencing assays. Provide support for data quality control and assessment, analysis, and reporting for multiple research projects within the framework of strict adherence to the principles of reproducible analysis and literate programming. Participate as a key member of each project to which he or she is assigned and therefore expected to develop a solid understanding of the scientific hypotheses and considerations of the project. While being heavily engaged in data analysis considerations, the expectation is to actively participate in and contribute to the development of statistical methods and computational tools needed to address the scientific considerations of each project.

Work Performed

Data Analysis and Programming
Provide support for analysis of genomic data from array and high-throughput sequencing assays. This will include quality assessment analysis, downstream statistical analysis, and genomic annotation. The downstream analyses will include association analyses as well as supervised (e.g., machine learning) and unsupervised (e.g., class discovery) learning.

Contribute to statistical study design, including power and sample size calculations using existing software or by conducting simulation studies.
Understand the scientific objectives of each project to which he or she is assigned. Critically review study documents (e.g., protocols), and the relevant biology and medical literature.

Independently validate analysis data sets and analysis results programmatically.

Documentation (software, analysis, website)
Use systems for dynamic report generation (e.g., knitr or Jupyter) to generate reproducible and literate reports.
Contribute to the development, testing, documentation, and deployment of data analysis pipelines, designed for use on local, cloud server, and cluster resources, for pre-processing of genomic data.

Contributions to methods research and tools development
Possess a solid understanding, including strengths and limitations, of any method or tool used for the analysis of the data. Conduct critical reviews of any relevant technical documentation.

Use modern programming tools and frameworks for data science, including the R tidyverse and python pandas ecosystems, to conduct elegant, efficient and reproducible data programming tasks. Use various data models (e.g., hdf5), and relational (e.g., PostgreSQL) and non-relational (eg., MongoDB) databases to store and manage data.

Contribute to the writing of methods and software papers. Conduct simulation studies, conduct data analysis, and contribute to programming and documentation of code.

Software & paper review
Continually extend his or her knowledge and expertise in statistical methods (e.g., competing risks and cause-specific hazard analysis) and computational algorithms, and successfully apply them to the projects.

Conduct critical reviews of existing analysis methods and tools and present the findings to the team so as to help with the assessment of the feasibility and appropriateness for adopting new methods and tools.

Administrative tasks and meetings
Prepare material, including figures, listings, and tables, for team, department, and national presentations, scientific meetings, abstracts, and papers. Critically review reports to ensure that the methodology and results are accurately reported.

Prepare preliminary statistical reports and contribute to final study reports as needed. Work closely with investigators to ensure the project results and conclusions are presented accurately.

Manage multiple competing deadlines and coordinate the needs for each project.

The team uses a commercial project management system to manage its projects. Actively use this system and be prepared to report on the progress of the projects.

All other duties as assigned.

The above statements describe the general nature and level of work being performed. This is not intended to be an exhaustive list of all responsibilities and duties required. Employees may be directed to perform job-related tasks other than those specifically presented in this description.

The intent of this job description is to be representative of the level and the types of duties and responsibilities that will be required of this position and shall not be construed as a declaration of the total specific duties and responsibilities.

Environment
The DCI Bioinformatics team members are extensively engaged with the research and educational initiatives and programs of the Duke Department of Biostatistics and Bioinformatics, including the Duke Center of Statistical Genetics and Genomics. The team includes faculty, staff, and graduate student interns. The team fosters a highly collaborative environment. Team members are expected and encouraged to actively seek guidance from DCI Bioinformatics faculty and senior staff. Each staff person is assigned to a faculty member to receive scientific and career mentoring.


Preferences
The minimum educational requirement for this position is a bachelor degree in the biological sciences with demonstrable training and skills and training in data analysis, scientific and data programming, mathematics (linear algebra, real analysis, numerical optimization, discrete mathematics), computer science, and statistics; or a bachelor degree in quantitative sciences (e.g., statistics, mathematics, physics, or theoretical computer science) with formal training or experience in molecular biology and genetics.
  • A master's degree or formal graduate training in statistics, biostatistics, mathematics, physics, or theoretical computer science is strongly preferred
  • Minimum of three years working as scientific programmer or as quantitative researcher (e.g., biostatistician) in an academic or research setting
  • Experience analyzing genomic data (e.g., from high throughput sequencing or high-dimensional array platforms) is strongly preferred
  • Solid understanding of the key elements of molecular biology and population genetics
  • Working experience with the GNU/Linux operating system and using UNIX tools (e.g., sed, awk)
  • Experience using programming languages (e.g., C/C++, python, scala) for scientific computing
  • Experience using and embedding scientific libraries (e.g., Eigen, Cuba, GSL, NLopt, numpy)
  • Experience using R for programming and data analysis
  • Experience using extension packages from the Bioconductor package for data analysis
  • Experience using software frameworks for machine learning (e.g., scikit-learn, tensorflow)




Requisition Number
401281434

Location
Durham

Duke Entity
MEDICAL CENTER

Job Code
2895 BIOINFORMATICIAN I

Job Family Level
80

Exempt/Non-Exempt
Exempt

Full Time / Part Time
FULL TIME

Regular / Temporary
Regular

Shift
First/Day

Minimum Qualifications
Duke University is an Affirmative Action/Equal Opportunity Employer committed to providing employment opportunity without regard to an individual's age, color, disability, genetic information, gender, gender expression, gender identity, national origin, race, religion,sexual orientation, or veteran status.Essential Physical Job Functions:Certain jobs at Duke University and Duke University Health System may include essential job 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.

Education

Work requires a B.S. in the Biological Sciences with demonstrable computational skills; or a B.S. in Computer Science with a strong interest in Biology/Genomics. M.S. preferred.

Experience

OR AN EQUIVALENT COMBINATION OF RELEVANT EDUCATION AND/OR EXPERIENCE

Auto req ID

91213BR

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

Essential Physical Job Functions: Certain jobs at Duke University and Duke University Health System may include essential job 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.

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