Specialist: Bioinformatics Programmer
https://aprecruit.ucsf.edu/JPF05202

The Krogan Lab is looking for a motivated individual to join our bioinformatics and computational biology team. We are a highly dynamic and collaborative laboratory, applying proteomics, functional genomics, and computational biology to unravel the molecular networks underpinning a broad range of complex biological and biomedical problems.

We value candidates who have the aptitude, motivation, and curiosity that drive ongoing learning in the diverse biology, biological research systems, and computational systems we use or that we are developing (with your help) in our lab.

Duties will include:

• Applying our existing analysis pipelines to proteomics and other 'omics datasets to identify proteins, protein interactions, pathways, networks, and other cell biology involved in disease and other health-relevant systems.
  
• Modifying existing analysis pipelines; developing or adopting new methods; and evaluating new/improved methods.
  
• Building computational tools and maintaining computational infrastructure to support analysis and data management in the lab.

Requirements:

• Junior Specialist- A bachelor's degree (or equivalent degree) or at least four years of research experience.
• Assistant Specialist- A master's degree or a bachelor's degree with three or more years of research experience.
• Experience with data analysis and graphical data presentation using the R programming language; or experience in a similar language such as Python and a willingness to learn R.
• Experience with analysis of 'omics datasets, characterized by multiple thousands of measurements across a few tens of conditions and replicates
• Familiarity with biological systems.
• Experience with biological research.
• Strong communication skills and ability to work in a collaborative team.
• Applicants must meet the required qualifications at the time of appointment.
• Application materials must state qualifications and/or if pending upon submission.

Desirable skills/experience/knowledge:

• Understanding of biological networks, such as protein interaction networks, and their presentation
• Demonstrated understanding of linear regression models and ANOVA
• Experience and familiarity with null hypothesis testing and p.value adjustments for multiple tests such as through FDR estimation
• Familiarity with data clustering
• Familiarity with dimensionality reduction methods (PCA, SVD, NMF, etc)
• Familiarity with over-representation or enrichment analysis such as via hypergeometric tests or GSEA
• Experience with SQL and database construction/design
• Experience with R/Shiny or other data-analysis-oriented web package
• Experience working in a Linux or other Unix-like command line environment.
• Familiarity with machine learning algorithms and their application to biological problems.
• Familiarity with the use of artificial intelligence systems to solve biological problems such as Alphafold.

Problem Solving:

Common:
Individual MS runs are of variable quality, so employee needs to inspect, assess, and present which if any need to be removed to improve quality of results.
Data or figure formats are not correct to match publication standards and need to be translated, adjusted, reformatted etc.

Less frequent/more complex:
Translate genes from a non-human model to orthologous human genes.
Normalization of protein intensity between MS runs failed to account for systematic technical differences; employee needs to detect the problem and apply alternate normalization procedures.

Refer to supervisor:
Software versions on shared resources aren't compatible and need to be upgraded.
Collaborators disagree on proper analysis procedures, and we need to choose and justify a single procedure.

Please apply online at https://aprecruit.ucsf.edu/JPF05202, with a CV, cover letter, and three references.

See Table 24B for the salary range for this position. A reasonable estimate for this position is $53,100-$68,300.

As a University employee, you will be required to comply with all applicable University policies and/or collective bargaining agreements, as may be amended from time to time. Federal, state, or local government directives may impose additional requirements.

UC San Francisco seeks candidates whose experience, teaching, research, or community service has prepared them to contribute to our commitment to diversity and excellence. The University of California is an Equal Opportunity/Affirmative Action Employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, age or protected veteran status.