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Most protocols for the high-throughput directed evolution of enzymes rely on random encapsulation to link phenotype and genotype. In order to optimize these approaches, or compare one to another, one needs a measure of their performance at…
Chemotaxis-driven invasions have been proposed across a broad spectrum of biological processes, from cancer to ecology. The influential system of equations introduced by Keller and Segel has proven a popular choice in the modelling of such…
Existing studies comparing individual-based models of growing cell populations and their continuum counterparts have mainly focused on homogeneous populations, in which all cells have the same phenotypic characteristics. However,…
Single-cell RNA-seq data are challenging because of the sparseness of the read counts, the tiny expression of many relevant genes, and the variability in the efficiency of RNA extraction for different cells. We consider a simple…
In genomics studies, the investigation of the gene relationship often brings important biological insights. Currently, the large heterogeneous datasets impose new challenges for statisticians because gene relationships are often local. They…
Small-molecule drug discovery requires simultaneous optimization of numerous properties of candidate molecules. These properties can be investigated through the analysis of high-dimensional biological signatures, such as cell morphology and…
We present an algorithm for the stochastic simulation of gene expression and heterogeneous population dynamics. The algorithm combines an exact method to simulate molecular-level fluctuations in single cells and a constant-number Monte…
The genetic basis of multiple phenotypes such as gene expression, metabolite levels, or imaging features is often investigated by testing a large collection of hypotheses, probing the existence of association between each of the traits and…
Genomic sequence analysis plays a crucial role in various scientific and medical domains. Traditional machine-learning approaches often struggle to capture the complex relationships and hierarchical structures of sequence data when working…
Heterogeneity is a hallmark of complex diseases. Regression-based heterogeneity analysis, which is directly concerned with outcome-feature relationships, has led to a deeper understanding of disease biology. Such an analysis identifies the…
High throughput sequencing is a technology that allows for the generation of millions of reads of genomic data regarding a study of interest, and data from high throughput sequencing platforms are usually count compositions. Subsequent…
In order to ensure the reliability of the explanations of machine learning models, it is crucial to establish their advantages and limits and in which case each of these methods outperform. However, the current understanding of when and how…
The advent of plant phenomics, coupled with the wealth of genotypic data generated by next-generation sequencing technologies, provides exciting new resources for investigations into and improvement of complex traits. However, these new…
Phenotypic heterogeneity is a strategy commonly used by bacteria to rapidly adapt to changing environmental conditions. Here, we study the interplay between phenotypic heterogeneity and genetic diversity in spatially extended populations.…
The antinuclear antibody detection with human epithelial cells is a popular approach for autoimmune diseases diagnosis. The manual evaluation demands time, effort and capital, and automation in screening can greatly aid the physicians in…
Recent work reports disparate performance for intersectional racial groups across face recognition tasks: face verification and identification. However, the definition of those racial groups has a significant impact on the underlying…
A Profile Mixture Model is a model of protein evolution, describing sequence data in which sites are assumed to follow many related substitution processes on a single evolutionary tree. The processes depend in part on different amino acid…
The development of high throughput single-cell sequencing technologies now allows the investigation of the population level diversity of cellular transcriptomes. This diversity has shown two faces. First, the expression dynamics (gene to…
Many biological systems regulate phenotypic heterogeneity as a fitness-maximising strategy in uncertain and dynamic environments. Analysis of such strategies is typically confined both to a discrete set of environmental conditions, and to a…
Sequencing technologies have revolutionised the field of molecular biology. We now have the ability to routinely capture the complete RNA profile in tissue samples. This wealth of data allows for comparative analyses of RNA levels at…