Quantitative Biology
While analysing rare blood cell aggregates remains challenging in automated haematology, they could markedly advance label-free functional diagnostics. Conventional flow cytometers efficiently perform cell counting with leukocyte…
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…
MicroRNAs (miRs) are robust regulators of gene expression, implicated in most biological processes. microRNAs predominantly downregulate the expression of genes post-transcriptionally and each miR is predicted to target several hundred…
A common approach in neuroscience is to study neural representations as a means to understand a system -- increasingly, by relating the neural representations to the internal representations learned by computational models. However, a…
Accurate prediction of antibody-antigen (Ab-Ag) binding affinity is essential for therapeutic design and vaccine development, yet the performance of current models is limited by noisy experimental labels, heterogeneous assay conditions, and…
We develop a general modelling framework for compartmental epidemiological systems structured by continuous variables which are linked to the levels of expression of compartment-specific traits. We start by formulating an individual-based…
Diffusion and anomalous diffusion are widely observed and used to study movement across organisms, resulting in extensive use of the mean and mean-squared displacement (MSD). However, these measures - corresponding to specific displacement…
We investigate how environmental flows influence spatial pattern formation and population dynamics using two nonlocal models of population dynamics, which we couple to two different stationary flows. Combining numerical simulations and…
This study demonstrates how to construct the solutions of a more general form of population dynamics models via a blend of variational iterative method with Sumudu transform. In this paper, population growth models are formulated in the…
Cell phenotype dynamic homeostasis contrasts with the inherent randomness of intracellular reactions. Although feedback control of master regulatory genes (MRG) is a key strategy for maintaining gene network expression ranges limited,…
Vaccines not only directly protect vaccinated individuals but also contribute to protect the entire population via indirect herd-immunity benefits. However, researchers have long struggled to quantify these indirect effects at the…
Current brain-computer interfaces primarily decode single motor variables, limiting their ability to support natural, high-bandwidth neural control that requires simultaneous extraction of multiple correlated motor dimensions. We introduce…
Calhoun's Rat Utopia experiments demonstrated a puzzling population trajectory: initial growth, plateau, and eventually a total collapse of the rat population despite abundant resources. This paper proposes a hypothesis that the enclosure's…
A consensus tree is a phylogenetic tree that synthesizes a given collection of phylogenetic trees, all of which share the same leaf labels but may have different topologies, typically obtained through bootstrapping. Our research focuses on…
Drug-drug interactions (DDIs) are a major concern in polypharmacy. Public databases often provide only qualitative descriptions without pharmacokinetic context. We present an interactive web tool that integrates 191,541 descriptive DDI…
Disordered proteins play essential roles in myriad cellular processes, yet their structural characterization remains a major challenge due to their dynamic and heterogeneous nature. We here present a community-driven initiative to address…
Methods: We have developed a software suite (DataSet Tracker) for real-time analysis designed to run on computers, smartphones, and smart glasses hardware and suitable for resource-constrained, on-the-fly computing in microscopes without…
In both human and monkeys the observation and execution of actions produced the activation of a network consisting of parietal and frontal areas. Although this network is involved in the encoding of the action goal, it does not consider the…
Characterizing judgments of similarity within a perceptual or semantic domain, and making inferences about the underlying structure of this domain from these judgments, has an increasingly important role in cognitive and systems…
We show how to localize and quantify the functional evolutionary constraints on natural proteins. The method compares the perturbations caused by local sequence variants to the energetics of the protein folding process and to the…