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Experimental evidence suggests that epidermal growth factor receptor (EGFR)-mediated activation of the signaling protein phospholipase C gamma plays a critical role in a cancer cell's phenotypic decision to either proliferate or to migrate…
Cell differentiation in multicellular organisms is a complex process whose mechanism can be understood by a reductionist approach, in which the individual processes that control the generation of different cell types are identified.…
This paper explores the transgenerational DNA methylation pattern (DNA methylation transmitted from one generation to the next) via a clustering approach. Beta regression is employed to model the transmission pattern from parents to their…
Classifier-free guidance (CFG) is a widely used technique for controllable generation in diffusion and flow-based models. Despite its empirical success, CFG relies on a heuristic linear extrapolation that is often sensitive to the guidance…
A crucial step in the regulation of gene expression is binding of transcription factor (TF) proteins to regulatory sites along the DNA. But transcription factors act at nanomolar concentrations, and noise due to random arrival of these…
Tree-child networks are one of the most prominent network classes for modeling evolutionary processes which contain reticulation events. Several recent studies have addressed counting questions for bicombining tree-child networks in which…
Modelling and understanding directional gene networks is a major challenge in biology as they play an important role in the architecture and function of genetic systems. Copula Directional Dependence (CDD) can measure the directed…
Among the main actors of organism development there are morphogens, which are signaling molecules diffusing in the developing organism and acting on cells to produce local responses. Growth is thus determined by the distribution of such…
Embryonic development leads to the reproducible and ordered appearance of complexity from egg to adult. The successive differentiation of different cell types, that elaborates this complexity, result from the activity of gene networks and…
Transcriptomic foundation models pretrained with masked language modeling can achieve low pretraining loss yet produce poor cell representations for downstream tasks. We introduce whole-cell expression decoding (WCED), where models…
We present schema redescription as a methodology to characterize canalization in automata networks used to model biochemical regulation and signalling. In our formulation, canalization becomes synonymous with redundancy present in the logic…
The shape of a cell contains essential information about its function within the biological system. Segmenting these structures from large-scale 3D microscopy images is challenging, limiting clinical insights especially for microglia,…
Biofilms are microbial collectives that occupy a diverse array of surfaces. The function and evolution of biofilms are strongly influenced by the spatial arrangement of different strains and species within them, but how spatiotemporal…
Protein structure prediction and folding are fundamental to understanding biology, with recent deep learning advances reshaping the field. Diffusion-based generative models have revolutionized protein design, enabling the creation of novel…
Dielectric barrier discharges (DBDs) are widely used in applications such as ozone generation and volatile organic compound treatment, where performance can be enhanced through catalyst integration. A fundamental understanding of reactive…
The particle-scale dynamics of granular materials have commonly been characterized by the self-diffusion coefficient $D$. However, this measure discards the collective and topological information known to be an important characteristic of…
Cell membranes phase separate into ordered ${\rm L_o}$ and disordered ${\rm L_d}$ domains depending on their compositions. This membrane compartmentalization is heterogeneous and regulates the localization of specific proteins related to…
The human body is able to generate a diverse set of high affinity antibodies, the soluble form of B cell receptors (BCRs), that bind to and neutralize invading pathogens. The natural development of BCRs must be understood in order to design…
The total-evidence approach to divergence-time dating uses molecular and morphological data from extant and fossil species to infer phylogenetic relationships, species divergence times, and macroevolutionary parameters in a single coherent…
The BFW model introduced by Bohman, Frieze, and Wormald [Random Struct. Algorithms, 25, 432 (2004)] and recently investigated in the framework of discontinuous percolation by Chen and D'Souza [Phys. Rev. Lett., 106, 115701 (2011)], is…