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温维亮,郭新宇 ,张颖,顾生浩,赵春江
《中国工程科学》 2023年 第25卷 第4期 页码 227-238 doi: 10.15302/J-SSCAE-2023.04.015
用于定义系统表现特征的基因型与表型仓库数据库的信息图式构造方法 Article
Shahab POURTALEBI,Imre HORVÁTH
《信息与电子工程前沿（英文）》 2016年 第17卷 第9期 页码 862-884 doi: 10.1631/FITEE.1600997
关键词： 信息物理系统；软件工具箱；预实体化设计；系统表现特征；仓库；数据库图式；基因型系统表现特征；表型系统表现特征；实例系统表现特征；信息模式构造
基于就医人群的中国多囊卵巢综合征女性的临床表型和治疗结局—— 身体质量指数与地理分布的影响 Article
高敬书, 马红丽, 王宇, 杨新鸣, 曹义娟, 张蓓, 韩丛辉, 吴效科
《工程（英文）》 2021年 第7卷 第2期 页码 170-177 doi: 10.1016/j.eng.2020.12.006
徐健, 马波, 苏晓泉, 黄适, 徐欣, 周学东, 黄巍, Rob Knight
《工程（英文）》 2017年 第3卷 第1期 页码 66-70 doi: 10.1016/J.ENG.2017.01.020
方法学创新一直是微生物组学研究的核心驱动力。我们认为在未来五到十年，微生物组的方法学体系在研究理念与技术平台方面将发生三大变革：①从监测菌群“结构”变化向监测菌群“功能/状态”变化的变革；②从细胞“群体”分析精度向细胞“个体”分析精度的转变；③从“数据分析”向“数据科学”的跨越。在这里我们针对实现上述三大方法学变革需要克服的关键科学或技术挑战，重点介绍了部分中国微生物组分析方法学研究团队及其国际合作伙伴的最新工作进展。我们相信中国微生物组计划应把握住当前这一重要机遇，通过在微生物组分析方法学前沿开展富有雄心、远见、创意与竞争力的交叉合作研究，为国际微生物组计划贡献一系列“中国制造”的新方法、新工具和新仪器
代谢组扩展生物学的“旁中心法则”——对理解基因组学-糖组学-代谢组学-表观基因组学互作的意义
Albert Stuart Reece
《工程（英文）》 2023年 第26卷 第7期 页码 16-16 doi: 10.1016/j.eng.2022.07.011
The central dogma of biology holds that the transcription of DNA into RNA and the translation of RNA into proteins forms the primary axis of biological activity [1]. Following major advances in the description of the complex glycan and lipid chains that are added onto these basic building blocks, the glycome and lipidome have recently been added to this doctrine as an exciting new extension named the ‘‘paracentral dogma” [2]. However, it has been pointed out that biological systems can include many layers, which are described in modern omics technology platforms relating to both cell-intrinsic and cell-extrinsic layers of control, including metabolomic, microbiomic, immunological, epigenomic, epitranscriptomic, proteomic and phosphoproteomic layers [3].
It is well known that stem and progenitor cells have a metabolism that is based on glycolysis and glutaminolysis [4]. Although this provides less energy to the cell than oxidative phosphorylation, it suffices for these cells’ needs, since such cells are generally relatively quiescent and normally suppress energy-intensive processes such as genome duplication and transcription. Moreover, it has been shown that the high intracellular lactate levels involved in such states not only inhibits the key gatekeeper enzymes of oxidative phosphorylation (i.e., pyruvate dehydrogenase and carnitine palmitoyl acyltransferase) but also actually covalently modifies them by lactylation in order to maintain this inhibited metabolic–epigenomic state [5]. In addition, intermediate metabolism and nutrients are the source of the very extensive library of post-translational modifications to DNA, RNA, and proteins, as well as supplying cellular energy for many of the required reactions. Hence, the metabolic state locks in and reinforces the epigenomic state, and the metabolome and epigenome thereby play mutually reinforcing roles. This self-reinforcing coordination explains why it is so difficult to generate induced pluripotent cells and is a contributory explanation for why the described protocols typically have such low cellular yields.
These concepts become even more important when it is considered that cancer cells are de-differentiated, similarly rely on glycolysis and glutaminolysis, and are similarly metabolically–epigenomically–genomically synchronized. The disruption of this metabolic system is a key focus of mechanistic cancer research.
These important considerations imply that the descriptive and predictive power of the newly described ‘‘paracentral dogma” of biology may be usefully and meaningfully extended by including the metabolome, along with the genome, transcriptome, proteome, glycome, and lipidome, to describe cell-intrinsic regulation—not only in terms of another omics analytical layer but also as a fully predictive and interactive partner in the symphonic-like multilayer coordination that evidently comprises cellular regulatory layering.
时间序列多组学整合分析揭示原代肝细胞体外培养去分化过程伴随非降解性泛素化修饰的增加 Article
姜正一, 孙泽宇, 欧阳晓希, 赵亚磊, 周梦豪, 王保红, 李启睿, 范林骁, 张赛男, 李兰娟
《工程（英文）》 2020年 第6卷 第11期 页码 1302-1314 doi: 10.1016/j.eng.2020.02.011
Daniel Richard Leff, Guang-Zhong Yang
《工程（英文）》 2015年 第1卷 第3期 页码 277-279 doi: 10.15302/J-ENG-2015075
本文主要关注大数据分析对改善健康、预防和检测早期疾病以及个性化干预措施的潜在影响，讨论了大数据分析在建立患者电子健康档案以获得更好的临床决策支持中的可能作用。笔者研究了药物遗传学的发展，以更好地理解患者对化学疗法产生不同反应的原因。此外，笔者评估了在线健康交流的发展， 以及如何利用这些数据检测公共健康威胁和控制传染病。
系统表现特征实例化和构成的信息模式构造 Article
Shahab POURTALEBI, Imre HORVÁTH
《信息与电子工程前沿（英文）》 2017年 第18卷 第9期 页码 1396-1415 doi: 10.1631/FITEE.1601235
关键词： 系统表现特征；信息模式构造；数据库纲要；基因型系统表现特征；表型系统表现特征；系统表现特征实例；软件工具箱；系统层级设计；信息物理系统
新孢子虫病——分子流行病学及发病机制综述 Review
Asis Khan, Jahangheer S. Shaik, Patricia Sikorski, Jitender P. Dubey, Michael E. Grigg
《工程（英文）》 2020年 第6卷 第1期 页码 10-19 doi: 10.1016/j.eng.2019.02.010
人类蛋白质N-糖基化的十二年全基因组关联研究 Review
Anna Timoshchuk, Sodbo Sharapov, Yurii S. Aulchenko
《工程（英文）》 2023年 第26卷 第7期 页码 17-31 doi: 10.1016/j.eng.2023.03.013
Most human-secreted and membrane-bound proteins have covalently attached oligosaccharide chains, or glycans. Glycosylation influences the physical and chemical properties of proteins, as well as their biological functions. Unsurprisingly, alterations in protein glycosylation have been implicated in a growing number of human diseases, and glycans are increasingly being considered as potential therapeutic targets, an essential part of therapeutics, and biomarkers. Although glycosylation pathways are biochemically well-studied, little is known about the networks of genes that guide the cell- and tissue-specific regulation of these biochemical reactions in humans in vivo. The lack of a detailed understanding of the mechanisms regulating glycome variation and linking the glycome to human health and disease is slowing progress in clinical applications of human glycobiology. Two of the tools that can provide much sought-after knowledge of human in vivo glycobiology are human genetics and genomics, which offer a powerful data-driven agnostic approach for dissecting the biology of complex traits. This review summarizes the current state of human populational glycogenomics. In Section 1, we provide a brief overview of the N-glycan's structural organization, and in Section 2, we give a description of the major blood plasma glycoproteins. Next, in Section 3, we summarize, systemize, and generalize the results from current N-glycosylation genome-wide association studies (GWASs) that provide novel knowledge of the genetic regulation of the populational variation of glycosylation. Until now, such studies have been limited to an analysis of the human blood plasma N-glycome and the N-glycosylation of immunoglobulin G and transferrin. While these three glycomes make up a rather limited set compared with the enormous multitude of glycomes of different tissues and glycoproteins, the study of these three does allow for powerful analysis and generalization. Finally, in Section 4, we turn to genes in the established loci, paying particular attention to genes with strong support in Section 5. At the end of the review, in Sections 6 and 7, we describe special cases of interest in light of new discoveries, focusing on possible mechanisms of action and biological targets of genetic variation that have been implicated in human protein N-glycosylation.
郑庆华,师斌,董博
《中国工程科学》 2023年 第25卷 第2期 页码 221-231 doi: 10.15302/J-SSCAE-2023.07.005
方向,于连超,任思源,熊行创
《中国工程科学》 2023年 第25卷 第3期 页码 230-238 doi: 10.15302/J-SSCAE-2023.07.021
标准参考数据是一类高质量科学数据，兼具计量科学特征和技术标准属性，是国家重要的科技基础和战略资源。我国标准参考数据的研究与建设基本处于空白状态，大幅落后于国际先进水平，造成科学研究和生产的系统性风险。本文详细阐明标准参考数据的科学内涵、外延特征及其战略价值，深度分析美国标准参考数据的发展脉络、管理体系、国际影响及其实践应用，在此基础上梳理我国标准参考数据发展现状，重点指出其中存在的概念不清晰、顶层设计不足、数据资源积累匮乏、管理体系缺失等关键问题，并系统地设计了我国标准参考数据建设路径。研究建议，建立健全标准参考数据政策制度体系；强化研究与建设经费保障；加强宣传教育，加快人才培养；汇集多方力量，加大国际合作。
关键词： 科学数据；计量溯源；标准化；标准参考数据
信息科学应引领未来的生物医学研究 Perspective
Kenta Nakai
《工程（英文）》 2019年 第5卷 第6期 页码 1155-1158 doi: 10.1016/j.eng.2019.07.023
笔者从长期回顾的角度阐述了对人工智能（AI）/数据科学与生物医学之间关系的看法。随着新技术的不断出现，现代生物医学的发展持续加速。与物理学不同，在生物学中没有发现（或很少有）主导定律。因此，在生物学中，“数据到知识”方法很重要。类似的方法可能有助于解决基因组序列解释中的问题，如确定患者基因组中的癌症驱动突变。最近，新一代测序（NGS）的爆炸性发展已产生大量数据，并且这种趋势将加速。这些数据可以视为气候模拟中的网格数据点。数据科学和人工智能对于这些数据的综合解释/模拟都将变得至关重要，并将在未来的精密医学中起主导作用。
标题 作者 时间 类型 操作
10x Genomics单细胞转录组测序及多组学数据挖掘技术
2019年08月02日
会议信息
新孢子虫病——分子流行病学及发病机制综述
Asis Khan, Jahangheer S. Shaik, Patricia Sikorski, Jitender P. Dubey, Michael E. Grigg
期刊论文
第七届中国图学大会
2019年08月08日
会议信息
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