Related papers: Representing and decomposing genomic structural va…
Sequencing a genome to determine an individual's DNA produces an enormous number of short nucleotide subsequences known as reads, which must be reassembled to reconstruct the full genome. We present a method for analyzing this type of data…
Despite the apparent ease with which a sheet of paper is crumpled and tossed away, crumpling dynamics are often considered a paradigm of complexity. This complexity arises from the infinite number of configurations a disordered crumpled…
Translating metabolic networks into dynamic models is difficult if kinetic constants are unknown. Structural Kinetic Modelling (SKM) replaces reaction elasticities by independent random numbers. Here I propose a variant that accounts for…
We study the mathematical properties of a general model of cell division structured with several internal variables. We begin with a simpler and specific model with two variables, we solve the eigenvalue problem with strong or weak…
The ability to absorb mutations while retaining structure and function, or mutational robustness, is a remarkable property of natural proteins. In this Letter, we use a computational model of organismic evolution [Zeldovich et al, PLOS Comp…
Single-cell RNA-sequencing technologies may provide valuable insights to the understanding of the composition of different cell types and their functions within a tissue. Recent technologies such as spatial transcriptomics, enable the…
Anatomical trees play an important role in clinical diagnosis and treatment planning. Yet, accurately representing these structures poses significant challenges owing to their intricate and varied topology and geometry. Most existing…
Background: DNA, RNA, and protein sequence motifs can be recognition sites for biological functions such as regulation, DNA base modification, and molecular binding in general. The gain and loss of such motifs can carry important…
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…
With the development of high throughput sequencing technology, it becomes possible to directly analyze mutation distribution in a genome-wide fashion, dissociating mutation rate measurements from the traditional underlying assumptions.…
Random copying is a simple model for population dynamics in the absence of selection, and has been applied to both biological and cultural evolution. In this work, we investigate the effect that spatial structure has on the dynamics. We…
In the analysis of spatially resolved transcriptomics data, detecting spatially variable genes (SVGs) is crucial. Numerous computational methods exist, but varying SVG definitions and methodologies lead to incomparable results. We review 33…
Graphs are naturally used to describe the structures of various real-world systems in biology, society, computer science etc., where subgraphs or motifs as basic blocks play an important role in function expression and information…
The GC-content is very variable in different genome regions and species but although many hypothesis we still do not know the reason why. Here we show that a relationship exists with the mutation rate, in particular we noticed a new…
Several formulations have long existed in the literature in the form of continuous mixtures of normal variables where a mixing variable operates on the mean or on the variance or on both the mean and the variance of a multivariate normal…
Most existing neural networks for learning graphs address permutation invariance by conceiving of the network as a message passing scheme, where each node sums the feature vectors coming from its neighbors. We argue that this imposes a…
Semantic segmentation has a broad range of applications in a variety of domains including land coverage analysis, autonomous driving, and medical image analysis. Convolutional neural networks (CNN) and Vision Transformers (ViTs) provide the…
It has been shown that genome spatial structures largely affect both genome activity and DNA function. Knowing this, many researchers are currently attempting to accurately model genome structures. Despite these increased efforts there…
Research in quantitative evolutionary genomics and systems biology led to the discovery of several universal regularities connecting genomic and molecular phenomic variables. These universals include the log-normal distribution of the…
Genomes contain the mutational footprint of an organism's evolutionary history, shaped by diverse forces including ecological factors, selective pressures, and life history traits. The sequentially Markovian coalescent (SMC) is a versatile…