Quantitative Biology
Topological data analysis (TDA) detects geometric structure in biological data. However, many TDA algorithms are memory intensive and impractical for massive datasets. Here, we introduce a statistical protocol that reduces TDA's memory…
All parts of the hawthorn tree (Crataegus spp.), including fruits, flowers, and leaves, have been used as a source of bioactive compounds. Thus, in this investigation, the twigs of two species of hawthorn plant of Crataegus azarolus (C.…
Antimicrobial resistance (AMR) poses a significant public health and economic challenge, increasing treatment costs and reducing antibiotic effectiveness. This study employs machine learning to analyze genomic and epidemiological data from…
Using past behaviors to guide future actions is essential for fostering cooperation in repeated social dilemmas. Traditional memory-based strategies that focus on recent interactions have yielded valuable insights into the evolution of…
Decoding bimanual hand movements from intracortical recordings remains a critical challenge for brain-computer interfaces (BCIs), due to overlapping neural representations and nonlinear interlimb interactions. We introduce BiND (Bimanual…
Mean-field models provide a link between microscopic neuronal activity and macroscopic brain dynamics. Their derivation depends on simplifying assumptions, such as all-to-all connectivity, limiting their biological realism. To overcome…
The fundamental laws governing proteoform dynamics have yet to be formulated. As a result, it is unclear how a specific proteoform, a distinct molecular variant of a protein, dynamically shapes its own future by evolving into new modes that…
Determining associations among different species from citizen science databases is challenging due to observer behavior and intrinsic density variations that give rise to correlations that do not imply species associations. This paper…
We propose and analyze a model for the dynamics of the flow into and out of a nest for the arboreal turtle ant $\textit{Cephalotes goniodontus}$ during foraging to investigate a possible mechanism for the emergence of oscillations. In our…
Simulation-based inference provides a powerful framework for cryo-electron microscopy, employing neural networks in methods like CryoSBI to infer biomolecular conformations via learned latent representations. This latent space represents a…
T-cells play a key role in adaptive immunity by mounting specific responses against diverse pathogens. An effective binding between T-cell receptors (TCRs) and pathogen-derived peptides presented on Major Histocompatibility Complexes (MHCs)…
This work reflects upon what Immersion can mean from the perspective of an Artificial Intelligence (AI). Applying the lens of immersive learning theory, it seeks to understand whether this new perspective supports ways for AI participation…
miRNA mRNA relations are closely linked to several biological processes and disease mechanisms In a recent study we tested the performance of large language models LLMs on extracting miRNA mRNA relations from PubMed PubMedBERT achieved the…
Despite the thousands of genes implicated in age-related phenotypes, effective interventions for aging remain elusive, a lack of advance rooted in the multifactorial nature of longevity and the functional interconnectedness of the molecular…
Citrus greening, or Huanglongbing (HLB), is a serious disease affecting citrus crops, with no known cure. Early detection is essential, but current methods are often expensive. To address this, a low-cost, portable sensor was developed to…
Single-cell RNA sequencing (scRNA-seq) provides unprecedented insights into cellular heterogeneity, enabling detailed analysis of complex biological systems at single-cell resolution. However, the high dimensionality and technical noise…
Recent advances in generative biology have enabled the design of novel proteins, creating significant opportunities for drug discovery while also introducing new risks, including the potential development of synthetic bioweapons. Existing…
This study explores the deployment of three machine learning (ML) approaches for real-time prediction of glucose, lactate, and ammonium concentrations in cell culture processes, using Raman spectroscopy as input features. The research…
Many ecosystems can undergo important qualitative changes, including sudden transitions to alternative stable states, in response to perturbations or increments in conditions. Such 'tipping points' are often preceded by declines in aspects…
Microbiomes are complex systems comprised of many interacting species. Species can survive harsh or changing conditions by rapid adaptation, a process accelerated by the exchange of genetic material between different species through…