POSITION SUMMARY

The Gage lab is seeking a Computational Biology Tech I to work collaboratively on projects studying neurodevelopment and neurological disease. The ideal candidate will have a background in bioinformatics, computer science, and/or software engineering. Under the direction of senior computational researchers and analysts, they will be responsible for implementing and running analysis pipelines for large-scale functional genomics datasets, generating intuitive data visualizations, and working with lab researchers to answer specific biological questions through the lens of functional genomics.

ESSENTIAL FUNCTIONS

(100%) Functional genomics pipeline development and data processing

• Implement, optimize, and run computational pipelines for functional genomics data including but not limited to bulk and single-cell RNA-seq and ATAC-seq.
• Develop scripts and conduct analysis of genomics counts data including but not limited to quality control, normalization, batch correction, principal component analysis, clustering, and differential analysis.
• Generate intuitive data visualizations from genomics data analyses
• Work on UNIX-like high-performance compute cluster environment
• Work on google cloud platform computing environment
• Present pipeline performance and analysis results in one-on-one and small group meetings.

EXPERIENCE: 

Required:

• No professional experience required
• Knowledge/Familiarity with the following gained through academic experience:
  • Experience working on a UNIX-like operating system in a high-performance computing environment
  • Programming experience in Bash, Python and R
  • Familiarity with Illumina sequencing technology and RNA-seq
  • Hands-on single-cell genomics experience:
  • Downstream analysis in Seurat and/or Scanpy environments either in a lab and/or the following courses: (1) BENG183, Applied Genomic Technologies and (2) CSE185, Advanced Bioinformatics Laboratory

Preferred:

• Hands-on single-cell genomics experience:
  • Alignment and quantification of sequencing reads using CellRanger and/or STARsolo pipelines
• Familiarity with creating and using isolated computational environments using conda and/or Docker containers
• Familiarity with supervised and unsupervised machine learning techniques including regression, classification, and clustering
• Pipeline development experience in Snakemake, Nextflow, and/or the workflow development language (WDL)
• Experience executing genomics pipelines in the cloud

EDUCATION

Required:

• Enrolled in a bioinformatics-focused BS program

Preferred:

• Undergraduate coursework in biological sciences related field.

SKILLS AND ABILITIES

Required:

• Proven organizational and time management skills to successfully complete tasks prioritized by the supervisor.
• Strong communication skills (both verbal and written) needed to interact professionally and effectively in the work environment.
• Some ability to read, comprehend, and discuss research papers and materials.
• Ability to interact diplomatically and professionally with lab researchers.
• Experience with Standard business office equipment and commonly used software and tools, such as Microsoft Office, electronic mail, and the internet.

Preferred:

• Theoretical and practical knowledge of biological sciences (particularly molecular and cellular biology).

SPECIAL CONDITIONS OF EMPLOYMENT

• Must be willing to work in an animal-related research environment.
• Must be willing to work a flexible schedule to support research needs.
• Successful completion of the Institute’s background investigation.
• Must be willing to sign a confidentiality agreement.

PHYSICAL REQUIREMENTS/MENTAL ACTIVITIES/ENVIRONMENTAL CONDITIONS

This position will require constant seeing, sitting, touching/feeling, analyzing, calculating, and working inside.