AIMC Topic: Phylogeny

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A Machine Learning Pipeline to Screen Large In Vivo Molecular Data to Curate Disease Signatures of High Translational Potential.

Methods in molecular biology (Clifton, N.J.) Jan 1, 2025
A significantly low success rate of human clinical studies has long been attributed to a capability gap, namely, an ineffective translation of the animal data to the human context. To bridge this capability gap, several correcting measures have been ...
Disease Models, Animal Translational Research, Biomedical Machine Learning Computational Biology Algorithms Proteomics Phylogeny Genomics Animals Humans
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Unveiling the ghost: machine learning's impact on the landscape of virology.

The Journal of general virology Jan 1, 2025
The complexity and speed of evolution in viruses with RNA genomes makes predictive identification of variants with epidemic or pandemic potential challenging. In recent years, machine learning has become an increasingly capable technology for address...
Humans Genome, Viral Viruses Virology Phylogeny Computational Biology Machine Learning
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BetaAlign: a deep learning approach for multiple sequence alignment.

Bioinformatics (Oxford, England) Dec 26, 2024
MOTIVATION: Multiple sequence alignments (MSAs) are extensively used in biology, from phylogenetic reconstruction to structure and function prediction. Here, we suggest an out-of-the-box approach for the inference of MSAs, which relies on algorithms ...
Natural Language Processing Sequence Alignment Deep Learning Computational Biology Algorithms Phylogeny Software
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Deep learning insights into distinct patterns of polygenic adaptation across human populations.

Nucleic acids research Dec 11, 2024
Response to spatiotemporal variation in selection gradients resulted in signatures of polygenic adaptation in human genomes. We introduce RAISING, a two-stage deep learning framework that optimizes neural network architecture through hyperparameter t...
Humans Genomics Models, Genetic Genome, Human Phylogeny Deep Learning Neural Networks, Computer Multifactorial Inheritance Genetics, Population Selection, Genetic Adaptation, Physiological
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Deep learning revealed the distribution and evolution patterns for invertible promoters across bacterial lineages.

Nucleic acids research Nov 27, 2024
Invertible promoters (invertons) are crucial regulatory elements in bacteria, facilitating gene expression changes under stress. Despite their importance, their prevalence and the range of regulated gene functions are largely unknown. We introduced D...
Genome, Bacterial Metagenome Evolution, Molecular Gene Expression Regulation, Bacterial Promoter Regions, Genetic Biofilms Bacteria Phylogeny Deep Learning
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Do protein language models learn phylogeny?

Briefings in bioinformatics Nov 22, 2024
Deep machine learning demonstrates a capacity to uncover evolutionary relationships directly from protein sequences, in effect internalising notions inherent to classical phylogenetic tree inference. We connect these two paradigms by assessing the ca...
Phylogeny Humans Deep Learning Proteins Machine Learning INDEL Mutation Evolution, Molecular
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Learning genotype-phenotype associations from gaps in multi-species sequence alignments.

Briefings in bioinformatics Nov 22, 2024
Understanding the genetic basis of phenotypic variation is fundamental to biology. Here we introduce GAP, a novel machine learning framework for predicting binary phenotypes from gaps in multi-species sequence alignments. GAP employs a neural network...
Ascorbic Acid Sequence Alignment L-Gulonolactone Oxidase Phylogeny Humans Genotype Neural Networks, Computer Genetic Association Studies Machine Learning Phenotype Animals
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Integrating Contact Tracing Data to Enhance Outbreak Phylodynamic Inference: A Deep Learning Approach.

Molecular biology and evolution Nov 1, 2024
Phylodynamics is central to understanding infectious disease dynamics through the integration of genomic and epidemiological data. Despite advancements, including the application of deep learning to overcome computational limitations, significant cha...
Humans COVID-19 Contact Tracing Phylogeny SARS-CoV-2 Deep Learning Disease Outbreaks Hong Kong
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Tree Sequences as a General-Purpose Tool for Population Genetic Inference.

Molecular biology and evolution Nov 1, 2024
As population genetic data increase in size, new methods have been developed to store genetic information in efficient ways, such as tree sequences. These data structures are computationally and storage efficient but are not interchangeable with exis...
Neural Networks, Computer Phylogeny Genetics, Population
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Identification of putative coral pathogens in endangered Caribbean staghorn coral using machine learning.

Environmental microbiology Sep 1, 2024
Coral diseases contribute to the rapid decline in coral reefs worldwide, and yet coral bacterial pathogens have proved difficult to identify because 16S rRNA gene surveys typically identify tens to hundreds of disease-associate bacteria as putative p...
Endangered Species Phylogeny Coral Reefs Anthozoa Vibrio Bacteria Machine Learning Caribbean Region RNA, Ribosomal, 16S Animals
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