Related papers: Etude de classification des bacteriophages
Horizontal gene transfer is an important contributor to evolution. According to Walter M.\ Fitch, two genes are xenologs if they are separated by at least one HGT. More formally, the directed Fitch graph has a set of genes is its vertices,…
Phylogenetic trees are simple models of evolutionary processes. They describe conditionally independent divergent evolution of taxa from common ancestors. Phylogenetic trees commonly do not have enough flexibility to adequately model all…
De novo assembly is the process of reconstructing the genome sequence of an organism from sequencing reads. Genome sequences are essential to biology, and assembly has been a central problem in bioinformatics for four decades. Until…
In an effort to catalog insect biodiversity, we propose a new large dataset of hand-labelled insect images, the BIOSCAN-Insect Dataset. Each record is taxonomically classified by an expert, and also has associated genetic information…
Bulges are of different types, morphologies and kinematics, from pseudo-bulges, close to disk properties (Sersic index, rotation fraction, flatenning), to classical de Vaucouleurs bulges, close to elliptical galaxies. Secular evolution and…
Phylogenetic networks extend phylogenetic trees to allow for modeling reticulate evolutionary processes such as hybridization. They take the shape of a rooted, directed, acyclic graph, and when parameterized with evolutionary parameters,…
Biological sequence comparison is a key step in inferring the relatedness of various organisms and the functional similarity of their components. Thanks to the Next Generation Sequencing efforts, an abundance of sequence data is now…
Orthology is a central concept in evolutionary and comparative genomics, used to relate corresponding genes in different species. In particular, orthologs are needed to infer species trees. In this chapter, we introduce the fundamental…
The Hecke category is bigraded. For completeness, we classify gradings on the Hecke category. We also classify object-preserving autoequivalences.
Bacteriophages, phages for short, are viruses of bacteria. The majority of phages contain a double-stranded DNA genome packaged in a capsid at a density of ~500 mg/ml. This high density requires substantial compression of the normal B form…
The BIOSCAN project, led by the International Barcode of Life Consortium, seeks to study changes in biodiversity on a global scale. One component of the project is focused on studying the species interaction and dynamics of all insects. In…
Species tree estimation is a complex problem, due to the fact that different parts of the genome can have different evolutionary histories than the genome itself. One of the causes for this discord is incomplete lineage sorting (also called…
We model the competition between recombination and point mutation in microbial genomes, and present evidence for two distinct phases, one uniform, the other genetically diverse. Depending on the specifics of homologous recombination, we…
Gene regulatory network of lambda phage is one the best studied model systems in molecular biology. More 50 years of experimental study has provided a tremendous amount of data at all levels: physics, chemistry, DNA, protein, and function.…
Ancestral sequence reconstruction is a key task in computational biology. It consists in inferring a molecular sequence at an ancestral species of a known phylogeny, given descendant sequences at the tip of the tree. In addition to its many…
Sequence comparison across multiple organisms aids in the detection of regions under selection. However, resource limitations require a prioritization of genomes to be sequenced. This prioritization should be grounded in two considerations:…
The human-associated microbiome is closely tied to human health and is of substantial clinical interest. Metagenomics-based tools are emerging for clinical diagnostics, tracking the spread of diseases, and surveillance of potential…
Foraminifera are single-celled marine organisms, which may have a planktic or benthic lifestyle. During their life cycle they construct shells consisting of one or more chambers, and these shells remain as fossils in marine sediments.…
The evolution in coding DNA sequences brings new flexibility and freedom to the codon words, even as the underlying nucleotides get significantly ordered. These curious contra-rules of gene organisation are observed from the distribution of…
Academic literature retrieval is concerned with the selection of papers that are most likely to match a user's information needs. Most of the retrieval systems are limited to list-output models, in which the retrieval results are isolated…