Jan Aerts
KU Leuven, Department of Electrical Engineering (ESAT), Faculty Member
Research Interests:
This work presents a joint spatial modeling framework to improve estimation of the spatial distribution of the latent COVID‐19 incidence in Belgium, based on test‐confirmed COVID‐19 cases and crowd‐sourced symptoms data as reported in a... more
This work presents a joint spatial modeling framework to improve estimation of the spatial distribution of the latent COVID‐19 incidence in Belgium, based on test‐confirmed COVID‐19 cases and crowd‐sourced symptoms data as reported in a large‐scale online survey. Correction is envisioned for stochastic dependence between the survey's response rate and spatial COVID‐19 incidence, commonly known as preferential sampling, but not found significant. Results show that an online survey can provide valuable auxiliary data to optimize spatial COVID‐19 incidence estimation based on confirmed cases in situations with limited testing capacity. Furthermore, it is shown that an online survey on COVID‐19 symptoms with a sufficiently large sample size per spatial entity is capable of pinpointing the same locations that appear as test‐confirmed clusters, approximately 1 week earlier. We conclude that a large‐scale online study provides an inexpensive and flexible method to collect timely inform...
Research Interests:
Background COVID-19 mortality, excess mortality, deaths per million population (DPM), infection fatality ratio (IFR) and case fatality ratio (CFR) are reported and compared for many countries globally. These measures may appear objective,... more
Background COVID-19 mortality, excess mortality, deaths per million population (DPM), infection fatality ratio (IFR) and case fatality ratio (CFR) are reported and compared for many countries globally. These measures may appear objective, however, they should be interpreted with caution. Aim We examined reported COVID-19-related mortality in Belgium from 9 March 2020 to 28 June 2020, placing it against the background of excess mortality and compared the DPM and IFR between countries and within subgroups. Methods The relation between COVID-19-related mortality and excess mortality was evaluated by comparing COVID-19 mortality and the difference between observed and weekly average predictions of all-cause mortality. DPM were evaluated using demographic data of the Belgian population. The number of infections was estimated by a stochastic compartmental model. The IFR was estimated using a delay distribution between infection and death. Results In the study period, 9,621 COVID-19-relate...
Research Interests:
Visual biases and more generally cognitive biases are a part of human life. Often to the frustration of the rational decision makers we aspire to be. Research into these biases has sparked a recent burst in interest, and more and more... more
Visual biases and more generally cognitive biases are a part of human life. Often to the frustration of the rational decision makers we aspire to be. Research into these biases has sparked a recent burst in interest, and more and more people are aware of possible pitfalls. In this paper, we argue that the consequences of biases during data analysis have to be considered rather than the occurrences themselves. In applying this, we distinguish between (visual) analysis for exploration and validation. Especially the latter turns out to be hard in some cases, indicated by a qualitative measure we call validation cost. Examples are provided of situations with a high validation cost and the role of visualization is discussed in these cases. For cases with a low validation cost, we argue that biases leading to false positives are far better than trying to avoid biases and ending up with false negatives.
Research Interests:
Research Interests:
Today location information on aircraft and vessels is collected worldwide and readily available to analysts. When analyzing such data for a large area or a long period of time, the sheer size of the dataset becomes a challenge. Especially... more
Today location information on aircraft and vessels is collected worldwide and readily available to analysts. When analyzing such data for a large area or a long period of time, the sheer size of the dataset becomes a challenge. Especially when one wants to work interactively at both overview and detail scales. We present a scalable approach to visualize such data by treating it as a set of trajectories simplified at different error rates. When combined with tiling and GPU-based visualization, we can interactively and visually analyze a dataset of 1 billion position records on a workstation.
Research Interests:
Research on the microbiome has boomed recently, which resulted in a wide range of tools, packages, and algorithms to analyze microbiome data. Here we investigate and map currently existing tools that can be used to perform visual analysis... more
Research on the microbiome has boomed recently, which resulted in a wide range of tools, packages, and algorithms to analyze microbiome data. Here we investigate and map currently existing tools that can be used to perform visual analysis on the microbiome, and associate the including methods, visual representations and data features to the research objectives currently of interest in microbiome research. The analysis is based on a combination of a literature review and workshops including a group of domain experts. Both the reviewing process and workshops are based on domain characterization methods to facilitate communication and collaboration between researchers from different disciplines. We identify several research questions related to microbiomes, and describe how different analysis methods and visualizations help in tackling them.
Research Interests:
Different genomic resources in chicken were integrated through the Wageningen chicken BAC library. First, a BAC anchor map was created by screening this library with two sets of markers: microsatellite markers from the consensus linkage... more
Different genomic resources in chicken were integrated through the Wageningen chicken BAC library. First, a BAC anchor map was created by screening this library with two sets of markers: microsatellite markers from the consensus linkage map and markers created from BAC end sequencing in chromosome walking experiments. Second, Hin dIII digestion fingerprints were created for all BACs of the Wageningen chicken BAC library. Third, cytogenetic positions of BACs were assigned by FISH. These integrated resources will facilitate further chromosome-walking experiments and whole-genome sequencing.
Research Interests:
Research Interests: Biology()
()
Research Interests:
Precision medicine as a framework for disease diagnosis, treatment, and prevention at the molecular level has entered clinical practice. From the start, genetics has been an indispensable tool to understand and stratify the biology of... more
Precision medicine as a framework for disease diagnosis, treatment, and prevention at the molecular level has entered clinical practice. From the start, genetics has been an indispensable tool to understand and stratify the biology of chronic and complex diseases in precision medicine. However, with the advances in biomedical and omics technologies, quantitative proteomics is emerging as a powerful technology complementing genetics. Quantitative proteomics provide insight about the dynamic behaviour of proteins as they represent intermediate phenotypes. They provide direct biological insights into physiological patterns, while genetics accounting for baseline characteristics. Additionally, it opens a wide range of applications in clinical diagnostics, treatment stratification, and drug discovery. In this mini-review, we discuss the current status of quantitative proteomics in precision medicine including the available technologies and common methods to analyze quantitative proteomic...
Research Interests:
Research Interests:
Although COVID-19 has been spreading throughout Belgium since February, 2020, its spatial dynamics in Belgium remain poorly understood, due to the limited testing of suspected cases. We analyse data of COVID-19 symptoms, as self-reported... more
Although COVID-19 has been spreading throughout Belgium since February, 2020, its spatial dynamics in Belgium remain poorly understood, due to the limited testing of suspected cases. We analyse data of COVID-19 symptoms, as self-reported in a weekly online survey, which is open to all Belgian citizens. We predict symptoms' incidence using binomial models for spatially discrete data, and we introduce these as a covariate in the spatial analysis of COVID-19 incidence, as reported by the Belgian government during the days following a survey round. The symptoms' incidence predictions explain a significant proportion of the variation in the relative risks based on the confirmed cases, and exceedance probability maps of the symptoms' incidence and the confirmed cases' relative risks pinpoint the same high-risk region. We conclude that these results can be used to develop public monitoring tools in scenarios with limited lab testing capacity, and to supplement test-based in...
Research Interests:
ObjectiveScrutiny of COVID-19 mortality in Belgium over the period 8 March – 9 May 2020 (Weeks 11-19), using number of deaths per million, infection fatality rates, and the relation between COVID-19 mortality and excess death... more
ObjectiveScrutiny of COVID-19 mortality in Belgium over the period 8 March – 9 May 2020 (Weeks 11-19), using number of deaths per million, infection fatality rates, and the relation between COVID-19 mortality and excess death rates.DataPublicly available COVID-19 mortality (2020); overall mortality (2009 – 2020) data in Belgium and demographic data on the Belgian population; data on the nursing home population; results of repeated sero-prevalence surveys in March-April 2020.Statistical methodsReweighing, missing-data handling, rate estimation, visualization.ResultsBelgium has virtually no discrepancy between COVID-19 reported mortality (confirmed and possible cases) and excess mortality. There is a sharp excess death peak over the study period; the total number of excess deaths makes April 2020 the deadliest month of April since WWII, with excess deaths far larger than in early 2017 or 2018, even though influenza-induced January 1951 and February 1960 number of excess deaths were si...
Research Interests:
Research Interests:
Single-cell RNA-seq allows building cell atlases of any given tissue and infer the dynamics of cellular state transitions during developmental or disease trajectories. Both the maintenance and transitions of cell states are encoded by... more
Single-cell RNA-seq allows building cell atlases of any given tissue and infer the dynamics of cellular state transitions during developmental or disease trajectories. Both the maintenance and transitions of cell states are encoded by regulatory programs in the genome sequence. However, this regulatory code has not yet been exploited to guide the identification of cellular states from single-cell RNA-seq data. Here we describe a computational resource, called SCENIC (Single Cell rEgulatory Network Inference and Clustering), for the simultaneous reconstruction of gene regulatory networks (GRNs) and the identification of stable cell states, using single-cell RNA-seq data. SCENIC outperforms existing approaches at the level of cell clustering and transcription factor identification. Importantly, we show that cell state identification based on GRNs is robust towards batch-effects and technical-biases. We applied SCENIC to a compendium of single-cell data from the mouse and human brain a...
Research Interests: Computer Science, Algorithms, Technology, Computational Biology, Biology, and 14 moreInference, Biological Sciences, Single cell analysis, Brain, Humans, Mice, Animals, Cell, Cluster Analysis, Gene Regulatory Networks, Transcription Factor, Compendium, Gene expression profiling, and Medical and Health Sciences
The identification of disease-causing genes in Mendelian disorders has been facilitated by the detection of rare disease-causing variation through exome sequencing experiments. These studies rely on population databases to filter a... more
The identification of disease-causing genes in Mendelian disorders has been facilitated by the detection of rare disease-causing variation through exome sequencing experiments. These studies rely on population databases to filter a majority of the putatively neutral variation in the genome and additional filtering steps using either cohorts of diseased individuals or familial information to narrow down the list of candidate variants. Recently, new computational methods have been proposed to prioritize variants by scoring them not only based on their potential impact on protein function but also on their relevance given the available information on the disease under study. Usually these diseases comprise several phenotypic presentations, which are separately prioritized and then aggregated into a global score. In this study we compare several simple (e.g. maximum and mean score) and more complex aggregation methods (e.g. order statistics, parametric modeling) in order to obtain the b...
Research Interests:
The Cosmopolitan Chicken Project is an artistic undertaking of renowned artist Koen Vanmechelen. In this project, the artist interbreeds domestic chickens from different countries aiming at the creation of a true Cosmopolitan Chicken as a... more
The Cosmopolitan Chicken Project is an artistic undertaking of renowned artist Koen Vanmechelen. In this project, the artist interbreeds domestic chickens from different countries aiming at the creation of a true Cosmopolitan Chicken as a symbol for global diversity. The unifying theme is the chicken and the egg, symbols that link scientific, political, philosophical and ethical issues. The Cosmopolitan Chicken Research Project is the scientific component of this artwork. Based on state of the art genomic techniques, the project studies the effect of the crossing of chickens on the genetic diversity. Also, this research is potentially applicable to the human population. The setup of the CC®P is quite different from traditional breeding experiments: starting from the crossbreed of two purebred chickens (Mechelse Koekoek x Poule de Bresse), every generation is crossed with a few animals from another breed. For 26 of these purebred and crossbred populations, genetic diversity was measu...
Research Interests: Biology, Medicine, Genetic Diversity, Population, Pubmed, and 2 moreBreed and Crossbreed(Breed and Crossbreed)
(Breed and Crossbreed)
Research Interests:
Research Interests:
Theoretical part of visualisation course.
Research Interests:
<b>Copyright information:</b>Taken from "Whole genome linkage disequilibrium maps in cattle"http://www.biomedcentral.com/1471-2156/8/74BMC Genetics 2007;8():74-74.Published online 25 Oct 2007PMCID:PMC2174945.parent... more
<b>Copyright information:</b>Taken from "Whole genome linkage disequilibrium maps in cattle"http://www.biomedcentral.com/1471-2156/8/74BMC Genetics 2007;8():74-74.Published online 25 Oct 2007PMCID:PMC2174945.parent were used.
High-throughput and high-resolution experimental methods in biology pose enormous challenges for cur-rent biological data visualization approaches. To address these challenges, researchers in the visualization and bioinformatics... more
High-throughput and high-resolution experimental methods in biology pose enormous challenges for cur-rent biological data visualization approaches. To address these challenges, researchers in the visualization and bioinformatics communities need to engage in the design, implementation, application, and evaluation of novel visualization techniques and tools that provide insight into large and highly complex data sets. BioVis 2015- the fifth Symposium on Biological Data Visualization- brought together researchers from the visualization, bioinformatics, and biology communities to establish an interdisciplinary dialogue and promote the sharing of expertise between both meeting participants and the communities at large. The meeting educated, inspired, and engaged visualization researchers in pro-blems in biological data visualization as well as bioinfor-matics and biology researchers in state-of-the-art visualization research. The symposium serves as a plat-form for researchers from thes...
With InVITe, we are working towards intuitive visualization to support review of iterative modifications on text documents. In order to accomplish this, we perform simple matching of text snippets between the two versions of text, across... more
With InVITe, we are working towards intuitive visualization to support review of iterative modifications on text documents. In order to accomplish this, we perform simple matching of text snippets between the two versions of text, across a large range of parameter settings. Next, an overview graphic indicating the effect of parameter space on the output allows the user to select those combinations that are of interest. Finally, such selection will display an alluvial diagram with annotations and covering different resolutions. With this tool, co-authors can keep an overview of changes made, both structural and local.
Research Interests:
Research Interests:
Research Interests:
Research Interests:
Research Interests:
Research Interests:
Research Interests:
Discussions and detailed methods directly cited in the main paper; supplementary references; supplementary tables; supplementary figure legends. Format: PDF Size: 360KB
Research Interests:
An interactive visualisation tool (Aracari) was developed to analyze eQTL data. Aracari consists of two linked viewing modes: a gene expression view and a SNP view. An eQTL data set with spiked-in simulated data was provided by the... more
An interactive visualisation tool (Aracari) was developed to analyze eQTL data. Aracari consists of two linked viewing modes: a gene expression view and a SNP view. An eQTL data set with spiked-in simulated data was provided by the BioVis2012 visualisation contest and analyzed by a non-domain expert; the results were assessed against the list of known spiked-in signals. Using this visualization tool, we were able to identify nine genes relevant to a disease while the defacto-standard biological experts eQTL toolkit (PLINK) ...
KULeuven. ...
Research Interests:
This tutorial describes how to use the Ruby API to the Ensembl Core and Variation databases. It is intended as an introduction and demonstration of the general API concepts. This tutorial is not comprehensive, but it will hopefully enable... more
This tutorial describes how to use the Ruby API to the Ensembl Core and Variation databases. It is intended as an introduction and demonstration of the general API concepts. This tutorial is not comprehensive, but it will hopefully enable to reader to become productive quickly, and facilitate a rapid understanding of the underlying systems. This tutorial assumes at least some familiarity with Ruby. It is the first of a three-part-tutorial: overview of the Ruby API system, installation and a minimal script (= part 1); the API to the ...
Research Interests: Bioinformatics, Computer Science, Information Retrieval, Ontology, Visualization, and 15 moreSemantic Web, Knowledge Representation, Medicine, Databases, Data Integration, Software, Semantic Interoperability, Data Science, Integration, Data Sharing, Gene, Data Models, Sequences, Glycomics, and Metabolic Pathways
Research Interests:
Research Interests:
Dendrograms are graphical representations of binary tree structures resulting from agglomerative hierarchical clustering. In Life Science, a cluster heat map is a widely accepted visualization technique that utilizes the leaf order of a... more
Dendrograms are graphical representations of binary tree structures resulting from agglomerative hierarchical clustering. In Life Science, a cluster heat map is a widely accepted visualization technique that utilizes the leaf order of a dendrogram to reorder the rows and columns of the data table. The derived linear order is more meaningful than a random order, because it groups similar items together. However, two consecutive items can be quite dissimilar despite proximity in the order. In addition, there are 2n-1 possible orderings given n input elements as the orientation of clusters at each merge can be flipped without affecting the hierarchical structure. We present two modular leaf ordering methods to encode both the monotonic order in which clusters are merged and the nested cluster relationships more faithfully in the resulting dendrogram structure. We compare dendrogram and cluster heat map visualizations created using our heuristics to the default heuristic in R and seriat...
Research Interests:
BioHackathon 2010 was the third in a series of meetings hosted by the Database Center for Life Sciences (DBCLS) in Tokyo, Japan. The overall goal of the BioHackathon series is to improve the quality and accessibility of life science... more
BioHackathon 2010 was the third in a series of meetings hosted by the Database Center for Life Sciences (DBCLS) in Tokyo, Japan. The overall goal of the BioHackathon series is to improve the quality and accessibility of life science research data on the Web by bringing together representatives from public databases, analytical tool providers, and cyber-infrastructure researchers to jointly tackle important challenges in the area of in silico biological research. The theme of BioHackathon 2010 was the…
Research Interests:
The interaction between biological researchers and the bioinformatics tools they use is still hampered by incomplete interoperability between such tools. To ensure interoperability initiatives are effectively deployed, end-user... more
The interaction between biological researchers and the bioinformatics tools they use is still hampered by incomplete interoperability between such tools. To ensure interoperability initiatives are effectively deployed, end-user applications need to be aware of, and support, best practices and standards. Here, we report on an initiative in which software developers and genome biologists came together to explore and raise awareness of these issues: BioHackathon 2009. Developers in attendance came from diverse backgrounds, with experts in Web services, workflow tools, text mining and visualization. Genome biologists provided expertise and exemplar data from the domains of sequence and pathway analysis and glyco-informatics. One goal of the meeting was to evaluate the ability to address real world use cases in these domains using the tools that the developers represented. This resulted in i) a workflow to annotate 100,000 sequences from an invertebrate species; ii) an integrated system ...
Research Interests:
Origins of the chicken genome consortium; historical background for the genome including evolution, domestication and natural history, and agricultural relevance; implications for human and chicken biology. Format: PDF Size: 360KB
A survey of genetic diversity of cattle suggests two domestication events in Asia and selection by husbandry.