Michiel Van Bel

Expert Bioinformatician
(Group member from 2006 until 2012)


+ 32 (0) 9 33 13 695

Research

PLAZA

My current main interests consist of helping with the development of the PLAZA comparative genomics platform. This includes website design and development, as well as developing visualization applications and writing parsing programs.

Splice site prediction

As a precursor to alternative splicing research, I started working on the more "simple" problem of single splice site prediction. This research is still ongoing, and is currently seen in the software package FunSiP. This program is modeled after the SpliceMachine software, and further extends the capabilities of its so-called feature extraction.

Alternative Splicing prediction

The research consisting of the prediction of alternative splicing events in Arabidopsis thaliana is currently on hold, until further notice.

Papers

(19) Schmidt, M., Van Bel, M., Woloszynska, M., Slabbinck, B., Martens, C., De Block, J., Coppens, F., Van Lijsebettens, M. (2017) Plant-RRBS, a bisulfite and next-generation sequencing-based methylome profiling method enriching for coverage of cytosine positions . BMC Plant Biology (In Press).

(18) Kreft, L., Botzki, A., Coppens, F., Vandepoele, K., Van Bel, M. (2017) PhyD3: a phylogenetic tree viewer with extended phyloXML support for functional genomics data visualization. Bioinformatics (In Press).

(17) Van de Velde, J., Van Bel, M., Van Eechoutte, D., Vandepoele, K. (2016) A Collection of Conserved Non-Coding Sequences to Study Gene Regulation in Flowering Plants. Plant Physiol. pp.00821.2016. [Epub ahead of print].

(16) Yue, K., Sandal, P., Williams, C., Murphy, E., Stest, E., Nikonovora, N., Ramakrishna, P., Czyzewicz, N., Montero Morales, L., Kumpf, R., Lin, Z., Van de Cotte, B., Iqbal, M., Van Bel, M., Van De Slijke, E., Meyer, M.R., Gadeyne, A., Zipfel, C., De Jaeger, G., Van Montagu, M., Van Damme, D., Gevaert, O., Rao, A.G., Beeckman, T., De Smet, I. (2015) PP2A-3 interacts with ACR4 and regulates formative cell division in the Arabidopsis root. PNAS 113(5):1447-52.

(15) Walton, A., Stes, E., Cybulski, N., Van Bel, M., Iñigo, S., Nagels Durand, A., Timmerman, D., Heyman, J., Pauwels, L., De Veylder, L., Goossens, A., De Smet, I., Coppens, F., Goormachtig, S., Gevaert, O. (2015) It's time for some "site"-seeing: novel tools to monitor the ubiquitin landscape in Arabidopsis thaliana. The Plant Cell 28(1):6-16.

(14) Olvera-Carrillo, Y., Van Bel, M., Van Hautegem, T., Fendrych, M., Huysmans, M., Simaskova, M., van Durme, M., Buscaill, P., Rivas, S., Coll, N.S., Coppens, F., Maere, S., Nowack, M.K. (2015) A conserved core of PCD indicator genes discriminates developmentally and environmentally induced programmed cell death in plants. Plant Physiol. 169(4):2684-99.

(13) * De Witte, D., * Van de Velde, J., Decap, D., Van Bel, M., Audenaert, P., Demeester, P., Dhoedt, B., * Vandepoele, K., * Fostier, J. (2015) BLSSpeller: exhaustive comparative discovery of conserved cis-regulatory elements. Bioinformatics 31(23):3758-66. *contributed equally

(12) Nelissen, B., Eeckhout, D., Demuynck, K., Persiau, G., Walton, A., Van Bel, M., Vervoort, M., Candaele, J., De Block, J., Aesaert, S., Van Lijsebettens, M., Goormachtig, S., Vandepoele, K., Van Leene, J., Muszynski, M., Gevaert, O., Inzé, D., De Jaeger, G. (2015) Dynamic Changes in ANGUSTIFOLIA3 Complex Composition Reveal a Growth Regulatory Mechanism in the Maize Leaf. The Plant Cell 27(6):1605-19.

(11) Proost, S., Van Bel, M., Vaneechoutte, D., Van de Peer, Y., Inzé, D., Mueller-Roeber, B., Vandepoele, K. (2015) PLAZA 3.0: an access point for plant comparative genomics. Nucleic Acids Research 43(Database issue):D974-81.

(10) Vargas, L., Santa Brígida, A. B., Mota Filho, J.P., de Carvalho, T. G., Rojas, C. A., Vaneechoutte, D., Van Bel, M., Farrinelli, L., Ferreira, P. C.G., Vandepoele, K., Hemerly, A. S. (2014) Drought tolerance conferred to sugarcane by association with Gluconacetobacter diazotrophicus: a transcriptomic view of hormone pathways. PLoS One 9(12):e114744.

(9) Sonnhammer, E., Gabaldon, T., Sousa da Silva, A.W., Martin, F., Robinson-Rechavi, M., Boeckmann, B., Thomas, E., Dessimoz, C., Vandepoele, K., Van Bel, M., Quest for Orthologs consortium, (2014) Big Data and Other Challenges in the Quest for Orthologs. Bioinformatics 30(21):2993-8.

(8) Van Bel, M., Proost, S., Van Neste, C., Deforce, D., Van de Peer, Y., Vandepoele, K. (2013) TRAPID: an efficient online tool for the functional and comparative analysis of de novo RNA-Seq transcriptomes. Genome Biol. 14(12):R134.

(7) Vandepoele, K., Van Bel, M., Richard, G., Van Landeghem, S., Verhelst, B., Moreau, H., Van de Peer, Y., Grimsley, N., Piganeau, G. (2013) pico-PLAZA, a genome database of microbial photosynthetic eukaryotes. Environ. Microbiol. 15(8):2147-53.

(6) Moreau, H., Verhelst, B., Couloux, A., Derelle, E., Rombauts, S., Grimsley, N., Van Bel, M., Poulain, J., Katinka, M., Hohmann-Marriott, M., Piganeau, G., Rouzé, P., Da Silva, C., Wincker, P., Van de Peer, Y., Vandepoele, K. (2012) Gene functionalities and genome structure in Bathycoccus prasinos reflect cellular specializations at the base of the green lineage . Genome Biol. 13, R74.

(5) Movahedi, S., Van Bel, M., Heyndrickx, KS., Vandepoele, K. (2012) Comparative co-expression analysis in plant biology. Plant, Cell & Environment 35(10):1787-98.

(4) Dessimoz, C., Gabaldon, T., Roos, D. S., Sonnhammer, E., Herrero, J., Altenhoff, A., Apweiler, R., Blake, J., Boeckmann, B., Bridge, A., Bruford, E., Cherry, M., Conte, M., Dannie, D., Datta, R., Entfellner, J., Ebersberger, I., Galperin, M., Joseph, J., Koestler, T., Kriventseva, E., Lecompte, O., Leunissen, J., Lewis, S., Linard, B., Livstone, M., Lu, H., Martin, F., Mazumder, R., Miele, V., Muffato, M., Perriere, G., Punta, M., Rouard, M., Schmitt, T., Schreiber, F., Silva, E.P., Sjolander, K., Skunca, N., Stanley, M., Szklarczyk, R., Thomas, E., Uchiyama, I., Van Bel, M., Vandepoele, K., Vilella, A., Yates, J.R., Zdobnov, E. (2012) Toward Community Standards in the Quest for Orthologs. Bioinformatics 28, 900-4.

(3) * Van Bel, M., * Proost, S., Wischnitzki, E., Movahedi, S., Scheerlinck, C., Van de Peer, Y., Vandepoele, K. (2012) Dissecting plant genomes with the PLAZA comparative genomics platform. Plant Physiol. 158(2):590-600. *contributed equally

(2) * 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

(1) Van Bel, M., Saeys, Y., Van de Peer, Y. (2008) FunSiP : A Modular and Extensible Classifier for the Prediction of Functional Sites in DNA. Bioinformatics 24(13):1532-3.











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