Positions in Swaney lab at UCSF

If you have questions, or would like to be considered for a position, please contact Danielle Swaney (danielle.swaney@ucsf.edu).

Position 1: Protein-protein interaction mass spectrometry

This position will focused on the characterization of protein-protein interactions related to autism spectrum disorder. The qualified candidate will utilize large-scale affinity purification mass spectrometry (AP-MS) to investigate specific and/or unique protein complexes involved in autism spectrum disorder. This data will be combined with genetic interaction maps to further analyze functions of each protein complex.

As an independent investigator, the qualified candidate will not only execute necessary experiments, but also provide scientific oversight of the project, including review and advice on experimental design, data interpretation, and long-term planning to his team and colleagues, who will together write manuscripts for publication when the project reaches the appropriate point. The candidate will consult with Dr. State and Prof. Krogan to define the project direction, set milestone, and evaluate progress. Position will be located at UCSF-Mission Bay in San Francisco.

Position 2: Bioinformatics

Bioinformatics Specialist for a Proteomics Core facility. The candidate will be responsible for collaborating with researchers and participating in the experimental and statistical design of projects, and in the biological interpretation of the resulting data. The candidate will be responsible for applying the appropriate algorithms, computational and modeling techniques and statistical methodologies to analyze and visualize data primarily generated through high-throughput proteomics experiments. The candidate is expected to create effective proteomics databases and to develop/maintain web-based tools for disseminating information to collaborators. The candidate will also have the opportunity to develop novel pipelines for analyzing and interpreting proteomics data, and integrating it with other types of data. This position has some flexibility to have the primary location at either UCSF-Mission Bay in San Francisco, or Sanford Burnham Institute in San Diego. Some travel will be required.

Preferred qualifications:

PhD in bioinformatics, statistics, mathematics, computer science or a related discipline together with relevant research experience in generalized and/or linear mixed models, machine learning algorithms, experimental design, general statistical, and other commonly applied techniques in statistical omics data analysis. Highly qualified candidates with a BS or MS will be considered.

Understanding of large-scale proteomics data and placing it in a biological context, as well as experience working with other omics data such as transcriptomics, genomics, lipidomics, and metabolomics.

Strong computational skills and prior experience with Unix/Linux and Windows environments, as well as programming, creating applications and packages in R.

Skill in relational database design, implementation, optimization, and storage procedures

Experience with programming language preferred such as C/C++, Java, Python, and .NET, and familiarity with data visualization tools and in GUI development.

Ability to develop web sites and set up effective sharing of data and analysis tools.

Position 3: Pathogenesis proteomics

We are looking for a talented PhD level scientist with experience in proteomics, to support collaborative mass spectrometry efforts between UCSF and Berkeley. Qualified candidates would have experience in proteomics experimental design, sample preparation, instrument operation and maintenance, and data analysis. Candidates with an interest in using these skills to study bacterial pathogenesis are particularly encourage to apply.