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

项目摘要 布赖恩哈斯是一个有成就的高级计算生物学家和生物信息学 布罗德研究所的程序员，他为许多癌症研究活动做出了贡献 在主任阿维夫·雷格夫的指导下他开发了几个非常 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，并撰写或合著了数十篇领先的科学手稿， 期刊15年多来，他利用基因组和转录组 分析以深入了解包括病原体在内的各种生物体的生物学， 疾病的动物媒介，最近是癌症。他扮演了一个关键的角色， 开发由国家癌症研究所资助的Trinity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。 在这个NCI R50提案中，我们建议根据Regev的 导师，以支持他（1）继续开发开源软件，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，以最大限度地提高可访问性和影响力，（3） 将这些工具应用于大量的癌症转录组数据， TCGA和其他大规模的努力，以及（4）将由此产生的结果作为 这些努力的配套资源。根据他过去对生物信息学的贡献 科学研究以及他从布罗德癌症研究所获得的支持 我们相信哈斯作为一个 NCI癌症研究专家。

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.