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Measuring the electrophoretic mobility of molecules is a powerful experimental approach for investigating biomolecular processes. A frequent challenge in the context of single-particle measurements is throughput, limiting the obtainable…

In genome mapping experiments, long DNA molecules are stretched by confining them to very narrow channels, so that the locations of sequence-specific fluorescent labels along the channel axis provide large-scale genomic information. It is…

There is a growing interest in measuring the cell wall mechanical property at different locations in single walled cells. We present an inference scheme that maps relative surface elastic modulus distributions along the cell wall based on…

We report the development of a scanning force microscope based on an ultra-sensitive silicon nitride membrane transducer. Our development is made possible by inverting the standard microscope geometry - in our instrument, the substrate is…

A conditional diffusion model has been developed to analyze intricate conductance fluctuations called universal conductance fluctuations or quantum fingerprints appearing in quantum transport phenomena. The model reconstructs impurity…

A theoretical calculation is presented to describe the confined motion of transmembrane molecules in cell membranes. The study is analytic, based on Master equations for the probability of the molecules moving as random walkers, and leads…

Network inference approaches are now widely used in biological applications to probe regulatory relationships between molecular components such as genes or proteins. Many methods have been proposed for this setting, but the connections and…

Modeling and simulation are transforming all fields of biology. Tools like AlphaFold have revolutionized structural biology, while molecular dynamics simulations provide invaluable insights into the behavior of macromolecules in solution or…

In Schiebinger et al. (2017), the authors use optimal transport of measures on empirical distributions arising from biological experiments to relate the single cell RNA sequencing profiles for induced pluripotent stem cells differentiating.…

Traction Force Microscopy (TFM) is a technique used to determine the tensions that a biological cell conveys to the underlying surface. Typically, TFM requires culturing cells on gels with fluorescent beads, followed by bead displacement…

Data-driven methods offer efficient and robust solutions for analyzing complex dynamical systems but rely on the assumption of I.I.D. data, driving the development of generalization techniques for handling environmental differences. These…

Conformational dynamics of biomolecules are of fundamental importance for their function. Single-molecule F\"orster Resonance Energy Transfer (smFRET) is a powerful approach to inform on the structure and the dynamics of labeled molecules.…

We tackle the problem of inferring node labels in a partially labeled graph where each node in the graph has multiple label types and each label type has a large number of possible labels. Our primary example, and the focus of this paper,…

Infrared spectroscopy is the technique of choice for chemical identification of biomolecules through their vibrational fingerprints. However, infrared light interacts poorly with nanometric size molecules. Here, we exploit the unique…

In recent years Bayesian Inference has become an efficient tool to analyse single molecule trajectories. Recently, high density single molecule tagging, Langevin Equation modelling and Bayesian Inference [10] have been used to infer…

Determining the trajectories of cells and their lineages or ancestries in live-cell experiments are fundamental to the understanding of how cells behave and divide. This paper proposes novel online algorithms for jointly tracking and…

Transport of liquid mixtures through porous membranes is central to processes such as desalination, chemical separations and energy harvesting, with ultrathin membranes made from novel 2D nanomaterials showing exceptional promise. Here we…

We present a framework to take advantage of existing labels at inference, called \textit{exemplars}, in order to improve the performance of object detection in medical images. The method, \textit{exemplar diffusion}, leverages existing…

In this paper we study subdiffusion in a system with a thin membrane. At the beginning, the random walk of a particle is considered in a system with a discrete time and space variable and then the probability describing the evolution of the…

Mesoscale molecular assemblies on the cell surface, such as cilia and filopodia, integrate information, control transport and amplify signals. Synthetic devices mimicking these structures could sensitively monitor these cellular functions…