{"title":"Setting the foundation for helminths systems biology","authors":"A. Sánchez-Flores","doi":"10.4161/sysb.23113","DOIUrl":"https://doi.org/10.4161/sysb.23113","url":null,"abstract":"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.","PeriodicalId":90057,"journal":{"name":"Systems biomedicine (Austin, Tex.)","volume":"93 1","pages":"11 - 5"},"PeriodicalIF":0.0,"publicationDate":"2013-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4161/sysb.23113","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70654003","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Network as biomarker","authors":"Rotem Ben-Hamo, S. Efroni","doi":"10.4161/sysb.26474","DOIUrl":"https://doi.org/10.4161/sysb.26474","url":null,"abstract":"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.","PeriodicalId":90057,"journal":{"name":"Systems biomedicine (Austin, Tex.)","volume":"1 1","pages":"35 - 41"},"PeriodicalIF":0.0,"publicationDate":"2013-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4161/sysb.26474","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70655829","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Somin Eunice Lee, A Paul Alivisatos, Mina J Bissell
{"title":"Toward plasmonics-enabled spatiotemporal activity patterns in three-dimensional culture models.","authors":"Somin Eunice Lee, A Paul Alivisatos, Mina J Bissell","doi":"10.4161/sysb.22834","DOIUrl":"https://doi.org/10.4161/sysb.22834","url":null,"abstract":"<p><p>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.</p>","PeriodicalId":90057,"journal":{"name":"Systems biomedicine (Austin, Tex.)","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2013-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4161/sysb.22834","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31859095","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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