A5012611425- Evolution and Paleontology Studies
- Genomics and Phylogenetic Studies
- Evolution and Genetic Dynamics
- Genetic diversity and population structure
- Radiomics and Machine Learning in Medical Imaging
- Data Analysis with R
- Bayesian Methods and Mixture Models
- Immunotherapy and Immune Responses
- vaccines and immunoinformatics approaches
- Scientific Computing and Data Management
- Machine Learning in Bioinformatics
- Geology and Paleoclimatology Research
- T-cell and B-cell Immunology
- Image Processing and 3D Reconstruction
- Advanced Breast Cancer Therapies
- Cardiovascular Health and Risk Factors
- Microbial infections and disease research
- Educational Tools and Methods
- Biomedical Text Mining and Ontologies
- Research Data Management Practices
- Fish biology, ecology, and behavior
- Physiological and biochemical adaptations
- Advanced Proteomics Techniques and Applications
- Educational Assessment and Pedagogy
- Soil Geostatistics and Mapping
University of Groningen
2016-2023
Abstract In the field of phylogenetics, BEAST2 is one most widely used software tools. It comes with graphical user interfaces BEAUti 2, DensiTree and Tracer, to create configuration files interpret BEAST2's output files. However, when many different alignments or model setups are required, a workflow cumbersome. Here, we present free, libre open‐source package, babette : ‘BEAUti Tracer for R’, R programming language. creates input files, runs parses its results, all from an function call....
AbstractThis article introduces a dedicated, computer-supported method to construct and formatively assess open, annotated concept maps of Personal Professional Theories (PPTs). These theories are internalised, personal bodies formal practical knowledge, values, norms convictions that professionals use as reference interpret acquire direct their behaviour, which vocational students expected develop. Monitoring the development PPTs assessing quality difficult they are, essentially, mental...
Summary In the field of phylogenetics, BEAST2 is one most widely used software tools. It comes with graphical user interfaces BEAUti 2, DensiTree and Tracer, to create configuration files interpret BEAST2’s output files. However, when many different alignments or model setups are required, a workflow cumbersome. Here, we present free, libre open-source package, babette : ‘BEAUti Tracer for R’, R programming language. creates input files, runs parses its results, all from an function call. We...
Abstract Understanding macroevolution on islands requires knowledge of the closest relatives is-land species mainland. The evolutionary relationships between island and mainland can be reconstructed using phylogenies, to which models fitted understand dynamical processes colonisation diversification. But how much information is needed gain insight into islands? Here we first test whether turnover incomplete sampling leave recognis-able signatures in community phylogenetic data. We find...
Abstract Phylogenetic trees are currently routinely reconstructed from an alignment of character sequences (usually nucleotide sequences). Bayesian tools, such as MrBayes, RevBayes and BEAST2, have gained much popularity over the last decade, they allow joint estimation posterior distribution phylogenetic parameters underlying inference model. An important ingredient these approaches is species tree prior. In principle, framework allows for comparing different priors, which may elucidate...
Cytolytic T cell responses are predicted to be biased towards membrane proteins. The peptide-binding grooves of most alleles histocompatibility complex class I (MHC-I) relatively hydrophobic, therefore peptide fragments derived from human transmembrane helices (TMHs) presented more often as would expected based on their abundance in the proteome. However, physiological reason why proteins might over-presented is unclear. In this study, we show that over-presentation TMH-derived peptides...
Simulates and computes the (maximum) likelihood of a dynamical model island biota assembly through speciation, immigration extinction. See e.g. Valente et al. 2015. Ecology Letters 18: 844-852, .
Summary Phylogenetic trees are currently routinely reconstructed from an alignment of character sequences (usually nucleotide sequences). Bayesian tools, such as MrBayes, RevBayes and BEAST2, have gained much popularity over the last decade, they allow joint estimation posterior distribution phylogenetic parameters underlying inference model. An important ingredient these approaches is species tree prior. In principle, framework allows for comparing different priors, which may elucidate...
One can generate a phylogeny from DNA alignment and model of evolution.Selecting an evolutionary is non-trivial, as there are many.mcbette R package that determines the has most evidence for having generated alignment, set models.In this way, 'simple enough, but not simpler' be used to phylogeny.
Speciation and extinction of species are two the most fundamental processes that investigated in field evolutionary biology. Ideally, one would like to study these replicated isolated systems. Islands come close this setting if colonisation is rare. However, often we cannot directly measure when an island was colonised, a colonist speciated, or went extinct. We can, however, use genetic data reconstruct history community. With reconstructed can fit statistical models understand...
babette <sup> 1 </sup> is a package to work with BEAST2 2 ,a software platform for Bayesian evolutionary analysis from R. spin-off of my own academic research.As PhD I on models diversification: mathematical descriptionsof how species form new species.