Related papers: eQTL Studies: from Bulk Tissues to Single Cells
Understanding the relationship between spontaneous stochastic fluctuations and the topology of the underlying gene regulatory network is of fundamental importance for the study of single-cell stochastic gene expression. Here by solving the…
The effects of treatments on continuous outcomes can be estimated by the mean difference (i.e. by measurement units) and the relative effect scales (i.e. by percentages), both of which provide only a single effect size estimate over the…
Genetic association data from national biobanks and large-scale association studies have provided new prospects for understanding the genetic evolution of complex traits and diseases in humans. In turn, genomes from ancient human…
The methylation of DNA regulates gene expression. On cell division the methylation state of the DNA is typically inherited from parent to daughter cells. While the chemical bond between the methyl group and the DNA is very strong, changes…
The time taken for gene expression varies not least because proteins vary in length considerably. This paper uses an abstract, tuneable Boolean regulatory network model to explore gene expression time variation. In particular, it is shown…
Transcriptional regulatory network inference methods have been studied for years. Most of them relie on complex mathematical and algorithmic concepts, making them hard to adapt, re-implement or integrate with other methods. To address this…
Multidrug resistance consists of a series of genetic and epigenetic alternations that involve multifactorial and complex processes, which are a challenge to successful cancer treatments. Accompanied by advances in biotechnology and…
Algorithmic bias often arises as a result of differential subgroup validity, in which predictive relationships vary across groups. For example, in toxic language detection, comments targeting different demographic groups can vary markedly…
We consider quantitative extensions of the alternating-time temporal logics ATL/ATLs called quantitative alternating-time temporal logics (QATL/QATLs) in which the value of a counter can be compared to constants using equality, inequality…
Genome-wide experiments to map the DNA-binding locations of transcription-associated factors (TFs) have shown that the number of genes bound by a TF far exceeds the number of possible direct target genes. Distinguishing functional from…
Genome Wide Association Studies (GWAS) and eQTL analyses have produced a large and growing number of genetic associations linked to a wide range of human phenotypes. As of 2013, there were more than 11,000 SNPs associated with a trait as…
Epigenetic Tracking is a mathematical model of biological cells, originally conceived to study embryonic development. Computer simulations proved the capacity of the model to generate complex 3-dimensional cellular structures, and the…
Investigating the emergence of a particular cell type is a recurring theme in models of growing cellular populations. The evolution of resistance to therapy is a classic example. Common questions are: when does the cell type first occur,…
Neurons in the brain are often finely tuned for specific task variables. Moreover, such disentangled representations are highly sought after in machine learning. Here we mathematically prove that simple biological constraints on neurons,…
Quantum tangent kernel methods provide an efficient approach to analyzing the performance of quantum machine learning models in the infinite-width limit, which is of crucial importance in designing appropriate circuit architectures for…
The predictive probability of the next token (P_token) in large language models (LLMs) is inextricably linked to the probability of relevance for the next piece of information, the purchase probability of the next product, and the execution…
We investigate a statistical model for multidimensional epistasis. The genotype is devided into subsequences, and within each subsequence mutations which occur in a prescribed order are beneficial. The bit-string model used to represent the…
Cells continuously sense their surroundings to detect modifications and generate responses. Very often changes in extracellular concentrations initiate signaling cascades that eventually result in changes in gene expression. Increasing…
In this note we contribute to the recently developing study of "almost Boolean" quantum logics (i.e. to the study of orthomodular partially ordered sets that are naturally endowed with a symmetric difference). We call them enriched quantum…
Laboratory experiments with bacterial colonies, under well-controlled conditions often lead to evolutionary diversification, where at least two ecotypes emerge from an initially monomorphic population. Empirical evidence suggests that such…