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... Anorexia nervosa (AN) is a complex disorder with a strong genetic component. Comorbidities are frequent and there is substantial overlap with other disorders. The lack of understanding of the molecular and neuroanatomical causes has made it difficult to develop effective treatments and it is often difficult to treat in clinical practice. Recent advances in genetics have changed our understanding o ...
... Knowledge of the higher-level phylogenetic relationships of birds has grown substantially during the past two decades due to the application of genomic data. However, the nomenclature of higher-level taxa has not become more stable, due to the lack of regulation of taxon names above the level of superfamily by the ICZN, and the usage of rank-based nomenclature, which is not tied to clades in a phy ...
... A new era in 3D genome studies began with the development of the so-called ‘C-methods’, used for the analysis of spatial contacts between distant genomic elements. However, the idea that spatial genome organization, partitioning of the genome into structural/functional units, and the functional compartmentalization of the cell nucleus are important for the implementation of key functions of the ge ...
... With increase in the number of sequenced genomes, it is now recognized that graph-based pangenomes can provide a comprehensive platform to study diversity in a population or species, from point mutations to large chromosomal rearrangements. By incorporating concepts from graph theory, a graph-pangenome can be studied directly to identify genomic regions and genes that underlie important evolutiona ...
... The decreasing cost of sequencing and concomitant augmentation of publicly available genomes have created an acute need for automated software to assess genomic contamination. During the last 6 years, 18 programs have been published, each with its own strengths and weaknesses. Deciding which tools to use becomes more and more difficult without an understanding of the underlying algorithms. We revi ...
genomics, etc ; evolution; genetic variation; microorganisms; Show all 4 Subjects
Abstract:
... Micro-organisms play key roles in various ecosystems, but many of their functions and interactions remain undefined. To investigate the ecological relevance of microbial communities, new molecular tools are being developed. Among them, single-cell omics assessing genetic diversity at the population and community levels and linking each individual cell to its functions is gaining interest in microb ...
... Conventional multiple testing procedures often assume hypotheses for different features are exchangeable. However, in many scientific applications, additional covariate information regarding the patterns of signals and nulls are available. In this article, we introduce an FDR control procedure in large-scale inference problem that can incorporate covariate information. We develop a fast algorithm ...
... Assignment of individual cattle to a specific breed can often not rely on pedigree information. This is especially the case for local breeds for which the development of genomic assignment tools is required to allow individuals of unknown origin to be included to their herd books. A breed assignment model can be based on two specific stages: (a) the selection of breed‐informative markers and (b) t ...
... Despite the prevalence of high‐throughput sequencing in phylogenetics, many relationships remain difficult to resolve because of conflicting signal among genomic regions. Selection of different types of molecular markers from different genomic regions is required to overcome these challenges. For evolutionary studies in frogs, we introduce the publicly available FrogCap suite of genomic resources, ...
... Recent advances in both genomics and ecological modelling present new, multidisciplinary opportunities for resolving species boundaries and understanding the mechanisms that maintain their integrity in regions of contact. Here, we use a combination of high‐throughput DNA sequencing and ecological niche modelling to resolve species boundaries and niche divergence within the Speyeria atlantis‐hesper ...
... Ever since their first report in 1984, Antennapedia-type homeobox (Hox) genes have been involved in such a series of interesting observations, in particular due to their conserved clustered organization between vertebrates and arthropods, that one may legitimately wonder about the origin of this heuristic value. In this essay, I first consider different examples where Hox gene clusters have been i ...
genomics, etc ; aneurysm; dissection; gene frequency; patients; Show all 5 Subjects
Abstract:
... Mosaicisms are often overlooked in routine molecular diagnosis. Although not common, they are of great significance for accurate diagnosis and genetic counseling. In this study, we systematically evaluated the frequency of mosaicisms in both asymptomatic parents and affected patients with thoracic aortic aneurysm and dissection (TAAD). Next-generation sequencing (NGS) data from 1085 patients was r ...
genomics, etc ; Bayesian theory; models; phenotype; prediction; Show all 5 Subjects
Abstract:
... KEY MESSAGE: We propose a novel approach to the Bayesian optimization of multivariate genomic prediction models based on secondary traits to improve accuracy gains and phenotyping costs via efficient Pareto frontier estimation. Multivariate genomic prediction based on secondary traits, such as data from various omics technologies including high-throughput phenotyping (e.g., unmanned aerial vehicle ...
genomics, etc ; Sepiidae; ecology; evolution; genes; squid; Show all 6 Subjects
Abstract:
... Cephalopods have recently moved into the research focus due to the growing number of sequenced genomes, molecular tools, and laboratory culture (Albertin & Simakov, 2020). Genome data now allows us to ask how the many known novelties of cephalopod morphology are reflected in their genomes and gene regulation. A crucial gap in this understanding has been the limited information for the Nautilus, t ...
genomics, etc ; X chromosome; cells; regulatory sequences; Show all 4 Subjects
Abstract:
... Gjaltema et al. (2021) perform systematic screens to identify the long-sought cis-regulatory elements of Xist. They discover that distal elements give Xist a boost as cells exit pluripotency, while proximal elements restrict Xist expression to cells with two X chromosomes. ...
genomics, etc ; females; genes; humans; mice; transcriptomics; Show all 6 Subjects
Abstract:
... Mice have emerged as one of the most popular and valuable model organisms in the research of human biology. This is due to their genetic and physiological similarity to humans, short generation times, availability of genetically homologous inbred strains, and relatively easy laboratory maintenance. Therefore, following the release of the initial human reference genome, the generation of the mouse ...
... As a major food crop and model organism, rice has been mostly studied with the largest number of functionally characterized genes among all crops. We previously built the funRiceGenes database including ~ 2800 functionally characterized rice genes and ~ 5000 members of different gene families. Since being published, the funRiceGenes database has been accessed by more than 54,400 users with over 54 ...
genomics, etc ; DNA; genes; meiosis; mice; retrotransposons; Show all 6 Subjects
Abstract:
... PRDM9 drives recombination hotspots in some mammals, including mice and apes. Non-functional orthologs of PRDM9 are present in a wide variety of vertebrates, but why it is functionally maintained in some lineages is not clear. One possible explanation is that PRDM9 plays a role in ensuring that meiosis is successful. During meiosis, available DNA may be a limiting resource given the tight packagin ...
genomics, etc ; Populus; ammonium; microRNA; plantlets; rhizosphere; Show all 6 Subjects
Abstract:
... BACKGROUND: The net ammonium fluxes differ among the different root zones of Populus, but the physiological and microRNA regulatory mechanisms are unclear. OBJECTIVE: To elucidate the physiological and miRNA regulatory mechanisms, we investigated the two root zones displaying significant differences in net NH₄⁺ effluxes of P. × canescens. METHODS: Populus plantlets were cultivated with 500 μM NH₄C ...
genomics, etc ; Internet; biomarkers; neoplasms; therapeutics; uncertainty; Show all 6 Subjects
Abstract:
... Tumor mutational burden (TMB) refers to the number of somatic mutations in a tumor per megabase and is a biomarker for response to immune checkpoint inhibitor therapy. Immune checkpoint inhibitors are currently approved for tumors with TMB greater than or equal to 10 mutations/megabase. Many laboratories are currently reporting TMB values based upon targeted resequencing panels with limited genomi ...