Related papers: Category theory for genetics II: genotype, phenoty…
The recent explosion of genetic and high dimensional biobank and 'omic' data has provided researchers with the opportunity to investigate the shared genetic origin (pleiotropy) of hundreds to thousands of related phenotypes. However,…
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…
In the past decade, Genome-Wide Association Studies (GWAS) have delivered an increasingly broad view of the genetic basis of human phenotypic variation. One of the major developments from GWAS is polygenic scores, a genetic predictor of an…
Statistically resolving the underlying haplotype pair for a genotype measurement is an important intermediate step in gene mapping studies, and has received much attention recently. Consequently, a variety of methods for this problem have…
High-dimensional phenotypes hold promise for richer findings in association studies, but testing of several phenotype traits aggravates the grand challenge of association studies, that of multiple testing. Several methods have recently been…
We consider the problem of detecting and estimating the strength of association between a trait of interest and alleles or haplotypes in a small genomic region (e.g. a gene or a gene complex), when no direct information on that region is…
We show how field- and information theory can be used to quantify the relationship between genotype and phenotype in cases where phenotype is a continuous variable. Given a sample population of phenotype measurements, from various known…
Polynomial functors are useful in the theory of data types, where they are often called containers. They are also useful in algebra, combinatorics, topology, and higher category theory, and in this broader perspective the polynomial aspect…
Identifying phenotypes plays an important role in furthering our understanding of disease biology through practical applications within healthcare and the life sciences. The challenge of dealing with the complexities and noise within…
Understanding the genetic basis of complex traits is a longstanding challenge in the field of genomics. Genome-wide association studies (GWAS) have identified thousands of variant-trait associations, but most of these variants are located…
Gene duplication is believed to play a major role in the evolution of genomic complexity. The presence of a duplicate removes the constraint of natural selection upon the gene, leading to its likely loss of function or, occasionally, the…
Decoding the genome confers the capability to predict characteristics of the organism(phenotype) from DNA (genotype). We describe the present status and future prospects of genomic prediction of complex traits in humans. Some highly…
Genotype networks are a method used in systems biology to study the "innovability" of a set of genotypes having the same phenotype. In the past they have been applied to determine the genetic heterogeneity, and stability to mutations, of…
The linking genotype to phenotype is the fundamental aim of modern genetics. We focus on study of links between gene expression data and phenotype data through integrative analysis. We propose three approaches. 1) The inherent complexity of…
Motivation: Genome-Wide Association Studies (GWAS) seek to identify causal genomic variants associated with rare human diseases. The classical statistical approach for detecting these variants is based on univariate hypothesis testing, with…
Pedigrees, or family trees, are graphs of family relationships that are used to study inheritance. A fundamental problem in computational biology is to find, for a pedigree with $n$ individuals genotyped at every site, a set of…
In this paper I consider all possible properties from commutative algebra for polynomial composites and monoid domains. The aim is full characterization of these structures. I start with the examination of group, ring, modules properties,…
The purpose of this paper is to develop a theory of bimonads and Hopf monads on arbitrary categories thus providing the possibility to transfer the essentials of the theory of Hopf algebras in vector spaces to more general settings. There…
Deep generative models open new avenues for simulating realistic genomic data while preserving privacy and addressing data accessibility constraints. While previous studies have primarily focused on generating gene expression or haplotype…
Modern categories of spectra such as that of Elmendorf et al equipped with strictly symmetric monoidal smash products allows the introduction of symmetric monoids providing a new way to study highly coherent commutative ring spectra. These…