Thomas Van Parys

Software Developer (Group member since 2007) + 32 (0) 9 33 13 825 VIB / Ghent University Bioinformatics & Systems Biology Technologiepark 927 B-9052 Gent BELGIUM

CV

• 1999 - 2003: Industrial Engineering (Informatics) at Hogeschool Gent
• 2003 - 2005: Master Computer Sciences (Software Development) at Ghent University
• 2005 - 2007: Webmaster HiPEAC (ELIS - Ghent University)
• 2007 - now: Software development at VIB (PSB - BEG)

Research

Development of tools and visualizations.

• Software development: Java, Python, Bash, Cytoscape Apps, ...
• Web development: PHP, CakePHP, HTML/CSS, JavaScript, JQuery, Drupal, ...
• Sysadmin: Linux, Git, Apache, MySQL, ...

Papers

(10) Van Parys, T., Melckenbeeck, I., Houbraken, M., Audenaert, P., Colle, J., Pickavet, M., Demeester, P., Van de Peer, Y. (2017) A Cytoscape app for motif enumeration with ISMAGS. Bioinformatics 33(3):461-463.

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(9) * Artaza, H., * Hong, N.C., * Corpas, M., * Corpuz, A., * Hooft, R., * Jimenez, R.C., * Leskošek, B., * Olivier, B.G., * Stourac, J., * Vařeková, R.S., * Van Parys, T., * Vaughan, D. (2016) Top 10 metrics for life science software good practices. F1000Research 5(ELIXIR):2000. *contributed equally

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(8) Xie, G.-C., Tzfadia, O., Levy, AA., Weithorn, E., Peled-Zehavi, H., Van Parys, T., Van de Peer, Y., Galili, G. (2016) hfAIM: a reliable bioinformatics approach for in silico genome-wide identification of autophagy-associated atg8-interacting motifs in various organisms. Autophagy 12(5):876-87.

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(7) Van Landeghem, S., Van Parys, T., Dubois, M., Inzé, D., Van de Peer, Y. (2016) Diffany: an ontology-driven framework to infer, visualise and analyse differential molecular networks. BMC Bioinformatics 17(1):18.

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(6) Vermeirssen, V., De Clercq, I., Van Parys, T., Van Breusegem, F., Van de Peer, Y. (2014) Arabidopsis ensemble reverse-engineered gene regulatory network discloses interconnected transcription factors in oxidative stress. The Plant Cell 26(12):4656-4679.

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(5) Abeel, T., Van Parys, T., Saeys, Y., Galagan, J., Van de Peer, Y. (2012) GenomeView: a next-generation genome browser. Nucleic Acids Res. 40(2):e12.

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(4) Kano, Y., Björne, J., Ginter, F., Salakoski, T., Buyko, E., Hahn, U., Cohen, K. B., Verspoor, K., Roeder, C., Hunter, L.E., Kilicoglu, H., Bergler, S., Van Landeghem, S., Van Parys, T., Van de Peer, Y., Miwa, S., Ananiadou, S., Neves, M., Pascual-Montano, A., Ozgur, A., Radev, D.R., Riedel, S., Saetre, R., Chun, H.W., Kim, J.R., Pyysalo, S., Ohta, T., Tsujii, J. (2011) U-Compare bio-event meta-service: compatible BioNLP event extraction services. BMC Bioinformatics 12:481.

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(3) * Audenaert, P., * Van Parys, T., Brondel, F., Pickavet, M., Demeester, P., Van de Peer, Y., Michoel, T. (2011) CyClus3D: a Cytoscape plugin for clustering network motifs in integrated networks. Bioinformatics 27(11):1587-8. *contributed equally

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(2) Joshi, A., Van Parys, T., Van de Peer, Y., Michoel, T. (2010) Characterizing regulatory path motifs in integrated networks using perturbational data. Genome Biol. 11(3):R32.

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(1) * Proost, S., * Van Bel, M., Sterck, L., Billiau, K., Van Parys, T., Van de Peer, Y., Vandepoele, K. (2009) PLAZA: a comparative genomics resource to study gene and genome evolution in plants. The Plant Cell 21(12):3718-31. *contributed equally

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