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You searched for: Subject "genomics" Remove constraint Subject: "genomics"
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1. Genetics of anorexia nervosa: An overview of genome-wide association studies and emerging biological links

Author:
Clara de Jorge Martínez; Gull Rukh; Michael J. Williams; Santino Gaudio; Samantha Brooks; Helgi B. Schiöth
Source:
Journal of genetics and genomics 2022 v.49 no.1 pp. 1-12
ISSN:
1673-8527
Subject:
genomics,   etc   ; anorexia nervosa; comorbidity;     Show all 3 Subjects
Abstract:
... 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 ...
DOI:
10.1016/j.jgg.2021.09.005

2. Phylogenetic definitions for 25 higher-level clade names of birds

Author:
George Sangster; Edward L. Braun; Ulf S. Johansson; Rebecca T. Kimball; Gerald Mayr; Alexander Suh
Source:
Avian research 2022 v.13 pp. 100027
ISSN:
2053-7166
Subject:
genomics,   etc   ; birds; phylogeny; research;     Show all 4 Subjects
Abstract:
... 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 ...
DOI:
10.1016/j.avrs.2022.100027

3. The twisted path of the 3D genome: where does it lead?

Author:
Sergey V. Razin; Omar L. Kantidze
Source:
Trends in biochemical sciences 2022 pp. -
ISSN:
0968-0004
Subject:
genomics,   etc   ; cell nucleus; genes;     Show all 3 Subjects
Abstract:
... 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 ...
DOI:
10.1016/j.tibs.2022.04.006

4. Are we there yet? Driving the road to evolutionary graph-pangenomics

Author:
Sariel Hübner
Source:
Current opinion in plant biology 2022 v.66 pp. 102195
ISSN:
1369-5266
Subject:
genomics,   etc   ; mathematical theory; plant biology;     Show all 3 Subjects
Abstract:
... 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 ...
DOI:
10.1016/j.pbi.2022.102195

5. Contamination detection in genomic data: more is not enough

Author:
Luc Cornet; Denis Baurain
Source:
Genome biology 2022 v.23 no.1 pp. 60
ISSN:
1474-760X
Subject:
genomics,   etc   ; automation; computer software; genome;     Show all 4 Subjects
Abstract:
... 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 ...
DOI:
10.1186/s13059-022-02619-9

6. Contribution of single-cell omics to microbial ecology

Author:
S. Mauger; C. Monard; C. Thion; P. Vandenkoornhuyse
Source:
Trends in ecology & evolution 2022 v.37 no.1 pp. 67-78
ISSN:
0169-5347
Subject:
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 ...
DOI:
10.1016/j.tree.2021.09.002

7. Covariate Adaptive False Discovery Rate Control With Applications to Omics-Wide Multiple Testing

Author:
Xianyang Zhang; Jun Chen
Source:
Journal of the American Statistical Association 2022 v.117 no.537 pp. 411-427
ISSN:
1537-274X
Subject:
genomics,   etc   ; algorithms; data collection; models;     Show all 4 Subjects
Abstract:
... 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 ...
DOI:
10.1080/01621459.2020.1783273

8. Development of a genomic tool for breed assignment by comparison of different classification models: Application to three local cattle breeds

Author:
Hélène Wilmot; Jeanne Bormann; Hélène Soyeurt; Xavier Hubin; Géry Glorieux; Patrick Mayeres; Carlo Bertozzi; Nicolas Gengler
Source:
Journal of animal breeding and genetics 2022 v.139 no.1 pp. 40-61
ISSN:
0931-2668
Subject:
genomics,   etc   ; cattle; herds; models; pedigree;     Show all 5 Subjects
Abstract:
... 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 ...
DOI:
10.1111/jbg.12643

9. FrogCap: A modular sequence capture probe‐set for phylogenomics and population genetics for all frogs, assessed across multiple phylogenetic scales

Author:
Carl R. Hutter; Kerry A. Cobb; Daniel M. Portik; Scott L. Travers; Perry L. Wood Jr.; Rafe M. Brown
Source:
Molecular ecology resources 2022 v.22 no.3 pp. 1100-1119
ISSN:
1755-098X
Subject:
genomics,   etc   ; ecology; exons; introns; phylogeny;     Show all 5 Subjects
Abstract:
... 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, ...
DOI:
10.1111/1755-0998.13517

10. Genomics and ecological modelling clarify species integrity in a confusing group of butterflies

Author:
Erin O. Campbell; Zachary G. MacDonald; Edward V. Gage; Randy V. Gage; Felix A. H. Sperling
Source:
Molecular ecology 2022 v.31 no.8 pp. 2400-2417
ISSN:
0962-1083
Subject:
genomics,   etc   ; DNA; gene flow; introgression;     Show all 4 Subjects
Abstract:
... 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 ...
DOI:
10.1111/mec.16407

11. The (unusual) heuristic value of Hox gene clusters; a matter of time?

Author:
Denis Duboule
Source:
Developmental biology 2022 v.484 pp. 75-87
ISSN:
0012-1606
Subject:
genomics,   etc   ; evolution; homeotic genes; vertebrates;     Show all 4 Subjects
Abstract:
... 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 ...
DOI:
10.1016/j.ydbio.2022.02.007

12. A systematic study of mosaicism in heritable thoracic aortic aneurysm and dissection

Author:
Hang Yang; Guoyan Zhu; Weizhen Zhou; Mingyao Luo; Yujing Zhang; Yinhui Zhang; Chang Shu; Zhou Zhou
Source:
Genomics 2022 v.114 no.1 pp. 196-201
ISSN:
0888-7543
Subject:
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 ...
DOI:
10.1016/j.ygeno.2021.12.002

13. Bayesian optimization of multivariate genomic prediction models based on secondary traits for improved accuracy gains and phenotyping costs

Author:
Kosuke Hamazaki; Hiroyoshi Iwata
Source:
Theoretical and applied genetics 2022 v.135 no.1 pp. 35-50
ISSN:
0040-5752
Subject:
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 ...
DOI:
10.1007/s00122-021-03949-1

14. Beyond “living fossils”: Can comparative genomics finally reveal novelty?

Author:
Gustavo Sanchez; Oleg Simakov; Daniel S. Rokhsar
Source:
Molecular ecology resources 2022 v.22 no.1 pp. 9-11
ISSN:
1755-098X
Subject:
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 ...
DOI:
10.1111/1755-0998.13488

15. Lesson of regulatory anatomy: Using integrated functional genomics to dissect the X-inactivation center

Author:
Elphège P. Nora
Source:
Molecular cell 2022 v.82 no.1 pp. 10-12
ISSN:
1097-2765
Subject:
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. ...
DOI:
10.1016/j.molcel.2021.12.009

16. Mouse genomic and cellular annotations

Author:
Helen Long; Richard Reeves; Michelle M. Simon
Source:
Mammalian genome 2022 v.33 no.1 pp. 19-30
ISSN:
0938-8990
Subject:
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 ...
DOI:
10.1007/s00335-021-09936-7

17. New Data and New Features of the FunRiceGenes (Functionally Characterized Rice Genes) Database: 2021 Update

Author:
Fangfang Huang; Yingru Jiang; Tiantian Chen; Haoran Li; Mengjia Fu; Yazhou Wang; Yufang Xu; Yang Li; Zhengfu Zhou; Lihua Jia; Yidan Ouyang; Wen Yao
Source:
Rice 2022 v.15 no.1 pp. 23
ISSN:
1939-8425
Subject:
genomics,   etc   ; databases; food crops; genes; rice;     Show all 5 Subjects
Abstract:
... 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 ...
DOI:
10.1186/s12284-022-00569-1

18. PRDM9-directed recombination hotspots depleted near meiotically transcribed genes

Author:
Enrique J. Schwarzkopf; Omar E. Cornejo
Source:
Gene 2022 v.813 pp. 146123
ISSN:
0378-1119
Subject:
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 ...
DOI:
10.1016/j.gene.2021.146123

19. Physiological characteristics and miRNA sequencing of two root zones with contrasting ammonium assimilation patterns in Populus

Author:
Jing Zhou; Jiang ting Wu
Source:
Genes & genomics 2022 v.44 no.1 pp. 39-51
ISSN:
1976-9571
Subject:
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 ...
DOI:
10.1007/s13258-021-01156-2

20. Visualization of the Effect of Assay Size on the Error Profile of Tumor Mutational Burden Measurement

Author:
Nathanael G. Bailey
Source:
Genes 2022 v.13 no.3 pp. -
ISSN:
2073-4425
Subject:
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 ...
DOI:
10.3390/genes13030432