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The Journal of Nutrition Jan 2007The human can be thought of as a human-microbe hybrid, and the health of this superorganism will be affected by intrinsic properties such as human genetics, diurnal... (Review)
Review
The human can be thought of as a human-microbe hybrid, and the health of this superorganism will be affected by intrinsic properties such as human genetics, diurnal cycles, and age and by extrinsic factors such as lifestyle choices (food and drink, drug intake) and the acquisition of a stable "healthy" gut microflora (the so-called microbiome). Alterations in this superorganism will be manifest in the metabolite complement within its serum and urine samples. The unraveling of this metabolic compartmentalization in this complex ecosystem will certainly be a challenge for systems biology and necessary for defining human health at the molecular level. Within the systems biology framework, functional analyses at the level of gene expression (transcriptomics), protein translation (proteomics), and, more recently, the metabolite network (metabolomics) have become increasingly popular. Metabolomics experiments aim to quantify all metabolites in a cellular system (cell or tissue) under defined states and at different time points so that the dynamics of any biotic, abiotic, or genetic perturbation can be accurately assessed. This article provides an overview of metabolomics and discusses how data are generated and analyzed within a systems biology framework. The role of metabolomics in nutrigenomics is also discussed, as are the concepts of the human being a superorganism and the complexities required to be overcome to understand human health and disease.
Topics: Animals; Computational Biology; Diet; Genomics; Humans; Metabolic Networks and Pathways; Systems Biology
PubMed: 17182837
DOI: 10.1093/jn/137.1.259S -
Genomics, Proteomics & Bioinformatics Oct 2022Recently developed technologies to generate single-cell genomic data have made a revolutionary impact in the field of biology. Multi-omics assays offer even greater... (Review)
Review
Recently developed technologies to generate single-cell genomic data have made a revolutionary impact in the field of biology. Multi-omics assays offer even greater opportunities to understand cellular states and biological processes. The problem of integrating different omics data with very different dimensionality and statistical properties remains, however, quite challenging. A growing body of computational tools is being developed for this task, leveraging ideas ranging from machine translation to the theory of networks, and represents another frontier on the interface of biology and data science. Our goal in this review is to provide a comprehensive, up-to-date survey of computational techniques for the integration of single-cell multi-omics data, while making the concepts behind each algorithm approachable to a non-expert audience.
Topics: Computational Biology; Multiomics; Genomics; Algorithms
PubMed: 36581065
DOI: 10.1016/j.gpb.2022.11.013 -
Life Sciences, Society and Policy Aug 2017Metaphors are not just decorative rhetorical devices that make speech pretty. They are fundamental tools for thinking about the world and acting on the world. The...
Metaphors are not just decorative rhetorical devices that make speech pretty. They are fundamental tools for thinking about the world and acting on the world. The language we use to make a better world matters; words matter; metaphors matter. Words have consequences - ethical, social and legal ones, as well as political and economic ones. They need to be used 'responsibly'. They also need to be studied carefully - this is what we want to do through this editorial and the related thematic collection. In the context of synthetic biology, natural and social scientists have become increasingly interested in metaphors, a wave of interest that we want to exploit and amplify. We want to build on emerging articles and books on synthetic biology, metaphors of life and the ethical and moral implications of such metaphors. This editorial provides a brief introduction to synthetic biology and responsible innovation, as well as a comprehensive review of literature on the social, cultural and ethical impacts of metaphor use in genomics and synthetic biology. Our aim is to stimulate an interdisciplinary and international discussion on the impact that metaphors can have on science, policy and publics in the context of synthetic biology.
Topics: Biology; Genomics; Humans; Language; Metaphor; Molecular Biology; Social Behavior; Social Responsibility; Synthetic Biology; Systems Biology; Thinking
PubMed: 28849542
DOI: 10.1186/s40504-017-0061-y -
Journal of Dental Research Oct 2022Oral and craniofacial tissues are uniquely adapted for continuous and intricate functioning, including breathing, feeding, and communication. To achieve these vital... (Review)
Review
Oral and craniofacial tissues are uniquely adapted for continuous and intricate functioning, including breathing, feeding, and communication. To achieve these vital processes, this complex is supported by incredible tissue diversity, variously composed of epithelia, vessels, cartilage, bone, teeth, ligaments, and muscles, as well as mesenchymal, adipose, and peripheral nervous tissue. Recent single cell and spatial multiomics assays-specifically, genomics, epigenomics, transcriptomics, proteomics, and metabolomics-have annotated known and new cell types and cell states in human tissues and animal models, but these concepts remain limitedly explored in the human postnatal oral and craniofacial complex. Here, we highlight the collaborative and coordinated efforts of the newly established Oral and Craniofacial Bionetwork as part of the Human Cell Atlas, which aims to leverage single cell and spatial multiomics approaches to first understand the cellular and molecular makeup of human oral and craniofacial tissues in health and to then address common and rare diseases. These powerful assays have already revealed the cell types that support oral tissues, and they will unravel cell types and molecular networks utilized across development, maintenance, and aging as well as those affected in diseases of the craniofacial complex. This level of integration and cell annotation with partner laboratories across the globe will be critical for understanding how multiple variables, such as age, sex, race, and ancestry, influence these oral and craniofacial niches. Here, we 1) highlight these recent collaborative efforts to employ new single cell and spatial approaches to resolve our collective biology at a higher resolution in health and disease, 2) discuss the vision behind the Oral and Craniofacial Bionetwork, 3) outline the stakeholders who contribute to and will benefit from this network, and 4) outline directions for creating the first Human Oral and Craniofacial Cell Atlas.
Topics: Animals; Epigenomics; Genomics; Humans; Metabolomics; Proteomics; Tooth
PubMed: 36154725
DOI: 10.1177/00220345221110768 -
Molecular Systems Biology Nov 2023Spatial omics has emerged as a rapidly growing and fruitful field with hundreds of publications presenting novel methods for obtaining spatially resolved information for... (Review)
Review
Spatial omics has emerged as a rapidly growing and fruitful field with hundreds of publications presenting novel methods for obtaining spatially resolved information for any omics data type on spatial scales ranging from subcellular to organismal. From a technology development perspective, spatial omics is a highly interdisciplinary field that integrates imaging and omics, spatial and molecular analyses, sequencing and mass spectrometry, and image analysis and bioinformatics. The emergence of this field has not only opened a window into spatial biology, but also created multiple novel opportunities, questions, and challenges for method developers. Here, we provide the perspective of technology developers on what makes the spatial omics field unique. After providing a brief overview of the state of the art, we discuss technological enablers and challenges and present our vision about the future applications and impact of this melting pot.
Topics: Genomics; Proteomics; Metabolomics; Computational Biology; Mass Spectrometry
PubMed: 37842805
DOI: 10.15252/msb.202110571 -
Chemical Reviews Nov 2016The electronics surrounding us in our daily lives rely almost exclusively on electrons as the dominant charge carrier. In stark contrast, biological systems rarely use... (Review)
Review
The electronics surrounding us in our daily lives rely almost exclusively on electrons as the dominant charge carrier. In stark contrast, biological systems rarely use electrons but rather use ions and molecules of varying size. Due to the unique combination of both electronic and ionic/molecular conductivity in conducting and semiconducting organic polymers and small molecules, these materials have emerged in recent decades as excellent tools for translating signals between these two realms and, therefore, providing a means to effectively interface biology with conventional electronics-thus, the field of organic bioelectronics. Today, organic bioelectronics defines a generic platform with unprecedented biological recording and regulation tools and is maturing toward applications ranging from life sciences to the clinic. In this Review, we introduce the field, from its early breakthroughs to its current results and future challenges.
Topics: Biology; Biosensing Techniques; Drug Delivery Systems; Electrical Equipment and Supplies; Electrodes; Electronics
PubMed: 27367172
DOI: 10.1021/acs.chemrev.6b00146 -
Hepatology (Baltimore, Md.) Aug 2014Medicine is expected to benefit from combining usual cellular and molecular studies with high-throughput methods (genomics, transcriptomics, proteomics, and... (Review)
Review
Medicine is expected to benefit from combining usual cellular and molecular studies with high-throughput methods (genomics, transcriptomics, proteomics, and metabolomics). These methods, collectively known as omics, permit the determination of thousands of molecules (variations within genes, RNAs, proteins, metabolites) within a tissue, cell, or biological fluid. The use of these methods is very demanding in terms of the design of the study, acquisition, storage, analysis, and interpretation of the data. When carried out properly, these studies can reveal new etiological pathways, help to identify patients at risk for disease, and predict the response to specific treatments. Here we review these omics methods and mention several applications in hepatology research.
Topics: Gastroenterology; Genomics; Humans; Liver Diseases; Metabolomics; Proteomics; Systems Biology
PubMed: 24449428
DOI: 10.1002/hep.27023 -
BMC Medical Genomics Sep 2020
Topics: Computational Biology; Congresses as Topic; Gene Expression Profiling; Genetics, Medical; Genomics; Mutation; Neoplasms; Systems Biology
PubMed: 32948185
DOI: 10.1186/s12920-020-00786-x -
Nature Chemical Biology Aug 2007The increasing availability of data related to genes, proteins and their modulation by small molecules has provided a vast amount of biological information leading to...
The increasing availability of data related to genes, proteins and their modulation by small molecules has provided a vast amount of biological information leading to the emergence of systems biology and the broad use of simulation tools for data analysis. However, there is a critical need to develop cheminformatics tools that can integrate chemical knowledge with these biological databases and simulation approaches, with the goal of creating systems chemical biology.
Topics: Animals; Biological Assay; Cell Physiological Phenomena; Computational Biology; Databases, Factual; Drug Design; Genomics; Humans; Models, Chemical; Models, Molecular; Molecular Biology; Peptide Library; Proteomics; Research; Systems Biology
PubMed: 17637771
DOI: 10.1038/nchembio0807-447 -
BMC Genomics 2014Synergistically integrating multi-layer genomic data at systems level not only can lead to deeper insights into the molecular mechanisms related to disease initiation...
Synergistically integrating multi-layer genomic data at systems level not only can lead to deeper insights into the molecular mechanisms related to disease initiation and progression, but also can guide pathway-based biomarker and drug target identification. With the advent of high-throughput next-generation sequencing technologies, sequencing both DNA and RNA has generated multi-layer genomic data that can provide DNA polymorphism, non-coding RNA, messenger RNA, gene expression, isoform and alternative splicing information. Systems biology on the other hand studies complex biological systems, particularly systematic study of complex molecular interactions within specific cells or organisms. Genomics and molecular systems biology can be merged into the study of genomic profiles and implicated biological functions at cellular or organism level. The prospectively emerging field can be referred to as systems genomics or genomic systems biology. The Mid-South Bioinformatics Centre (MBC) and Joint Bioinformatics Ph.D. Program of University of Arkansas at Little Rock and University of Arkansas for Medical Sciences are particularly interested in promoting education and research advancement in this prospectively emerging field. Based on past investigations and research outcomes, MBC is further utilizing differential gene and isoform/exon expression from RNA-seq and co-regulation from the ChiP-seq specific for different phenotypes in combination with protein-protein interactions, and protein-DNA interactions to construct high-level gene networks for an integrative genome-phoneme investigation at systems biology level.
Topics: Genetic Research; Genomics; Systems Biology
PubMed: 25558922
DOI: 10.1186/1471-2164-15-S11-I1