Quantitative Biology
Motivation: Standard genome-wide association studies in cancer genomics rely on statistical significance with multiple testing correction, but systematically fail in underpowered cohorts. In TCGA breast cancer (n=967, 133 deaths), low event…
Bioinformatic analysis of microbiota revealed that certain metabolic pathways are associated with low- and high- residual feed intake (HRFI and LRFI), such as the amino-acid biosynthesis pathway and the tRNA-aminoacyl synthesis pathway. The…
The dynamics of tumor-immune interactions within a complex tumor microenvironment are typically modeled using a system of ordinary differential equations or partial differential equations. These models introduce some unknown parameters that…
We investigate here various properties of the responses of excitable systems subject to periodic forcing and noise. While the properties of intrinsic oscillators, subject to added periodic signals, are well understood, much less is known…
Do brains and language models converge toward the same internal representations of the world? Recent years have seen a rise in studies of neural activations and model alignment. In this work, we review 25 fMRI-based studies published…
Building a working mental model of a protein typically requires weeks of reading, cross-referencing crystal and predicted structures, and inspecting ligand complexes, an effort that is slow, unevenly accessible, and often requires…
Recent advances in neural interfacing have enabled significant improvements in human-computer interaction, rehabilitation, and neuromuscular diagnostics. Motor unit (MU) decomposition from surface electromyography (sEMG) is a key technique…
The scientific study of the retina has reached a remarkable state of completion. We can now explain many aspects of early visual processing based on a relatively simple model of neural circuitry in the retina. The same model, with different…
High-dimensional neural activity often reside in a low-dimensional subspace, referred to as neural manifolds. Grid cells in the medial entorhinal cortex provide a periodic spatial code that are organized near a toroidal manifold,…
Identifying DNA- (DBPs) and RNA-binding proteins (RBPs) is crucial for the understanding of cell function, molecular interactions as well as regulatory functions. Owing to their high similarity, most of the existing approaches face…
Sequence data, such as DNA, RNA, and protein sequences, exhibit intricate, multi-scale structures that pose significant challenges for conventional analysis methods, particularly those relying on alignment or purely statistical…
Our brain learns to update its mental model of the environment by abstracting sensory experiences for adaptation and survival. Learning to categorize sounds is one essential abstracting process for high-level human cognition, such as speech…
Protein fitness optimization involves finding a protein sequence that maximizes desired quantitative properties in a combinatorially large design space of possible sequences. Recent advances in steering protein generative models (e.g.,…
Proteins and other macromolecules exist not in a single state but as dynamic ensembles of interconverting conformations, which are essential for catalysis, allosteric regulation, and molecular recognition. While AI-based structure…
Social interactions are fundamental in animal groups, including humans, and can take various forms, such as competition, cooperation, or kinship. Understanding these interactions in marine environments has been historically challenging due…
The rise of neurotechnologies, especially in combination with AI-based methods for brain data analytics, has given rise to concerns around the protection of mental privacy, mental integrity and cognitive liberty - often framed as…
In Hopfield-type associative memory models, memories are stored in the connectivity matrix and can be retrieved subsequently thanks to the collective dynamics of the network. In these models, the retrieval of a particular memory can be…
Many Mendelian randomization (MR) papers have been conducted only in people of European ancestry, limiting transportability of results to the global population. Expanding MR to diverse ancestry groups is essential to ensure equitable…
Recurrent neural networks with balanced excitation and inhibition exhibit irregular asynchronous dynamics, which is fundamental for cortical computations. Classical balance mechanisms require strong external inputs to sustain finite firing…
Traumatic brain injury (TBI) disrupts thalamocortical connectivity, contributing to cognitive impairment and post-traumatic epilepsy (PTE). This study presents a novel tractography-based framework that leverages diffusion maps to capture…