Related papers: InferenceMAP: Mapping of Single-Molecule Dynamics …
Single cell responses are shaped by the geometry of signaling kinetic trajectories carved in a multidimensional space spanned by signaling protein abundances. It is however challenging to assay large number (>3) of signaling species in…
Cellular tissue behavior is a multiscale problem. At the cell level, out of equilibrium, biochemical reactions drive physical cell-cell interactions in a typical active matter process. Cell modeling computer simulations are a robust tool to…
The development of single-cell and spatial transcriptomics has revolutionized our capacity to investigate cellular properties, functions, and interactions in both cellular and spatial contexts. However, the analysis of single-cell and…
Proteins move and deform to ensure their biological functions. Despite significant progress in protein structure prediction, approximating conformational ensembles at physiological conditions remains a fundamental open problem. This paper…
The cellular Potts model (CPM) is a powerful computational method for simulating collective spatiotemporal dynamics of biological cells. To drive the dynamics, CPMs rely on physics-inspired Hamiltonians. However, as first principles remain…
Current efforts in the biomedical sciences and related interdisciplinary fields are focused on gaining a molecular understanding of health and disease, which is a problem of daunting complexity that spans many orders of magnitude in…
Human physiology and pathology arise from the coordinated interactions of diverse single cells. However, analyzing single cells has been limited by the low sensitivity and throughput of analytical methods. DNA sequencing has recently made…
We review methods of data analysis for biophysical data with a special emphasis on single molecule applications. Our review is intended for anyone, from student to established researcher. For someone just getting started, we focus on…
This paper develops a conceptual extension of the Kinetic Theory of Active Particles, building upon the framework introduced in [2]. Living systems cannot be adequately described within classical single-scale paradigms, even when refined.…
BosonSampling is a well-defined scheme for demonstrating quantum supremacy with photons in near term. Although relying only on multi-photon interference in nonadaptive linear-optical networks, it is hard to simulate classically. Here we…
Seamless situational awareness provided by modern radar systems relies on effective methods for multiobject tracking (MOT). This paper presents a graph-based Bayesian method for nonlinear and high-dimensional MOT problems that embeds…
Generators of space-time dynamics in bioimaging have become essential to build ground truth datasets for image processing algorithm evaluation such as biomolecule detectors and trackers, as well as to generate training datasets for deep…
We introduce a graphical method originating from the computer graphics domain that is used for the arbitrary and intuitive placement of cells over a two-dimensional manifold. Using a bitmap image as input, where the color indicates the…
Quantitative analysis of the dynamics of tiny cellular and sub-cellular structures, known as particles, in time-lapse cell microscopy sequences requires the development of a reliable multi-target tracking method capable of tracking numerous…
This paper aims to efficiently compute transport maps between probability distributions arising from particle representation of bio-physical problems. We develop a bidirectional DeepParticle (BDP) method to learn and generate solutions…
The application of single-cell molecular profiling coupled with spatial technologies has enabled charting cellular heterogeneity in reference tissues and in disease. This new wave of molecular data has highlighted the expected diversity of…
Single-cell multi-omics (scMulti-omics) refers to the paired multimodal data, such as Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-seq), where the regulation of each cell was measured from different modalities, i.e.…
Fluorescence spectroscopy is an image correlation technique to analyze and characterize the molecular dynamics from a sequence of fluorescence images. Many image correlation techniques have been developed for different applications [1]. But…
Collectively coordinated cell migration plays a role in tissue embryogenesis, cancer, homeostasis and healing. To study these processes, different cell-based modelling approaches have been developed, ranging from lattice-based cellular…
We propose an approach to analysing single trajectories of a particle, which moves randomly on a landscape distinct parts of which result in sufficiently various diffusion coefficients. The method based on the mapping the cumulative sum of…