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Comptes Rendus Biologies 2016The origins of genetics are to be found in Gregor Mendel's memoir on plant hybridization (1865). However, the word 'genetics' was only coined in 1906, to designate the... (Review)
Review
The origins of genetics are to be found in Gregor Mendel's memoir on plant hybridization (1865). However, the word 'genetics' was only coined in 1906, to designate the new science of heredity. Founded upon the Mendelian method for analyzing the products of crosses, this science is distinguished by its explicit purpose of being a general 'science of heredity', and by the introduction of totally new biological concepts (in particular those of gene, genotype, and phenotype). In the 1910s, Mendelian genetics fused with the chromosomal theory of inheritance, giving rise to what is still called 'classical genetics'. Within this framework, the gene is simultaneously a unit of function and transmission, a unit of recombination, and of mutation. Until the early 1950s, these concepts of the gene coincided. But when DNA was found to be the material basis of inheritance, this congruence dissolved. Then began the venture of molecular biology, which has never stopped revealing the complexity of the way in which hereditary material functions.
Topics: Animals; Epigenomics; Genes; Genetics; History, 19th Century; History, 20th Century; History, 21st Century; Humans; Molecular Biology; Plants
PubMed: 27263362
DOI: 10.1016/j.crvi.2016.05.009 -
Molecular & Cellular Proteomics : MCP Jun 2023The world has witnessed a steady rise in both non-infectious and infectious chronic diseases, prompting a cross-disciplinary approach to understand and treating disease.... (Review)
Review
The world has witnessed a steady rise in both non-infectious and infectious chronic diseases, prompting a cross-disciplinary approach to understand and treating disease. Current medical care focuses on treating people after they become patients rather than preventing illness, leading to high costs in treating chronic and late-stage diseases. Additionally, a "one-size-fits all" approach to health care does not take into account individual differences in genetics, environment, or lifestyle factors, decreasing the number of people benefiting from interventions. Rapid advances in omics technologies and progress in computational capabilities have led to the development of multi-omics deep phenotyping, which profiles the interaction of multiple levels of biology over time and empowers precision health approaches. This review highlights current and emerging multi-omics modalities for precision health and discusses applications in the following areas: genetic variation, cardio-metabolic diseases, cancer, infectious diseases, organ transplantation, pregnancy, and longevity/aging. We will briefly discuss the potential of multi-omics approaches in disentangling host-microbe and host-environmental interactions. We will touch on emerging areas of electronic health record and clinical imaging integration with muti-omics for precision health. Finally, we will briefly discuss the challenges in the clinical implementation of multi-omics and its future prospects.
Topics: Humans; Genomics; Proteomics; Multiomics; Metabolomics; Neoplasms
PubMed: 37119971
DOI: 10.1016/j.mcpro.2023.100561 -
Experimental & Molecular Medicine Sep 2020Advances in single-cell isolation and barcoding technologies offer unprecedented opportunities to profile DNA, mRNA, and proteins at a single-cell resolution. Recently,... (Review)
Review
Advances in single-cell isolation and barcoding technologies offer unprecedented opportunities to profile DNA, mRNA, and proteins at a single-cell resolution. Recently, bulk multiomics analyses, such as multidimensional genomic and proteogenomic analyses, have proven beneficial for obtaining a comprehensive understanding of cellular events. This benefit has facilitated the development of single-cell multiomics analysis, which enables cell type-specific gene regulation to be examined. The cardinal features of single-cell multiomics analysis include (1) technologies for single-cell isolation, barcoding, and sequencing to measure multiple types of molecules from individual cells and (2) the integrative analysis of molecules to characterize cell types and their functions regarding pathophysiological processes based on molecular signatures. Here, we summarize the technologies for single-cell multiomics analyses (mRNA-genome, mRNA-DNA methylation, mRNA-chromatin accessibility, and mRNA-protein) as well as the methods for the integrative analysis of single-cell multiomics data.
Topics: Animals; Biotechnology; Computational Biology; Epigenomics; Gene Expression Profiling; Genomics; Humans; Organ Specificity; Proteomics; Single-Cell Analysis; Transcriptome
PubMed: 32929225
DOI: 10.1038/s12276-020-0420-2 -
BMC Genomics Jan 2018The 16th International Conference on Bioinformatics (InCoB) was held at Tsinghua University, Shenzhen from September 20 to 22, 2017. The annual conference of the...
The 16th International Conference on Bioinformatics (InCoB) was held at Tsinghua University, Shenzhen from September 20 to 22, 2017. The annual conference of the Asia-Pacific Bioinformatics Network featured six keynotes, two invited talks, a panel discussion on big data driven bioinformatics and precision medicine, and 66 oral presentations of accepted research articles or posters. Fifty-seven articles comprising a topic assortment of algorithms, biomolecular networks, cancer and disease informatics, drug-target interactions and drug efficacy, gene regulation and expression, imaging, immunoinformatics, metagenomics, next generation sequencing for genomics and transcriptomics, ontologies, post-translational modification, and structural bioinformatics are the subject of this editorial for the InCoB2017 supplement issues in BMC Genomics, BMC Bioinformatics, BMC Systems Biology and BMC Medical Genomics. New Delhi will be the location of InCoB2018, scheduled for September 26-28, 2018.
Topics: Animals; Computational Biology; Genomics; High-Throughput Nucleotide Sequencing; Humans; Systems Biology
PubMed: 29363432
DOI: 10.1186/s12864-017-4326-x -
Analytica Chimica Acta Jan 2021Recent advances in high-throughput technologies have enabled the profiling of multiple layers of a biological system, including DNA sequence data (genomics), RNA... (Review)
Review
Recent advances in high-throughput technologies have enabled the profiling of multiple layers of a biological system, including DNA sequence data (genomics), RNA expression levels (transcriptomics), and metabolite levels (metabolomics). This has led to the generation of vast amounts of biological data that can be integrated in so-called multi-omics studies to examine the complex molecular underpinnings of health and disease. Integrative analysis of such datasets is not straightforward and is particularly complicated by the high dimensionality and heterogeneity of the data and by the lack of universal analysis protocols. Previous reviews have discussed various strategies to address the challenges of data integration, elaborating on specific aspects, such as network inference or feature selection techniques. Thereby, the main focus has been on the integration of two omics layers in their relation to a phenotype of interest. In this review we provide an overview over a typical multi-omics workflow, focusing on integration methods that have the potential to combine metabolomics data with two or more omics. We discuss multiple integration concepts including data-driven, knowledge-based, simultaneous and step-wise approaches. We highlight the application of these methods in recent multi-omics studies, including large-scale integration efforts aiming at a global depiction of the complex relationships within and between different biological layers without focusing on a particular phenotype.
Topics: Biomedical Research; Computational Biology; Genomics; Metabolomics; Phenotype
PubMed: 33248648
DOI: 10.1016/j.aca.2020.10.038 -
Current Biology : CB Jan 2018Interview with Martin Raff, Emeritus Professor of Cell Biology and Affiliated Member of the MRC Laboratory for Molecular Cell Biology at University College London, by...
Interview with Martin Raff, Emeritus Professor of Cell Biology and Affiliated Member of the MRC Laboratory for Molecular Cell Biology at University College London, by Jordan Raff, group leader at the Sir William Dunn School of Pathology, University of Oxford.
Topics: Allergy and Immunology; Boston; Cell Biology; Developmental Biology; History, 20th Century; History, 21st Century; London; Neurobiology; Quebec
PubMed: 29412897
DOI: 10.1016/j.cub.2017.12.001 -
Journal of Translational Medicine Nov 2021
Topics: Proteomics; Signal Transduction; Systems Biology; Translational Research, Biomedical
PubMed: 34847911
DOI: 10.1186/s12967-021-03148-y -
International Journal of Molecular... Aug 2020Medical genomics relies on next-gen sequencing methods to decipher underlying molecular mechanisms of gene expression. This special issue collects materials originally...
Medical genomics relies on next-gen sequencing methods to decipher underlying molecular mechanisms of gene expression. This special issue collects materials originally presented at the "Centenary of Human Population Genetics" Conference-2019, in Moscow. Here we present some recent developments in computational methods tested on actual medical genetics problems dissected through genomics, transcriptomics and proteomics data analysis, gene networks, protein-protein interactions and biomedical literature mining. We have selected materials based on systems biology approaches, database mining. These methods and algorithms were discussed at the Digital Medical Forum-2019, organized by I.M. Sechenov First Moscow State Medical University presenting bioinformatics approaches for the drug targets discovery in cancer, its computational support, and digitalization of medical research, as well as at "Systems Biology and Bioinformatics"-2019 (SBB-2019) Young Scientists School in Novosibirsk, Russia. Selected recent advancements discussed at these events in the medical genomics and genetics areas are based on novel bioinformatics tools.
Topics: Algorithms; Computational Biology; Data Mining; Genetics, Medical; High-Throughput Nucleotide Sequencing; Humans; Systems Biology
PubMed: 32872128
DOI: 10.3390/ijms21176224 -
The Plant Cell Sep 2019
Topics: Cell Biology; Genomics; History, 21st Century; Humans; Plant Cells; Publications; Synthetic Biology
PubMed: 31311835
DOI: 10.1105/tpc.19.00547 -
Advances in Nutrition (Bethesda, Md.) Nov 2014Metabolic pathways are tightly regulated in a tissue-specific manner to maintain whole-body homeostasis. Nutrients and hormones control these pathways at the level of...
Metabolic pathways are tightly regulated in a tissue-specific manner to maintain whole-body homeostasis. Nutrients and hormones control these pathways at the level of transcription, translation, and/or post-translation. Genomic and proteomic tools have been predominantly used to understand metabolic regulation, and only a few studies used metabolomics approaches. Metabolomics is a powerful, unbiased approach that allows comprehensive metabolic analysis of physiologic measurements and energy balance. Thus, nutrimetabolomics can expedite our ability to identify metabolic diseases that are influenced by nutrients and to develop targeted diet-based treatments. Presentations at this symposium reviewed current resources and platforms for metabolic profiling along with statistical and bioinformatics tools for data and pathway analyses. Specific applications of metabolomics were illustrated in nutritional and disease conditions, including polycystic ovary syndrome, diabetes, and obesity and in host-gut microbiome interactions.
Topics: Computational Biology; Congresses as Topic; Energy Metabolism; Humans; Metabolic Networks and Pathways; Metabolomics; Nutritional Status; Proteomics; Stearoyl-CoA Desaturase; Systems Biology
PubMed: 25398743
DOI: 10.3945/an.114.006684