Related papers: Making mathematical online resources FAIR: at the …
The reproduction and replication of research results has become a major issue for a number of scientific disciplines. In computer science and related computational disciplines such as systems biology, the challenges closely revolve around…
The reliability of a phylogenetic inference method from genomic sequence data is ensured by its statistical consistency. Bayesian inference methods produce a sample of phylogenetic trees from the posterior distribution given sequence data.…
The FAIR (Findable, Accessible, Interoperable, and Reusable) data principles [1] promote the interoperability of scientific data by encouraging the use of persistent identifiers, standardized vocabularies, and formal metadata structures.…
A phylogenetic tree shows the evolutionary relationships among species. Internal nodes of the tree represent speciation events and leaf nodes correspond to species. A goal of phylogenetics is to combine such trees into larger trees, called…
Designing sustainable systems involves complex interactions between environmental resources, social impact/adoption, and financial costs/benefits. In a constrained world, achieving a balanced design across those dimensions has become…
With the advent of open source software, a veritable treasure trove of previously proprietary software development data was made available. This opened the field of empirical software engineering research to anyone in academia. Data that is…
We study the problem of learning a latent tree graphical model where samples are available only from a subset of variables. We propose two consistent and computationally efficient algorithms for learning minimal latent trees, that is, trees…
treePL uses a penalised likelihood approach to produce a dated phylogeny in a maximum likelihood framework. Since its publication in 2012, few resources have been developed to explain how to use it properly. In this guide, I provide a…
Reviewing scientific literature is a cumbersome, time consuming but crucial activity in research. Leveraging a scholarly knowledge graph, we present a methodology and a system for comparing scholarly literature, in particular research…
Phylogenetic inference-the derivation of a hypothesis for the common evolutionary history of a group of species- is an active area of research at the intersection of biology, computer science, mathematics, and statistics. One assumes the…
A concise and measurable set of FAIR (Findable, Accessible, Interoperable and Reusable) principles for scientific data is transforming the state-of-practice for data management and stewardship, supporting and enabling discovery and…
The evolutionary relationships between species are typically represented in the biological literature by rooted phylogenetic trees. However, a tree fails to capture ancestral reticulate processes, such as the formation of hybrid species or…
In molecular phylogeny, relationships among organisms are reconstructed using DNA or protein sequences and are displayed as trees. A linear increase in the number of sequences results in an exponential increase of possible trees. Thus,…
The expanding need for an open information sharing infrastructure to promote scholarly communication led to the pioneering establishment of arXiv.org, now maintained by the Cornell University Library. To be sustainable, the repository…
The statistical estimation of phylogenies is always associated with uncertainty, and accommodating this uncertainty is an important component of modern phylogenetic comparative analysis. The birth-death polytomy resolver is a method of…
In mathematics, LaTeX is the de facto standard to prepare documents, e.g., scientific publications. While some formulae are still developed using pen and paper, more complicated mathematical expressions used more and more often with…
I propose an approach to identify, among several strategies of phylogenetic analysis, those producing the most accurate results. This approach is based on the hypothesis that the more a result is reproduced from independent data, the more…
Recent years have seen a rapid expansion of the model space explored in statistical phylogenetics, emphasizing the need for new approaches to statistical model representation and software development. Clear communication and representation…
Computer simulations are an important tool for studying the mechanics of biological evolution. In particular, in silico work with agent-based models provides an opportunity to collect high-quality records of ancestry relationships among…
Tree matching techniques have been investigated in many fields, including web data mining and extraction, as a key component to analyze the content of web documents, existing tree matching approaches, like Tree-Edit Distance (TED) or…