Related papers: A Category of Genes
In this paper we develope a categorical theory of relations and use this formulation to define the notion of quantization for relations. Categories of relations are defined in the context of symmetric monoidal categories. They are shown to…
Interactions are ubiquitous across biological systems. These interactions can be abstracted as patterns of connections among distinct units such as genes, proteins, individual organisms, or species which form a hierarchy of biological…
Category theory has foundational importance because it provides conceptual lenses to characterize what is important in mathematics. Originally the main lenses were universal mapping properties and natural transformations. In recent decades,…
How does the genome encode the form of the organism? What is the nature of this genomic code? Inspired by recent work in machine learning and neuroscience, we propose that the genome encodes a generative model of the organism. In this…
Networks of gene regulation govern morphogenesis, determine cell identity and regulate cell function. But we have little understanding, at the local level, of which logics are biologically preferred or even permitted. To solve this puzzle,…
Gene-gene interactions are often regarded as playing significant roles in influencing variabilities of complex traits. Although much research has been devoted to this area, to date a comprehensive statistical model that addresses the…
Multicellular self-organization drives development in biological organisms, yet a comprehensive theory is lacking as basic properties of cells can complicate common approaches. Framing such properties by dynamic graphs led to new…
Gene-gene and gene-environment interactions are widely believed to play significant roles in explaining the variability of complex traits. While substantial research exists in this area, a comprehensive statistical framework that addresses…
Relation of genome sizes to organisms complexity is still described rather equivocally. Neither the number of genes (G-value), nor the total amount of DNA (C-value) correlates consistently with phenotype complexity. Using information theory…
Many people are familiar with the physico-chemical properties of gene sequences. In this paper I present a mathematical perspective: how do mathematical principles such as information theory, coding theory, and combinatorics influence the…
Gene expression is a central process to any form of life. It involves multiple temporal and functional scales that extend from specific protein-DNA interactions to the coordinated regulation of multiple genes in response to intracellular…
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…
A cell's behavior is a consequence of the complex interactions between its numerous constituents, such as DNA, RNA, proteins and small molecules. Cells use signaling pathways and regulatory mechanisms to coordinate multiple processes,…
The development of mathematics has been characterized by the increasing interconnectivity of seemingly separate disciplines. Such interplay has been facilitated by a massive development in formalism; category theory has provided a common…
DNA rearrangement processes recombine gene segments that are organized on the chromosome in a variety of ways. The segments can overlap, interleave or one may be a subsegment of another. We use directed graphs to represent segment…
We outline the global control architecture of genomes. A theory of genomic control information is presented. The concept of a developmental control network called a cene (for control gene) is introduced. We distinguish parts-genes from…
Genetic interaction measures how different genes collectively contribute to a phenotype, and can reveal functional compensation and buffering between pathways under genetic perturbations. Recently, genome-wide screening for genetic…
By linking conceptual theories with observed data, generative models can support reasoning in complex situations. They have come to play a central role both within and beyond statistics, providing the basis for power analysis in molecular…
It is widely acknowledged that there is a diversity problem in genomics stemming from the vast underrepresentation of non-European genetic ancestry populations. While many challenges exist to address this gap, a major complicating factor is…
In mathematical phylogenetics, evolutionary relationships are often represented by trees and networks. The latter are typically used whenever the relationships cannot be adequately described by a tree, which happens when so-called…