ATD: Collaborative Research: Statistical Ensembles for the Identification of Bacterial Genomes
ATD:合作研究:用于鉴定细菌基因组的统计集合
基本信息
- 批准号:1410771
- 负责人:
- 金额:$ 49.53万
- 依托单位:
- 依托单位国家:美国
- 项目类别:Continuing Grant
- 财政年份:2013
- 资助国家:美国
- 起止时间:2013-08-01 至 2016-07-31
- 项目状态:已结题
- 来源:
- 关键词:
项目摘要
This research focuses on reducing bioterrorism threat by integrating tools from genomics and statistics in ways that have not been previously examined. The investigators develop novel statistical theory and computational tools for accurate pathogen detection based on next generation sequencing data. Key research directions involve (i) classification by sequence enrichment; (ii) comparison of empirical clusterings and reference genomes; and (iii) shrinkage estimation and model selection in hierarchical log-linear models. In addition to an in-depth characterization of the theoretical properties of these new statistical inference techniques, the investigators perform a thorough assessment of their practical importance in the context of the detection and identification of bacterial genomes. This assessment is done using publicly available data from sources such as the Human Microbiome Project, the NCBI Short Read Archive, the European Bioinformatics Institute, and the Broad Institute. The applicability of this new methodology is broad and relates to high-dimensional settings in which choosing an appropriate class of candidate statistical models is difficult. The investigators study statistical ensembles, combinations of techniques that have been shown to provide more reliable inferences than any single statistical approach. As opposed to existing work which combines models from the same class, this new framework concerns ensembles that cross class boundaries and optimally combine inferences from multiple models from several model classes. These ensembles are expected to have distinct advantages over existing approaches, such as robustness to model misspecification and improved predictive performance.The new statistical methodology developed in this proposal has the potential to substantially improve the response of federal and international agencies to a bioterrorism attack through a rapid identification of differences in microbial genomes and their accurate classification as harmless or potentially pathogenic. The impact of these algorithms for pathogen detection on both information technology and civil infrastructure is maximized through their implementation in user-friendly, open-source computational tools and software that will be freely available to the public. The project also has a significant educational and mentorship component for students and postdoctoral fellows who are interested in enhancing our ability to respond rapidly and appropriately to (i) incidents of bioterrorism, and (ii) microbial threats to public health.
这项研究的重点是减少生物恐怖主义的威胁,通过整合工具,从基因组学和统计学的方式,以前没有检查。研究人员开发了新的统计理论和计算工具,用于基于下一代测序数据进行准确的病原体检测。主要研究方向包括(i)序列富集分类;(ii)经验聚类和参考基因组的比较;(iii)分层对数线性模型中的收缩估计和模型选择。除了深入表征这些新统计推断技术的理论特性外,研究人员还对其在细菌基因组检测和识别方面的实际重要性进行了彻底评估。该评估使用来自人类微生物组项目,NCBI Short Read Archive,欧洲生物信息学研究所和Broad Institute等来源的公开数据进行。这种新方法的适用性是广泛的,涉及到高维设置中,选择一个合适的类的候选统计模型是困难的。研究人员研究统计集成,已被证明比任何单一的统计方法提供更可靠的推断技术的组合。相对于现有的工作,从同一类的模型相结合,这个新的框架涉及的合奏,跨类边界和最佳的联合收割机从多个模型类的推断。这些集成预计将有明显的优势,现有的方法,如鲁棒性的模型误指定和改进的预测performance.The新的统计方法中开发的这一建议有可能大大提高反应的联邦和国际机构的生物恐怖主义袭击,通过快速识别微生物基因组的差异和准确的分类为无害或潜在的致病性。这些用于病原体检测的算法对信息技术和民用基础设施的影响通过在用户友好的开放源码计算工具和软件中实施而最大化,这些工具和软件将免费提供给公众。该项目也有一个重要的教育和指导组成部分,为学生和博士后研究员谁有兴趣提高我们的能力,以迅速和适当地应对(一)生物恐怖主义事件,和(ii)微生物对公共卫生的威胁。
项目成果
期刊论文数量(0)
专著数量(0)
科研奖励数量(0)
会议论文数量(0)
专利数量(0)
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Jennifer Clarke其他文献
Quantitative modeling of the survival of emListeria monocytogenes/em in soy sauce-based acidified food products
基于酱油酸化食品中单核细胞增生李斯特氏菌存活的定量建模
- DOI:
10.1016/j.ijfoodmicro.2022.109635 - 发表时间:
2022-06-02 - 期刊:
- 影响因子:5.200
- 作者:
Onay B. Dogan;Jayne Stratton;Ana Arciniega;Jennifer Clarke;Mark L. Tamplin;Andreia Bianchini;Bing Wang - 通讯作者:
Bing Wang
Body composition, pre‐diabetes and cardiovascular disease risk in early schizophrenia
早期精神分裂症的身体成分、糖尿病前期和心血管疾病风险
- DOI:
- 发表时间:
2017 - 期刊:
- 影响因子:2
- 作者:
M. Strassnig;Jennifer Clarke;S. Mann;G. Remington;R. Ganguli - 通讯作者:
R. Ganguli
<strong>Glucosylceramide synthase inhibition reduces α-synuclein pathology and improves cognition in murine models of synucleinopathy</strong>
- DOI:
10.1016/j.ymgme.2015.12.427 - 发表时间:
2016-02-01 - 期刊:
- 影响因子:
- 作者:
S. Pablo Sardi;Catherine Viel;Jennifer Clarke;Christopher Treleaven;Hyejung Park;James Dodge;John Marshall;Mandy Cromwell;John Leonard;Bing Wang;Seng H. Cheng;Lamya Shihabuddin - 通讯作者:
Lamya Shihabuddin
23 ESTABLISHING THE SPECIFIC CONTRIBUTION OF ADHERENT AND INVASIVE <em>ESCHERICHIA COLI</em> TO THE ONSET OF INFLAMMATORY BOWEL DISEASE
- DOI:
10.1053/j.gastro.2019.01.237 - 发表时间:
2019-02-01 - 期刊:
- 影响因子:
- 作者:
Hatem Kittana;João Carlos Gomes-Neto;Kari Heck;Jason Sughroue;Rafael Segura Muñoz;Liz A. Cody;Yibo Xian;Sara Mantz;Robert Schmaltz;Jesse Hostetter;Jennifer Clarke;Steve Kachman;Andrew Benson;Jens Walter;Amanda Ramer-Tait - 通讯作者:
Amanda Ramer-Tait
Sa1667: DIGESTIVE TRACT RESECTIONS LEADING TO AN OSTOMY INFLUENCE THE RISK OF CIRCULATING FOOD-SPECIFIC-IGG WHEN COMPARED TO OTHER DIGESTIVE ILLNESSES
- DOI:
10.1016/s0016-5085(22)61088-6 - 发表时间:
2022-05-01 - 期刊:
- 影响因子:
- 作者:
Walker K. Carson;Joseph Baumert;Jennifer Clarke;Jacques Izard - 通讯作者:
Jacques Izard
Jennifer Clarke的其他文献
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{{ truncateString('Jennifer Clarke', 18)}}的其他基金
Open Access Block Award 2024 - National Physical Laboratory NPL
2024 年开放存取块奖 - 国家物理实验室 NPL
- 批准号:
EP/Z532344/1 - 财政年份:2024
- 资助金额:
$ 49.53万 - 项目类别:
Research Grant
Open Access Block Award 2023 - National Physical Laboratory NPL
2023 年开放存取块奖 - 国家物理实验室 NPL
- 批准号:
EP/Y529795/1 - 财政年份:2023
- 资助金额:
$ 49.53万 - 项目类别:
Research Grant
Open Access Block Award 2022 - National Physical Laboratory NPL
2022 年开放存取块奖 - 国家物理实验室 NPL
- 批准号:
EP/X526861/1 - 财政年份:2022
- 资助金额:
$ 49.53万 - 项目类别:
Research Grant
ATD: Collaborative Research: Statistical Ensembles for the Identification of Bacterial Genomes
ATD:合作研究:用于鉴定细菌基因组的统计集合
- 批准号:
1120404 - 财政年份:2011
- 资助金额:
$ 49.53万 - 项目类别:
Continuing Grant
RUI: Foraging Behavior and the Role of Social Transmission
RUI:觅食行为和社会传播的作用
- 批准号:
9514137 - 财政年份:1996
- 资助金额:
$ 49.53万 - 项目类别:
Continuing Grant
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