Featured RNA-Seq Job – Sequence Pipeline Developer

University of California – San Francisco (San Francisco, CA)

Req Number – 42709BR
Job Title – Sequence Pipeline Developer
Job Code and Payroll Title – 7275 PROGRAMMER/ANALYST III
Location – Mission Bay
Department Name – Psychiatry
Work Days – Monday – Friday, 8:00 am – 5:00 pm
Shift – Days
Shift Length – 8 Hours

Job Summary

Next-generation sequencing has revolutionized the understanding of human genetics, including identifying genes associated with specific diseases using exome/genome sequencing, regulatory machinery using ChIP-Seq, and co-expression modules using RNA-Seq. The Psychiatry Department at UCSF is developing a bioinformatics core that will develop and maintain bioinformatics pipelines for processing exome, genome, ChIP-Seq, and RNA-Seq data using the latest tools to facilitate this research. Once the basic pipelines are in place we will develop and share downstream analytic tools (e.g. systems analysis, gene enrichment tests, clinical feedback). In addition, we will collaborate with researchers at UCSF to develop customized pipelines for specific solutions. Finally, we will use this framework to assess and implement novel genomic technologies, such as single molecule sequencing.

The Sequence Pipeline Developer will join a highly motivated team of bioinformaticians including several Programmer/Analysts, PhD students, and postdocs in the Sanders lab and collaborating labs. University level experience in biology and genetics would be a great asset, but not required. We are especially keen to hire an individual who is highly motivated and capable of both working in a team and independent problem solving.

Computational resources: UCSF has several high-performance computing clusters (HPCCs) for processing genomic data. The majority of genomic work is performed on the Institute of Human Genetics (IHG) cluster, which has a dedicated system admin. We also intend to utilize cloud-computing resources (e.g. AWS) to minimize processing time and simplify collaboration across sites, departments, and institutions.

Genomics resources: UCSF has several genomics cores with Illumina sequencing instruments, including numerous HiSeq 2500s and MiSeqs. The Psychiatry Department has access to large datasets of exome,

This person will develop a bioinformatic pipeline to process genomic data, including next generation sequencing data and microarray data. The pipeline will enable the processing of whole exome, whole genome, RNA-Seq, and ChIP-Seq data. In addition, the individual will work to visualize and filter the results from these analyses to find genomic loci of interest clinically and scientifically. Finally, he/she will implement these pipelines on a commercial cloud environment (e.g. AWS) to facilitate collaboration with other institutions.

Required Qualifications

  • BS degree in Computer Science/Biological Sciences, or equivalent
  • Familiarity with statistical analysis
  • Prior systems administration experience with a UNIX/Linux system
  • Proficient at shell scripting
  • Prior experience with data management, storage, transfer, analysis
  • Prior experience in system operations (sysops)
  • Experience with multiple programming methods for example: R, C/C++, Java, html, PHP, SQL
  • Proficient at Python and/or Perl programming
  • Interested in learning about genetics and next generation sequencing
  • Excellent written and oral communication skills
  • Excellent problem solving skills
  • Strong organizational skills
  • Attention to detail
  • Ability to pick up new techniques quickly
  • Proven ability to work within a team to accomplish specific goals at specified times
  • Demonstrates excellent attendance and professionalism

Preferred Qualifications

  • MS degree in Computer Science/Statistics/Biological Sciences, or equivalent
  • Background in biological data processing, especially in human genetics
  • Experience with parallelized/distributed computing on high-performance computing clusters and/or Cloud servers
  • Experience with Adobe Photoshop and/or Digital Animation
  • Proven record of excelling in a large team environment (15 plus individuals) but still possess an independent work ethic
  • Outstanding job reference

Department Of Psychiatry

The UCSF Department of Psychiatry is among the nation’s foremost resources in the field of child, adolescent and adult mental health. Psychiatry faculty members are recognized for their leadership roles in state of the art, comprehensive, and compassionate patient care, pioneering research, excellence in training the next generation of leaders, advancing public policy to advance mental health, and commitment to diversity.

About UCSF

The University of California, San Francisco (UCSF) is a leading university dedicated to promoting health worldwide through advanced biomedical research, graduate-level education in the life sciences and health professions, and excellence in patient care. It is the only campus in the 10-campus UC system dedicated exclusively to the health sciences.

Equal Employment Opportunity The University of California San Francisco is an Equal Opportunity/Affirmative Action Employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, national origin, disability, or protected veteran status. Further information about the University of California, San Francisco, is available at diversity.ucsf.edu. UCSF seeks candidates whose skills, and personal and professional experience, have prepared them to contribute to our commitment to diversity and excellence, and the communities we serve.


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