Related papers: A Comparison of the Pathway Tools Software with th…
Accurate prediction of cancer progression remains a challenge due to the high heterogeneity of molecular omics data across patients. While biologically informed models have improved the interpretability of these predictions, a persistent…
Integration of transcriptomic and metabolomic data improves functional interpretation of disease-related metabolomic phenotypes, and facilitates discovery of putative metabolite biomarkers and gene targets. For this reason, these data are…
Recent developments in AI have provided assisting tools to support pathologists' diagnoses. However, it remains challenging to incorporate such tools into pathologists' practice; one main concern is AI's insufficient workflow integration…
The analysis and interpretation of relationships between biological molecules is done with the help of networks. Networks are used ubiquitously throughout biology to represent the relationships between genes and gene products. Network…
Diagnosing diseases through histopathology whole slide images (WSIs) is fundamental in modern pathology but is challenged by the gigapixel scale and complexity of WSIs. Trained histopathologists overcome this challenge by navigating the…
Advances in optical microscopy scanning have significantly contributed to computational pathology (CPath) by converting traditional histopathological slides into whole slide images (WSIs). This development enables comprehensive digital…
Tumors bearing Ras mutations are notoriously difficult to treat. Drug combinations targeting the Ras protein or its pathway have also not met with success. Pathway drug cocktails, which are combinations aiming at parallel pathways, appear…
Biological organisms are composed of numerous interconnected biochemical processes. Diseases occur when normal functionality of these processes is disrupted. Thus, understanding these biochemical processes and their interrelationships is a…
Backgr: Digital pathology images are increasingly used both for diagnosis and research, because slide scanners are nowadays broadly available and because the quantitative study of these images yields new insights in systems biology.…
With high-throughput biotechnologies generating unprecedented quantities of data, researchers are faced with the challenge of locating and comparing an exponentially growing number of programs and websites dedicated to computational…
Pathway enrichment analysis has become a key tool for biomedical researchers to gain insight into the underlying biology of differentially expressed genes, proteins and metabolites. It reduces complexity and provides a system-level view of…
Background: The study of genome-scale metabolic models and their underlying networks is one of the most important fields in systems biology. The complexity of these models and their description makes the use of computational tools an…
Despite the promises of data-driven artificial intelligence (AI), little is known about how we can bridge the gulf between traditional physician-driven diagnosis and a plausible future of medicine automated by AI. Specifically, how can we…
Podocytes, specialized epithelial cells that envelop the glomerular capillaries, play a pivotal role in maintaining renal health. The current description and quantification of features on pathology slides are limited, prompting the need for…
Path planning is an essential component of mobile robotics. Classical path planning algorithms, such as wavefront and rapidly-exploring random tree (RRT) are used heavily in autonomous robots. With the recent advances in machine learning,…
Pathology is the study of microscopic inspection of tissue, and a pathology diagnosis is often the medical gold standard to diagnose disease. Pathology images provide a unique challenge for computer-vision-based analysis: a single pathology…
Exploring the structural topology of genome-based large-scale metabolic network is essential for investigating possible relations between structure and functionality. Visualization would be helpful for obtaining immediate information about…
Addressing the functionality of genomes is one of the most important and challenging tasks of today's biology. In particular the ability to link genotypes to corresponding phenotypes is of interest in the reconstruction and biotechnological…
Pathologists diagnose cancer using gigapixel whole-slide images (WSIs), but the current digital workflow is fragmented. These multiscale datasets often exceed 100,000 x 100,000 pixels, yet standard 2D monitors restrict the field of view.…
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…