Related papers: OrfMapper: A Web-Based Application for Visualizing…
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…
Neural network models of real-world systems, such as industrial processes, made from sensor data must often rely on incomplete data. System states may not all be known, sensor data may be biased or noisy, and it is not often known which…
High-dimensional omics datasets are routinely visualized as heatmaps, where color intensities reveal co-expression patterns and correlations. However, modern omics technologies increasingly generate matrices so large that existing visual…
Summary: Most cellular tasks are performed not by individual proteins, but by groups of functionally associated proteins, often referred to as modules. In a protein assocation network modules appear as groups of densely interconnected…
A genome-scale reconstruction of human metabolism, Recon 2, is available but no interface exists to interactively visualise its content integrated with omics data and simulation results. We manually drew a comprehensive map, ReconMap 2.0,…
Rapid technological advances have allowed for molecular profiling across multiple omics domains from a single sample for clinical decision making in many diseases, especially cancer. As tumor development and progression are dynamic…
The potential benefits of applying machine learning methods to -omics data are becoming increasingly apparent, especially in clinical settings. However, the unique characteristics of these data are not always well suited to machine learning…
The Mapper algorithm, a technique within topological data analysis (TDA), constructs a simplified graphical representation of high-dimensional data to uncover its underlying shape and structural patterns. The algorithm has attracted…
Motivation: The Mapper algorithm is an essential tool to explore shape of data in topology data analysis. With a dataset as an input, the Mapper algorithm outputs a graph representing the topological features of the whole dataset. This…
Communication and networking research introduces new protocols and standards with an increasing number of researchers relying on real experiments rather than simulations to evaluate the performance of their new protocols. A number of…
Protein quantification and analysis are well-accepted approaches for biomarker discovery but are limited to identification without structural information. High-throughput omics data (i.e., genomics, transcriptomics, and proteomics) have…
Schematic maps are in daily use to show the connectivity of subway systems and to facilitate travellers to plan their journeys effectively. This study surveys up-to-date algorithmic approaches in order to give an overview of the state of…
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…
Background: Cancers are highly heterogeneous with different subtypes. These subtypes often possess different genetic variants, present different pathological phenotypes, and most importantly, show various clinical outcomes such as varied…
We consider the analysis of high dimensional data given in the form of a matrix with columns consisting of observations and rows consisting of features. Often the data is such that the observations do not reside on a regular grid, and the…
Background: It is well known that the development of cancer is caused by the accumulation of somatic mutations within the genome. For oncogenes specifically, current research suggests that there is a small set of "driver" mutations that are…
International initiatives such as METABRIC (Molecular Taxonomy of Breast Cancer International Consortium) have collected several multigenomic and clinical data sets to identify the undergoing molecular processes taking place throughout the…
Local feature matching is an essential component in many visual applications. In this work, we propose OAMatcher, a Tranformer-based detector-free method that imitates humans behavior to generate dense and accurate matches. Firstly,…
Matrices often represent important information in scientific applications and are involved in performing complex calculations. But systematically testing these applications is hard due to the oracle problem. Metamorphic testing is an…
To facilitate understanding the architecture of a software system, we developed SArF Map technique that visualizes software architecture from feature and layer viewpoints using a city metaphor. SArF Map visualizes implicit software features…