VERMONT INBRE: BIOINFORMATICS CORE

佛蒙特州因布雷：生物信息学核心

• 批准号: 7610033
• 负责人: JEFFREY P. BOND
• 金额: $ 25.76万
• 依托单位: UNIVERSITY OF VERMONT & ST AGRIC COLLEGE
• 依托单位国家: 美国
• 财政年份: 2007
• 资助国家: 美国
• 起止时间: 2007-07-01 至 2008-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7610033
• 关键词: Award; Bioinformatics; Bos taurus; Calendar; Categories; Cattle; Centers of Research Excellence; Clinical Research; Computer Retrieval of Information on Scientific Projects Database; Consult; Custom; Data Analyses; Databases; Development; Directories; Drosophila genus; Electronic Mail; Electronics; Event; Experimental Designs; Facility Construction Funding Category; Faculty; Funding; Genetic; Genotype; Grant; Human; Human Resources; Immunobiology; Individual; Institution; Internet; Laboratories; Mass Spectrum Analysis; Medicine; Mercury; Numbers; Oligonucleotide Microarrays; Open Reading Frames; Participant; Pattern; Phase I Clinical Trials; Positioning Attribute; Principal Investigator; Process; Publications; Published Directory; Regulation; Reporting; Research; Research Infrastructure; Research Personnel; Research Project Grants; Research Support; Resources; Robot; Sampling; Science; Service Statistics; Services; Source; Streptococcus mutans; Technology; Toxic effect; Toxoplasma gondii; United States National Institutes of Health; Vermont; base; college; data management; interest; lectures; malignant breast neoplasm; member; novel; outreach; programs; protein structure function; success

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

该子项目是利用该技术的众多研究子项目之一 资源由 NIH/NCRR 资助的中心拨款提供。子项目和 研究者 (PI) 可能已从 NIH 的另一个来源获得主要资金， 因此可以在其他 CRISP 条目中表示。列出的机构是 对于中心来说，它不一定是研究者的机构。 佛蒙特州遗传学网络生物信息学核心 (BC) 亮点 2006年9月 2007年4月11日 对于三个 BC 目标中的每一个，我们都重印了目标，然后总结了要点。 目标 1 提供生物信息学服务，使研究人员在研究经费方面更具竞争力。 服务包括实验设计以及数据管理和分析。 这些服务将包括对涉及寡核苷酸微阵列、LC-质谱和蛋白质结构/功能的实验项目的支持。 更一般地说，BC 支持自定义数据库的开发。 由于 VGN 微阵列设施取得了巨大成功，生物信息学核心服务强调了微阵列数据分析。 VGN 通过 INBRE 资金支持微阵列数据分析职位，该职位现在已主要转变为医学院支持和联邦对个人研究人员的研究资助相结合。 因此，我们利用 INBRE 资金增加了微阵列数据分析职位，该职位随后转向自我维持。 亮点： + 微阵列用户有 24 名 NIH 资助的研究人员（2006 财年）、17 个 UVM 部门以及很高比例的初级研究人员（表 1）。 大约一半的服务支持人类表达或基因型分析（下表），但这些设施也支持特殊兴趣，例如牛、变形链球菌和弓形虫研究。 + 支持 NIH R01 资助米德尔伯里学院的一名研究员 (Grace Spatafora)。 除了表达统计数据的计算之外，服务还包括基于相关表达模式的共同调节识别，以及新颖的开放阅读框架的识别。 五名米德尔伯里学院的本科生参与了这项研究。 + BCRF 向 Hyman Muss 博士提供一项新资助，用于人类乳腺癌样本的微阵列研究。 + 美国农业部向 Thomas McFadden 博士拨款用于牛微阵列研究。 + 向 Matthew Rand 博士提供 NIH R01 资助，用于甲基汞毒性的基因芯片研究。 + Ralph Budd 博士因包括基因芯片研究在内的免疫生物学研究而获得 COBRE 奖。 参与 COBRE 的三名研究人员在他们的研究中使用微阵列。 + 支持初级教员 Giselle Sholler 博士参与临床研究，其中包括神经母细胞瘤治疗的 I 期临床试验。 目标 2 向学士学位机构 (BPI) 提供实验室/讲座模块。 生物信息学核心为 VGN 外展协调员 Janet Murray 博士在其生物信息学和微阵列模块的持续开发过程中提供了一些咨询服务。 然而，Murray 博士现在独立运作得非常好，因此生物信息学和微阵列外展模块的成功值得完全归功于外展核心。 目标 3 支持电子网络管理基础设施的发展。 VGN 发起了佛蒙特州科学技术专家数据库的建设，此后该数据库的范围不断扩大，成为 VGN ERIS 项目。简而言之，ERIS 的基本思想是利用公共人员名录、书目引文数据库、资助奖项数据库和日历中的信息来提供有关人们的专业知识和兴趣、研究项目、出版物和活动的信息。 这些信息将通过全州范围内的电子邮件公告、网页和自动通知参与者新条目的机器人进行交换。报告期内，ERIS 用于发布 13 项全州公告。 PI 类别# 教职人员 41 NIH 资助，2006 财年 24 初级教师 13 机构3 UVM 部门 17 表 1. 涉及微阵列的项目的主要研究者 (PI)。 芯片数量 ATH1-121501 27 牛 52 Dros基因组1 8 果蝇_2 6 HG-U133A 123 HG-U133A_2 94 HG-U133_Plus_2 8 MG_U74Av2 34 MOE430A 34 映射250K_Nsp 34 映射250K_Sty 5 鼠标430A_2 38 鼠标430_2 6 Mu11KsubA 4 RAE230A 38 RG_U34A 19 S_mutans530155 17 Tgondiia520372 9 总计 556 表 2. 由 VGN 微阵列设备或 VGN 生物信息学核心处理的芯片