Related papers: Etude de classification des bacteriophages
Bi-clustering is a useful approach in analyzing biological data when observations come from heterogeneous groups and have a large number of features. We outline a general Bayesian approach in tackling bi-clustering problems in moderate to…
Throughout the evolution of biological species on Earth, cells and organs have developed many complex structures and processes to ensure their interactions with individual chemical molecules (small and macromolecular) and nanoscale objects…
Understanding the structure and dynamics of biological networks is one of the important challenges in system biology. In addition, increasing amount of experimental data in biological networks necessitate the use of efficient methods to…
With the astonishing rate that the genomic and metagenomic sequence data sets are accumulating, there are many reasons to constrain the data analyses. One approach to such constrained analyses is to focus on select subsets of gene families…
Background: Significance analysis plays a major role in identifying and ranking genes, transcription factor binding sites, DNA methylation regions, and other high-throughput features for association with disease. We propose a new approach,…
We present a new method for detecting and identifying bacteria by measuring impedance fluctuations (impedance noise) caused by ion release by the bacteria during phage infestation. This new method significantly increases the measured signal…
The phage $\lambda$ infection of an \textit{E. coli} cell has become a paradigm for understanding the molecular processes involved in gene expression and cell signaling. This system provides an example of a genetic switch, as cells with…
We introduce the concept of an abstract evolution system, which provides a convenient framework for studying generic mathematical structures and their properties. Roughly speaking, an evolution system is a category endowed with a selected…
Marine microalgae are widespread in the ocean and play a crucial role in the ecosystem. Automatic identification and location of marine microalgae in microscopy images would help establish marine ecological environment monitoring and water…
Several approaches were proposed to describe the geomorphology of drainage networks and the abiotic/biotic factors determining their morphology. There is an intrinsic complexity of the explicit qualification of the morphological variations…
Network representations of systems from various scientific and societal domains are neither completely random nor fully regular, but instead appear to contain recurring structural building blocks. These features tend to be shared by…
Biological cells, by definition, are the basic units which contain the fundamental molecules of life of which all living things are composed. Understanding how they function and differentiating cells from one another therefore is of…
Recent attacks of various viruses with having deep and extensive impact at a global scale has warranted that microbiome be studied extensively and in a robust analytic framework. Microbiome typically refers to the collective genomes of such…
Changing base composition during the evolution of biological sequences can mislead some of the phylogenetic inference techniques in current use. However, detecting whether such a process has occurred may be difficult, since convergent…
The ability to quickly and accurately identify microbial species in a sample, known as metagenomic profiling, is critical across various fields, from healthcare to environmental science. This paper introduces a novel method to profile…
Phylogenomics is a new field which applies to tools in phylogenetics to genome data. Due to a new technology and increasing amount of data, we face new challenges to analyze them over a space of phylogenetic trees. Because a space of…
The classification of life should be based upon the fundamental mechanism in the evolution of life. We found that the global relationships among species should be circular phylogeny, which is quite different from the common sense based upon…
Precision and reliability of barcode-based biodiversity assessment can be affected at several steps during acquisition and analysis of the data. Identification of barcodes is one of the crucial steps in the process and can be accomplished…
Clustering objects into synthetic groups is a natural activity of any science. Astrophysics is not an exception and is now facing a deluge of data. For galaxies, the one-century old Hubble classification and the Hubble tuning fork are still…
Comparative and evolutive ecologists are interested in the distribution of quantitative traits among related species. The classical framework for these distributions consists of a random process running along the branches of a phylogenetic…