Featured RNA-Seq Job – Computational Biology / Bioinformatician

Job ID – 6204
Type – Regular Full-Time
Company – Fred Hutchinson Cancer Research Center
Location  -US-WA-Seattle

Overview

Cures Start Here. At Fred Hutchinson Cancer Research Center, home to three Nobel laureates, interdisciplinary teams of world-renowned scientists seek new and innovative ways to prevent, diagnose and treat cancer, HIV/AIDS and other life-threatening diseases. Fred Hutch’s pioneering work in bone marrow transplantation led to the development of immunotherapy, which harnesses the power of the immune system to treat cancer. An independent, nonprofit research institute based in Seattle, Fred Hutch houses the nation’s first and largest cancer prevention research program, as well as the clinical coordinating center of the Women’s Health Initiative and the international headquarters of the HIV Vaccine Trials Network. Careers Start Here.

About the Division

The mission of the Vaccine and Infectious Diseases Division (VIDD) of the Fred Hutchinson Cancer Research Center is to eliminate or minimize the worldwide impact of globally significant infectious diseases.  The Division shares the Center’s values of scientific excellence, respect, openness, and innovation in the pursuit of its mission.

The Bioinformatician will develop analytical pipelines for the analysis of high-throughput assay data including RNA-Seq (and single-cell RNA-seq), microarrays, and/or high-dimensional single-cell assays (e.g. CyTOF, Fluidigm) generated through large collaborative projects such as the HIV Vaccine Trials Network, the Collaboration for AIDS Vaccine Discovery and the Human Immunology Project Consortium. He/She will then use computational approaches to integrate results from one or more high-throughput assay types along with immunological and clinical endpoints to help predict how the immune system responds to a particular infection or vaccination.

The Bioinformatician will integrate a dynamic team of (bio)-statisticians, bioinformaticians, computer scientists, and programmers lead by Dr. Raphael Gottardo at the Fred Hutchinson Cancer Research Center (FHCRC). The FHCRC provides a highly interactive and supportive environment for junior investigators to grow and develop their future career; it consistently ranks in the top places to work in academia, as surveyed by The Scientist.

Responsibilities

The Bioinformatician will independently determine programmatic approaches to problems, and develop computational tools and software programs that are computationally efficient, effective, and well documented for public release. He/She will apply these tools to large datasets to generate novel biological insights and will communicate results to collaborators via conference calls and lab meetings. He/She will also be expected to contribute to manuscript preparation and to give presentation at both national international meetings.

Additional responsibilities may include some or all of the following:

1. Analysis
   1. Communicate with collaborators to understand and develop requirements and specifications for analysis.
   2. Develop reproducible pipeline for data analysis of specific assay data (e.g., single-cell RNA-Seq)
   3. Integrate multiple data types using system approaches for generating novel biological insights
   4. Write detailed reports to be used to disseminate results to collaborators and prepare manuscripts

2. Data management and high performance computing
   1. Implement creative solutions for large volume data management challenges (e.g. databases)
   2. Create reusable high performance computing solutions for processing large data sets (e.g. write specific parallel code or scripts to send multiple jobs to a queue)

Qualifications

Minimum Qualifications

• MS degree in computer science, bioinformatics, statistics, biostatistics or related field; or BS and 2 or more years related experience.
• Proficient in R and another programming language
• Experience with version control tools (preferably git)

Preferred Qualifications

• Proficient with Bioconductor and C/C++
• Experience with relational databases, database schema design, SQL, postgress, and/or netCDF / HDF5 file formats
• Familiarity with bioinformatics workflows and online databases and web servers such as the Gene Expression Omnibus and the UCSC genome browser
• Familiarity with high performance computing and computing clusters
• Knowledge of JavaScript including D3.js, extJS or jquery or similar

Expectation

• Must be organized and detail-oriented, with good oral and written communication skills

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