Open Software and Resource Development Leveraging Next-gen Sequencing Data to Facilitate Computational Analysis of Cancer Biology

开放软件和资源开发利用下一代测序数据促进癌症生物学的计算分析

• 批准号: 10001054
• 负责人: Brian Haas
• 金额: $ 33.97万
• 依托单位: BROAD INSTITUTE, INC.
• 依托单位国家: 美国
• 财政年份: 2016
• 资助国家: 美国
• 起止时间: 2016-09-15 至 2021-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10001054
• 关键词: Animals; Bioinformatics; Biology; Cancer Biology; Cancer Research Project; Cells; Clinical Research; Collection; Communities; Companions; Computer Analysis; Computer software; Data; Disease Vectors; Funding; Genome; Infrastructure; Institutes; Journals; Malignant Neoplasms; Manuscripts; Mentorship; Methods; Mutation; Organism; Play; RNA Splicing; Research Activity; Research Support; Resource Development; Resources; Role; Software Tools; Specialist; The Cancer Genome Atlas; Transcript; Wages; anticancer research; base; computer infrastructure; data portal; data resource; insight; next generation sequencing; open source; pathogen; software development; tool; transcriptome; transcriptome sequencing; tumor heterogeneity

Project Summary Brian Haas is an accomplished Senior Computational Biologist and bioinformatics programmer at the Broad Institute who contributes to many cancer research activities under the mentorship of Unit Director Aviv Regev. He has developed several very popular open-source bioinformatics software tools to support genome and transcriptome studies, and has authored or co-authored dozens of manuscripts in leading scientific journals. For more than 15 years, he has leveraged genome and transcriptome analyses to gain insights into the biology of diverse organisms, including pathogens, animal vectors of disease, and most recently cancer. He played a critical role in developing the NCI-funded Trinity Cancer Transcriptome Analysis Toolkit, a suite of software that uses RNA-Seq data to capture cancer mutations, fusion transcripts, evidence of aberrant splicing and expression, and exploration of tumor heterogeneity through single cell transcriptome analysis. In this NCI R50 proposal, we propose salary support for Haas under Regev's mentorship, to support him in (1) continuing to develop open-source software for use by the cancer research community, (2) integrating these tools into NCI-supported infrastructures including the NCI Cloud to maximize accessibility and impact, (3) applying these tools to large collections of cancer transcriptome data made available via TCGA and other large-scale efforts, and (4) making the resulting findings available as companion resources to these efforts. Based on his past contributions to bioinformatics and scientific research and the support he has gained from the Broad Institute cancer research programs and abroad, we believe Haas will be tremendously successful as a NCI Cancer Research Specialist.

项目摘要 布莱恩·哈斯是一位颇有成就的高级计算生物学家和生物信息学专家 布罗德研究所的程序员，参与了许多癌症研究活动 在科长阿维夫·雷格夫的指导下。他已经发展出了几个非常 支持基因组和转录组的流行开源生物信息学软件工具 研究，并在领先的科学领域撰写或合著了数十篇手稿 日记。在超过15年的时间里，他利用基因组和转录组 分析以深入了解不同生物体的生物学，包括病原体， 动物传播疾病的媒介，以及最近的癌症。他扮演了关键的角色 开发NCI资助的三位一体癌症转录组分析工具包，一套 使用RNA-Seq数据捕获癌症突变、融合转录本、 异常剪接和表达的证据以及肿瘤异质性的探索 通过单细胞转录组分析。 在这份NCI R50提案中，我们建议根据Regev的 指导，支持他(1)继续开发开放源码软件，供 癌症研究社区，(2)将这些工具整合到NCI支持的 包括NCI云在内的基础设施可最大限度地提高可访问性和影响力，(3) 将这些工具应用于通过以下途径提供的大量癌症转录组数据 TCGA和其他大规模努力，以及(4)将结果作为 这些努力的配套资源。基于他过去对生物信息学的贡献 和科学研究以及他从布罗德癌症研究所获得的支持 研究计划和国外，我们相信哈斯将非常成功作为一个 NCI癌症研究专家。