In the midst of an outbreak or sustained epidemic, reliable prediction of transmission risks and patterns of spread is critical to inform public health programs. Projections of transmission growth or decline among specific risk groups can aid in opti...
Deciphering the relationship between a gene and its genomic context is fundamental to understanding and engineering biological systems. Machine learning has shown promise in learning latent relationships underlying the sequence-structure-function par...
IEEE/ACM transactions on computational biology and bioinformatics
Apr 3, 2024
We show that an iterative ansatz of deep learning and human intelligence guided simplification may lead to surprisingly simple solutions for a difficult problem in phylogenetics. Distinguishing Farris and Felsenstein trees is a longstanding problem i...
Molecular phylogenetics and evolution
Mar 31, 2024
Machine learning has increasingly been applied to a wide range of questions in phylogenetic inference. Supervised machine learning approaches that rely on simulated training data have been used to infer tree topologies and branch lengths, to select s...
The global spread of the SARS-CoV-2 pandemic, originating in Wuhan, China, has had profound consequences on both health and the economy. Traditional alignment-based phylogenetic tree methods for tracking epidemic dynamics demand substantial computati...
B cell receptors (BCRs) denote antigen specificity, while corresponding cell subsets indicate B cell functionality. Since each B cell uniquely encodes this combination, physical isolation and subsequent processing of individual B cells become indispe...
Cladistics : the international journal of the Willi Hennig Society
Feb 28, 2024
A phylogenetic graph search relies on a large number of highly parameterized search procedures (e.g. branch-swapping, perturbation, simulated annealing, genetic algorithm). These procedures vary in effectiveness over datasets and at alternative point...
The increasing prevalence of antibiotic resistance in Cutibacterium acnes (C. acnes) requires the search for alternative therapeutic strategies. Antimicrobial peptides (AMPs) offer a promising avenue for the development of new treatments targeting C....
Auricularia cornea is an important edible mushroom crop in China but the occurrence of cobweb disease has cause significance economic loss in its production. The rate of disease occurrence is 16.65% all over the country. In the present study, a new p...
The trends of the last 20 years in biotechnology were revealed using artificial intelligence and natural language processing (NLP) of publicly available data. Implementing this "science-of-science" approach, we capture convergent trends in the field ...
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