Graduate Group in Bioinformatics seeks a second renewal of its training program in Bioinformatics and Computational Biology. The program focuses on training young scientists who can serve as leaders in research at the interface between computation and biology. Emphasis areas include these fields as well as Complex Biological Systems and Quantitative Genetics and Genomics. The training plan for coursework, enrichment activities, and research reflects the fundamentally collaborative culture at UCSF. Thus, both the formal and informal features of the program have been designed to bring together students from different disciplines and train them for team-based problem solving. Although the focus is on computational research, all students must perform an experimental rotation and are heavily exposed to experimental biology in many other aspects of their training. As a result, our graduates understand the sources of their experimental data as well as how to manipulate it and are prepared to interact in multidisciplinary teams that require an understanding of both """"""""wet"""""""" and """"""""dry"""""""" scientific cultures. We recruit a diverse and talented group of students with computational and quantitative backgrounds and train them to tackle challenging problems in biology at scales that span the molecular to the phenotypic. Because UCSF is a health sciences campuses, many of our students do research explicitly associated with human health and disease. The special features of our program are: Collaborative and inter-disciplinary research. Training faculty are heavily involved in collaborative research, both within and outside of UCSF. Many of their labs (and trainees) are involved in Consortia or Centers created to address problems that cannot be solved from a single viewpoint but require contributions from many disciplines. Student publications reflect this culture as do student initiated journal clubs and interest groups bringing together students from multiple disciplines for """"""""Research in Progress"""""""" talks. An innovative curriculum and special training features. Our core values of collaboration and inter- disciplinary research involve first-year students in team-based and hands-on learning. These special features of First Year training begins with a """"""""Bootcamp"""""""" experience taught by senior students and then proceeds to a major integrative biological """"""""Systems"""""""" course in the fall quarter featuring student teams chosen to span their different backgrounds. A Core curriculum follows in the winter to teach relevant fundamentals. The spring quarter has been refactored to provide a menu of in-depth """"""""mini-courses"""""""" held in a small group format for substantive interactions with faculty with deep research involvement in each area. Significant training in communication and preparation for diverse careers. Students get intensive training in oral and written communication taught in formal courses designed in part by professional staff. Many other venues teach these skills more informally. Students also are given many opportunities to participate in internships, career preparation workshops, and medical education.

Public Health Relevance

The huge volume of data continually produced by genomic and related projects offers enormous opportunities for improving our understanding of human health and alleviating disease. The UCSF Bioinformatics Training Program aims to train a new generation of scientific leaders at the interface of computation and biology who will be needed to make effective use of these data.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Institutional National Research Service Award (T32)
Project #
5T32GM067547-12
Application #
8686873
Study Section
(TWD)
Program Officer
Marcus, Stephen
Project Start
2003-07-01
Project End
2018-06-30
Budget Start
2014-07-01
Budget End
2015-06-30
Support Year
12
Fiscal Year
2014
Total Cost
Indirect Cost
Name
University of California San Francisco
Department
Pharmacology
Type
Schools of Pharmacy
DUNS #
City
San Francisco
State
CA
Country
United States
Zip Code
94143
Wilson, Michael R; O'Donovan, Brian D; Gelfand, Jeffrey M et al. (2018) Chronic Meningitis Investigated via Metagenomic Next-Generation Sequencing. JAMA Neurol 75:947-955
Bradley, Patrick H; Nayfach, Stephen; Pollard, Katherine S (2018) Phylogeny-corrected identification of microbial gene families relevant to human gut colonization. PLoS Comput Biol 14:e1006242
White Bear, J; Long, Thavy; Skinner, Danielle et al. (2018) Predictions of novel Schistosoma mansoni - human protein interactions consistent with experimental data. Sci Rep 8:13092
Cario, Clinton L; Witte, John S (2018) Orchid: a novel management, annotation and machine learning framework for analyzing cancer mutations. Bioinformatics 34:936-942
Mavor, David; Barlow, Kyle A; Asarnow, Daniel et al. (2018) Extending chemical perturbations of the ubiquitin fitness landscape in a classroom setting reveals new constraints on sequence tolerance. Biol Open 7:
Saha, Suvrajit; Nagy, Tamas L; Weiner, Orion D (2018) Joining forces: crosstalk between biochemical signalling and physical forces orchestrates cellular polarity and dynamics. Philos Trans R Soc Lond B Biol Sci 373:
Hendel, Nathan L; Thomson, Matthew; Marshall, Wallace F (2018) Diffusion as a Ruler: Modeling Kinesin Diffusion as a Length Sensor for Intraflagellar Transport. Biophys J 114:663-674
Barlow, Kyle A; Ó Conchúir, Shane; Thompson, Samuel et al. (2018) Flex ddG: Rosetta Ensemble-Based Estimation of Changes in Protein-Protein Binding Affinity upon Mutation. J Phys Chem B 122:5389-5399
Kang, Hyun Min; Subramaniam, Meena; Targ, Sasha et al. (2018) Multiplexed droplet single-cell RNA-sequencing using natural genetic variation. Nat Biotechnol 36:89-94
Milgrom, Peter; Horst, Jeremy A; Ludwig, Sharity et al. (2018) Topical silver diamine fluoride for dental caries arrest in preschool children: A randomized controlled trial and microbiological analysis of caries associated microbes and resistance gene expression. J Dent 68:72-78

Showing the most recent 10 out of 125 publications