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Contact tracing is an effective method to control emerging diseases. Since the 1980's, mathematical modelers are developing a consistent theory for contact tracing, with the aim to find effective and efficient implementations of contact…
Computational models have great potential to accelerate bioscience, bioengineering, and medicine. However, it remains challenging to reproduce and reuse simulations, in part, because the numerous formats and methods for simulating various…
Recently developed technologies to generate single-cell genomic data have made a revolutionary impact in the field of biology. Multi-omics assays offer even greater opportunities to understand cellular states and biological processes.…
Cataloging the neuronal cell types that comprise circuitry of individual brain regions is a major goal of modern neuroscience and the BRAIN initiative. Single-cell RNA sequencing can now be used to measure the gene expression profiles of…
Medical texts, particularly electronic medical records (EMRs), are a cornerstone of modern healthcare, capturing critical information about patient care, diagnoses, and treatments. These texts hold immense potential for advancing clinical…
Contact (or mixing, or more generally connectivity) matrices are a fundamental component of modelling and inference for infectious disease epidemiology. Their structure and parametrisation directly accounts for the frequency of interactions…
Understanding the biological mechanisms of disease is crucial for medicine, and in particular, for drug discovery. AI-powered analysis of genome-scale biological data holds great potential in this regard. The increasing availability of…
In many tissues, cell type varies over single-cell length-scales, creating detailed spatial heterogeneities fundamental to physiological function. To gain understanding of this relationship between tissue function and detailed structure,…
Nearly all cell models explicitly or implicitly deal with the biophysical constraints that must be respected for life to persist. Despite this, there is almost no systematicity in how these constraints are implemented, and we lack a…
Composition is a powerful principle for systems biology, focused on the interfaces, interconnections, and orchestration of distributed processes to enable integrative multiscale simulations. Whereas traditional models focus on the structure…
We propose the Riskman ontology and shapes for representing and analysing information about risk management for medical devices. Risk management is concerned with taking necessary precautions to ensure that a medical device does not cause…
Reproducibility is a cornerstone of science, as the replication of findings is the process through which they become knowledge. It is widely considered that many fields of science are undergoing a reproducibility crisis. This has led to the…
Cell detection, segmentation and classification are essential for analyzing tumor microenvironments (TME) on hematoxylin and eosin (H&E) slides. Existing methods suffer from poor performance on understudied cell types (rare or not present…
Recent advances in single cell sequencing and multi-omics techniques have significantly improved our understanding of biological phenomena and our capacity to model them. Despite combined capture of data modalities showing similar progress,…
Deciphering cell type heterogeneity is crucial for systematically understanding tissue homeostasis and its dysregulation in diseases. Computational deconvolution is an efficient approach estimating cell type abundances from a variety of…
Epigenetic Tracking is a mathematical model of biological cells, originally conceived to study embryonic development. Computer simulations proved the capacity of the model to generate complex 3-dimensional cellular structures, and the…
With the completion of human genome mapping, the focus of scientists seeking to explain the biological complexity of living systems is shifting from analyzing the individual components (such as a particular gene or biochemical reaction) to…
Molecular Communication (MC) is a communication strategy that uses molecules as carriers of information, and is widely used by biological cells. As an interdisciplinary topic, it has been studied by biologists, communication theorists and a…
Cell heterogeneity and the inherent complexity due to the interplay of multiple molecular processes within the cell pose difficult challenges for current single-cell biology. We introduce an approach that identifies a disease phenotype from…
The fundamental understanding of how cells physically interact with each other and their environment is key to understanding their organisation in living tissues. Over the past decades several computational methods have been developed to…