Related papers: Distinguishing Cell Phenotype Using Cell Epigenoty…
The positioning of new cellular walls during cell division plays a key role in shaping plant tissue organization. The influence of cell geometry on the positioning of division planes has been previously captured into various geometrical…
Important objectives in cancer research are the prediction of a patient's risk based on molecular measurements such as gene expression data and the identification of new prognostic biomarkers (e.g. genes). In clinical practice, this is…
Motivation. Association studies have been widely used to search for associations between common genetic variants observations and a given phenotype. However, it is now generally accepted that genes and environment must be examined jointly…
In cell differentiation, a cell of a less specialized type becomes one of a more specialized type, even though all cells have the same genome. Transcription factors and epigenetic marks like histone modifications can play a significant role…
Cell motility in dense cell collectives is pivotal in various diseases like cancer metastasis and asthma. A central aspect in these phenomena is the heterogeneity in cell motility, but identifying the motility of individual cells is…
Current efforts in the biomedical sciences and related interdisciplinary fields are focused on gaining a molecular understanding of health and disease, which is a problem of daunting complexity that spans many orders of magnitude in…
Metagenomics provides a powerful new tool set for investigating evolutionary interactions with the environment. However, an absence of model-based statistical methods means that researchers are often not able to make full use of this…
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…
Complexity in biology is often described using a multi-map architecture, where the genotype, representing the encoded information, is mapped to the functional level, known as the phenotype, which is then connected to a latent phenotype we…
Unpaired image-to-image translation methods aim at learning a mapping of images from a source domain to a target domain. Recently, these methods proved to be very useful in biological applications to display subtle phenotypic cell…
Genetic differences between individuals associated to quantitative phenotypic traits, including disease states, are usually found in non-coding genomic regions. These genetic variants are often also associated to differences in expression…
Cellular form and function emerge from complex mechanochemical systems within the cytoplasm. No systematic strategy currently exists to infer large-scale physical properties of a cell from its many molecular components. This is a…
Computer vision-based methods have valuable use cases in precision medicine, and recognizing facial phenotypes of genetic disorders is one of them. Many genetic disorders are known to affect faces' visual appearance and geometry. Automated…
We discuss the mathematical modelling of two of the main mechanisms which pushed forward the emergence of multicellularity: phenotype divergence in cell differentiation, and between-cell cooperation. In line with the atavistic theory of…
A mechanism of sympatric speciation is presented based on the interaction-induced developmental plasticity of phenotypes. First, phenotypes of individuals with identical genotypes split into a few groups, according to instability in the…
Background: Single-cell RNA sequencing (scRNA-seq) yields valuable insights about gene expression and gives critical information about complex tissue cellular composition. In the analysis of single-cell RNA sequencing, the annotations of…
Inferring microbial interaction networks from abundance patterns is an important approach to advance our understanding of microbial communities in general and the human microbiome in particular. Here we suggest discriminating two levels of…
Populations can become spatially organised through chemotaxis autoattraction, wherein population members release their own chemoattractant. Standard models of this process usually assume phenotypic homogeneity, but recent studies have shed…
Comparisons of single-cell RNA sequencing (scRNA-seq) data across species can reveal links between cellular gene expression and the evolution of cell functions, features, and phenotypes. These comparisons invoke evolutionary histories, as…
We consider a setting in which we have a treatment and a large number of covariates for a set of observations, and wish to model their relationship with an outcome of interest. We propose a simple method for modeling interactions between…