Genomic neighborhood
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Spatial multi-omic studies have emerged as a promising approach to comprehensively analyze cells in tissues, enabling the joint analysis of multiple data modalities like transcriptome, epigenome, proteome, and metabolome in parallel or even the same tissue section. This review focuses on the recent advancements in spatial multi-omics technologies, including novel data modalities and computational approaches.
17p vicwell 29-02-2024 5 2 Download
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We develop a method, VIPER, to impute the zero values in single-cell RNA sequencing studies to facilitate accurate transcriptome quantification at the single-cell level. VIPER is based on nonnegative sparse regression models and is capable of progressively inferring a sparse set of local neighborhood cells that are most predictive of the expression levels of the cell of interest for imputation.
15p vigalileogalilei 27-02-2022 32 1 Download
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Genomes computationally inferred from large metagenomic data sets are often incomplete and may be missing functionally important content and strain variation. We introduce an information retrieval system for large metagenomic data sets that exploits the sparsity of DNA assembly graphs to efficiently extract subgraphs surrounding an inferred genome.
16p viarchimedes 26-01-2022 6 0 Download
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Researchers discover lncRNAs can act as decoys or sponges to regulate the behavior of miRNAs. Identification of lncRNA-miRNA interactions helps to understand the functions of lncRNAs, especially their roles in complicated diseases. Computational methods can save time and reduce cost in identifying lncRNA-miRNA interactions, but there have been only a few computational methods.
12p viansan2711 30-07-2021 6 1 Download
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In previous studies, gene neighborhoods—spatial clusters of co-expressed genes in the genome-have been defined using arbitrary rules such as requiring adjacency, a minimum number of genes, a fixed window size, or a minimum expression level.
17p viwyoming2711 16-12-2020 6 1 Download
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Cross-species comparisons of gene neighborhoods (also called genomic contexts) in microbes may provide insight into determining functionally related or co-regulated sets of genes, suggest annotations of previously un-annotated genes, and help to identify horizontal gene transfer events across microbial species.
8p viwyoming2711 16-12-2020 16 1 Download
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Functional annotation of bacterial genomes is an obligatory and crucially important step of information processing from the genome sequences into cellular mechanisms. However, there is a lack of computational methods to evaluate the quality of functional assignments.
11p viflorida2711 30-10-2020 6 1 Download
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Large enzyme families may contain functionally diverse members that give rise to clusters in a sequence similarity network (SSN). In prokaryotes, the genome neighborhood of a gene-product is indicative of its function and thus, a genome neighborhood network (GNN) deduced for an SSN provides strong clues to the specific function of enzymes constituting the different clusters.
13p viflorida2711 30-10-2020 8 1 Download
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The order of genes in bacterial genomes is not random; for example, the products of genes belonging to an operon work together in the same pathway. The cotranslational assembly of protein complexes is deemed to conserve genomic neighborhoods even stronger than a common function.
8p vicolorado2711 23-10-2020 27 1 Download
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In February of 2011, the Melman boys were at it again opening Paris Club and Studio Paris in Chicago’s River North neighborhood solidifying the already known truth that they too had a knack for opening and operating hot new restaurants. The menu, created by Chef Jean Joho is approachable French dining in a casual urban setting. Upstairs is Studio Paris, one of Chicago’s hottest nightlife destinations.
60p loginnhanh 25-04-2013 68 7 Download
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Discovering what lies behind a hill or beyond a neighborhood can be as simple as taking a short walk. But curiosity and the urge to make new dis- coveries usually require people to undertake journeys much more adven- turesome than a short walk, and scientists oft en study realms far removed from everyday observation—sometimes even beyond the present means of travel or vision.
0p cronus75 14-01-2013 46 2 Download
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“Epigenetics” as introduced by ConradWaddington in 1946, is defined as a set of interactions between genes and the surrounding environment, which determines the phenotype or physical traits in an organism, (Murrell et al., 2005;Waddington, 1942). Initial research focused on genomic regions such as heterochromatin and euchromatin based on dense and relatively loose DNA packing, since these were known to contain inactive and active genes respectively, (Yasuhara et al., 2005).
218p yeutinh98 22-09-2012 59 11 Download
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Tuyển tập các báo cáo nghiên cứu về y học được đăng trên tạp chí y học quốc tế cung cấp cho các bạn kiến thức về ngành y đề tài: Genomic neighborhoods for Arabidopsis retrotransposons: a role for targeted integration in the distribution of the Metaviridae...
16p thulanh19 09-11-2011 41 1 Download