For the official list, see the KU Leuven database.

• Heylen D, Peeters J, Aerts J, Ertaylan G & Hooyberghs J
  BioMOBS: A multi-omics visual analytics workflow for biomolecular insight generation
  PLoS One 18(12):e0295361 (2023)
  


• Kafetzaki D, Poblome J & Aerts J
  Fuzzy Typological (Re)Arrangement - A Prototype of Rethinking the Typology of Roman Tablewares from Sagalassos, Southwest Anatolia.
  Journal of Archaeological Method and Theory (2023)
  


• Bach B, Keck M, Rajabiyazdi F, et al.
  Challenges and Opportunities in Data Visualization Education - A Call to Action
  arXiv (2023)
  


• Bot DM, Peeters J & Aerts J
  The Challenge of Branch-Aware Data Manifold Exploration
  EuroVIS 2023 (2023)
  


• Vranckx M, Faes C, Molenberghs G et al
  A Spatial Model to Jointly Analyze Self-reported Survey Data of COVID-19 Symptoms and Official COVID-19 Incidence Data
  Biometrical Journal 65(1):2100186 (2023)
  


• Klein K, Marai GE, Nieselt KK & Zupan B
  Visualization of Biological Data - From Analysis to Communication (Dagstuhl Seminar 21401)
  (2022)
  


• Aerts J, Aigner W, Bach B et al
  Me-ifestos for visualization empowerment in teaching (and learning?)
  In Alt.Vis 2022 (9) (2022)
  


• Vranckx M, Faes C, Molenberghs G, Hens N, Beutels P, Van Damme P, Aerts J & Petrof O
  A Joint Spatial Model to Analyse Self-Reported Survey Data of COVID-19 Symptoms and Lagged Surveillance-Based COVID-19 Incidence Data
  Biometrical Journal (2022)
  


• Panagiotidou G, Poblome J, Aerts J & Vande Moere A
  Designing a Data Visualisation for Interdisciplinary Scientists. How to Transparently Convey Data Frictions?
  Computer Supported Cooperative Work (CSCW) 31(4): 633-667 (2022)
  


• Bot DM, Peeters J & Aerts J
  EProM - Exploration of Protein Modifications
  Bio+MedVis @IEEE VIS 2022 (2022)
  


• Kyndt E & Aerts J
  Addressing 'Wicked Problems' Using Visual Analysis.
  In: Goller M et al (eds) Methods for Researching Professional Learning and Development. Professional and Practice-based Learning, vol 33. Springer, Cham. (2022)
  


• Molenberghs G et al
  COVID-19 Mortality, Excess Mortality, Deaths per Million and Infection Fatality Ratio, Belgium, 9 March 2020 to 28 June 2020.
  Eurosurveillance 27 (7) (2022)
  


• Peeters J, Thas O, Shkedy Z, Kodalci L et al.
  Exploring the Microbiome Analysis and Visualization Landscape
  Frontiers in Bioinformatics (2021)
  


• Bot DM, Peeters J, Kafetzaki D & Aerts J
  Human-in-the-Loop Integration of Complex and Noisy Data (VAST MC2)
  (2021)
  


• Aerts J, Peeters J, Bot J, Kafetzaki D & Lamqaddam H
  Remote Instruction for Data Visualization Design - A Report From the Trenches
  IEEE Computer Graphics and Applications (2021)
  


• Alcaide D & Aerts J
  Spanning Trees as Approximation of Data Structures
  IEEE Transactions on Visualization and Computer 27(10): 3994-4008 (2021)
  


• Correa Rojo A, Heylen D, Aerts J, Thas O, Hooyberghs J, Ertaylan G & Valkenborg D
  Towards building a quantitative proteomics toolbox in precision medicine: a mini-review
  Front Physiol 12:723510 (2021) (2021)
  


• Alcaide D, Aerts J.
  A visual analytic approach for the identification of ICU patient subpopulations using ICD diagnostic codes
  PeerJ Computer Science 7:e430 (2021)
  


• Neyens N et al.
  Can COVID-19 symptoms as reported in a large-scale online survey be used to optimise spatial predictions of COVID-19 incidence risk in Belgium?
  Spatial and Spatio-temporal Epidemiology, 35:100379 (2020)
  


• Panagiotidou G, Aerts J & Vande Moere A
  GoCo: A Gamified Activity for Winnowing Visualization Projects with Interdisciplinary Experts
  IEEE VIS Workshop on Data Vis Activities (2020)
  


• Molenberghs G et al.
  Belgian COVID-19 mortality, excess deaths, number of deaths per million, and infection fatality rates (8 March - 9 May 2020)
  Preprint at https://doi.org/10.1101/2020.06.20.20136234 (2020)
  


• Papadimitriou S, Gazzo A, Versbraegen N, Nachtegael C, Aerts J et al.
  Predicting disease-causing variant combinations
  Proceedings of the National Academy of Sciences 116(24):11878-11887 (2019)
  


• Ardeshirdavani A, Zamani Esteki M, Alcaide D, Masset H, Ding J, Sifrim A, Aerts J, Voet T, Moreau Y & Vermeesch J
  HiVA: a web platform for haplotyping and copy number analysis of single-cell genomes
  Proceedings of the European Human Genetics Conference, Gothenburg, Sweden, 16P.37A p (2019)
  


• Brosens K, Aerts J, Alen K et al.
  Slow Digital Art History in Action: Project Cornelia’s Computational Approach to Seventeenth-century Flemish Creative Communities
  Visual Resources 1-20 (2019)
  


• Knudsen S, Aerts J, Archambault D, et al.
  Unifying the framework of Multi-Layer Network and Visual Analytics
  Dagstuhl Reports 9(2):19-23 (2019)
  


• Faria R, Triant D, Perdomo-Sabogal A, Overduin B, Bleidorn C, Isabel Bermudez Santana C, Langenberger D, Marco Dall’Olio G, Indrischek H, Aerts J, Engelhardt J, Engelken J, Liebal K, Fasold M, Robb S, Grath S, Raj Kolora SR, Carvalho T, Salzburger W, Jovanovic V & Nowick K
  Introducing evolutionary biologists to the analysis of big data: guidelines to organize extended bioinformatics training courses
  Evolution: Education and Outreach, 11:8 (2018)
  


• Moerman T, Aibar Santos S, Bravo González-Blas C, Simm J, Moreau Y, Aerts J & Aerts S
  GRNBoost2 and Arboreto: efficient and scalable inference of gene regulatory networks
  Bioinformatics (2018)
  


• Lamqaddam H, Aerts J, Brosens K & Verbert K
  NAHR: a visual representation of social networks as support for art history research
  Proceedings of the 10th Nordic Conference on Human-Computer Interaction: 634-641 (2018)
  


• Alcaide D & Aerts J
  MCLEAN: Multilevel Clustering Exploration As Network
  PeerJ Computer Science 4:e145 (2018)
  


• Aerts J, Gehlenborg N, Marai GE & Nieselt KK
  Visualization of Biological Data - Crossroads (Dagstuhl Seminar 18161)
  Dagstuhl Reports 8(4):32-71 (2018)
  


• Brosens K, Aerts J, Alen K, Beerens RJ, Cardoso B, De Prekel I, Ivanova A, Lamqaddam H, Molenberghs G, Slegten A, Truyen F, Van der Stighelen K & Verbert K
  Slow Digital Art History in Action: Project Cornelia’s Computational Approach to Seventeenth-century Flemish Creative Communities
  Visual Resources 35 (2018)
  


• Kyndt E & Aerts J
  Op maat matchen, een wicked probleem dat een innovatieve aanpak vraagt
  Leren Duaal Leren. Dekocker V. & Sodermans A.K. (Red.); Leuven: Acco (2018)
  


• Aibar S, Bravo González-Blas C, Moerman T, Imrichova H, Hulselmans G, Rambow F, Marine JC, Geurts P, Aerts J, van den Oord J, Kalender Atak Z, Wouters J & Aerts S
  SCENIC: single-cell regulatory network inference and clustering
  Nature Methods 14(11):1083 (2017)
  


• Brosens K, Aerts J, Alen K, Slegten A & Truyen F
  Visualizing and Analyzing Complex and Dynamic Networks of Flemish Tapestry Entrepreneurs (1640–1720)
  Leonardo 50(5):503 (2017)
  


• Brosens K, Aerts J, Alen K, Slegten A & Truyen F
  Visualizing and Analyzing Complex and Dynamic Networks of Flemish Tapestry Entrepreneurs (1640–1720)
  Leonardo - Art, Science and Technology, 49 (2), art.nr. 10.1162/LEON_a_01276 (2016)
  


• Lamqaddam H & Aerts J
  InVITe - Towards Intuitive Visualization of Iterations over Text
  Eurographics Conference on Visualization (EuroVis) Posters Track (2016)
  


• Tranchevent LC, Ardeshirdavani A, ElShal S, Alcaide D, Aerts J, Auboeuf D & Moreau Y
  Candidate gene prioritization with Endeavour
  Nucleic Acids Research 44:117-121 (2016)
  


• Alcaide D, Thiyagarajan J, Lamqaddam H, Nualart J & Aerts J
  Visual Anomaly Detection in Spatio-Temporal Data using Element-Specific References
  VAST Challenge (2016)
  


• Aerts J et al
  Highlights from the 5th Symposium on Biological Data Visualization: Part 2.
  BMC Bioinformatics 16(Suppl 11): S1 (2015)
  


• Chua A, Sakai R, Aerts J & Vande Moere A
  A three step process to design visualisations for GeoTemporal analysis
  IEEE Conference on Visual Analytics Science and Technology, VAST 2014 - Proceedings: 349–350 (2014)
  


• Winand R et al
  Assessing transmissibility of HIV-1 drug resistance mutations from treated and from drug-naive individuals
  Aids 29(15): 2045–2052 (2015)
  


• Verbeiren T & Aerts J
  A pragmatic approach to biases in visual data analysis
  DECISIVe : Workshop on Dealing with Cognitive Biases in Visualisations, IEEE VIS2014 (2014)
  


• Sakai R & Aerts J
  Card sorting techniques for domain characterization in problem-driven visualization research
  Eurographics Conference on Visualization (EuroVis) (2015)
  


• Sakai R & Aerts J
  Sequence Diversity Diagram for Comparative Analysis of Multiple Sequence Alignments.
  BMC Proceedings 8: S9 (2014)
  


• Pougach K, Voet A, Kondrashov F, Voordeckers K, Christiaens JF, Baying B, Benes V et al
  Duplication of a Promiscuous Transcription Factor Drives the Emergence of a New Regulatory Network.
  Nature Communications 5 (January): 4868 (2014)
  


• Sakai R, Winand R, Verbeiren T, Vande Moere A & Aerts J
  Dendsort: Modular Leaf Ordering Methods for Dendrogram Representations in R.
  F1000Research 3 (January): 177 (2014)
  


• Winand R, Hens K, Dondorp W, De Wert G, Moreau Y, Vermeesch JR, Liebaers I & Aerts J
  In Vitro Screening of Embryos by Whole-Genome Sequencing : Now, in the Future or Never ?
  Hum Reprod 29(4):842-851 (2014)
  


• Pavlopoulos GA, Kumar P, Sifrim A, Sakai R, Lin ML, Voet T, Moreau Y & Aerts J
  Meander: Visually Exploring the Structural Variome Using Space-Filling Curves.
  Nucleic Acids Research (11) (April 19): 1–9 (2013)
  


• Sakai R, Moisse M, Reumers J & Aerts J
  Pipit: Visualizing Functional Impacts of Structural Variations.
  Bioinformatics (Oxford, England) 29 (17) (September 1): 2206–2207 (2013)
  


• Pavlopoulos G, Oulas A, Iacucci E, Sifrim A, Moreau Y, Schneider R, Aerts J & Iliopoulos I
  Unraveling genomic variation from next generation sequencing data
  BioData Mining, 6 (13), 1-25 (2013)
  


• Sakai R, Sifrim A, Vande Moere A & Aerts J
  TrioVis: A Visualisation Approach for Filtering Genomic Variants of Parent-Child Trios.
  Bioinformatics (Oxford, England) (May 8): 2–3 (2013)
  


• Sifrim A, Popovic D, Tranchevent LC, Ardeshirdavani A, Sakai R, Konings P, Vermeesch JR, Aerts J, De Moor B & Moreau Y
  eXtasy: Variant Prioritization by Genomic Data Fusion.
  Nature Methods 10 (11) (November): 1083–1084 (2013)
  


• Bartlett CW, Cheong SY, Hou L, Paquette J, Lum PY, Jaeger G, Battke F et al
  An eQTL Biological Data Visualization Challenge and Approaches from the Visualization Community.
  BMC Bioinformatics 13 Suppl 8 (Suppl 8) (January): S8 (2012)
  


• Bonnal RJP, Aerts J, Githinji G, Goto N, Maclean D, Miller CA, Mishima H et al
  Biogem : An Effective Tool Based Approach for Scaling up Open Source Software Development in Bioinformatics.
  Bioinformatics: 28(7):1035-1037 (2012)
  


• Johansson S, Irgens H, Chudasama KK, Molnes J, Aerts J, Roque FS, Jonassen I et al
  Exome Sequencing and Genetic Testing for MODY.
  PloS One 7 (5) (January): e38050 (2012)
  


• Sifrim A, Van Houdt JK, Tranchevent LC, Nowakowska B, Sakai R, Pavlopoulos GA, Devriendt K, Vermeesch JR, Moreau Y & Aerts J
  Annotate-It: A Swiss-Knife Approach to Annotation, Analysis and Interpretation of Single Nucleotide Variation in Human Disease.
  Genome Medicine 4 (9) (September 26): 73 (2011)
  


• Katayama T, Wilkinson MD, Vos R, Kawashima T, Kawashima S, Nakao M, Yamamoto Y et al
  The 2nd DBCLS BioHackathon: Interoperable Bioinformatics Web Services for Integrated Applications.
  Journal of Biomedical Semantics 2 (1) (August 2): 4 (2011)
  


• Moschopoulos CN, Pavlopoulos GA, Iacucci E, Aerts J, Likothanassis S, Schneider R & Kossida S
  Which Clustering Algorithm Is Better for Predicting Protein Complexes?
  BMC Research Notes 4 (1) (December 20): 549 (2011)
  


• Pavlopoulos GA, Hooper SD, Sifrim A, Schneider R & Aerts J
  Medusa: A Tool for Exploring and Clustering Biological Networks.
  BMC Research Notes 4 (1) (January): 384 (2011)
  


• Pavlopoulos GA, Secrier M, Moschopoulos CN, Soldatos TG, Kossida S, Aerts J, Schneider R & Bagos Pantelis
  Using Graph Theory to Analyze Biological Networks.
  BioData Mining 4 (1): 10 (2011)
  


• Strozzi F & Aerts J
  A Ruby API to Query the Ensembl Database for Genomic Features.
  Bioinformatics (Oxford, England) (January): 1–2 (2011)
  


• Conrad DF, Pinto D, Redon R, Feuk L, Gokcumen O, Zhang Y, Aerts J, et al
  Origins and Functional Impact of Copy Number Variation in the Human Genome.
  Nature 464 (April): 704–712 (2010)
  


• Goto N, Prins P, Nakao M, Bonnal R, Aerts J & Katayama T
  BioRuby: Bioinformatics Software for the Ruby Programming Language.
  Bioinformatics 26 (20) (August): 2617–2619 (2010)
  


• Kalay E, Yigit G, Aslan Y, Brown KE, Pohl E, Bicknell LS, Kayserili H et al
  CEP152 Is a Genome Maintenance Protein Disrupted in Seckel Syndrome.
  Nature Genetics 43 (1) (December): 23–26 (2010)
  


• The DBCLS BioHackathon Consortium
  The DBCLS BioHackathon: Standardization and Interoperability for Bioinformatics Web Services and Workflows.
  Journal of Biomedical Semantics (2010)
  


• The Wellcome Trust Case Control Consortium
  Genome-Wide Association Study of CNVs in 16,000 Cases of Eight Common Diseases and 3,000 Shared Controls.
  Nature 464 (7289): 713–720 (2010)
  


• Aerts J & Tyler-Smith C
  Structural Variation in Great Ape Genomes.
  In: Encyclopedia of Life Sciences (2009)
  


• Aerts J & Law A
  An Introduction to Scripting in Ruby for Biologists.
  BMC Bioinformatics 10: 221 (2009)
  


• Connelley T, Aerts J, Law A, and Morrison WI
  Genomic Analysis Reveals Extensive Gene Duplication within the Bovine TRB Locus.
  BMC Genomics 10 (January): 192 (2009)
  


• Elsik CG, Tellam RL, Gibbs RA, Worley KC, Muzny DM, Weinstock GM, Adelson DL et al
  The Genome Sequence of Taurine Cattle: A Window to Ruminant Biology and Evolution.
  Science 324 (5926): 522–528 (2009)
  


• Gibbs RA, Taylor JF, Van Tassell CP, Barendse W, Eversole KA, Gill CA, Green RD et al
  Genome-Wide Survey of SNP Variation Uncovers the Genetic Structure of Cattle Breeds.
  Science 324 (5926): 528–532 (2009)
  


• McKay SD, Schnabel RD, Murdoch BM, Matukumalli LK, Aerts J, Coppieters W, Crews D et al
  An Assessment of Population Structure in Eight Breeds of Cattle Using a Whole Genome SNP Panel.
  BMC Genetics 9 (January): 37 (2008)
  


• Taylor DF, Field D, Sansone SA, Aerts J, Apweiler R, Ashburner M, Ball CA et al
  Promoting Coherent Minimum Reporting Guidelines for Biological and Biomedical Investigations: The MIBBI Project.
  Nature Biotechnology 26 (8) (August): 889–96 (2008)
  


• Aerts J, Megens HJ, Veenendaal T, Ovcharenko I, Crooijmans R, Gordon L, Stubbs L & Groenen M
  Extent of Linkage Disequilibrium in Chicken.
  Cytogenetic and Genome Research (2007)
  


• McKay SD, Schnabel RD, Murdoch BM, Aerts J, Gill CA, Gao C, Li C et al
  Construction of Bovine Whole-Genome Radiation Hybrid and Linkage Maps Using High-Throughput Genotyping.
  Animal Genetics 38 (2) (April): 120–5 (2007)
  


• McKay SD, Schnabel RD, Murdoch BM, Matukumalli LK, Aerts J, Coppieters W, Crews D et al
  Whole Genome Linkage Disequilibrium Maps in Cattle.
  BMC Genetics 8: 74 (2007)
  


• Snelling WM, Chiu R, Schein JE, Hobbs M, Abbey CA, Adelson DL, Aerts J et al
  A Physical Map of the Bovine Genome
  Genome Biology 8 (8) (January): R165 (2007)
  


• Jann OC, Aerts J, Jones M, Hastings N, Law A, McKay S, Marques E et al
  A Second Generation Radiation Hybrid Map to Aid the Assembly of the Bovine Genome Sequence
  BMC Genomics 7 (January): 283 (2006)
  


• Aerts J, Veenendaal T, van der Poel JJ, Crooijmans RPMA & Groenen MAM
  Chromosomal Assignment of Chicken Clone Contigs by Extending the Consensus Linkage Map.
  Animal Genetics 36 (3) (June): 216–22 (2005)
  


• Aerts J, Jungerius BJ & Groenen MAM
  POSA: Perl Objects for DNA Sequencing Data Analysis.
  BMC Genomics 5 (1) (August): 60 (2003)
  


• International Chicken Genome Sequencing Consortium
  Sequence and Comparative Analysis of the Chicken Genome Provide Unique Perspectives on Vertebrate Evolution.
  Nature 432 (December): 695–777 (2004)
  


• Wallis JW, Aerts J, Groenen MAM, Crooijmans RPMA, Layman D, Graves TA, Scheer DE et al
  A Physical Map of the Chicken Genome.
  Nature 432 (December): 761–764 (2004)
  


• Aerts J, Crooijmans R, Cornelissen S, Hemmatian K, Veenendaal T, Jaadar A, Van Der Poel J, Fillon V, Vignal A & Groenen M
  Integration of Chicken Genomic Resources to Enable Whole-Genome Sequencing.
  Cytogenetic and Genome Research 303: 297–303 (2003)
  


• Aerts J, Wetzels Y, Cohen N & Aerssens J
  Data Mining of Public SNP Databases for the Selection of Intragenic SNPs.
  Human Mutation 20 (3) (September): 162–73 (2002)