VERMONT INBRE: BIOINFORMATICS CORE

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This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. Vermont Genetics Network Bioinformatics Core (BC) Highlights September 2006  April 11, 2007 For each of the three BC Aims we reprint the aim and then summarize highlights. AIM 1 Provide bioinformatics services that make investigators more competitive for research funding. Services include experimental design as well as data management and analysis. These services will include support for experimental programs involving oligonucleotide microarrays, LC-Mass spectrometry, and protein structure/function. More generally, the BC supports development of custom databases. Bioinformatics Core services have emphasized microarray data analysis because of the overwhelming success of the VGN Microarray Facility. The VGN supported a microarray data analysis position with INBRE funds, a position that has now moved largely to a combination of College of Medicine support and federal research grants to individual investigators. Thus we used INBRE funds to add a microarray data analysis position that subsequently moved to self-sustainability. Highlights: + The microarray user 24 NIH-funded investigators (FY2006), 17 departments of UVM, and a high proportion of junior investigators (Table 1). About half of the services support human expression or genotype analysis (bottom table) but these facilities also support special interests such as Bos Taurus, Streptococcus mutans, and Toxoplasma gondii research. + Support for an NIH R01 grant to an investigator (Grace Spatafora) at Middlebury College. In addition to calculation of expression statistics, services included identification of co-regulation based on correlated expression patterns, and identification of novel open reading frames. Five Middlebury College undergraduates participated in this research. + A new BCRF grant to Dr. Hyman Muss for microarray studies on human breast cancer samples. + A USDA grant to Dr. Thomas McFadden for bovine microarray studies. + An NIH R01 grant to Dr. Matthew Rand for GeneChip studies of methyl mercury toxicity. + A COBRE award to Dr. Ralph Budd for immunobiology research that includes GeneChip studies. Three of the investigators participating in this COBRE use microarray in their research. + Support for a junior faculty member, Dr. Giselle Sholler, involved in clinical research that includes a Phase I clinical trial of a neuroblatoma therapy. AIM 2 Provide laboratory/lecture modules to Baccalaureate Institutions (BPI). The Bioinformatics Core provided some consulting services to Dr. Janet Murray, VGN Outreach coordinator, during ongoing development of her Bioinformatics and Microarray modules. However, that Dr. Murray is now functioning exceptionally well independently so the Outreach Core deserves full credit for the success of Bioinformatics and Microarray Outreach Modules. AIM 3 Support the development of administrative infrastructure for electronic networks. The VGN initiated construction of a database of Vermont Experts in Science and Technology, which has since grown in scope to become the VGN ERIS Project. Briefly, the idea underlying ERIS is to take advantage of information in public personnel directories, bibliographic citation databases, grant award databases, and calendars to provide information about people's expertise and interests, research projects, publications, and events. This information will be exchanged through statewide email announcements, a web page, and robots that automatically notify participants of new entries. ERIS was used to make 13 statewide announcements during the reporting period. PI Category # Faculty members 41 NIH-funded, FY06 24 Junior faculty 13 Institutions 3 UVM Departments 17 Table 1. Principal Investigators (PI) on projects that involve microarrays. Chip Number ATH1-121501 27 Bovine 52 DrosGenome1 8 Drosophila_2 6 HG-U133A 123 HG-U133A_2 94 HG-U133_Plus_2 8 MG_U74Av2 34 MOE430A 34 Mapping250K_Nsp 34 Mapping250K_Sty 5 Mouse430A_2 38 Mouse430_2 6 Mu11KsubA 4 RAE230A 38 RG_U34A 19 S_mutans530155 17 Tgondiia520372 9 TOTAL 556 Table 2. Chips processed by the VGN Microarray Facility or by the VGN Bioinformatics Core