Related papers: PhaBOX: A web server for identifying and character…
Phylogenetic analysis, which allow to understand the evolution of bacterial and viral epidemics, requires large quantities of data to be analysed and processed for knowledge extraction. One of the major challenges consists on the…
Bacteriophages are central to microbial ecosystems for balancing bacterial populations and promoting evolution by applying strong selection pressure. Here we review some of the known aspects that modulate phage-bacteria interaction in a way…
We introduce a new, simplified model of proteins, which we call protein metastructure. The metastructure of a protein carries information about its secondary structure and $\beta$-strand conformations. Furthermore, protein metastructure…
Tandem repeats in proteins identification, classification and curation is a complex process that requires manual processing from experts, processing power and time. There are recent and relevant advances applying machine learning for…
Reproducibility and reusability of the results of data-based modeling studies are essential. Yet, there has been -- so far -- no broadly supported format for the specification of parameter estimation problems in systems biology. Here, we…
Modern biomedical applications often involve time-series data, from high-throughput phenotyping of model organisms, through to individual disease diagnosis and treatment using biomedical data streams. Data and tools for time-series analysis…
We introduce a unified Python package for the prediction of protein biophysical properties, streamlining previous tools developed by the Bio2Byte research group. This suite facilitates comprehensive assessments of protein characteristics,…
Bacteriophages are viruses infecting bacteria and archaea. Many phage species cause infections which lead to the certain death of the infected prokaryotic host cell and the release of a large batch of phage progeny, yet they have been able…
Due to the recent advances in high-throughput sequencing technologies, it becomes possible to directly analyze microbial communities in the human body and in the environment. Knowledge of how microbes interact with each other and form…
Phages are one of the most present groups of organisms in the biosphere. Their identification continues and their taxonomies are divergent. However, due to their evolution mode and the complexity of their species ecosystem, their…
Information on protein-protein interactions (PPIs) not only advances our understanding of molecular biology but also provides important clues for target selection in drug discovery and the design of PPI inhibitors. One of the techniques…
The explosion in known microbial diversity in the last two decades has made it abundantly clear that microbes in the environment do not exist in isolation; they are members of communities. Accordingly, omics approaches such as metagenomics…
Phage display is a powerful laboratory technique used to study the interactions between proteins and other molecules, whether other proteins, peptides, DNA or RNA. The under-utilisation of this data in conjunction with deep learning models…
Protein quantification and analysis are well-accepted approaches for biomarker discovery but are limited to identification without structural information. High-throughput omics data (i.e., genomics, transcriptomics, and proteomics) have…
Motivation: Parameter estimation is a cornerstone of data-driven modeling in systems biology. Yet, constructing such problems in a reproducible and accessible manner remains challenging. The PEtab format has established itself as a powerful…
The human habitat is a host where microbial species evolve, function, and continue to evolve. Elucidating how microbial communities respond to human habitats is a fundamental and critical task, as establishing baselines of human microbiome…
When planktonic bacteria adhere together to a surface, they begin to form biofilms, or communities of bacteria. Biofilm formation in a host can be extremely problematic if left untreated, especially since antibiotics can be ineffective in…
Phishing attacks remain a persistent threat to online security, demanding robust detection methods. This study investigates the use of machine learning to identify phishing URLs, emphasizing the crucial role of feature selection and model…
Protein-peptide molecular docking is a difficult modeling problem. It is even more challenging when significant conformational changes that may occur during the binding process need to be predicted. In this chapter, we demonstrate the…
Understanding how microbes interact with each other is key to revealing the underlying role that microorganisms play in the host or environment and to identifying microorganisms as an agent that can potentially alter the host or…