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

这个子项目是许多研究子项目中利用 资源由NIH/NCRR资助的中心拨款提供。子项目和 调查员(PI)可能从NIH的另一个来源获得了主要资金， 并因此可以在其他清晰的条目中表示。列出的机构是 该中心不一定是调查人员的机构。 佛蒙特州遗传学网络生物信息学核心(BC)亮点 2006年09月2007年04月11日 对于BC的三个目标，我们重印目标，然后总结要点。 目标1提供生物信息学服务，使研究人员在研究资金方面更具竞争力。服务包括实验设计以及数据管理和分析。这些服务将包括支持涉及寡核苷酸微阵列、LC-MS和蛋白质结构/功能的实验计划。更广泛地说，BC支持定制数据库的开发。 由于VGN微阵列设施取得了压倒性的成功，生物信息学核心服务部门强调了微阵列数据分析。VGN用INBRE基金支持一个微阵列数据分析职位，这个职位现在基本上已经转移到医学院支持和联邦研究资助个人研究人员的结合上。因此，我们使用INBRE资金增加了一个微阵列数据分析职位，该职位随后转向自我维持。 亮点： +微阵列使用者有24名由NIH资助的研究人员(2006财年)，UVM的17个部门，以及较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分析(下表)，但这些设施也支持特殊的兴趣，如牛、变形链球菌和弓形虫研究。 +支持向米德尔伯里学院的一名研究员(Grace Spatafora)提供NIH R01拨款。除了计算表达统计数据外，服务还包括基于相关表达模式的协同调控识别，以及新的开放阅读框架的识别。米德尔伯里学院的五名本科生参与了这项研究。 +向海曼·穆斯博士提供新的BCRF赠款，用于对人类乳腺癌样本进行微阵列研究。 +美国农业部为托马斯·麦克法登博士提供的牛微阵列研究拨款。 +向马修·兰德博士授予NIH R01拨款，用于甲基汞毒性的基因芯片研究。 +授予拉尔夫·巴德博士包括基因芯片研究在内的免疫生物学研究的科布尔奖。参与这项研究的三名研究人员在他们的研究中使用了微阵列。 +支持初级教员吉赛尔·肖勒博士参与临床研究，其中包括神经母细胞瘤疗法的I期临床试验。 目标2向文凭院校(BPI)提供实验室/讲座单元。 在生物信息学和微阵列模块的持续开发期间，生物信息学核心为VGN外联协调员Janet Murray博士提供了一些咨询服务。然而，默里博士现在独立运作得非常好，因此生物信息学和微阵列扩展模块的成功应完全归功于外联核心。 目标3支持发展电子网络的行政基础设施。 VGN开始建立佛蒙特州科学和技术专家数据库，该数据库的范围后来扩大，成为VGN ERIS项目。简而言之，ERIS的基本思想是利用公共人事目录、书目引文数据库、奖励奖数据库和日历中的信息来提供关于人们的专业知识和兴趣、研究项目、出版物和事件的信息。这些信息将通过全州范围的电子邮件公告、网页和自动通知参与者新条目的机器人来交换。在本报告所述期间，使用ERIS在全州范围内发布了13项公告。 PI类别# 教职员工41 NIH资助，06-24财年 初级教员13 院校3 密歇根州立大学17个部门 表1.涉及微阵列项目的首席调查人员(PI)。 芯片号 ATH1-121501 27 牛52 DrosGenome1 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 -11KsubA 4 RAE230A 38 RG_U34A 19 S_变种人530155 17 泰国520372 9 总计556 表2.VGN微阵列设备或VGN生物信息学核心处理的芯片