Molecular Profiling and Computational Biology

About

The Molecular Profiling and Computational Biology Core assists researchers in a variety of tasks designing experiments and interpreting results from sequence-based assays, including genome-scale and targeted assays of host (e.g., human) and viral sequences, and the design and interpretation of micro-biome communities. This includes assays such as genome and RNA sequencing, mass spectrometry, and other high throughput technologies.

Investigators at CFAR can partner with Core faculty for appropriate design and analysis of experiments.    Access to consulting expertise advanced computational tools and software expertise ensures high-level quality control. The Core will also facilitate access to assay technologies, such as sequencing, arrays, or other high throughput technologies available at any of our institutes associated facilities.  All activities—from project-related work to analytical tool development—serve as practical case studies in the Core’s formal training sessions in sequence analysis.

On this page: 

Services, ActivitiesPeople, Contact

Services

For researchers looking to include HIV sequence analysis in an ongoing or proposed project, we offer support for all aspects of experiment design, data generation, quality control and data analysis

CFAR members can submit questions or request meetings to discuss specific analysis strategies, and solicit advice on experiment design and novel research studies.

Expertise is provided in the areas of microarray, high-throughput DNA sequencing, genomics, & proteomics data, and for combining data with public bioinformatics resources, including expertise specific to viral sequence analysis. 

Classes and hands-on computing labs are offered periodically to introduce genomics and proteomics techniques and analysis tools to CFAR staff allowing them to work independently.

As new technologies of likely general use are identified this resource works with other center investigators or shared resources to acquire and deploy those computational techniques.

A key aspect of the Core is to provide access to computational tools (some web-based, others standalone) required to interpret sequence data, including phylogenic analysis, classification/clustering, processing RNA- or DNA- sequence data.

Activities

The Core resource makes experimental design and processing of microarray, high-throughput sequencing and mass-spectrometry based platforms broadly available to researchers across the Center through expertise in data analysis, consulting, training and technology development. The following coordinated initiatives are provided generally at no cost to CFAR members.

1. Consulting - An email help-desk (see below) is staffed for users to submit questions, request meetings to discuss specific analysis strategies, and solicit advice on experiment design and novel research studies.

2. Data processing and analysis - Expertise is provided in the areas of microarray, high-throughput DNA sequencing, genomics, & proteomics data, and for combining data with public bioinformatics resources, including expertise specific to viral sequence analysis (described below).

3. Training - Classes and hands-on computing labs are offered periodically to introduce genomics and proteomics techniques and analysis tools to CFAR staff allowing them to work independently.

4. Technology Development and Acquisition -- As new technologies of likely general use are identified this resource works with other center investigators or shared resources to acquire and deploy those computational techniques. CFAR Investigators with a need to access new computational technologies can request developments through the resource; priority is given to those technologies that will be used by multiple CFAR members, and approval is provided by the scientific steering committee.

5. Development, maintenance, support and access to software: A key aspect of the Core is to provide access to computational tools (some web-based, others standalone) required to interpret sequence data, including phylogenic analysis, classification/clustering, processing RNA- or DNA- sequence data. A current list of software algorithms can be found here: http://indra.mullins.microbiol.washington.edu/ and also here http://matsen.fhcrc.org/software.html.

People

Martin McIntosh, Core Co-Director, Full Member and Program head of Computational Biology, FHCRC, and lead for host sequence analysis.

James I. Mullins, PhD , Core Co-Director, Professor of Microbiology, Medicine and Laboratory Medicine, and lead for viral sequence analysis.

Erick Matsen, Assistant Member Computational Biology, FHCRC, and lead on microbiome analysis and advanced viral sequence analysis.

Matt Fitzgibbon and  Kavita Garg, core director and executive director.

Sara Zriny, Core Manager.

Contact

To receive services, users should send a brief email to CFARcompbio@fhcrc.org that includes a few sentences describing, briefly, the nature of your questions and your contact information.  Core leaders will use this description to assign your request to an appropriate staff member who will contact you for follow-up.  Most often you will be contacted by a staff member the same day as the request.  Follow-up may include a one-on-one meeting, or possibly email or phone exchanges if that is adequate.