Results 21 to 30 of about 43,570 (212)
BMC Bioinformatics, 2017 Background The canonical code, although prevailing in complex genomes, is not universal. It was shown the canonical genetic code superior robustness compared to random codes, but it is not clearly determined how it evolved towards its current form.
José Santos, Ángel Monteagudo
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Automatic differentiation and the optimization of differential equation models in biology
Frontiers in Ecology and Evolution, 2022 A computational revolution unleashed the power of artificial neural networks. At the heart of that revolution is automatic differentiation, which calculates the derivative of a performance measure relative to a large number of parameters. Differentiation
Steven A. Frank
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Analysis of epistatic interactions and fitness landscapes using a new geometric approach
BMC Evolutionary Biology, 2007 Background Understanding interactions between mutations and how they affect fitness is a central problem in evolutionary biology that bears on such fundamental issues as the structure of fitness landscapes and the evolution of sex.
Elena Santiago F +4 more
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Predictable properties of fitness landscapes induced by adaptational tradeoffs
eLife, 2020 Fitness effects of mutations depend on environmental parameters. For example, mutations that increase fitness of bacteria at high antibiotic concentration often decrease fitness in the absence of antibiotic, exemplifying a tradeoff between adaptation to ...
Suman G Das +4 more
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PLoS Genetics, 2019 Characterizing the fitness landscape, a representation of fitness for a large set of genotypes, is key to understanding how genetic information is interpreted to create functional organisms.
Victoria O Pokusaeva +13 more
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Many Activities, One Structure: Functional Plasticity of Ribozyme Folds
Molecules, 2016 Catalytic RNAs, or ribozymes, are involved in a number of essential biological processes, such as replication of RNA genomes and mobile genetic elements, RNA splicing, translation, and RNA degradation.
Matthew W.L. Lau +1 more
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Mutational robustness changes during long-term adaptation in laboratory budding yeast populations
eLife, 2022 As an adapting population traverses the fitness landscape, its local neighborhood (i.e., the collection of fitness effects of single-step mutations) can change shape because of interactions with mutations acquired during evolution.
Milo S Johnson, Michael M Desai
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On simplified global nonlinear function for fitness landscape: a case study of inverse protein folding. [PDF]
PLoS ONE, 2014 The construction of fitness landscape has broad implication in understanding molecular evolution, cellular epigenetic state, and protein structures. We studied the problem of constructing fitness landscape of inverse protein folding or protein design ...
Yun Xu, Changyu Hu, Yang Dai, Jie Liang
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Inferring protein fitness landscapes from laboratory evolution experiments.
PLoS Computational Biology, 2023 Directed laboratory evolution applies iterative rounds of mutation and selection to explore the protein fitness landscape and provides rich information regarding the underlying relationships between protein sequence, structure, and function.
Sameer D'Costa +4 more
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Gut microbiome and aging—A dynamic interplay of microbes, metabolites, and the immune system
FEBS Letters, EarlyView.Age‐dependent shifts in microbial communities engender shifts in microbial metabolite profiles. These in turn drive shifts in barrier surface permeability of the gut and brain and induce immune activation. When paired with preexisting age‐related chronic inflammation this increases the risk of neuroinflammation and neurodegenerative diseases.
Aaron Mehl, Eran Blacher
wiley +1 more source