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Gene regulatory networks (GRNs) define the regulatory relationships among molecules such as transcription factors, chromatin remodelers, and target genes. GRNs play a critical role in diverse biological processes, including development,…
Cell differentiation is an important process in living organisms. Differentiation is mostly based on binary decisions with the progenitor cells choosing between two specific lineages. The differentiation dynamics have both deterministic and…
Single-cell transcriptomics, epigenomics, and other 'omics applied at single-cell resolution can significantly advance hypotheses and understanding of glial biology. Omics technologies are revealing a large and growing number of new glial…
Medical errors are a major public health concern and a leading cause of death worldwide. Many healthcare centers and hospitals use reporting systems where medical practitioners write a preliminary medical report and the report is later…
A ubiquitous way that cells share information is by exchanging molecules. Yet, the fundamental ways that this information exchange is influenced by intracellular dynamics remain unclear. Here we use information theory to investigate a…
Cell segmentation is a fundamental task for computational biology analysis. Identifying the cell instances is often the first step in various downstream biomedical studies. However, many cell segmentation algorithms, including the recently…
Large language models excel at interpreting complex natural language instructions, enabling them to perform a wide range of tasks. In the life sciences, single-cell RNA sequencing (scRNA-seq) data serves as the "language of cellular…
Despite fluorescent cell-labelling being widely employed in biomedical studies, some of its drawbacks are inevitable, with unsuitable fluorescent probes or probes inducing a functional change being the main limitations. Consequently, the…
Background: Citation analysis has become an important tool for research performance assessment in the medical sciences. However, different areas of medical research may have considerably different citation practices, even within the same…
Cellular signaling is essential in information processing and decision making. Therefore, a variety of experimental approaches have been developed to study signaling on bulk and single-cell level. Single-cell measurements of signaling…
To understand the relationship between the chirality of individual cells and that of tissues and organisms, we have developed a chiral polarized particle model to investigate the movement of cell populations on substrates. Our model…
Biomedical entity linking (BEL) is the task of grounding entity mentions to a knowledge base. It plays a vital role in information extraction pipelines for the life sciences literature. We review recent work in the field and find that, as…
The knowledge of cell molecular mechanisms implicated in human diseases is expanding and should be converted into guidelines for deciphering pathological cell signaling and suggesting appropriate treatment. The basic assumption is that…
Automatically generated radiology reports often receive high scores from existing evaluation metrics but fail to earn clinicians' trust. This gap reveals fundamental flaws in how current metrics assess the quality of generated reports. We…
This paper describes a new type of spreadsheet which mitigates the errors caused by incorrect range referencing in formulae. This spreadsheet is composed of structured worksheets called tables which contain a hierarchical organization of…
Identification of disease subtypes and corresponding biomarkers can substantially improve clinical diagnosis and treatment selection. Discovering these subtypes in noisy, high dimensional biomedical data is often impossible for humans and…
Recently, microRNAs (miRNAs) have emerged as central posttranscriptional regulators of gene expression. miRNAs regulate many key biological processes, including cell growth, death, development and differentiation. This discovery is…
Automated analysis of tissue sections allows a better understanding of disease biology and may reveal biomarkers that could guide prognosis or treatment selection. In digital pathology, less abundant cell types can be of biological…
Information of relevance to the organism often is represented by the concentrations of particular molecules inside a cell. As outside observers we can now measure these concentrations precisely, but the cell's own mechanisms must be…
The evaluation of cell tracking results steers the development of tracking methods, significantly impacting biomedical research. This is quantitatively achieved by means of evaluation metrics. Unfortunately, current metrics favor local…