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Motivation: In this paper we present the latest release of EBIC, a next-generation biclustering algorithm for mining genetic data. The major contribution of this paper is adding support for big data, making it possible to efficiently run…
Current research in biology heavily depends on the availability and efficient use of information. In order to build new knowledge, various sources of biological data must often be combined. Semantic Web technologies, which provide a common…
The applicability of computational models to the biological world is an active topic of debate. We argue that a useful path forward results from abandoning hard boundaries between categories and adopting an observer-dependent, pragmatic…
Increasing emphasis on data and quantitative methods in the biomedical sciences is making biological research more computational. Collecting, curating, processing, and analysing large genomic and imaging data sets poses major computational…
Machine learning has proved to be a useful tool for extracting knowledge from scientific data in numerous research fields, including astrophysics, genomics, and molecular dynamics. Often, data sets from these research areas need to be…
The field of ageing science has gone through remarkable progress in recent decades, yet many fundamental questions remain unanswered or unexplored. Here we present a curated list of 100 open problems in ageing and longevity science. These…
Raman spectroscopy is a non-destructive and label-free chemical analysis technique, which plays a key role in the analysis and discovery cycle of various branches of science. Nonetheless, progress in Raman spectroscopic analysis is still…
In this research, we provide a comprehensive empirical summary of the Python Package Repository, PyPI, including both package metadata and source code covering 178,592 packages, 1,745,744 releases, 76,997 contributors, and 156,816,750…
The study of trajectories is often a core task in several research fields. In environmental modelling, trajectories are crucial to study fluid pollution, animal migrations, oil slick patterns or land movements. In this contribution, we…
Data exploration is an important step of every data science and machine learning project, including those involving textual data. We provide a novel language tool, in the form of a publicly available Python library for extracting patterns…
Cultural phylogenies, or "trees" of culture, are typically built using methods from biology that use similarities and differences in artifacts to infer the historical relationships between the populations that produced them. While these…
As a result of a hundred million years of evolution, living animals have adapted extremely well to their ecological niche. Such adaptation implies species-specific interactions with their immediate environment by processing sensory cues and…
Recently, much attention has been given to understanding recombination events along a chromosome in a variety of field. For instance, many population genetics problems are limited by the inaccuracy of inferred evolutionary histories of…
We introduce BioTrove, the largest publicly accessible dataset designed to advance AI applications in biodiversity. Curated from the iNaturalist platform and vetted to include only research-grade data, BioTrove contains 161.9 million…
There has been an increasing recognition of the value of data and of data-based decision making. As a consequence, the development of data science as a field of study has intensified in recent years. However, there is no systematic and…
This paper aims at identifying emerging computational intelligence trends for the design and modeling of complex biometric-enabled infrastructure and systems. Biometric-enabled systems are evolving towards deep learning and deep inference…
Phylogenomics heavily relies on well-curated sequence data sets that consist, for each gene, exclusively of 1:1-orthologous. Paralogs are treated as a dangerous nuisance that has to be detected and removed. We show here that this severe…
Drosophila melanogaster, a small dipteran of African origin, represents one of the best-studied model organisms. Early work in this system has uniquely shed light on the basic principles of genetics and resulted in a versatile collection of…
Pattern-based file access is a fundamental but often under-documented aspect of computational research. The Python glob module provides a simple yet powerful way to search, filter, and ingest files using wildcard patterns, enabling scalable…
One of the important questions in biological evolution is to know if certain changes along protein coding genes have contributed to the adaptation of species. This problem is known to be biologically complex and computationally very…