• 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)

:: General media ::

  • De Standaard, 04/06/2014, “Je smartphone als dokter”
  • Aerts J. Enhancing genomic analysis through ICT and visualisation. Projects, Insight Publishers, p28-31 (2013)
  • Scheire, L. & Van Tendeloo, H. (2012) Wat cellen voorspellen: de genetica van de toekomst. Humo, 3725/04, 10-15