Related papers: InferenceMAP: Mapping of Single-Molecule Dynamics …
Background: Connectivity mapping is a process to recognize novel pharmacological and toxicological properties in small molecules by comparing their gene expression signatures with others in a database. A simple and robust method for…
Phytoplankton are a crucial component of aquatic ecosystems, and effective monitoring of them can provide valuable insights into ocean environments and ecosystem changes. Traditional phytoplankton monitoring methods are often complex and…
We present a theory for analyzing residence times of single molecules in a fixed detection area of a scanning tunneling microscope (STM). The approach is developed for one-dimensional molecule diffusion and can be extended to two dimensions…
Modern biology and biomedicine are undergoing a big-data explosion needing advanced computational algorithms to extract mechanistic insights on the physiological state of living cells. We present the motivation for the Cell Physiome: a…
A set of rules is defined to systematically number the groups and the atoms of organic molecules and, particularly, of polypeptides in a modular manner. Supported by this numeration, a set of internal coordinates is defined. These…
Human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) are an effective tool for studying cardiac function and disease, and hold promise for screening drug effects on human tissue. Changes to motion patterns in these cells…
Spatially Resolved Transcriptomics (SRT) is a cutting-edge technique that captures the spatial context of cells within tissues, enabling the study of complex biological networks. Recent graph-based methods leverage both gene expression and…
In immunological studies, the characterization of small, functionally distinct cell subsets from blood and tissue is crucial to decipher system level biological changes. An increasing number of studies rely on assays that provide…
The rapid development of digital pathology and modern deep learning has facilitated the emergence of pathology foundation models that are expected to solve general pathology problems under various disease conditions in one unified model,…
Membrane proteins often need to be inserted into or attached on the cell membrane to perform their functions. Understanding their transmembrane topology and conformational dynamics during insertion is crucial for elucidating their roles.…
Exploring the use of individual molecules as active components in electronic devices has been at the forefront of nanoelectronics research in recent years. Compared to semiconductor microelectronics, modeling transport in single-molecule…
Modern single-cell flow and mass cytometry technologies measure the expression of several proteins of the individual cells within a blood or tissue sample. Each profiled biological sample is thus represented by a set of hundreds of…
Pancreatic $\beta-$cells regulate insulin secretion through complex oscillations, which are vital for glucose control and diabetes research. In this paper, an existing mathematical model of $\beta-$cell dynamics is analyzed using a…
The pathway is a biological term that refers to a series of interactions between molecules in a cell that causes a certain product or a change in the cell. Pathway analysis is a powerful method for gene expression analysis. Through pathway…
Proteins are essential component of human life and their structures are important for function and mechanism analysis. Recent work has shown the potential of AI-driven methods for protein structure prediction. However, the development of…
The aim of this chapter is to convey the importance and usefulness of mathematical modelling as a tool to achieve a deeper understanding of stem cell biology. We introduce key mathematical concepts (random walk theory, differential…
Mammalian cells have about 30,000-fold more protein molecules than mRNA molecules. This larger number of molecules and the associated larger dynamic range have major implications in the development of proteomics technologies. We examine…
Long-term biomolecular dynamics are critical for understanding key evolutionary transformations in molecular systems. However, capturing these processes requires extended simulation timescales that often exceed the practical limits of…
Network models provide a powerful framework for analysing single-cell count data, facilitating the characterisation of cellular identities, disease mechanisms, and developmental trajectories. However, uncertainty modeling in unsupervised…
Computation of biological processes creates great promise for everyday life and great challenges for physical scientists. Simulations of molecular dynamics appeal to biologists as a natural extension of structural biology. Once biologists…