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42 results for “substitution models”
Ions release from hydroxyapatite and substituted hydroxyapatites in different immersion liquids: In vitro experiments and theoretical modelling study
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Supplementary material for: nQMaker: estimating time non-reversible amino acid substitution models
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Modeling wetland functions: Is space-to-time substitution of perimeter-area relation appropriate?
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Data from: Mixture models of nucleotide sequence evolution that account for heterogeneity in the substitution process across sites and across lineages
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Data from: Validation of the What Matters Index: a brief, patient-reported index that guides care for chronic conditions and can substitute for computer-generated risk models
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Data from: SNP discovery in non-model organisms: strand-bias and base-substitution errors reduce conversion rates
Single nucleotide polymorphisms (SNPs) have become the marker of choice for genetic studies in organisms of conservation, commercial or biological interest. Most SNP discovery projects in nonmodel organisms apply a strategy for identifying putative SNPs based on filtering rules that account for random sequencing errors. Here, we analyse data used to develop 4723 novel SNPs for the commercially important deep-sea fish, orange roughy (Hoplostethus atlanticus), to assess the impact of not accounting for systematic sequencing errors when filtering identified polymorphisms when discovering SNPs. We used SAMtools to identify polymorphisms in a velvet assembly of genomic DNA sequence data from seven individuals. The resulting set of polymorphisms were filtered to minimize 'bycatch'—polymorphisms caused by sequencing or assembly error. An Illumina Infinium SNP chip was used to genotype a final set of 7714 polymorphisms across 1734 individuals. Five predictors were examined for their effect on the probability of obtaining an assayable SNP: depth of coverage, number of reads that support a variant, polymorphism type (e.g. A/C), strand-bias and Illumina SNP probe design score. Our results indicate that filtering out systematic sequencing errors could substantially improve the efficiency of SNP discovery. We show that BLASTX can be used as an efficient tool to identify single-copy genomic regions in the absence of a reference genome. The results have implications for research aiming to identify assayable SNPs and build SNP genotyping assays for nonmodel organisms.
Data from: PartitionFinder: combined selection of partitioning schemes and substitution models for phylogenetic analyses.
In phylogenetic analyses of molecular sequence data, partitioning involves estimating independent models of molecular evolution for different sets of sites in a sequence alignment. Choosing an appropriate partitioning scheme is an important step in most analyses because it can affect the accuracy of phylogenetic reconstruction. Despite this, partitioning schemes are often chosen without explicit statistical justification. Here, we describe two new objective methods for the combined selection of best-fit partitioning schemes and nucleotide substitution models. These methods allow millions of partitioning schemes to be compared in realistic timeframes, and so permit the objective selection of partitioning schemes even for large multi-locus DNA datasets. We demonstrate that these methods significantly outperform previous approaches, including the ad hoc selection of partitioning schemes (e.g. partitioning by gene or codon position), and a recently proposed hierarchical clustering method. We have implemented these methods in an open-source program, PartitionFinder. This program allows users to select partitioning schemes and substitution models using a range of information-theoretic metrics (e.g. the BIC, AIC, and AICc). We hope that PartitionFinder will encourage the objective selection of partitioning schemes, and thus lead to improvements in phylogenetic analyses. PartitionFinder is written in Python and runs under Mac OSX 10.4 and above. The program, source code, and a detailed manual are freely available from .
Data from: Elevated substitution rate estimates from ancient DNA: model violation and bias of Bayesian methods
The increasing ability to extract and sequence DNA from non-contemporaneous tissue offers biologists the opportunity to analyze ancient DNA (aDNA) together with modern DNA (mDNA) to address the taxonomy of extinct species, evolutionary origins, historical phylogeography and biogeography. Perhaps more exciting are recent developments in coalescence-based Bayesian inference that offer the potential to use temporal information from aDNA and mDNA for the estimation of substitution rates and divergence dates as an alternative to fossil and geological calibration. This comes at a time of growing interest in the possibility of time dependency for molecular rate estimates. Here we provide a critical assessment of Bayesian MCMC analysis for the estimation of substitution rate using simulated samples of aDNA and mDNA. We conclude that the current models and priors employed in Bayesian MCMC analysis of heterochronous mtDNA are susceptible to an upward bias in the estimation of substitution rates due to model misspecification when the data comes from populations with less than simple demographic histories, including sudden short-lived population bottlenecks or pronounced population structure. However when model misspecification is only mild, then the 95% HPD intervals provide adequate frequentist coverage of the true rates.
Data from: Accurate estimation of substitution rates with neighbour-dependent models in a phylogenetic context
Most models and algorithms developed to perform statistical inference from DNA data make the assumption that substitution processes affecting distinct nucleotide sites are stochastically independent. This assumption ensures both mathematical and computational tractability, but is in disagreement with observed data in many situations -- one well-known example being CpG dinucleotide hypermutability in mammalian genomes. In this paper, we consider the class of RN95+YpR substitution models, which allows neighbour-dependent effects -- including CpG hypermutability -- to be taken into account, through transitions between pyrimidine-purine dinucleotides. We show that it is possible to adapt inference methods originally developed under the assumption of independence between sites to RN95+YpR models, using a mathematically rigorous framework provided by specific structural properties of this class of models. We assess how efficient this approach is at inferring the CpG hypermutability rate from aligned DNA sequences. The method is tested on simulated data and compared against several alternatives; the results suggest that it delivers a high degree of accuracy at a low computational cost. We then apply our method to an alignment of ten DNA sequences from primate species. Model comparisons within the RN95+YpR class show the importance of taking into account neighbour-dependent effects. An application of the method to the detection of hypomethylated islands is discussed.
Data from: Phylogenetic relationship among horseshoe crab species: effect of substitution models on phylogenetic analyses
The horseshoe crabs, known as living fossils, have maintained their morphology almost unchanged for the past 150 million years. The little morphological differentiation among horseshoe crab lineages has resulted in substantial controversy concerning the phylogenetic relationship among the extant species of horseshoe crabs, especially among the three species in the Indo-Pacific region. Previous studies suggest that the three species constitute a phylogenetically unresolvable trichotomy, the result of a cladogenetic process leading to the formation of all three Indo-Pacific species in a short geological time. Data from two mitochondrial genes (for 16S ribosomal rRNA and cytochrome oxidase subunit I) and one nuclear gene (for coagulogen) in the four species of horseshoe crabs and outgroup species were used in a phylogenetic analysis with various substitution models. All three genes yield the same tree topology, with Tachypleus-gigas and Carcinoscorpius-rotundicauda grouped together as a monophyletic taxon. This topology is significantly better than all the alternatives when evaluated with the RELL (resampling estimated log-likelihood) method.
Data from: Elevated substitution rate estimates from ancient DNA: model violation and bias of Bayesian methods
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Data from: Synthesis, characterization and modelling of zinc and silicate co-substituted hydroxyapatite
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Data from: A new hierarchy of phylogenetic models consistent with heterogeneous substitution rates
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Data from: Phylogenetic relationship among horseshoe crab species: effect of substitution models on phylogenetic analyses
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Data from: Accurate estimation of substitution rates with neighbour-dependent models in a phylogenetic context
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Data from: PartitionFinder: combined selection of partitioning schemes and substitution models for phylogenetic analyses.
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Data from: ModelOMatic: fast and automated comparison between RY, nucleotide, amino acid, and codon substitution models
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Data from: SNP discovery in non-model organisms: strand-bias and base-substitution errors reduce conversion rates
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The Tissue-Engineered Human Psoriatic Skin Substitute: A Valuable In Vitro Model to Identify Genes with Altered Expression in Lesional Psoriasis
GEO Series GSE120464. Homo sapiens. 13 samples. Type: Expression profiling by array.
Data from: Kinetic study of catalytic CO2 hydration by metal-substituted biomimetic carbonic anhydrase model complexes
The rapid rise of the CO2 level in the atmosphere has spurred the development of CO2 capture methods such as the use of biomimetic complexes that mimic carbonic anhydrase. In this study, model complexes with tris(2-pyridylmethyl)amine (TPA) were synthesized using various transition metals (Zn2+, Cu2+ and Ni2+) to control the intrinsic proton-donating ability. The pKa of the water coordinated to the metal, which indicates its proton-donating ability, was determined by potentiometric pH titration and found to increase in the order [(TPA)Cu(OH2)]2+ < [(TPA)Ni(OH2)]2+ < [(TPA)Zn(OH2)]2+. The effect of pKa on the CO2 hydration rate was investigated by stopped-flow spectrophotometry. Because the water ligand in [(TPA)Zn(OH2)]2+ had the highest pKa, it would be more difficult to deprotonate it than those coordinated to Cu2+ and Ni2+. It was therefore expected that the complex would have the slowest rate for the reaction of the deprotonated water with CO2 to form bicarbonate. However, it was confirmed that [(TPA)Zn(OH2)]2+ actually had the fastest CO2 hydration rate because the substitution of bicarbonate with water (bicarbonate release) occurred easily.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
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DANDI Archive for NWB datasets
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International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.