Ryo Sakai

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


Novel visualization paradigm for structural variations and genome comparison


Jan Aerts, Yves Moreau



International Journal Papers

  1. 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).

  2. 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. .

  3. 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.

  4. 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.

  5. 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.

  6. Sakai R., Sifrim A., Vande Moere A., Aerts J., "TrioVis: a visualization approach for filtering genomic variants of parent–child trios", Bioinformatics, vol. 29, no. 14, Aug. 2013, pp. 1801-1802.

  7. 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.

  8. 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).

  9. 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. 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.

  2. 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.