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Scientific inference is often undermined by the vast but rarely explored "multiverse" of defensible modelling choices, which can generate results as variable as the phenomena under study. We introduce RobustiPy, an open-source Python…
Gene innovation is a key mechanism on the evolution and phenotypic diversity of life forms. There is a need for tools able to study gene innovation across an increasingly large number of genomic sequences to maximally capitalise our…
Biological networks exhibit intricate architectures deemed to be crucial for their functionality. In particular, gene regulatory networks, which play a key role in information processing in the cell, display non-trivial architectural…
Information is a key concept in evolutionary biology. Information is stored in biological organism's genomes, and used to generate the organism as well as to maintain and control it. Information is also "that which evolves". When a…
Many aspects of macroevolutionary theory and our understanding of biotic responses to global environmental change derive from literature-based compilations of palaeontological data. Existing manually assembled databases are, however,…
Delivering effective data analytics is of crucial importance to the interpretation of the multitude of biological datasets currently generated by an ever increasing number of high throughput techniques. Logic programming has much to offer…
In an effort to overcome the data deluge in computational biology and bioinformatics and to facilitate bioinformatics research in the era of big data, we identify some of the most influential algorithms that have been widely used in the…
By providing a framework of accounting for the shared ancestry inherent to all life, phylogenetics is becoming the statistical foundation of biology. The importance of model choice continues to grow as phylogenetic models continue to…
Array programming provides a powerful, compact, expressive syntax for accessing, manipulating, and operating on data in vectors, matrices, and higher-dimensional arrays. NumPy is the primary array programming library for the Python…
We propose methods for the analysis of hierarchical clustering that fully use the multi-resolution structure provided by a dendrogram. Specifically, we propose a loss for choosing between clustering methods, a feature importance score and a…
While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims…
Computational methods have reshaped the landscape of modern biology. While the biomedical community is increasingly dependent on computational tools, the mechanisms ensuring open data, open software, and reproducibility are variably…
Advances in molecular technologies underlie an enormous growth in the size of data sets pertaining to biology and biomedicine. These advances parallel those in the deep learning subfield of machine learning. Components in the differentiable…
Understanding how genotypes map onto phenotypes, fitness, and eventually organisms is arguably the next major missing piece in a fully predictive theory of evolution. We refer to this generally as the problem of the genotype-phenotype map.…
The scale, variety, and quantity of publicly-available NLP datasets has grown rapidly as researchers propose new tasks, larger models, and novel benchmarks. Datasets is a community library for contemporary NLP designed to support this…
Since its conception in 2006, differential privacy has emerged as the de-facto standard in data privacy, owing to its robust mathematical guarantees, generalised applicability and rich body of literature. Over the years, researchers have…
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…
Biological tree (BioTree) analysis is a foundational tool in biology, enabling the exploration of evolutionary and differentiation relationships among organisms, genes, and cells. Traditional tree construction methods, while instrumental in…
The protein-protein interaction (PPI) network provides an overview of the complex biological reactions vital to an organism's metabolism and survival. Even though in the past PPI network were compared across organisms in detail, there has…
Understanding the evolution of complexity is an important topic in a wide variety of academic fields. Implications of better understanding complexity include increased knowledge of major evolutionary transitions and the properties of living…