Quantitative Biology
Sex chromosomes have evolved repeatedly across the Tree of Life, yet their evolutionary fates differ strikingly. In sharp contrast to mammals and birds with degenerated, stable Y/W chromosomes, in most amphibians, teleosts, non avian…
In multicellular organisms, cells coordinate their activities through cell-cell communication (CCC), which is crucial for development, tissue homeostasis, and disease progression. Recent advances in single-cell and spatial omics…
Drug synergy is profoundly influenced by cellular context, as variations in protein interaction landscapes and pathway activities across cell types reshape how drugs act in combination. Most existing models overlook this heterogeneity,…
Spatial Transcriptomics (ST) is a technology that measures gene expression profiles within tissue sections while retaining spatial context. It reveals localized gene expression patterns and tissue heterogeneity, both of which are essential…
Understanding the growth and form of shapes is one of the most fundamental problems in biology. While many prior works have analyzed the beak shapes of Darwin's finches, other cranial features are relatively less explored. In this work, we…
Neural systems face the challenge of maintaining reliable representations amid variations from plasticity and spontaneous activity. In particular, the spontaneous dynamics in neuronal circuit is known to operate near a highly variable…
Previous pandemics, including influenza pandemics and Covid-19, have disproportionately impacted M\=aori and Pacific populations in Aotearoa New Zealand. The reasons for this are multi-faceted, including differences in socioeconomic…
Speciation is often associated with geographical barriers that limit gene flow. However, species can also emerge in continuous homogeneous environments through isolation by distance. When the environment is not homogeneous, natural…
Biodiversity assessments depend critically on the spatial scale at which species richness is measured. How species richness accumulates with sampling area is influenced by natural and anthropogenic processes whose effects vary across…
Grid cells in the medial entorhinal cortex (MEC) and place cells in the hippocampus (HC) both form spatial representations. Grid cells fire in triangular grid patterns, while place cells fire at specific locations and respond to contextual…
In chemical safety assessment, validation studies rely on reference compound lists to evaluate the applicability of alternative methods prior to regulatory acceptance. These lists are expected to cover multiple aspects, including chemical…
Biochemical and environmental modeling typically relies on reaction networks to represent complex transformations. While the Linkage Class Decomposition (LCD) partitions networks based on visual standard connectivity, it often misaligns…
Understanding how simple local interactions give rise to emergent exploration patterns is a fundamental question in statistical physics. We introduce a minimal model of two coupled agents that avoid retracing their own paths while being…
Optic deconvolution in light microscopy (LM) refers to recovering the object details from images, revealing the ground truth of samples. Traditional explicit methods in LM rely on the point spread function (PSF) during image acquisition.…
For mathematical and experimental ease, models with time varying parameters are often simplified to assume constant parameters. However, this simplification can potentially lead to identifiability issues (lack of uniqueness of parameter…
Light microscopy is a widespread and inexpensive imaging technique facilitating biomedical discovery and diagnostics. However, light diffraction barrier and imperfections in optics limit the level of detail of the acquired images. The…
Planning entails identifying sequences of actions to reach a goal, yet we still have incomplete knowledge of how problem constraints, such as difficulty and available time, influence the visual strategies supporting plan construction, both…
Hippocampal neurons exhibit precise phase locking to network oscillations, but the computational principle governing this temporal precision is still unclear. Neural information is conveyed jointly by firing rates and spike timing, but…
Adeno-associated viral (AAV) vectors are widely used delivery platforms in gene therapy, and the design of improved capsids is key to expanding their therapeutic potential. A central challenge in AAV bioengineering, as in protein design…
We propose a model of the functional architecture of curvature-sensitive cells in the primary visual cortex. The model accounts for the modular and hierarchical organization of the cortex, the horizontal connectivity, and the shape of…