Quantitative Biology
Automated radiology report generation has gained increasing attention with the rise of deep learning and large language models. However, fully generative approaches often suffer from hallucinations and lack clinical grounding, limiting…
In the last century, most sensorimotor studies of cortical neurons relied on average firing rates. Rate coding is efficient for fast sensorimotor processing that occurs within a few seconds. Much less is known about the neural mechanisms…
It is known that listeners lose the ability to discriminate the direction of motion of a revolving sound (clockwise vs. counterclockwise) beyond a critical velocity ("the upper limit"), likely due to degraded front-back discrimination.…
Microbial populations exhibit a broad spectrum of nutrient utilization strategies, ranging from strategies utilizing diverse nutrients, called "generalists," to those being highly adapted to specific nutrients, called "specialists." The…
Biological evolution depends on the passing down to subsequent generations of genetic information encoding beneficial traits, and on the removal of unfit individuals by a selection mechanism. However, selection acts on phenotypes, and is…
Cell invasion and spatial pattern formation are two distinct manifestations of cellular self-organisation in development, regeneration, and disease. Here, we develop and analyse a unified theoretical framework that links these two seemingly…
Boolean networks are powerful mathematical tools for modeling the qualitative dynamics of genetic regulation. Yet inferred models often generate spurious attractors that lack biological viability. In this paper, we propose a parsimonious…
Predicting species persistence within ecological communities is a fundamental challenge for both empirical and theoretical ecology. Existing methods span from mechanistic models, whose parameters are difficult to estimate from data, to…
The evolutionary origins of structural features in reconstructed gene-regulatory networks (GRNs) remain poorly understood, especially given the random aspects of gene expression. Here, we extend a classical model of GRN evolution to allow a…
Black Sigatoka disease (BSD), also known as black leaf streak disease, is an airborne fungal infection caused by \textit{Pseudocercospora fijiensis} that severely impacts global banana and plantain production. Its persistence and resistance…
Identifying genes associated with diseases is crucial to understanding disease mechanisms and developing therapies. However, identification of individual genes associated with a disease often needs to be supplemented with clustering…
Mosquito vector competence is usually represented as a process in which once virus is detected in saliva, mosquitoes are assumed to remain infectious for life, implying an irreversible transition to the transmitting state. However, some…
Transfer RNAs (tRNAs) are essential components of the translational machinery. Their abundance and diversity shape decoding capacity and protein synthesis efficiency and accuracy. Because tRNA abundance is encoded in the genome through tDNA…
Cardiac digital twins hold great promise for personalized medicine, but they currently depend on complex constitutive models of tissue mechanics that are often over-parameterized for the clinical context. To address this, we introduce…
Gene drive alleles bias their own inheritance to offspring. They can fix in a wild-type population in spite of a fitness cost, and even lead to the eradication of the target population if the fitness cost is high. However, this outcome may…
Dengue virus transmission models commonly assume an exponential distribution for the mosquito extrinsic incubation period (EIP), potentially oversimplifying biological variability. We developed a stochastic mechanistic dengue transmission…
Non-invasive electrophysiology lacks methods that accurately reconstruct whole-brain spatiotemporal dynamics while incorporating individual cortical geometry, leaving current electroencephalography and magnetoencephalography source imaging…
AI chatbots are increasingly used for health advice, but their performance in psychiatric triage remains undercharacterized. Psychiatric triage is particularly challenging because urgency must often be inferred from thoughts, behavior, and…
Generating novel, biologically plausible three-dimensional morphological structures is a fundamental challenge in computational evolutionary biology, hampered by extreme data scarcity and the requirement that generated shapes respect…
Protein dynamics underlie many biological functions, yet remain difficult to characterize due to the high computational cost of molecular dynamics simulations and the scarcity of dynamic structural data. This survey reviews recent advances…