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Metabolic modelling has entered a mature phase with dozens of methods and software implementations available to the practitioner and the theoretician. It is not easy for a modeller to be able to see the wood (or the forest) for the trees.…
Visualisation is an effective way to facilitate the analysis and understanding of multivariate data. In the context of multi-objective optimisation, comparing to quantitative performance metrics, visualisation is, in principle, able to…
The recent explosion of genetic and high dimensional biobank and 'omic' data has provided researchers with the opportunity to investigate the shared genetic origin (pleiotropy) of hundreds to thousands of related phenotypes. However,…
There is a growing trend of applying machine learning methods to medical datasets in order to predict patients' future status. Although some of these methods achieve high performance, challenges still exist in comparing and evaluating…
The linking genotype to phenotype is the fundamental aim of modern genetics. We focus on study of links between gene expression data and phenotype data through integrative analysis. We propose three approaches. 1) The inherent complexity of…
Quite generally, constraint-based metabolic flux analysis describes the space of viable flux configurations for a metabolic network as a high-dimensional polytope defined by the linear constraints that enforce the balancing of production…
Dynamic graph visualization attracts researchers' concentration as it represents time-varying relationships between entities in multiple domains (e.g., social media analysis, academic cooperation analysis, team sports analysis). Integrating…
We present an algorithmic and visual grouping of participants and eye-tracking metrics derived from recorded eye-tracking data. Our method utilizes two well-established visualization concepts. First, parallel coordinates are used to provide…
The use of networks to integrate different genetic, proteomic, and metabolic datasets has been proposed as a viable path toward elucidating the origins of specific diseases. Here we introduce a new phenotypic database summarizing…
Automated phenotyping of plants for breeding and plant studies promises to provide quantitative metrics on plant traits at a previously unattainable observation frequency. Developers of tools for performing high-throughput phenotyping are,…
Hematotoxicity, drug-induced damage to the blood-forming system, is a frequent side effect of cytotoxic chemotherapy and poses a significant challenge in clinical practice due to its high inter-patient variability and limited…
The vast majority of connections between complex disease and common genetic variants were identified through meta-analysis, a powerful approach that enables large samples sizes while protecting against common artifacts due to population…
Information Visualization (InfoVis) systems utilize visual representations to enhance data interpretation. Understanding how visual attention is allocated is essential for optimizing interface design. However, collecting Eye-tracking (ET)…
The central nervous system is composed of many individual units -- from cells to areas -- that are connected with one another in a complex pattern of functional interactions that supports perception, action, and cognition. One natural and…
In the rapidly evolving field of metabolic engineering, the quest for efficient and precise gene target identification for metabolite production enhancement presents significant challenges. Traditional approaches, whether knowledge-based or…
We propose a method called integrated diffusion for combining multimodal datasets, or data gathered via several different measurements on the same system, to create a joint data diffusion operator. As real world data suffers from both local…
Variable importance, interaction measures, and partial dependence plots are important summaries in the interpretation of statistical and machine learning models. In this paper we describe new visualization techniques for exploring these…
Modern display environments offer great potential for involving multiple users in presentations, discussions, and data analysis sessions. By showing multiple views on multiple displays, information exchange can be improved, several…
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…
Metabolomic data can potentially enable accurate, non-invasive and low-cost prediction of coronary artery disease. Regression-based analytical approaches however might fail to fully account for interactions between metabolites, rely on a…