BIOINFORMATICIAN II

Location
Durham, NC
Posted
Mar 14, 2018
Institution Type
Four-Year Institution

diversity employer



BIOINFORMATICIAN II
STATISTICAL CENTER

Occupational Summary
Work with the Director of Biostatistics for the Duke Cancer Institute (DCI) and other faculty as needed on projects with high-dimensional 'omics data. Manages project responsibilities independently. Handles multiple competing projects and deadlines, and coordinates all the bioinformatic needs of each clinical trial/project. Performs intermediate and advanced statistical and bioinformatics analysis and programming for clinical research projects.

Work Performed

Research design, programming, and collaboration 70% Effort
  • Develop scalable and well documented software packages and analysis pipelines that conform to the principles of literate programming and good practices, and promote and facilitate the practice of reproducible analysis
  • Provide support for analysis of genomic data from array and high-throughput sequencing assays with strict adherence to the principles of reproducible analysis. 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.
  • Continually extend knowledge about biological, clinical and translational aspects of cancer research. Ensure that data analysis and reporting, and methods and tools development is informed by this knowledge
  • 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.
  • Conduct critical reviews of any relevant technical documentation, 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.
  • 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.
  • Conduct simulation studies, data analysis, and contribute to programming and documentation of code.
  • Prepare material, including figures, listings, and tables, for team, department, and national presentations, scientific meetings, abstracts, and papers.
  • Provide training and guidance to junior staff and student trainees with limited input from faculty supervisor
  • Collaborate with project leader, principal investigator, other clinical investigators, and external government or industry representatives to affect significant decisions regarding the trial/project, and to jointly achieve objectives and timelines.
  • Present information on topics relevant to statistics and statistical operations at internal statistics meetings.

Scientific writing, editing, and publication 20% Effort
  • Prepare preliminary statistical reports and contribute to final study reports as needed.
  • Critically review reports to ensure that the methodology and results are accurately reported.
  • Manage multiple competing deadlines and coordinate the needs for each project with limited input from faculty supervisor
  • Write technical papers as the (or a) lead author
  • Write software packages as the (or a) lead developer
  • Contribute substantial input, in terms of gathering information for and writing of grants and collaborative papers (e.g., write methods sections, supplementary material) with limited input from faculty supervisor
  • Prepare statistical method sections for inclusion in study protocols and/or manuscripts.
  • Take lead role in documenting SOPs and training material with limited input from faculty supervisor

Regulatory, data security/management, reproducibility, and project reporting 10% Effort
  • 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.
  • Take major responsibility for keeping projects on track and ensuring that deadlines are met with limited input from faculty supervisor
  • Use various data models (e.g., hdf5), and relational (e.g., PostgreSQL) and non-relational (e.g., Mongo DB) databases to store and manage data.
  • Understands and proactively remains abreast of guidelines from regulatory agencies as they apply to statistics, programming, and handling of clinical data; monitors compliance to required standards of own work and that of any individuals being mentored.
  • Monitors data collection, institutes procedures to assure data quality and guarantees study protocols are followed appropriately.
  • Handles and secures highly confidential and sensitive analyses and documentation.
  • Supports the preparation of Data and Safety Monitoring Board reports and final statistical and study reports, including those intended for regulatory submission, and collaborate with medical writers as needed.
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.

Preferences
Experience with R. Demonstrated ability to plan and carry out simulation studies in biostatistical methods work is highly desirable. Experience with advanced biostatistical techniques highly desirable, including observational data analysis, causal modeling, and randomized trial inference.



Requisition Number
401394957

Location
Durham

Duke Entity
MEDICAL CENTER

Job Code
2893 BIOINFORMATICIANII

Job Family Level
84

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, 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 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 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

Work requires at least 2 years of experience in bioinformatics. 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. OR AN EQUIVALENT COMBINATION OF RELEVANT EDUCATION AND/OR EXPERIENCE

Auto req ID

98637BR

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.

PI101595546

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