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德州大学UTH SBMI郑文进博士获科研经费支持:以数据科学和信息学推进癌症研究

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来源:HIT专家网        编译:沈建苗

郑文进

德克萨斯大学休斯顿健康科学中心(UTHealth)生物医学信息学学院(SBMI)副教授  郑文进博士

2017年8月16日,德克萨斯癌症防治与研究所(CPRIT)宣布了60笔新科研经费获得者的名单。德克萨斯大学休斯顿健康科学中心(UTHealth)生物医学信息学学院(SBMI)副教授郑文进(W. Jim Zheng)博士兼理科硕士是科研经费获得者之一。

郑文进博士是一位受过正规生物和计算机科学训练的生物信息学专家,于2013年加入SBMI。借助CPRIT的这笔科研经费,郑文进博士旨在“通过充分利用生物医学研究各个领域的专长,对各种类型癌症的数据进行多层次分析:从群体研究到患者个体研究,一直到分子研究和基因表达研究。”

郑文进博士的父亲郑夜明(Yeming Zheng)罹患肝癌后于1995年过世。郑文进博士回忆说:“父亲过世时,我在读研究生。正是在那段时间,我开始立志于努力攻克癌症。”

郑文进博士说,在过去的10-20年间,“技术促使生物医学研究发生了巨大变化,让我们由低通量的研究方法转变为高通量的研究方法。低通量的研究利用人力,而高通量的研究利用机器人。”郑文进博士还声称,正是由于这种转变,生物医学研究出现了“从产生数据到分析数据的重大转变”。这也表明了为何郑文进博士计划借助CPRIT科研经费来评估的数据在竭力消灭全球癌症瘟疫的工作中是如此重要。

这笔科研经费名为“建立癌症研究的数据科学和信息学中心”(即DSICCR),金额超过580万美元。据写给没有专业科研背景的人看的科研经费申请总结显示,该项目旨在将SBMI最前沿的数据科学和信息学研究转换成易于访问、高质量、易于使用的软件和服务,从而推进癌症研究工作。

张家杰博士是SBMI院长,兼Glassell家族基金会信息学卓越中心杰出教授(Distinguished Chair),他发表了一番真知灼见,特别指出:“大数据时代已让位于数据科学。”张院长继续声称,“数据科学成了普通意义上的信息学的代名词,它利用各种流程/方法,让未经解读的数据流经不同的(分析)渠道,得到能用于临床医疗、疾病防治和生物医学发现的宝贵信息或实用知识。郑博士的CPRIT科研经费将使用同样的方法,利用从诸多数据源获得的未经过滤的大数据,为癌症研究人员提供推进疾病防治工作所需要的工具。”

郑文进博士计划借助DSICCR实现的目标是:“使用超过1PB的数据构建一个庞大的用于计算和分析的基础设施,向癌症研究人员提供数据科学和信息学服务。”数据将来自诸多数据源,比如:美国国立卫生研究院(NIH)、国际研究团体、医院及诊所、付费人及其他资源。这让研究人员得以享用全球各地成千上万的患者病历和生物数据。

通过挖掘病历和数据,以了解共病情况(比如多少人患有两种不同的疾病)和疾病的关联性(比如胰腺发炎会导致胰腺癌),郑文进博士想要“让癌症研究人员了解最新方法及其在癌症研究中的应用。”

DSICCR最初将包括12个项目和12名来自UTHealth学校、德克萨斯大学MD安德森癌症中心以及德克萨斯农业机械大学等机构的研究人员。这些项目的三个总体目标是:让研究人员易于访问独特资源、向其他CPRIT技术中心提供服务,以及帮助癌症研究人员更有效地分析数据。

“研究人员在开展研究时向来基于假设,而详细深入的大数据分析意味着,研究人员可以基于数据、从经过筛选的信息中找到线索和事实。”郑文进博士进一步阐述道,“更深入地了解数据,有助于更高效地利用数据,研究人员可以进而根据分析数据发现的结果来形成假设。”

郑文进博士计划提供给癌症研究人员的工具将先在德克萨斯州内部共享,然后扩大到其他州。该项目的启动日期是今年9月1日,将于2022年8月31日结束。

【附英文原文】

SBMI associate professor awarded grant to advance cancer research

On Aug. 16, the Cancer Prevention & Research Institute of Texas (CPRIT) announced the awardees for 60 new grants. UTHealth School of Biomedical Informatics (SBMI) Associate Professor W. Jim Zheng, Ph.D., M.S. was one of the grant award recipients.

Zheng is a bioinformatician who joined SBMI in 2013 and is trained in several biological areas of study and computer science. With this CPRIT award, Zheng aims to “analyze data for all forms of cancer and all scales, while utilizing expertise in each area of biomedical research; from population studies to individual patients and all the way down to molecular and gene expression research.”

Zheng’s father, Yeming Zheng, died in 1995 after suffering from liver cancer. “When my father passed away, I was in graduate school,” Zheng noted. “My interests in working to fight and cure cancer started during that time.”

Over the past 10 to 20 years, “technology has ushered in a transition in biomedical research that has taken us from low-throughput to high-throughput research methods,” says Zheng. “Low-throughput research involves the use of humans and high-throughput research uses robotics.” Zheng also states that as a result of the transition, there has been a “paradigm shift from the data generation model to a data analysis model.” This demonstrates why the data Zheng plans to evaluate with the CPRIT grant is so critically important in the fight to end the global cancer epidemic.

The grant, titled “Data Science and Informatics Core for Cancer Research,” or DSICCR, is worth over $5.8 million. According to the grant submission lay summary, the project aims to translate the cutting-edge data science and informatics research at SBMI to easily accessible, high quality, and user-friendly software and services to advance cancer research.

SBMI Dean and Glassell Family Foundation Distinguished Chair in Informatics Excellence, Jiajie Zhang, Ph.D. shared his insight by noting that “the ‘Big Data’ era gave way to the term data science.” Zhang continued stating “data science, synonymous to informatics in a general sense, utilizes various processes to take uninterepreted data through several channels until the result is intelligence or actionable knowledge for clinical care, disease prevention and biomedical discovery. Dr. Zheng’s CPRIT grant uses that same methodology; he will take unfiltered ‘Big Data’ from many sources and give cancer researchers the tools they need to advance disease prevention.”

Zheng’s goal with DSICCR is to “build a large infrastructure using more than one petabyte of data to provide data science and informatics services to cancer researchers.” Data will come from sources like the National Institutes of Health (NIH), international consortia, hospitals and clinics, payers and other entities. This gives researchers access to tens of millions of patient records and biological data from across the globe.

By mining the records and data for co-morbidity (e.g. simultaneous presence of two chronic diseases or conditions in a patient) and disease correlation (e.g. can an inflamed pancreas lead to pancreatic cancer) Zheng wants to “keep cancer researchers informed about the latest methods and their application in cancer research.”

DSICCR will initially include 12 projects with 12 additional investigators from UTHealth schools, University of Texas MD Anderson Cancer Center, Texas A&M University and more.  The three overall objectives among the projects are to provide researchers with easy access to unique resources, offer services to other CPRIT core researchers and to help cancer researchers better analyze data.

“Researchers have historically been hypothesis-driven but detailed ‘Big Data’ analysis means researchers can be data-driven and find clues and facts from sifted information.” Zheng elaborated that “a better understanding of the data leads to more efficient uses of data; researchers can then develop hypotheses based on findings.”

The tools that Zheng plans to offer cancer researchers will be shared within Texas first, then expanded beyond state lines. The project start date is Sept. 1 of this year and it will conclude on Aug. 31 in 2022.

【责任编辑:谭啸】

 

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