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Determining cell identities in imaging sequences is an important yet challenging task. The conventional method for cell identification is via cell tracking, which is complex and can be time-consuming. In this study, we propose an innovative…
The fields of computing and biology have begun to cross paths in new ways. In this paper a review of the current research in biological computing is presented. Fundamental concepts are introduced and these foundational elements are explored…
Systems Biology has emerged in the last years as a new holistic approach based on the global understanding of cells instead of only being focused on their individual parts (genes or proteins), to better understand the complexity of human…
Motility is an essential factor for an organism's survival and diversification. With the advent of novel single-cell technologies, analytical frameworks and theoretical methods, we can begin to probe the complex lives of microscopic motile…
Pattern formation in biological tissues plays an important role in the development of living organisms. Since the classical work of Alan Turing, a pre-eminent way of modelling has been through reaction-diffusion mechanisms. More recently,…
Detecting microbial biomarkers used to predict disease phenotypes and clinical outcomes is crucial for disease early-stage screening and diagnosis. Most methods for biomarker identification are linear-based, which is very limited as…
A fundamental problem in medicine and biology is to assign states, e.g. healthy or diseased, to cells, organs or individuals. State assignment or making a diagnosis is often a nontrivial and challenging process and, with the advent of omics…
This paper presents a novel framework for the modeling of biological networks. It makes use of recent tools analyzing the robust satisfaction of properties of (hybrid) dynamical systems. The main challenge of this approach as applied to…
Cell formation problem is among the first obstacles the designer of cellular production systems must overcome. This paper presents a critical analysis of the various criteria and constraints considered in the literature. The objective is to…
Cytology is the branch of pathology which deals with the microscopic examination of cells for diagnosis of carcinoma or inflammatory conditions. Automation in cytology started in the early 1950s with the aim to reduce manual efforts in…
Microrheology, the study of fluids on micron length-scales, promises to reveal insights into cellular biology, including mechanical biomarkers of disease and the interplay between biomechanics and cellular function. Here a…
In multicellular organisms, relations among parts and between parts and the whole are contextual and interdependent. These organisms and their cells are ontogenetically linked: an organism starts as a cell that divides producing…
Radiology reports for the same patient examination may contain clinically meaningful discrepancies arising from interpretation differences, reporting variability, or evolving assessments. Systematic analysis of such discrepancies is…
Whole-cell computational models aim to predict cellular phenotypes from genotype by representing the entire genome, the structure and concentration of each molecular species, each molecular interaction, and the extracellular environment.…
Diseases involve complex processes and modifications to the cellular machinery. The gene expression profile of the affected cells contains characteristic patterns linked to a disease. Hence, biological knowledge pertaining to a disease can…
A brief informal overview on the BioPAX and SBML standards for formal presentation of complex biological knowledge.
Cell state discovery is crucial for understanding biological systems and enhancing medical outcomes. A key aspect of this process is identifying distinct biomarkers that define specific cell states. However, difficulties arise from the…
This article examines recent research in molecular communications from a telecommunications system design perspective. In particular, it focuses on channel models and state-of-the-art physical layer techniques. The goal is to provide a…
This study addresses the challenge of classifying cell shapes from noisy contours, such as those obtained through cell instance segmentation of histological images. We assess the performance of various features for shape classification,…
Pathology deals with the practice of discovering the reasons for disease by analyzing the body samples. The most used way in this field, is to use histology which is basically studying and viewing microscopic structures of cell and tissues.…