Deep learning (DL) is revolutionizing the development of artificial intelligence systems. For example, before 2015, humans were better than artificial machines at classifying images and solving many problems of computer vision (related to object localization and detection using images), but nowadays, artificial machines have surpassed the ability of humans in this specific task. This is just one example of how the application of these models has surpassed human abilities and the performance of other machine-learning algorithms. For this reason, DL models have been adopted for genomic selection (GS). In this article we provide insight about the power of DL in solving complex prediction tasks and how combining GS and DL models can accelerate the revolution provoked by GS methodology in plant breeding. Furthermore, we will mention some trends of DL methods, emphasizing some areas of opportunity to really exploit the DL methodology in GS; however, we are aware that considerable research is required to be able not only to use the existing DL in conjunction with GS, but to adapt and develop DL methods that take the peculiarities of breeding inputs and GS into consideration.
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http://dx.doi.org/10.1002/tpg2.20122 | DOI Listing |
Sci Rep
January 2025
Department of Neurology, The Fourth Affiliated Hospital of Guangxi Medical University, Liuzhou, Guangxi, China.
Benign paroxysmal vertigo (BPV) is a common cause of dizziness, and some patients are comorbid with psychiatric disorders such as depression, requiring intervention with antidepressants. However, the causal association between BPV, depression and antidepressants has not been clearly established. We used two-sample bidirectional Mendelian randomization (MR) to analyze the causal association between BPV, depression, and antidepressants.
View Article and Find Full Text PDFNat Commun
January 2025
State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Sciences, Beijing, China.
The relative contributions of mutation rate variation, selection, and recombination in shaping genomic variation in bacterial populations remain poorly understood. Here we analyze 3318 Yersinia pestis genomes, spanning nearly a century and including 2336 newly sequenced strains, to shed light on the patterns of genetic diversity and variation distribution at the population level. We identify 45 genomic regions ("hot regions", HRs) that, although comprising a minor fraction of the genome, are hotbeds of genetic variation.
View Article and Find Full Text PDFNat Commun
January 2025
Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland.
Nuclear speckles are membraneless organelles that associate with active transcription sites and participate in post-transcriptional mRNA processing. During the cell cycle, nuclear speckles dissolve following phosphorylation of their protein components. Here, we identify the PP1 family as the phosphatases that counteract kinase-mediated dissolution.
View Article and Find Full Text PDFVet Res
January 2025
College of Veterinary Medicine, Jeonbuk National University, Iksan Campus, Iksan, 54596, Republic of Korea.
Fowl typhoid (FT) poses a significant threat to the poultry industry and can cause substantial economic losses, especially in developing regions. Caused by Salmonella Gallinarum (SG), vaccination can prevent FT. However, existing vaccines, like the SG9R strain, have limitations, including residual virulence and potential reversion of pathogenicity.
View Article and Find Full Text PDFMob DNA
January 2025
Department of Biology, La Sierra University, Riverside, CA, USA.
Background: Messenger RNA 3' untranslated regions (3'UTRs) control many aspects of gene expression and determine where the transcript will terminate. The polyadenylation signal (PAS) AAUAAA (AATAAA in DNA) is a key regulator of transcript termination and this hexamer, or a similar sequence, is very frequently found within 30 bp of 3'UTR ends. Short interspersed element (SINE) retrotransposons are found throughout genomes in high copy numbers.
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