Related papers: DendroPy 5: a mature Python library for phylogenet…
DeeProb-kit is a unified library written in Python consisting of a collection of deep probabilistic models (DPMs) that are tractable and exact representations for the modelled probability distributions. The availability of a representative…
Data gridding is a common task in astronomy and many other science disciplines. It refers to the resampling of irregularly sampled data to a regular grid. We present cygrid, a library module for the general purpose programming language…
One of the main properties of biological systems is modularity, which manifests itself at all levels of their organization, starting with the level of molecular genetics, ending with the level of whole organisms and their communities. In a…
A phylogeny describes the evolutionary history of an evolving population. Evolutionary search algorithms can perfectly track the ancestry of candidate solutions, illuminating a population's trajectory through the search space. However,…
The integration of bioinformatics predictions and experimental validation plays a pivotal role in advancing biological research, from understanding molecular mechanisms to developing therapeutic strategies. Bioinformatics tools and methods…
Study reproducibility is essential to corroborate, build on, and learn from the results of scientific research but is notoriously challenging in bioinformatics, which often involves large data sets and complex analytic workflows involving…
Process mining, i.e., a sub-field of data science focusing on the analysis of event data generated during the execution of (business) processes, has seen a tremendous change over the past two decades. Starting off in the early 2000's, with…
Sequence comparison and alignment has had an enormous impact on our understanding of evolution, biology, and disease. Comparison and alignment of biological networks will likely have a similar impact. Existing network alignments use…
Y haplogroup analyses are an important component of genealogical reconstruction, population genetic analyses, medical genetics and forensics. These fields are increasingly moving towards use of low-coverage, high throughput sequencing.…
BOLD, the Barcode of Life Data System, supports the acquisition, storage, validation, analysis, and publication of DNA barcodes, activities requiring the integration of molecular, morphological, and distributional data. Its pivotal role in…
Computer simulation has become one of the most important tools in scientific research in many disciplines. Benefiting from the dynamical trajectories regulated by versatile interatomic interactions, various material properties can be…
Software Heritage is the largest public archive of software source code and associated development history, as captured by modern version control systems. As of July 2023, it has archived more than 16 billion unique source code files coming…
The idea of the inheritance of biological processes, such as the developmental process or the life cycle of an organism, has been discussed in the biology literature, but formal mathematical descriptions and plausible data analysis…
Computing systems form the backbone of many aspects of our life, hence they are becoming as vital as water, electricity, and road infrastructures for our society. Yet, engineering long running computing systems that achieve their goals in…
This article highlights some of the basic concepts of bioinformatics and data mining. The major research areas of bioinformatics are highlighted. The application of data mining in the domain of bioinformatics is explained. It also…
Phylogenies (ancestry trees) depict the evolutionary history of an evolving population. In evolutionary computing, a phylogeny can reveal how an evolutionary algorithm steers a population through a search space, illuminating the…
The Persistent-Phylogeny Model is an extension of the widely studied Perfect-Phylogeny Model, encompassing a broader range of evolutionary phenomena. Biological and algorithmic questions concerning persistent phylogeny have been intensely…
Biosciences have been revolutionized by next generation sequencing (NGS) technologies in last years, leading to new perspectives in medical, industrial and environmental applications. And although our motivation comes from biosciences, the…
"Evolution behaves like a tinkerer" (Francois Jacob, Science, 1977). Software systems provide a unique opportunity to understand biological processes using concepts from network theory. The Debian GNU/Linux operating system allows us to…
Bioinformatics research is characterized by voluminous and incremental datasets and complex data analytics methods. The machine learning methods used in bioinformatics are iterative and parallel. These methods can be scaled to handle big…