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Current Biology : CB Oct 2020Florian Maderspacher introduces the microbiology special issue and asks how the study of microbes has shaped our understanding of evolution.
Florian Maderspacher introduces the microbiology special issue and asks how the study of microbes has shaped our understanding of evolution.
Topics: Bacteria; Biodiversity; Biological Evolution; Ecology; Environmental Microbiology; Microbial Interactions; Phylogeny
PubMed: 33022245
DOI: 10.1016/j.cub.2020.09.010 -
Genome Biology Jan 2012A report of the Wellcome Trust Functional Genomics and Systems Biology Conference, Hinxton, UK, 29 November to 1 December 2011.
A report of the Wellcome Trust Functional Genomics and Systems Biology Conference, Hinxton, UK, 29 November to 1 December 2011.
Topics: Computational Biology; Gene Expression; Gene Regulatory Networks; Genomics; Proteomics; Systems Biology; United Kingdom
PubMed: 22289510
DOI: 10.1186/gb-2012-13-1-312 -
BMC Genomics Dec 2019The goal of this editorial is to summarize the 2019 International Conference on Intelligent Biology and Medicine (ICIBM 2019) conference that took place on June 9-11,...
The goal of this editorial is to summarize the 2019 International Conference on Intelligent Biology and Medicine (ICIBM 2019) conference that took place on June 9-11, 2019 in The Ohio State University, Columbus, OH, and to provide an introductory summary of the seven articles presented in this supplement issue. ICIBM 2019 hosted four keynote speakers, four eminent scholar speakers, five tutorials and workshops, twelve concurrent sessions and a poster session, totaling 23 posters, spanning state-of-the-art developments in bioinformatics, genomics, next-generation sequencing (NGS) analysis, scientific databases, cancer and medical genomics, and computational drug discovery. A total of 105 original manuscripts were submitted to ICIBM 2019, and after careful review, seven were selected for this supplement issue. These articles cover methods and applications for functional annotations of miRNA targeting, clonal evolution of bacterial cells, gene co-expression networks that describe a given phenotype, functional binding site analysis of RNA-binding proteins, normalization of genome architecture mapping data, sample predictions based on multiple NGS data types, and prediction of an individual's genetic admixture given exonic single nucleotide polymorphisms data.
Topics: Computational Biology; Databases, Factual; Gene Regulatory Networks; Genomics; High-Throughput Nucleotide Sequencing; Humans; Internationality; Systems Biology
PubMed: 31888451
DOI: 10.1186/s12864-019-6326-5 -
Essays in Biochemistry Nov 2021In synthetic biology, biological cells and processes are dismantled and reassembled to make novel systems that do useful things. Designs are encoded by deoxyribonucleic...
In synthetic biology, biological cells and processes are dismantled and reassembled to make novel systems that do useful things. Designs are encoded by deoxyribonucleic acid (DNA); DNA makes biological (bio-)parts; bioparts are combined to make devices; devices are built into biological systems. Computers are used at all stages of the Design-Build-Test-Learn cycle, from mathematical modelling through to the use of robots for the automation of assembly and experimentation. Synthetic biology applies engineering principles of standardisation, modularity, and abstraction, enabling fast prototyping and the ready exchange of designs between synthetic biologists working around the world. Like toy building blocks, compatible modular designs enable bioparts to be combined and optimised easily; biopart specifications are shared in open registries. Synthetic biology is made possible due to major advances in DNA sequencing and synthesis technologies, and through knowledge gleaned in the field of systems biology. Systems biology aims to understand biology across scales, from the molecular and cellular, up to tissues and organisms, and describes cells as complex information-processing systems. By contrast, synthetic biology seeks to design and build its own systems. Applications of synthetic biology are wide-ranging but include impacting healthcare to improve diagnosis and make better treatments for disease; it seeks to improve the environment by finding novel ways to clean up pollution, make industrial processes for chemical synthesis sustainable, and remove the need for damaging farming practices by making better fertilisers. Synthetic biology has the potential to change the way we live and help us to protect the future of our planet.
Topics: Agriculture; Synthetic Biology; Systems Biology
PubMed: 34693448
DOI: 10.1042/EBC20200059 -
International Journal of Molecular... Jan 2024The advances in molecular biology techniques and omics approaches have made it possible to take giant steps in applied research in life sciences [...].
The advances in molecular biology techniques and omics approaches have made it possible to take giant steps in applied research in life sciences [...].
Topics: Genomics; Proteomics; Systems Biology
PubMed: 38279361
DOI: 10.3390/ijms25021361 -
Drug Discovery Today Feb 2023Metabolomics enables the comprehensive and unbiased analysis of metabolites and lipids in biological systems. In conjunction with high-throughput activity screening, big... (Review)
Review
Metabolomics enables the comprehensive and unbiased analysis of metabolites and lipids in biological systems. In conjunction with high-throughput activity screening, big data and synthetic biology, metabolomics can guide the discovery of lead compounds with pharmacological activity from natural sources and the gut microbiome. In combination with other omics, metabolomics can further unlock the elucidation of compound toxicity, the mode of action and novel druggable targets of disease. Here, we discuss the workflows, limitations and future opportunities to leverage metabolomics and big data in conjunction with systems and synthetic biology for streamlining the discovery and development of molecules of pharmaceutical interest.
Topics: Metabolomics; High-Throughput Screening Assays; Systems Biology; Synthetic Biology
PubMed: 36427778
DOI: 10.1016/j.drudis.2022.103460 -
Current Opinion in Virology Dec 2014Recent technological advances have led to an explosion in the system-wide profiling of biological processes in the study of herpesvirus biology, herein referred to as... (Review)
Review
Recent technological advances have led to an explosion in the system-wide profiling of biological processes in the study of herpesvirus biology, herein referred to as '-omics'. In many cases these approaches have revealed novel virus-induced changes to host cell biology that can be targeted with new antiviral therapeutics. Despite these successes, -omics approaches are not widely applied in the study of roseoloviruses. Here we describe examples of how -omics studies have shaped our understanding of herpesvirus biology, and discuss how these approaches might be used to identify host and viral factors that mediate roseolovirus pathogenesis.
Topics: Gene Expression Profiling; Genomics; Host-Pathogen Interactions; Humans; Metabolomics; Proteomics; Roseolovirus; Systems Biology; Virology
PubMed: 25437230
DOI: 10.1016/j.coviro.2014.09.021 -
PLoS Biology Jan 2024Open science is key to PLOS Biology's mission, both in its daily operations and in the role we aspire to have in the scholarly ecosystem. Here, we reflect on open...
Open science is key to PLOS Biology's mission, both in its daily operations and in the role we aspire to have in the scholarly ecosystem. Here, we reflect on open science at the journal and discuss how and why we shall continue to hold it central to everything we do.
Topics: Biology; Periodicals as Topic
PubMed: 38285734
DOI: 10.1371/journal.pbio.3002516 -
Advances in Nutrition (Bethesda, Md.) Jul 2011In the last decade, advances in genomics, proteomics, and metabolomics have yielded large-scale datasets that have driven an interest in global analyses, with the... (Review)
Review
In the last decade, advances in genomics, proteomics, and metabolomics have yielded large-scale datasets that have driven an interest in global analyses, with the objective of understanding biological systems as a whole. Systems biology integrates computational modeling and experimental biology to predict and characterize the dynamic properties of biological systems, which are viewed as complex signaling networks. Whereas the systems analysis of disease-perturbed networks holds promise for identification of drug targets for therapy, equally the identified critical network nodes may be targeted through nutritional intervention in either a preventative or therapeutic fashion. As such, in the context of the nutritional sciences, it is envisioned that systems analysis of normal and nutrient-perturbed signaling networks in combination with knowledge of underlying genetic polymorphisms will lead to a future in which the health of individuals will be improved through predictive and preventative nutrition. Although high-throughput transcriptomic microarray data were initially most readily available and amenable to systems analysis, recent technological and methodological advances in MS have contributed to a linear increase in proteomic investigations. It is now commonplace for combined proteomic technologies to generate complex, multi-faceted datasets, and these will be the keystone of future systems biology research. This review will define systems biology, outline current proteomic methodologies, highlight successful applications of proteomics in nutrition research, and discuss the challenges for future applications of systems biology approaches in the nutritional sciences.
Topics: Computational Biology; Forecasting; Genomics; Humans; Metabolomics; Models, Biological; Nutritional Sciences; Proteomics; Systems Analysis; Systems Biology
PubMed: 22332076
DOI: 10.3945/an.111.000554 -
International Journal of Molecular... Jul 2023With the rapid introduction of high-throughput omics approaches such as genomics, transcriptomics, proteomics and metabolomics, the generation of large amounts of data...
With the rapid introduction of high-throughput omics approaches such as genomics, transcriptomics, proteomics and metabolomics, the generation of large amounts of data has become a fundamental aspect of modern biological research [...].
Topics: Computational Biology; Genomics; Proteomics; Metabolomics; Gene Expression Profiling
PubMed: 37511384
DOI: 10.3390/ijms241411625