Req #: 233667

Department: DEPARTMENT OF NEUROLOGICAL SURGERY

Posting Date: 05/08/2024

Closing Info: Open Until Filled

Salary: $5,469 - $9,000 per month

Shift: First Shift

Notes: As a UW employee, you will enjoy generous benefits and work/life programs. For a complete description of our benefits for this position, please visit our website, click here. (https://hr.uw.edu/benefits/wp-content/uploads/sites/3/2018/02/benefits-professional-staff-librarians-academic-staff-20230701_a11y.pdf )

As a UW employee, you have a unique opportunity to change lives on our campuses, in our state and around the world. UW employees offer their boundless energy, creative problem-solving skills and dedication to build stronger minds and a healthier world.

UW faculty and staff also enjoy outstanding benefits, professional growth opportunities and unique resources in an environment noted for diversity, intellectual excitement, artistic pursuits and natural beauty.

POSITION PURPOSE
Our lab is focused on understanding intratumoral heterogeneity in glioblastoma. We have shown in the past that cells within a tumor have dramatically different gene expression profiles. We use cutting edge techniques for single cell analysis such as single cell RNA-seq to interrogate tumor heterogeneity in primary patient samples that are harvested directly from the operating room. In parallel, we are trying to develop and characterize mouse and human culture models that recapitulate the heterogeneity seen in patient tumors in order to allow us to study how these processes affect treatment resistance and tumor evolution. These models include mouse xenografts, genetic mouse models, and human tissue culture models such as neurospheres and brain organoids.

DUTIES AND RESPONSIBILITIES This Research Scientist/Engineer 3 (E S UAW RSE) position will play an important role in the development and maintenance of bioinformatics pipelines used for QC and processing of high-throughput sequencing data as well as in the integrated analysis of large datasets. This position requires the ability to apply R and python algorithms to extract meaningful insight from complex omics data. Additional skills needed for this position include: HPC, bash scripting, machine learning, and Linux OS.

Bioinformatics Management: 90%

• Design, develop, and maintain research-related custom software used in a high-throughput, next-generation sequencing.

• Serve as a bioinformatics expert to guide wet lab scientists in data interpretation and troubleshooting bench experiments.

• Participate in developing, implementing and maintaining new workflows.

• Thrive in a fast-paced work environment that requires independent self-direction with an aptitude for team collaboration and open communication.

• Provide support in writing manuscripts, abstracts, and presentations.

• Present findings at group meetings and conferences, if necessary.

• Responsible for review and interpretation of omics results under direction of principal investigators.

• Develop and coordinate data analysis strategies and implementation for large research projects.

• Update variant curation strategies, variant scoring process, interpretation process, and reporting process on an ongoing basis.

• Develop expertise in interpreting genetic data from open source and proprietary analysis software and databases.

• Support/design of software tools to assist in more efficient variant review for the variant review

• scientist and affiliated faculty.

• Integrate omics data to extract meaningful insights into disease pathogenesis.Other Duties as Assigned: 10% MINIMUM REQUIREMENTS

• Bachelor’s degree in a related field and four years of relevant experience,

• Equivalent education/experience will substitute for all minimum qualifications except when there are legal requirements, such as a license/certification/registration. DESIRED QUALIFICATIONS

• Master’s degree in Bioinformatics.

• Proficient in the use of:

• R - Statistical analysis, machine learning, clustering, data visualization, data analysis.

• Bash/Unix command line/awk - Text parsing, and file manipulation and handling, GitHub & Bitbucket.

• Python - Bio python, DNA sequence manipulation, file manipulation, parsing.

• SQL - Data manipulation, database querying.

• Neo4J - data architecture.

• Mol Bio - PCR, ELISA, AGE/SDS-PAGE, Western blotting, Flow cytometry, DNA extraction, purification & quantification.

• Algorithms & Software - BLAST, FASTA, Sam tools, Bowtie2, Trinity, DeSeq2, Qiagen, Array studio, GSEA, CIBERSORT, BEAST2, Mummer, RBH, ITOL.

• Operating systems - Linux, Windows, MacOS, UGE (Univa grid engine), HPC (High-performance computing) multi-omics data integration. Application Process: The application process may include completion of a variety of online assessments to obtain additional information that will be used in the evaluation process. These assessments may include Work Authorization, Cover Letter and/or others. Any assessments that you need to complete will appear on your screen as soon as you select “Apply to this position”. Once you begin an assessment, it must be completed at that time; if you do not complete the assessment, you will be prompted to do so the next time you access your “My Jobs” page. If you select to take it later, it will appear on your "My Jobs" page to take when you are access ready. Please note that your application will not be reviewed, and you will not be considered for this position until all required assessments have been completed.

University of Washington is an affirmative action and equal opportunity employer. All qualified applicants will receive consideration for employment without regard to, among other things, race, religion, color, national origin, sexual orientation, gender identity, sex, age, protected veteran or disabled status, or genetic information.