Thomas Abeel
thomas@abeel.be
- http://www.abeel.be
| Broad Institute of MIT and Harvard Genome Sequencing and Analysis Program 7 Cambridge Center Cambridge, MA, 02142 http://www.broadinstitute.org |
VIB - Ghent University Department of Plant Systems Biology Bioinformatics & Evolutionary Genomics Technologiepark 927, 9000 Gent, Belgium http://bioinformatics.psb.ugent.be |
Publications and presentations
Journal articles
21) Galagan, J., Minch, K., Peterson, M., Lyubetskaya, A., Azizi, E., Sweet, L., Gomes, A., Rustad, T., Dolganov, G., Glotova, I., Abeel, T., Mawhinney, C., Kennedy, A., Allard, R., Brabant, W., Krueger, A., Jaini, S., Honda, B., Yu, W., Hickey, M., Zucker, J., Garay, C., Weiner, B., Sisk, P., Stolte, C., Camacho, D., Dreyfuss, J., Liu, Y., Dorhoi, A., Mollenkopf, H., Drogaris, P., Lamontagne, J., Zhou, Y., Piquenot, J., Tae Park, S., Raman, S., Kaufmann, S., Mohney, R., Chelsky, D., Moody, B., Sherman, D., Schoolnik, G., Van de Peer, Y., Iazzetti, P., Winkler, J. 2013. The Mycobacterium tuberculosis Regulatory Network and the Hypoxic Response. Nature. accepted
19) Goncearenco, A., Grynberg, P., Botvinnik, O., Macintyre, G., Abeel, T. 2012. Highlights from the Eighth International Society for Computational Biology (ISCB) Student Council Symposium 2012. BMC Bioinformatics. 13 (Supplement 18): A1
18) de Ridder, J., Abeel, T., Michaut, M., Satagopam, V., Gehlenborg, N. 2012. Don't Wear Your New Shoes (Yet): Taking the right steps to become a successful Principal Investigator. PLOS Computational Biology. 9 (1): e1002834
17) Sterck, L., Billiau, K., Abeel, T., Rouzé, P., Van de Peer, Y. 2012. ORCAE: online resource for community annotation of eukaryotes. Nature Methods. 9 (11): 1041
15) Van Landeghem, S., Björne, J., Abeel, T., De Baets, B., Salakoski, T., Van de Peer, Y. 2012. Semantically linking molecular entities in literature through entity relationships. BMC Bioinformatics. 13 (Suppl 11): S6
14) McGuire, A., Weiner, B., Park, S., Wapinski, I., Raman, S., Dolganov, G., Peterson, M., Riley, R., Zucker, J., Abeel, T., White, J., Sisk, P., Stolte, C., Koehrsen, M., Yamamoto, R., Iacobelli-Martinez, M., Kidd, M., Maer, A., Schoolnik, G., Regev, A., Galagan, J. 2012. Comparative analysis of Mycobacterium and related Actinomycetes yields insight into the evolution of Mycobacterium tuberculosis pathogenesis. BMC Genomics. 13 (1): 120
13) Grynberg, P., Abeel, T., Lopes, P., Macintyre, G., Pantano Rubiño, L. 2011. Highlights from the Seventh International Society for Computational Biology (ISCB) Student Council Symposium 2011. BMC Bioinformatics. 12 (Suppl 11): I1
12) Abeel, T., Van Parys, T., Saeys, Y., Galagan, J., Van de Peer, Y. 2011. GenomeView: a next-generation genome browser. Nucleic Acids Research. doi: 10.1093/nar/gkr995
11) Holder, J., Ulrich, J., DeBono, A., Godfrey, P., Desjardins, C., Zucker, J., Zeng, Q., Leach, A., Ghiviriga, I., Dancel, C., Abeel, T., Gevers, D., Kodira, C., Desany, B., Affourtit, J., Birren, B., Sinskey, A. 2011. Comparative and Functional Genomics of Rhodococcus opacus PD630 for Biofuels Development. PLoS Genetics. 7 (9): e1002219. doi:10.1371/journal.pgen.1002219
10) Van Landeghem, S., Abeel, T., Saeys, Y., Van de Peer, Y. 2010. Discriminative and informative features for biomolecular text mining with ensemble feature selection. Bioinformatics. 26 (18): i554-i560
9) Abeel, T., Van Landeghem, S., Morante, R., Van Asch, V., Van de Peer, Y., Daelemans, W., Saeys, Y. 2010. Highlights of the BioTM 2010 workshop on advances in bio text mining. BMC Bioinformatics. 11 (Suppl 5): I1
8) Klijn, C., Michaut, M., Abeel, T. 2010. Highlights from the 6th International Society for Computational Biology Student Council Symposium at the 18th Annual International Conference on Intelligent Systems for Molecular Biology . BMC Bioinformatics. 11 (Suppl 10): I1
7) Abeel, T., Helleputte, T., Van de Peer, Y., Dupont, P., Saeys, Y. 2010. Robust biomarker identification for cancer diagnosis with ensemble feature selection methods. Bioinformatics. 26 (3): 392-398
6) Abeel, T., De Ridder, J., Peixoto, L. 2009. Highlights from the 5th International Society for Computational Biology Student Council Symposium at the 17th Annual International Conference on Intelligent Systems for Molecular Biology and the 8th European Conference on Computational Biology. BMC Bioinformatics. 10 (Suppl 13): I1
5) Abeel, T., Van de Peer, Y., Saeys, Y. 2009. Java-ML: a machine learning library. Journal of Machine Learning Research. 10 (Apr): 931-934
4) Abeel, T., Van de Peer, Y., Saeys, Y. 2009. Towards a gold standard for promoter prediction evaluation. Bioinformatics. 25 (12): i313-i320
3) Abeel, T., Saeys, Y., Bonnet, E., Rouzé, P., Van de Peer, Y. 2008. Generic eukaryotic core promoter prediction using structural features of DNA. Genome Research. 18 (2): 310-323
2) Abeel, T., Saeys, Y., Rouzé, P., Van de Peer, Y. 2008. ProSOM: Core promoter prediction based on unsupervised clustering of DNA physical profiles. Bioinformatics. 24 (13): i24-i31
1) Saeys, Y., Abeel, T., Degroeve, S., Van de Peer, Y. 2007. Translation initiation site prediction on a genomic scale: beauty in simplicity. Bioinformatics. 23 (13): i418-i423
Lectures
11) Visualizing the next generation of sequencing data with GenomeView (invited)
VIB seminar 2012, 20/04/2012, Blankenberge, Belgium
VIB seminar 2012, 20/04/2012, Blankenberge, Belgium
10) GenomeView: Visualizing the next generation of sequencing data (contributed)
Illumina iDEA conference 2011, 14/6/2011-15/6/2011, San Diego, CA, USA
Illumina iDEA conference 2011, 14/6/2011-15/6/2011, San Diego, CA, USA
9) Visualizing HTS and comparative data with GenomeView (invited)
ABRF 2011, 19/2/2011-22/2/2011, San Antonio, TX, USA
ABRF 2011, 19/2/2011-22/2/2011, San Antonio, TX, USA
8) Visualizing HTS and comparative data with GenomeView (contributed)
ISMB, 11/7/2010-13/7/2010, Boston, MA, USA
ISMB, 11/7/2010-13/7/2010, Boston, MA, USA
7) Visualizing NGS data with GenomeView (invited)
Workshop on next generation sequencing data analysis, 31/5/2010-4/6/2010, Espoo, Finland
Workshop on next generation sequencing data analysis, 31/5/2010-4/6/2010, Espoo, Finland
6) Towards a gold standard for promoter prediction evaluation (contributed)
ISMB, 27/6/2009-2/7/2009, Stockholm, Sweden
ISMB, 27/6/2009-2/7/2009, Stockholm, Sweden
5) ProSOM: Core promoter prediction based on unsupervised clustering of DNA physical profiles (contributed)
ISMB, 19/7/2008-23/7/2008, Toronto, Canada
ISMB, 19/7/2008-23/7/2008, Toronto, Canada
4) ProSOM: Core promoter identification in the human genome (contributed)
Benelearn, 19/05/2008-20/05/2008, Spa, Belgium
Benelearn, 19/05/2008-20/05/2008, Spa, Belgium
3) Generic core promoter prediction (invited)
VIB science club genetics, 17/04/2008., Leuven, Belgium
VIB science club genetics, 17/04/2008., Leuven, Belgium
2) Generic eukaryotic core promoter prediction (contributed)
VIB seminar, 6/03/2008-7/03/2008, Blankenberge, Belgium,
VIB seminar, 6/03/2008-7/03/2008, Blankenberge, Belgium,
1) The structure of the promoter unravelled (contributed)
Benelux Bioinformatics Conference, 17/10/2006-18/10/2006, Wageningen, the Netherlands
Benelux Bioinformatics Conference, 17/10/2006-18/10/2006, Wageningen, the Netherlands
Proceedings
9) Van Landeghem, S., Abeel, T., De Baets, B., Van de Peer, Y. 2011. Detecting Entity Relations as a Supporting Task for Bio-Molecular Event Extraction. Proceedings of BioNLP Shared Task 2011 Workshop. Proceedings of BioNLP Shared Task 2011 Workshop. 147-148. Portland, Oregon, USA, Association for Computational Linguistics
8) Abeel, T., Van de Peer, Y., Saeys, Y. 2008. Towards robust feature selection techniques for high-dimensional datasets in biofinformatics. Proceedings of Benelux Bioinformatics Conference. Proceedings of the Benelux Bioinformatics Conference. 84. Maastrich, the Netherlands
7) Saeys, Y., Abeel, T., Van de Peer, Y. 2008. Towards robust feature selection techniques. Proceedings of Benelearn. Proceedings of Benelearn. 45-46. Spa, Belgium
6) Abeel, T., Saeys, Y., Van de Peer, Y. 2008. ProSOM: Core promoter identification in the human genome. Proceedings of Benelearn. Proceedings of Benelearn. 77-78. Spa, Belgium
5) Saeys, Y., Abeel, T., Van de Peer, Y. 2008. Robust Feature Selection using Ensemble Feature Selection Techniques. Proceedings of ECML/PKDD. Lecture Notes in Computer Science. 5212, 313-325. Antwerp, Belgium
4) Abeel, T., Saeys, Y., Bonnet, E., Rouzé, P., Van de Peer, Y. 2007. Eukaryotic core promoter prediction using structural features of DNA. Proceedings of Benelux Bioinformatics Conference. Proceedings of the Benelux Bioinformatics Conference. 29. Leuven, Belgium
3) Abeel, T., Saeys, Y., Van de Peer, Y. 2007. Core promoter prediction using ensembles of classifiers. Proceedings of Benelearn. 139-140. Amsterdam, the Netherlands
2) Abeel, T., Saeys, Y., Van de Peer, Y. 2006. The structure of the promoter unraveled. Proceedings of Benelux Bioinformatics Conference. Proceedings of the Benelux Bioinformatics Conference. 53. Wageningen, the Netherlands
1) Abeel, T., Saeys, Y., Van de Peer, Y. 2006. Improved core promoter prediction using ensembles of support vector machines. Proceedings of Benelearn. Proceedings of Benelearn. 180-181. Gent, Belgium
Posters
45) Sisk, P., Stolte, C., Abeel, T., Peterson, M., Zucker, J., Gomes, A., Lyubetskaya, A., Rustad, T., Minch, K., Glotova, I., Sherman, D., Galagan, J., 2011, TBDB: Publishing TB Systems Biology Data in an Interactive Genomic Context, Broad Retreat 2011, Boston, MA, USA
44) Abeel, T., Galagan, J., Van de Peer, Y., 2011, Visualizing sequencing and comparative data with GenomeView , Broad Retreat 2011, Boston, MA, USA
43) McGuire, A., Griggs, A., DesJardins, C., Godfrey, P., Haas, B., Wortman, J., Zucker, J., Abeel, T., Pearson, M., Zheng, Q., Strauss, J., Allen-Vercoe, E., Birren, B., , A., 2011, Comparative Analysis of Fusobacterium, Broad Retreat 2011, Boston, MA, USA
42) Abeel, T., Van Parys, T., Galagan, J., Van de Peer, Y., 2011, Visualizing the next generation of sequencing data , ISMB 2011, Vienna, Austria
41) Abeel, T., Van Parys, T., Galagan, J., Van de Peer, Y., 2011, Visualizing the next generation of sequencing data , Vizbi 2011, Boston, MA, USA
40) Abeel, T., Van Parys, T., Saeys, Y., Galagan, J., Van de Peer, Y., 2010, Visualizing the next generation of sequencing data , First European Student Council Symposium, Gent, Belgium
39) Abeel, T., Van Parys, T., Saeys, Y., Galagan, J., Van de Peer, Y., 2010, Visualizing the next generation of sequencing data, ECCB 2010, Gent, Belgium
38) Gomes, A., Boulanov, D., Galagan, J., Kaiser, N., Abeel, T., 2010, Predicting Operon Map in Mycobacterium Tuberculosis Using RNAseq Data and Conditional Random Field , ISMB, Boston, MA, USA
37) Abeel, T., Van Parys, T., Weiner, B., Galagan, J., Van de Peer, Y., 2010, Visualizing the next generation of sequencing data, ISMB, Boston, MA, USA
36) Abeel, T., Van Landeghem, S., Saeys, Y., Van de Peer, Y., 2010, Text mining meets feature selection, BioTM 2010 Workshop on Advances in Bio Text Mining, Gent, Belgium
35) Abeel, T., Van Parys, T., Saeys, Y., Galagan, J., Van de Peer, Y., 2010, Visualizing the next generation of sequencing data, 2nd StatSeq Workshop, Gent, Belgium
34) Abeel, T., Van Parys, T., Weiner, B., Saeys, Y., Galagan, J., Van de Peer, Y., 2010, GenomeView: next-generation sequencing visualization, VIB seminar 2010, Blankenberge, Belgium
33) Abeel, T., Van Parys, T., Weiner, B., Saeys, Y., Galagan, J., Van de Peer, Y., 2010, GenomeView: next-generation sequencing visualization, Workshop on Visualizing Biological Data 2010, Heidelberg, Germany
32) Abeel, T., Helleputte, T., Dupont, P., Saeys, Y., 2009, Robust biomarker identification for cancer diagnosis using ensemble feature selection methods, BBC 2009, Liege, Belgium
31) Weiner, B., Peterson, M., McGuire, A., Lun, D., Zucker, J., Abeel, T., White, J., Sherrid, A., Sherman, D., Galagan, J., 2009, Network modeling of Mycobacterium tuberculosis via integration of ChIP-Seq and Transcriptomics, TB sysbio meeting, Seattle, WA, USA
30) McGuire, A., Weiner, B., Riley, R., Peterson, M., Zucker, J., Abeel, T., Wapinski, I., White, J., Koehrsen, M., Pearson, M., 2009, Comparative Analysis of Mycobacterium tuberculosis, Broad Retreat, Boston, MA, USA
29) Gellesch, M., Stolte, C., Jen, D., Heilman, E., Abeel, T., Engels, R., Borenstein, D., Sykes, S., Sisk, P., Koehrsen, M., Pearson, M., 2009, Searching and Visualizing Polymorphisms in M. tuberculosis using Next Generation Sequencing, Broad Retreat, Boston, MA, USA
28) Abeel, T., Van Parys, T., Galagan, J., 2009, Visualization of next-generation sequencing data, Broad Retreat, Boston, MA, USA
27) Abeel, T., Van de Peer, Y., Saeys, Y., 2009, Java-ML: a Java Library for Data Mining, MLSB 2009, Ljubljana, Slovenia
26) Abeel, T., Helleputte, T., Dupont, P., Saeys, Y., 2009, Robust biomarker identification for cancer diagnosis using ensemble feature selection methods, MLSB 2009, Ljubljana, Slovenia
25) De Schutter, K., Lin, Y., Tiels, P., Van Hecke, A., Sterck, L., Abeel, T., Glinka, S., Weber-Lehmann, J., Rouzé, P., Van de Peer, Y., Callewaert, N., 2009, Genome sequence of the recombinant protein production host Pichia pastoris., BioMagnet 2009, Gent, Belgium
24) Abeel, T., Helleputte, T., Dupont, P., Saeys, Y., 2009, Robust biomarker identification for cancer diagnosis using ensemble feature selection methods, BioMagnet 2009, Gent, Belgium
23) De Schutter, K., Lin, Y., Tiels, P., Van Hecke, A., Sterck, L., Abeel, T., Glinka, S., Weber-Lehmann, J., Rouzé, P., Van de Peer, Y., Callewaert, N., 2009, Genome sequence of the recombinant protein production host Pichia pastoris., NGS2009, Barcelona, Spain
22) Abeel, T., Van de Peer, Y., Saeys, Y., 2009, Benchmarking promoter prediction software., ISMB/ECCB, Stockholm, Sweden
21) Abeel, T., White, J., Galagan, J., 2009, Comparative gene-finding in TB genomes, Third Annual New England Tuberculosis Symposium, Boston, MA, USA
20) Saeys, Y., Abeel, T., Van de Peer, Y., 2009, Robust biomarker identification using ensemble feature selection techniques, VIB seminar 2009, Blankenberge, Belgium
19) Abeel, T., Saeys, Y., Van de Peer, Y., 2008, Towards robust feature selection techniques for high-dimensional datasets in bioinformatics, BBC 2008, Maastricht, The Netherlands
18) Abeel, T., Saeys, Y., Van de Peer, Y., 2008, Ensemble feature selection improves selected feature stability, ECML - CIL student poster session, Antwerp, Belgium
17) Abeel, T., Saeys, Y., Van de Peer, Y., 2008, Improving Promoter Prediction Precision Using Ensemble Methods, MLSB 2008, Brussels, Belgium
16) Abeel, T., Saeys, Y., Rouzé, P., Van de Peer, Y., 2008, ProSOM: Core promoter prediction based on unsupervised clustering of DNA physical profiles, ISMB 2008, Toronto, Canada
15) Abeel, T., Saeys, Y., Van de Peer, Y., 2008, Improving precision of core promoter predictions, 4th ISCB Student Council Symposium, Toronto, Canada
14) Abeel, T., Saeys, Y., Van de Peer, Y., 2008, Core promoter prediction in eukaryote genomes, BioMAGNet-SymBioSys workshop, Leuven, Belgium
13) Abeel, T., Saeys, Y., Van de Peer, Y., 2007, Eukaryotic core promoter prediction using structural features of DNA, Benelux Bioinformatics Conference 2007 (BBC 2007), Leuven, Belgium
12) Abeel, T., Saeys, Y., Van de Peer, Y., 2007, The Java Machine Learning Library, Machine Learning in Systems Biology 2007 (MLSB2007), Evry, France
11) Abeel, T., Saeys, Y., Van de Peer, Y., 2007, Clustering to improve core promoter prediction, Second contact day of the Computational Intelligence and Learning doctoral school, Leuven, Belgium
10) Abeel, T., Saeys, Y., Van de Peer, Y., 2007, Core promoter identification using ensembles of classifiers, ISMB/ECCB 2007, Vienna, Austria
9) Abeel, T., Saeys, Y., Van de Peer, Y., 2007, Core promoter identification using ensembles of classifiers, Benelearn 2007, Amsterdam, The Netherlands
8) Abeel, T., Saeys, Y., Van de Peer, Y., 2007, Core promoter prediction for genome annotation, doctoral symposium of the faculty of Sciences, Gent, Belgium
7) Abeel, T., Saeys, Y., Van de Peer, Y., 2007, Fast and accurate promoter prediction in human, VIB seminar 2007, Blankenberge, Belgium
6) Abeel, T., Saeys, Y., Van de Peer, Y., 2007, Fast and accurate promoter prediction in human, BioMagnet kick-off meeting, Liege, Belgium
5) Abeel, T., Saeys, Y., Van de Peer, Y., 2006, The structure of the promoter unraveled, Young scientists day, Gembloux, Belgium
4) Abeel, T., Saeys, Y., Van de Peer, Y., 2006, Improved core promoter prediction using ensembles of support vector machines, International Workshop on Current Challenges in Kernel Methods (CCKM06), Brussels, Belgium
3) Abeel, T., Saeys, Y., Van de Peer, Y., 2006, Improved core promoter prediction using ensembles of support vector machines, Research contact day of the Computational Intelligence and Learning doctoral school, Brussels, Belgium
2) Abeel, T., Saeys, Y., Van de Peer, Y., 2006, Improved core promoter prediction using ensembles of support vector machines, Gent-Lille Workshop on Computational Biology, Lille, France
1) Abeel, T., Saeys, Y., Van de Peer, Y., 2006, Improved core promoter prediction using ensembles of support vector machines, Benelearn 2006, Gent, Belgium
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