AIMC Topic: Phylogeny
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Inferring Historical Introgression with Deep Learning.
Systematic biology
Nov 1, 2023
Resolving phylogenetic relationships among taxa remains a challenge in the era of big data due to the presence of genetic admixture in a wide range of organisms. Rapidly developing sequencing technologies and statistical tests enable evolutionary rel...
Automatic Differentiation is no Panacea for Phylogenetic Gradient Computation.
Genome biology and evolution
Jun 1, 2023
Gradients of probabilistic model likelihoods with respect to their parameters are essential for modern computational statistics and machine learning. These calculations are readily available for arbitrary models via "automatic differentiation" implem...
DEPP: Deep Learning Enables Extending Species Trees using Single Genes.
Systematic biology
May 19, 2023
Placing new sequences onto reference phylogenies is increasingly used for analyzing environmental samples, especially microbiomes. Existing placement methods assume that query sequences have evolved under specific models directly on the reference phy...
Inpactor2: a software based on deep learning to identify and classify LTR-retrotransposons in plant genomes.
Briefings in bioinformatics
Jan 19, 2023
LTR-retrotransposons are the most abundant repeat sequences in plant genomes and play an important role in evolution and biodiversity. Their characterization is of great importance to understand their dynamics. However, the identification and classif...
Optimization scheme of machine learning model for genetic division between northern Han, southern Han, Korean and Japanese.
Yi chuan = Hereditas
Nov 20, 2022
Han Chinese, Korean and Japanese are the main populations of East Asia, and Han Chinese presents a gradient admixture from north to south. There are differences among the East Asian populations in genetic structure. To achieve fine-scale genetic clas...
The Statistical Trends of Protein Evolution: A Lesson from AlphaFold Database.
Molecular biology and evolution
Oct 7, 2022
The recent development of artificial intelligence provides us with new and powerful tools for studying the mysterious relationship between organism evolution and protein evolution. In this work, based on the AlphaFold Protein Structure Database (Alph...
DeePVP: Identification and classification of phage virion proteins using deep learning.
GigaScience
Aug 11, 2022
BACKGROUND: Many biological properties of phages are determined by phage virion proteins (PVPs), and the poor annotation of PVPs is a bottleneck for many areas of viral research, such as viral phylogenetic analysis, viral host identification, and ant...
EPIMUTESTR: a nearest neighbor machine learning approach to predict cancer driver genes from the evolutionary action of coding variants.
Nucleic acids research
Jul 8, 2022
Discovering rare cancer driver genes is difficult because their mutational frequency is too low for statistical detection by computational methods. EPIMUTESTR is an integrative nearest-neighbor machine learning algorithm that identifies such marginal...
A LASSO-based approach to sample sites for phylogenetic tree search.
Bioinformatics (Oxford, England)
Jun 24, 2022
MOTIVATION: In recent years, full-genome sequences have become increasingly available and as a result many modern phylogenetic analyses are based on very long sequences, often with over 100 000 sites. Phylogenetic reconstructions of large-scale align...
Morphological Development at the Evolutionary Timescale: Robotic Developmental Evolution.
Artificial life
Jun 9, 2022
Evolution and development operate at different timescales; generations for the one, a lifetime for the other. These two processes, the basis of much of life on earth, interact in many non-trivial ways, but their temporal hierarchy-evolution overarchi...
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