Related papers: Etude de classification des bacteriophages
Bacteriophage viruses, one of the most abundant entities in our planet, lack the ability to move independently. Instead, they crowd fluid environments in anticipation of a random encounter with a bacterium. Once they land on the cell body…
Living systems can be understood as organized entities that capture, transform, and reproduce information. Classical gene-centered models explain adaptation through frequency changes driven by differential fitness, yet they often overlook…
Categorization is a fundamental function of minds, with wide ranging implications for the rest of the cognitive system. In humans, categories are shared and communicated between minds, thus requiring explanations at the population level. In…
At present, object recognition studies are mostly conducted in a closed lab setting with classes in test phase typically in training phase. However, real-world problem is far more challenging because: i) new classes unseen in the training…
The grand challenges in biology today are being shaped by powerful high-throughput technologies that have revealed the genomes of many organisms, global expression patterns of genes and detailed information about variation within…
The discovery of nucleic acids and the structure of DNA have brought considerable advances in the understanding of life. The development of next-generation sequencing technologies has led to a large-scale generation of data, for which…
Interacting proteins coevolve at multiple but interconnected scales, from the residue-residue over the protein-protein up to the family-family level. The recent accumulation of enormous amounts of sequence data allows for the development of…
Bacterial heterogeneity is pivotal for adaptation to diverse environments, posing significant challenges in microbial diagnostics and therapeutic interventions. Recent advancements in high-resolution optical microscopy have revolutionized…
Metagenomics is an approach for characterizing environmental microbial communities in situ, it allows their functional and taxonomic characterization and to recover sequences from uncultured taxa. For communities of up to medium diversity,…
Classification of proteins based on their structure provides a valuable resource for studying protein structure, function and evolutionary relationships. With the rapidly increasing number of known protein structures, manual and…
MetaScope is a fast and accurate tool for analyzing (host-associated) metagenome datasets. Sequence alignment of reads against the host genome (if requested) and against microbial Genbank is performed using a new DNA aligner called SASS.…
The ongoing explosion of genome sequence data is transforming how we reconstruct and understand the histories of biological systems. Across biological scales, from individual cells to populations and species, trees-based models provide a…
The marine environment is one of the most important sources for microbial biodiversity on the planet. These microbes are drivers for many biogeochemical processes, and their enormous genetic potential is still not fully explored or…
Phylogeny can be inferred using two sources of data from an organism: morphological data and molecular data. Historically, phylogenies were usually inferred using morphological characters, but some morphological features may not necessarily…
To tackle the challenge of producing tractable phylogenetic trees in contexts where complete information is available, we introduce APOGeT: an online, pluggable, clustering algorithm for a stream of genomes. It is designed to run alongside…
Phylogenetic trees are a central tool in understanding evolution. They are typically inferred from sequence data, and capture evolutionary relationships through time. It is essential to be able to compare trees from different data sources…
The rise in the availability of bacterial genomes defines a need for synthesis: abstracting from individual taxa, to see larger patterns of bacterial lifestyles across systems. A key concept for such synthesis in ecology is the niche, the…
Species complexes are groups of closely related populations exchanging genes through dispersal. We study the dynamics of the structure of species complexes in a class of metapopulation models where demes can exchange genetic material…
There exist a variety of star-galaxy classification techniques, each with their own strengths and weaknesses. In this paper, we present a novel meta-classification framework that combines and fully exploits different techniques to produce a…
Our understanding of planetary nebulae has been significantly enhanced as a result of several recent large surveys (Parker et al., these proceedings). These new discoveries suggest that the `PN phenomenon' is in fact more heterogeneous than…