Ryo Sakai

Contact address:
Kasteelpark Arenberg 10, bus 2446, B-3001 Leuven, Belgium
office: 03.11
phone: +32 16 32 74 95


Biological Data Visualization: Analysis and Design


Data visualization is an integral part of biological sciences and essential to enable dissemination of knowledge and sophisticated analysis of data. With advances in both biological data acquisition technologies and data-management and -processing technologies, researchers face challenges of developing better conjectures from the data that continue to increase in volume and complexity. Consequently, such data analysis often requires interdisciplinary expertise to address challenges in each case. In this thesis, we examine the design process of visualization projects from a wide range of application domains. The discussion includes the descriptive explanation of intermediate iterations towards the final design solution. The existing visualization model and framework are extended to characterise the design space of biological data visualization. Also, a practical 4-step guideline for visualization design is provided as an actionable evaluation method of visualization design. Careful retrospective analysis of each design case reveals that data visualization is ubiquitous, highlighting its vital role at different stages of data-intensive science.


    Prof. dr. ir. H. Hens, chair
    Prof. dr. ir. J. Aerts, supervisor
    Prof. dr. ir. Y. Moreau
    Prof. dr. ir. arch. A. Vande Moere
    Prof. dr. ir. S. Aerts
    Prof. dr. ir. J. Raes
    Dr. ir. J. Reumers
    Prof. dr. ir. J. Kennedy


International Journal Papers

  1. Stinckens A., Vereijken A., Ons E., Konings P., Van As P., Cuppens H., Moreau Y., Sakai R., Aerts J., Goddeeris B., Buys N., Vanmechelen K., Cassiman J.J., "Art meets science : The cosmopolitan chicken research project", Facts and views Vs. Obgyn, vol. 7, no. 3, 2015, pp. 163-172.

  2. Pougach K., Voet A., Kondrashov F.A., Voordeckers K., Christaens J.F., Baying B., Benes V., Sakai R., Aerts J., Zhu B., Van Dijck P., Verstrepen K., "Duplication of a promiscuous transcription factor drives the emergence of a new regulatory network", Nature communications, vol. 5, Sep. 2014, pp. 1-11 (Art. Nb 4868).

  3. Sakai R., Winand R., Verbeiren T., Vande Moere A., Aerts J., "dendsort: modular leaf ordering methods for dendrogram representations in R", F1000Research, vol. 3, no. 177, Jul. 2014, pp. 1-13.

  4. Sakai R., Aerts J., "Sequence Diversity Diagram for comparative analysis of multiple sequence alignments", BMC Proceedings, vol. 8, no. Suppl 2, Aug. 2014, pp. S9.

  5. Sakai R., Moisse M., Reumers J., Aerts J., "Pipit: visualizing functional impacts of structural variations", Bioinformatics, vol. 29, no. 17, Sep. 2013, pp. 2206-2207.

  6. Sifrim A., Popovic D., Tranchevent L.-C., Ardeshirdavani A., Sakai R., Konings P., Vermeesch J., Aerts J., De Moor B., Moreau Y., "eXtasy: Variant Prioritization By Genomic Data Fusion", Nature Methods, vol. 10, no. 11, Sep. 2013, pp. 1083-1084.

  7. Sakai R., Sifrim A., Vande Moere A., Aerts J., "TrioVis: a visualization approach for filtering genomic variants of parent×£hild trios", Bioinformatics, vol. 29, no. 14, Jul. 2013, pp. 1801-1802.

  8. 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, vol. 41, no. 11, Jun. 2013, e118 p.

  9. Bartlett C., Cheong S., Hou L., Paquette J., Lum P., J ̈ager G., Battke F., Vehlow C., Heinrich J., Nieselt K., Sakai R., Aerts J., Ray W., "An eQTL Biological Data Visualization Challenge and Approaches from the Visualization Community", BMC Bioinformatics, vol. 13, no. 8, 2012, pp. S8-(1-16).

  10. Sifrim A., Van Houdt J.K.J, Tranchevent L., Nowakowska B., Sakai R., Pavlopoulos G.A., Devriendt K., Vermeesch J.R., Moreau Y., Aerts J., "Annotate-it : a Swiss-knife approach to annotation, analysis and interpretation of single nucleotide variation in human disease", Genome Medicine, vol. 4, no. 73, 2012, pp. 1-12.

International Conference Papers

  1. Verbeiren T., Sakai R., Aerts J., "A Pragmatic Approach to Biases in Visual Data Analysis", in Proc. of the DECISIVE : Workshop on Dealing with Cognitive Biases in Visualisations (IEEE VIS2014), Paris, France, Nov. 2014, pp. 1-6.

  2. Sakai R., Aerts J., "Card Sorting Techniques for Domain Characterization in Problem-driven Visualization Research", in Eurographics Conference on Visualization (EuroVis) - Short Papers, (Bertini E., Kennedy J., and Puppo E., eds.), vol. 0 of emph{0}, The Eurographics Association (Geneve, Switzerland), 2015, pp. 121-125.

  3. Popovic D., Moschopoulos C., Sakai R., Sifrim A., Aerts J., Moreau Y., De Moor B., "A self-tuning genetic algorithm with applications in biomarker discovery", in Proc. of the IEEE 27th International Symposium on Computer-based Medical Systems (CBMS 2014), New York, USA, May 2014, pp. 233-238.


  1. Sakai R., Biological Data Visualization : Analysis and Design, PhD thesis, Faculty of Engineering, KU Leuven (Leuven, Belgium), May 2016, 183 p.