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Selecting an appropriate kernel is a central challenge in kernel-based spectral methods. In \emph{Kernelized Diffusion Maps} (KDM), the kernel determines the accuracy of the RKHS estimator of a diffusion-type operator and hence the quality…
It has recently been proposed that proteins embedded in lipidic bio-membranes can spontaneously self-organize into stable small clusters, or membrane nano-domains, due to the competition between short-range attractive and longer-range…
Deep clustering (DC) is often quoted to have a key advantage over $k$-means clustering. Yet, this advantage is often demonstrated using image datasets only, and it is unclear whether it addresses the fundamental limitations of $k$-means…
Eukaryotic cells are able to sense chemical gradients in a wide range of environments. We show that, if a cell is exposed to a highly variable environment, it may gain chemotactic accuracy by expressing multiple receptor types with varying…
Cells in multicellular organisms adhere to the extracellular matrix through two-dimensional clusters spanning a size range from very few to thousands of adhesion bonds. For many common receptor-ligand systems, the ligands are tethered to a…
Non-Hermitian systems hosting exceptional points (EPs) exhibit signal enhancement and unconventional mode dynamics. Going beyond isolated EPs, here we report on the existence of exceptional rings (ERs) in planar optical resonators with…
Many types of cells can sense external ligand concentrations with cell-surface receptors at extremely high accuracy. Interestingly, ligand-bound receptors are often internalized, a process also known as receptor-mediated endocytosis. While…
Unsupervised cell type identification is crucial for uncovering and characterizing heterogeneous populations in single cell omics studies. Although a range of clustering methods have been developed, most focus exclusively on intrinsic…
Tissue organization plays a crucial role in morphogenesis, wound healing and cancer metastasis. Hydra, known for its regenerative capabilities, serves as an excellent model for studying cellular structures, particularly in pattern formation…
Tissue boundaries pattern embryos, suppress tumours, and provide directional cues. Tissue boundaries are associated with supracellular cables formed by actin and the molecular motor non-muscle myosin II. Actomyosin cables generate tension…
Cells crawling through tissues migrate inside a complex fibrous environment called the extracellular matrix (ECM), which provides signals regulating motility. Here we investigate one such well-known pathway, involving mutually antagonistic…
Extracting an understanding of the underlying system from high dimensional data is a growing problem in science. Discovering informative and meaningful features is crucial for clustering, classification, and low dimensional data embedding.…
Cellular contractility, migration, and extracellular matrix (ECM) mechanics are critical for a wide range of biological processes including embryonic development, wound healing, tissue morphogenesis, and regeneration. Even though the…
Kernel spectral clustering corresponds to a weighted kernel principal component analysis problem in a constrained optimization framework. The primal formulation leads to an eigen-decomposition of a centered Laplacian matrix at the dual…
Kernel embeddings have emerged as a powerful tool for representing probability measures in a variety of statistical inference problems. By mapping probability measures into a reproducing kernel Hilbert space (RKHS), kernel embeddings enable…
The phenomenon where cells with elongated protrusions, such as neurons, communicate by contacting other cells and arrange themselves appropriately is termed cell sorting through haptotaxis. This phenomenon is described by partial…
The adhesion of cell membranes is mediated by the binding of membrane-anchored receptor and ligand proteins. In this article, we review recent results from simulations and theory that lead to novel insights on how the binding equilibrium…
Recent advancements in immune sequencing and experimental techniques are generating extensive T cell receptor (TCR) repertoire data, enabling the development of models to predict TCR binding specificity. Despite the computational challenges…
Constrictions in blood vessels and microfluidic devices can dramatically change the spatial distribution of passing cells or particles and are commonly used in biomedical cell sorting applications. However, the three-dimensional nature of…
Small extracellular vesicles (sEVs) are known to play an important role in the communication between distant cells and to deliver biological information throughout the body. To date, many studies have focused on the role of sEVs…