相关论文: Connecting the dots across time: Reconstruction of…

Developments in transcriptomics techniques have caused a large demand in tailored computational methods for modelling gene expression dynamics from experimental data. Recently, so-called single-cell experiments have revolutionised genetic…

Single-cell RNA sequencing (scRNA-seq), especially temporally resolved datasets, enables genome-wide profiling of gene expression dynamics at single-cell resolution across discrete time points. However, current technologies provide only…

Cells with the same genome can exist in different phenotypes. and can change between distinct phenotypes when subject to specific stimuli and microenvironments. Some examples include cell differentiation during development, reprogramming…

The study of moving particles (e.g. molecules, virus, vesicles, organelles, or whole cells) is crucial to decipher a plethora of cellular mechanisms within physiological and pathological conditions. Powerful live-imaging approaches enable…

Tethered particle motion experiments are versatile single-molecule techniques enabling one to address in vitro the molecular properties of DNA and its interactions with various partners involved in genetic regulations. These techniques…

This paper presents a novel method for the reconstruction of high-resolution temporal images in dynamic tomographic imaging, particularly for discrete objects with smooth boundaries that vary over time. Addressing the challenge of limited…

We show that the symmetries of image formation by scattering enable graph-theoretic manifold-embedding techniques to extract structural and timing information from simulated and experimental snapshots at extremely low signal. The approach…

Understanding the dynamic nature of biological systems is fundamental to deciphering cellular behavior, developmental processes, and disease progression. Single-cell RNA sequencing (scRNA-seq) has provided static snapshots of gene…

The ability of a cell to communicate with its environment is essential for key cellular functions like replication, metabolism, or cell fate decisions. The involved molecular mechanisms are highly dynamic and difficult to capture…

Causality implies that by measuring an absorption spectrum, the time-dependent linear response function can be retrieved. Recent experiments suggest a link between the shape of spectral lines observed in absorption spectroscopy with the…

Mathematical methods of step-by-step and combined shifts are proposed for experimental data processing to reconstruct the measuring system impulse response distorted by shift-invariant blur. Proposed methods base on direct non-blind…

Single-molecule experimental techniques track the real-time dynamics of molecules by recording a small number of experimental observables. Following these observables provides a coarse-grained, low-dimensional representation of the…

In this paper, we study the method to reconstruct dynamical systems from data without time labels. Data without time labels appear in many applications, such as molecular dynamics, single-cell RNA sequencing etc. Reconstruction of dynamical…

Reconstructing continuous signals from a small number of discrete samples is a fundamental problem across science and engineering. In practice, we are often interested in signals with 'simple' Fourier structure, such as bandlimited,…

Single-cell RNA sequencing (scRNA-seq) provides high-dimensional profiles of cellular states, enabling data-driven modeling of cellular dynamics over time. In practice, time-resolved scRNA-seq is collected at only a few discrete time points…

We present a probabilistic framework for modeling structured spatiotemporal dynamics from sparse observations, focusing on cardiac motion. Our approach integrates neural ordinary differential equations (NODEs), graph neural networks (GNNs),…

Single-molecule tracking (SMT) methods are under considerable expansion in many fields of cell biology, as the dynamics of cellular components in biological mechanisms becomes increasingly relevant. Despite the development of SMT…

Analyzing data from dynamical systems often begins with creating a reconstruction of the trajectory based on one or more variables, but not all variables are suitable for reconstructing the trajectory. The concept of nonlinear observability…

We consider the problem of reconstructing the paths of a set of points over time, where, at each of a finite set of moments in time the current positions of points in space are only accessible through some small number of their X-rays. This…

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…