定量生物学
Introduction: While the origin and evolution of proteins remain mysterious, advances in evolutionary genomics and systems biology are facilitating the historical exploration of the structure, function and organization of proteins and…
Robust machine learning for regulatory genomics is studied under biologically and technically induced distribution shifts. Deep convolutional and attention based models achieve strong in distribution performance on DNA regulatory sequence…
We present a new illusion that challenges our understanding of stereo vision. The illusion consists of a larger circle at 50cm, and smaller circle in front of it at 40cm, with constant angular sizes throughout. We move the larger circle…
Single-cell RNA sequencing (scRNA-seq) data exhibit strong and reproducible statistical structure. This has motivated the development of large-scale foundation models, such as TranscriptFormer, that use transformer-based architectures to…
Background: Human behavior shapes infectious disease dynamics, yet its integration into transmission models remains fragmented. Recent epidemics, particularly COVID-19, highlight the need for models capturing adaptation to perceived risk,…
There is growing evidence that independently trained AI systems come to represent the world in the same way. In other words, independently trained embeddings from text, vision, audio, and neural signals share an underlying geometry. We call…
The vast majority of biological sequences encode unknown functions and bear little resemblance to experimentally characterized proteins, limiting both our understanding of biology and our ability to harness functional potential for the…
Diversity-Generating Retroelements (DGRs) create rapid, targeted variation within specific genomic regions in phages and bacteria. They operate through stochastic retro-transcription of a template region (TR) into a variable region (VR),…
Natural birth and death are fundamental mechanisms of population dynamics in ecosystems and have played pivotal roles in shaping population dynamics. Nevertheless, in studies of cyclic competition systems governed by the rock-paper-scissors…
The loss of biodiversity due to the likely widespread extinction of species in the near future is a focus of current concern in conservation biology. One approach to measure the impact of this extinction is based on the predicted loss of…
Understanding the dynamic nature of brain connectivity is critical for elucidating neural processing, behavior, and brain disorders. Traditional approaches such as sliding-window correlation (SWC) characterize time-varying undirected…
Complex change is often described as "evolutionary" in economics, policy, and technology, yet most system dynamics models remain constrained to fixed state spaces and equilibrium-seeking behavior. This paper argues that evolutionary…
Following limb amputation and targeted muscle reinnervation (TMR), nerves that originally innervated agonist and antagonist muscles are rerouted into one or more residual target muscles. This rerouting profoundly alters the natural…
Neuronal systems often preserve their characteristic functions and signalling patterns, also referred to as regimes, despite parametric uncertainties and variations. For neural models having uncertain parameters with a known probability…
Background: Cognitive impairment in multiple sclerosis (MS) is driven by both focal inflammation and compartmentalized neurodegeneration, yet the relative effect of lesion-independent thalamic atrophy on information processing speed (IPS)…
A central challenge in cognitive neuroscience is to explain how semantic and episodic memory, two major forms of declarative memory, typically associated with cortical and hippocampal processing, interact to support learning, recall, and…
Phylogenetic inference, the task of reconstructing how related sequences evolved from common ancestors, is a central objective in evolutionary genomics. The current state-of-the-art methods exploit probabilistic models of sequence evolution…
Aquaporins (AQPs) and aquaglyceroporins (AQGPs) play a crucial role in regulating water transport and solute selectivity across biological membranes. Besides their biological relevance, AQPs have at-tracted growing interest as models for…
Synaptic transmission must balance the need for reliable signalling against the metabolic cost of achieving that reliability. How energetic constraints shape synaptic precision and its regulation during plasticity remains unclear. Here we…
Connecting the dynamics of biomolecular networks to experimentally measurable cell phenotypes remains a central challenge in systems biology. Here we introduce a model-based definition of phenotype as a partial steady state that is…