Collaborative Research: RUI: Investigating microbial metabolic and regulatory diversity by modeling gene activity states inferred from transcriptome data
合作研究:RUI:通过对转录组数据推断的基因活性状态进行建模来研究微生物代谢和调控多样性
基本信息
- 批准号:1715211
- 负责人:
- 金额:$ 27.12万
- 依托单位:
- 依托单位国家:美国
- 项目类别:Standard Grant
- 财政年份:2017
- 资助国家:美国
- 起止时间:2017-09-01 至 2020-08-31
- 项目状态:已结题
- 来源:
- 关键词:
项目摘要
Microorganisms have profound impacts on the environment, society and the ways that people interact with the world. This research will advance understanding of bacterial microorganisms by developing new computational technologies for combining very large sets of diverse data with models of how bacteria function in different environments. The results should allow for more accurate prediction of bacterial metabolism. The project will train a cadre of undergraduate students in mathematics, statistics, computer science, and life science and prepare them for careers in STEM fields. The methodological advancements from this work will be available for use by microbiologists and engineers to help them design new applications and processes that make use of microbial metabolic reactions. Breakthroughs in sequencing technology have set the stage for genome-scale understanding of microbial life. The next great challenge is to capture gene regulatory information in order to more accurately model the metabolic response of an organism to its environment. Prior work has developed and applied automated methods to create genome-scale metabolic models and developed a robust Bayesian statistical framework for estimating gene activity states of bacteria. These estimates are used as constraints in an integrated metabolic and regulatory model (iMRM), effectively incorporating information from large scale expression data into metabolic models. Additional work is needed to integrate such metabolic models with a wide range of alternative data sources, including transcriptional regulatory networks. To meet this need, this project will apply computational approaches for iterative cycles of model generation, experimental validation and feedback to generate better model outcomes. The results are expected to establish a rigorous statistical foundation for the generation and application of iMRMs by the scientific community. Further, the project incorporates undergraduate students in all aspects of the research as the primary research students.
微生物对环境、社会和人类与世界互动的方式有着深远的影响。这项研究将通过开发新的计算技术来促进对细菌微生物的理解,这些技术将非常大的不同数据集与细菌在不同环境中如何发挥作用的模型相结合。 结果应该允许更准确地预测细菌代谢。该项目将培养一批数学、统计学、计算机科学和生命科学的本科生,并为他们在STEM领域的职业生涯做好准备。这项工作的方法学进步将可供微生物学家和工程师使用,帮助他们设计利用微生物代谢反应的新应用和工艺。测序技术的突破为了解微生物生命的基因组规模奠定了基础。下一个巨大的挑战是捕获基因调控信息,以便更准确地模拟生物体对其环境的代谢反应。先前的工作已经开发和应用了自动化方法来创建基因组规模的代谢模型,并开发了一个强大的贝叶斯统计框架来估计细菌的基因活性状态。这些估计值用作综合代谢和调节模型(iMRM)中的约束,有效地将来自大规模表达数据的信息并入代谢模型中。需要更多的工作来整合这些代谢模型与广泛的替代数据源,包括转录调控网络。为了满足这一需求,本项目将采用计算方法进行模型生成、实验验证和反馈的迭代循环,以生成更好的模型结果。 预计这些结果将为科学界生成和应用iMRM建立严格的统计基础。此外,该项目将本科生纳入研究的各个方面,作为主要的研究学生。
项目成果
期刊论文数量(2)
专著数量(0)
科研奖励数量(0)
会议论文数量(0)
专利数量(0)
Implementing and evaluating a Gaussian mixture framework for identifying gene function from TnSeq data
实施和评估用于从 TnSeq 数据识别基因功能的高斯混合框架
- DOI:10.1142/9789813279827_0016
- 发表时间:2018
- 期刊:
- 影响因子:0
- 作者:Li, Kevin;Chen, Rachel;Lindsey, William;Best, Aaron;DeJongh, Matthew;Henry, Christopher;Tintle, Nathan
- 通讯作者:Tintle, Nathan
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Nathan Tintle其他文献
Assessment of the vitamin D status and its determinants in young healthy students from Palestine
巴勒斯坦年轻健康学生维生素 D 状况及其决定因素的评估
- DOI:
- 发表时间:
2023 - 期刊:
- 影响因子:2.5
- 作者:
Janina Susann Lenz;Nathan Tintle;F. Kerlikowsky;M. Badrasawi;Rana Zahdeh;R. Qasrawi;A. Hahn;J. Schuchardt - 通讯作者:
J. Schuchardt
Mental health service-seeking behavior in post-Soviet Ukraine
后苏联乌克兰的心理健康服务寻求行为
- DOI:
- 发表时间:
2023 - 期刊:
- 影响因子:2
- 作者:
Amanda Jiang;Rachel Ulrich;K. Van De Griend;Nathan Tintle;M. McCarthy;Daniela A. Beckelhymer - 通讯作者:
Daniela A. Beckelhymer
Trans Fatty Acid Biomarkers and Incident Type 2 Diabetes: Pooled Analysis from 10 Prospective Cohort Studies in the Fatty Acids and Outcome Research Consortium (FORCE) (OR33-02-19)
- DOI:
10.1093/cdn/nzz039.or33-02-19 - 发表时间:
2019-06-01 - 期刊:
- 影响因子:
- 作者:
Heidi Lai;Fumiaki Imamura;Andres Ardisson Korat;Rachel Murphy;Nathan Tintle;Julie Bassett;Jiaying Chen;Janine Kröger;Nita Forouhi;Matthias Schulze;William Harris;Vasan Ramachandran;Frank Hu;Graham Giles;Luc Djousse;Ingeborg Brouwer;Jason Wu;Matti Marklund;Renata Micha;Rozenn Lemaitre - 通讯作者:
Rozenn Lemaitre
P10-001-23 Circulating Omega-3 Fatty Acids Mediate and Moderate the Effect of FADS on Cardiovascular Biomarkers
- DOI:
10.1016/j.cdnut.2023.101668 - 发表时间:
2023-07-01 - 期刊:
- 影响因子:
- 作者:
Carmen Annevelink;Gregory Shearer;Nathan Tintle;Jason Westra - 通讯作者:
Jason Westra
Home- and Hospital-Based Cardiac Rehabilitation Exercise
家庭和医院心脏康复锻炼
- DOI:
10.1177/0193945916668326 - 发表时间:
2017 - 期刊:
- 影响因子:1.8
- 作者:
S. Dunn;L. M. Dunn;Madison P. Buursma;Jacob A. Clark;Lucas Vander Berg;Holli A. DeVon;Nathan Tintle - 通讯作者:
Nathan Tintle
Nathan Tintle的其他文献
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{{ truncateString('Nathan Tintle', 18)}}的其他基金
Expanding and assessing the art and practice of statistical thinking
扩展和评估统计思维的艺术和实践
- 批准号:
2235355 - 财政年份:2023
- 资助金额:
$ 27.12万 - 项目类别:
Standard Grant
Developing and Assessing a Conceptual Approach to an Algebra-based Second Course in Statistics
开发和评估基于代数的第二门统计学课程的概念方法
- 批准号:
1612201 - 财政年份:2016
- 资助金额:
$ 27.12万 - 项目类别:
Standard Grant
REU Site: Effects of political upheaval and ethnic discord on the mental health of a population
REU 网站:政治动乱和种族不和对人口心理健康的影响
- 批准号:
1560078 - 财政年份:2016
- 资助金额:
$ 27.12万 - 项目类别:
Standard Grant
Broadening the impact and evaluating the effectiveness of randomization-based curricula for introductory statistics
扩大基于随机化的统计入门课程的影响并评估其有效性
- 批准号:
1323210 - 财政年份:2014
- 资助金额:
$ 27.12万 - 项目类别:
Standard Grant
Collaborative Research: RUI: Developing Integrated Metabolic Regulatory Models (iMRMs) for the Investigation of Metabolic and Regulatory Diversity of Sequenced Microbes
合作研究:RUI:开发综合代谢调节模型(iMRM)用于研究测序微生物的代谢和调节多样性
- 批准号:
1330813 - 财政年份:2013
- 资助金额:
$ 27.12万 - 项目类别:
Standard Grant
Developing an Innovative Randomization-based Introductory Statistics Curriculum
开发基于随机化的创新统计入门课程
- 批准号:
1140629 - 财政年份:2012
- 资助金额:
$ 27.12万 - 项目类别:
Standard Grant
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