AIMC Topic: Phylogeny

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A deep learning approach to real-time HIV outbreak detection using genetic data.

PLoS computational biology Oct 14, 2022
Pathogen genomic sequence data are increasingly made available for epidemiological monitoring. A main interest is to identify and assess the potential of infectious disease outbreaks. While popular methods to analyze sequence data often involve phylo...
Humans Disease Outbreaks HIV Infections Europe HIV-1 Phylogeny Deep Learning
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Quartet Based Gene Tree Imputation Using Deep Learning Improves Phylogenomic Analyses Despite Missing Data.

Journal of computational biology : a journal of computational molecular cell biology Sep 1, 2022
Species tree estimation is frequently based on phylogenomic approaches that use multiple genes from throughout the genome. However, for a combination of reasons (ranging from sampling biases to more biological causes, as in gene birth and loss), gene...
Genome Genetic Speciation Computer Simulation Phylogeny Deep Learning Models, Genetic
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The origin and evolution of open habitats in North America inferred by Bayesian deep learning models.

Nature communications Aug 17, 2022
Some of the most extensive terrestrial biomes today consist of open vegetation, including temperate grasslands and tropical savannas. These biomes originated relatively recently in Earth's history, likely replacing forested habitats in the second hal...
Ecosystem Phylogeny Biological Evolution Deep Learning Fossils Bayes Theorem
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New feature extraction from phylogenetic profiles improved the performance of pathogen-host interactions.

Frontiers in cellular and infection microbiology Aug 2, 2022
MOTIVATION: The understanding of pathogen-host interactions (PHIs) is essential and challenging research because this potentially provides the mechanism of molecular interactions between different organisms. The experimental exploration of PHI is tim...
Computational Biology Machine Learning Host-Pathogen Interactions Phylogeny
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bHLHDB: A next generation database of basic helix loop helix transcription factors based on deep learning model.

Journal of bioinformatics and computational biology Jul 25, 2022
The basic helix loop helix (bHLH) superfamily is a large and diverse protein family that plays a role in various vital functions in nearly all animals and plants. The bHLH proteins form one of the largest families of transcription factors found in pl...
Plants Amino Acid Sequence Phylogeny Transcription Factors Animals Deep Learning Basic Helix-Loop-Helix Transcription Factors
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Invariant transformers of Robinson and Foulds distance matrices for Convolutional Neural Network.

Journal of bioinformatics and computational biology Jul 6, 2022
The evolutionary histories of genes are susceptible of differing greatly from each other which could be explained by evolutionary variations in horizontal gene transfers or biological recombinations. A phylogenetic tree would therefore represent the ...
Algorithms Phylogeny Gene Transfer, Horizontal Neural Networks, Computer Software
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Deep learning from phylogenies to uncover the epidemiological dynamics of outbreaks.

Nature communications Jul 6, 2022
Widely applicable, accurate and fast inference methods in phylodynamics are needed to fully profit from the richness of genetic data in uncovering the dynamics of epidemics. Standard methods, including maximum-likelihood and Bayesian approaches, gene...
Disease Outbreaks Phylogeny Computer Simulation Male Deep Learning Bayes Theorem Humans
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Evolution and dispersal of mitochondrial DNA haplogroup U5 in Northern Europe: insights from an unsupervised learning approach to phylogeography.

BMC genomics May 7, 2022
BACKGROUND: We combined an unsupervised learning methodology for analyzing mitogenome sequences with maximum likelihood (ML) phylogenetics to make detailed inferences about the evolution and diversification of mitochondrial DNA (mtDNA) haplogroup U5,...
Evolution, Molecular Unsupervised Machine Learning Genetics, Population Bayes Theorem Phylogeny Haplotypes DNA, Mitochondrial Humans Europe Phylogeography
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A new linear combination method of haplogroup distribution central vectors to model population admixtures.

Molecular genetics and genomics : MGG Apr 11, 2022
We introduce a novel population genetic approach suitable to model the origin and relationships of populations, using new computation methods analyzing Hg frequency distributions. Hgs were selected into groups which show correlated frequencies in sub...
Hungary Genetics, Population Artificial Intelligence Mercury Phylogeny Haplotypes Algorithms DNA, Mitochondrial
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Current progress and open challenges for applying deep learning across the biosciences.

Nature communications Apr 1, 2022
Deep Learning (DL) has recently enabled unprecedented advances in one of the grand challenges in computational biology: the half-century-old problem of protein structure prediction. In this paper we discuss recent advances, limitations, and future pe...
Computational Biology Systems Biology Proteins Phylogeny Deep Learning
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