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- Imanishi, T., et al.
(författare)
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Integrative annotation of 21,037 human genes validated by full-length cDNA clones
- 2004
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Ingår i: PLoS biology. - : Public Library of Science (PLoS). - 1544-9173 .- 1545-7885. ; 2:6, s. 856-875
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Tidskriftsartikel (refereegranskat)abstract
- The human genome sequence defines our inherent biological potential; the realization of the biology encoded therein requires knowledge of the function of each gene. Currently, our knowledge in this area is still limited. Several lines of investigation have been used to elucidate the structure and function of the genes in the human genome. Even so, gene prediction remains a difficult task, as the varieties of transcripts of a gene may vary to a great extent. We thus performed an exhaustive integrative characterization of 41,118 full-length cDNAs that capture the gene transcripts as complete functional cassettes, providing an unequivocal report of structural and functional diversity at the gene level. Our international collaboration has validated 21,037 human gene candidates by analysis of high-quality full-length cDNA clones through curation using unified criteria. This led to the identification of 5,155 new gene candidates. It also manifested the most reliable way to control the quality of the cDNA clones. We have developed a human gene database, called the H-Invitational Database (H-InvDB; http://www.h-invitational.jp/). It provides the following: integrative annotation of human genes, description of gene structures, details of novel alternative splicing isoforms, non-protein-coding RNAs, functional domains, subcellular localizations, metabolic pathways, predictions of protein three-dimensional structure, mapping of known single nucleotide polymorphisms (SNPs), identification of polymorphic microsatellite repeats within human genes, and comparative results with mouse full-length cDNAs. The H-InvDB analysis has shown that up to 4% of the human genome sequence (National Center for Biotechnology Information build 34 assembly) may contain misassembled or missing regions. We found that 6.5% of the human gene candidates (1,377 loci) did not have a good protein-coding open reading frame, of which 296 loci are strong candidates for non-protein-coding RNA genes. In addition, among 72,027 uniquely mapped SNPs and insertions/deletions localized within human genes, 13,215 nonsynonymous SNPs, 315 nonsense SNPs, and 452 indels occurred in coding regions. Together with 25 polymorphic microsatellite repeats present in coding regions, they may alter protein structure, causing phenotypic effects or resulting in disease. The H-InvDB platform represents a substantial contribution to resources needed for the exploration of human biology and pathology.
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- Kino, S., et al.
(författare)
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A scoping review on the use of machine learning in research on social determinants of health: Trends and research prospects
- 2021
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Ingår i: SSM - Population Health. - : Elsevier BV. - 2352-8273. ; 15
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Tidskriftsartikel (refereegranskat)abstract
- Background: Machine learning (ML) has spread rapidly from computer science to several disciplines. Given the predictive capacity of ML, it offers new opportunities for health, behavioral, and social scientists. However, it remains unclear how and to what extent ML is being used in studies of social determinants of health (SDH). Methods: Using four search engines, we conducted a scoping review of studies that used ML to study SDH (published before May 1, 2020). Two independent reviewers analyzed the relevant studies. For each study, we identified the research questions, Results, data, and algorithms. We synthesized our findings in a narrative report. Results: Of the initial 8097 hits, we identified 82 relevant studies. The number of publications has risen during the past decade. More than half of the studies (n = 46) used US data. About 80% (n = 66) utilized surveys, and 70% (n = 57) employed ML for common prediction tasks. Although the number of studies in ML and SDH is growing rapidly, only a few studies used ML to improve causal inference, curate data, or identify social bias in predictions (i.e., algorithmic fairness). Conclusions: While ML equips researchers with new ways to measure health outcomes and their determinants from non-conventional sources such as text, audio, and image data, most studies still rely on traditional surveys. Although there are no guarantees that ML will lead to better social epidemiological research, the potential for innovation in SDH research is evident as a result of harnessing the predictive power of ML for causality, data curation, or algorithmic fairness. © 2021
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