Related papers: A Category of Genes
The present article is the first of a series whose goal is to define a logical formalism in which it is possible to reason about genetics. In this paper, we introduce the main concepts of our language whose domain of discourse consists of a…
We introduce a categorical language in which it is possible to talk about DNA sequencing, alignment methods, CRISPR, homologous recombination, haplotypes, and genetic linkage. This language takes the form of a class of limit-sketches whose…
The Gene Ontology (GO) provides biologists with a controlled terminology that describes how genes are associated with functions and how functional terms are related to each other. These term-term relationships encode how scientists conceive…
Living organisms are the most complex, interesting and significant objects regarding all substructures of the universe. Life science is regarded as a science of the 21st century and one can expect great new discoveries in the near futures.…
The ultimate secret of all lives on earth is hidden in their genomes -- a totality of DNA sequences. We currently know the whole genome sequence of many organisms, while our understanding of the genome architecture on a systematic level…
Most genes are part of larger families of evolutionary related genes. The history of gene families typically involves duplications and losses of genes as well as horizontal transfers into other organisms. The reconstruction of detailed gene…
The phenotype of any organism on earth is, in large part, the consequence of interplay between numerous gene products encoded in the genome, and such interplay between gene products affects the evolutionary fate of the genome itself through…
Molecular phylogeny has focused mainly on improving models for the reconstruction of gene trees based on sequence alignments. Yet, most phylogeneticists seek to reveal the history of species. Although the histories of genes and species are…
The last decade has seen the advent and consolidation of ontology based tools for the identification and biological interpretation of classes of genes, such as the Gene Ontology. The information accumulated time-by-time and included in the…
A system level view of cellular processes for human and several organisms can be cap- tured by analyzing molecular interaction networks. A molecular interaction network formed of differentially expressed genes and their interactions helps…
With the completion of human genome mapping, the focus of scientists seeking to explain the biological complexity of living systems is shifting from analyzing the individual components (such as a particular gene or biochemical reaction) to…
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…
A hierarchical structure describing the inter-relationships of species has long been a fundamental concept in systematic biology, from Linnean classification through to the more recent quest for a 'Tree of Life.' In this paper we use an…
Much of the natural variation for a complex trait can be explained by variation in DNA sequence levels. As part of sequence variation, gene-gene interaction has been ubiquitously observed in nature, where its role in shaping the development…
A critical task in systems biology is the identification of genes that interact to control cellular processes by transcriptional activation of a set of target genes. Many methods have been developed to use statistical correlations in…
Genetic regulatory networks enable cells to respond to the changes in internal and external conditions by dynamically coordinating their gene expression profiles. Our ability to make quantitative measurements in these biochemical circuits…
The unprecedented pace of machine learning research has lead to incredible advances, but also poses hard challenges. At present, the field lacks strong theoretical underpinnings, and many important achievements stem from ad hoc design…
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 pathway is a biological term that refers to a series of interactions between molecules in a cell that causes a certain product or a change in the cell. Pathway analysis is a powerful method for gene expression analysis. Through pathway…
Gene interaction graphs aim to capture various relationships between genes and can represent decades of biology research. When trying to make predictions from genomic data, those graphs could be used to overcome the curse of dimensionality…