Systems biomedicine (Austin, Tex.)最新文献

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SyStem cell biology 系统细胞生物学

Systems biomedicine (Austin, Tex.)

Pub Date : 2013-01-01 DOI: 10.4161/sysb.25874

E. Meshorer

引用次数: 1

Setting the foundation for helminths systems biology 为蠕虫系统生物学奠定了基础

Systems biomedicine (Austin, Tex.)

Pub Date : 2013-01-01 DOI: 10.4161/sysb.23113

A. Sánchez-Flores

Next generation sequencing technologies and bioinformatics have provided cost-effective methods to obtain and analyze large amounts of genome and transcriptome data from many different organisms. This information has to be integrated in order to have a system-level understanding of any organism. Parasites, in particular helminths, present new challenges not only for systems biology but for many other disciplines in science because of their diversity and evolution. Helminths are adapted to a diverse set of niches and very little is known about how they interact and manipulate their hosts or how they sense and interpret the environment. In this review, different sequencing technologies are described and it is also discussed how to avoid possible biases in each of them. The technological advances in different ’omics approaches and bioinformatics allow us to study helminths in more detail in order to contribute to current knowledge of parasitology and underpin future explorations.

下一代测序技术和生物信息学为获取和分析来自许多不同生物体的大量基因组和转录组数据提供了经济有效的方法。这些信息必须综合起来，以便对任何生物体有一个系统级的了解。寄生虫，特别是蠕虫，由于其多样性和进化性，不仅对系统生物学，而且对许多其他科学学科都提出了新的挑战。蠕虫适应了各种各样的生态位，人们对它们如何相互作用和操纵宿主，以及它们如何感知和解读环境知之甚少。在这篇综述中，介绍了不同的测序技术，并讨论了如何避免每种技术中可能存在的偏差。不同组学方法和生物信息学的技术进步使我们能够更详细地研究寄生虫，从而为当前的寄生虫学知识做出贡献，并为未来的探索奠定基础。

引用次数: 1

Network as biomarker 网络作为生物标志物

Systems biomedicine (Austin, Tex.)

Pub Date : 2013-01-01 DOI: 10.4161/sysb.26474

Rotem Ben-Hamo, S. Efroni

Identifying robust biomarkers for cancer phenotypes has challenged the biological and pharmacological communities for many years, more so since the availability of screening methods that reveal the expression levels of all the genes in the genome. A host of different approaches have been used to address this lack of robustness. These methods have included a spectrum of approaches from gene enrichment analysis to network inference analysis. More recently, some methods that use the network properties of genes have demonstrated an ability to provide a more robust signature. In this review, we survey different network-as-biomarker methods used to identify various biomarkers and we discuss the critical role of networks in the progress toward personalized medicine. We also discuss the ability of the network to identify misguided processes, rather than the gene itself, as the core of distinctions among phenotypes. Discussions about the importance of the molecular pathway view and about processes (rather than the gene per se) at the core of understanding cancer are not new. However, this review focuses on the set of tools available for actually measuring the pathway, or the process, when the expression levels of their components are available.

多年来，确定癌症表型的可靠生物标志物一直是生物学和药理学领域面临的挑战，尤其是自从有了揭示基因组中所有基因表达水平的筛选方法以来。已经使用了许多不同的方法来解决这种缺乏鲁棒性的问题。这些方法包括从基因富集分析到网络推理分析的一系列方法。最近，一些利用基因网络特性的方法已经证明能够提供更强大的签名。在这篇综述中，我们调查了用于识别各种生物标志物的不同网络作为生物标志物的方法，并讨论了网络在个性化医疗进展中的关键作用。我们还讨论了网络识别错误过程的能力，而不是基因本身，作为表型之间区别的核心。关于分子途径观点和过程(而不是基因本身)在理解癌症的核心中的重要性的讨论并不新鲜。然而，这篇综述的重点是当它们的成分的表达水平可用时，可用于实际测量途径或过程的一组工具。

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引用次数: 4

Introducing Systems Biomedicine 生物医学导论

Systems biomedicine (Austin, Tex.)

Pub Date : 2013-01-01 DOI: 10.4161/SYSB.26099

S. Efroni

引用次数: 5

Toward plasmonics-enabled spatiotemporal activity patterns in three-dimensional culture models. 三维文化模型中等离子体的时空活动模式。

Systems biomedicine (Austin, Tex.)

Pub Date : 2013-01-01 DOI: 10.4161/sysb.22834

Somin Eunice Lee, A Paul Alivisatos, Mina J Bissell

Spatiotemporal activity patterns of proteases such as matrix metalloproteinases and cysteine proteases in organs have the potential to provide insight into how organized structural patterns arise during tissue morphogenesis and may suggest therapeutic strategies to repair diseased tissues. Toward imaging spatiotemporal activity patterns, recently increased emphasis has been placed on imaging activity patterns in three-dimensional culture models that resemble tissues in vivo. Here, we briefly review key methods, based on fluorogenic modifications either to the extracellular matrix or to the protease-of-interest, that have allowed for qualitative imaging of activity patterns in three-dimensional culture models. We highlight emerging plasmonic methods that address significant improvements in spatial and temporal resolution and have the potential to enable quantitative measurement of spatiotemporal activity patterns with single-molecule sensitivity.

蛋白酶(如基质金属蛋白酶和半胱氨酸蛋白酶)在器官中的时空活动模式有可能提供对组织形态发生过程中有组织结构模式如何产生的见解，并可能提出修复病变组织的治疗策略。在成像时空活动模式方面，近年来越来越重视在类似于活体组织的三维培养模型中成像活动模式。在这里，我们简要回顾了基于对细胞外基质或感兴趣的蛋白酶的荧光修饰的关键方法，这些方法允许在三维培养模型中对活动模式进行定性成像。我们重点介绍了新兴的等离子体方法，这些方法在空间和时间分辨率方面取得了重大进展，并有可能实现单分子灵敏度时空活动模式的定量测量。

引用次数: 10

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