Thomas Abeel

thomas@abeel.be - http://www.abeel.be
Delft University of Technology
Faculty of Electrical Engineering, Mathematics and Computer Science
Intelligent Systems - Delft Bioinformatics Lab
Mekelweg 4, 2628 CD Delft, The Netherlands
http://bioinformatics.tudelft.nl/
Broad Institute of MIT and Harvard
Genome Sequencing and Analysis Program
7 Cambridge Center
Cambridge, MA, 02142, USA
http://www.broadinstitute.org

Publications and presentations

Journal articles

43) Wollenberg, K., Desjardins, C., Zalutskaya, A., Slodovnikova, V., Oler, A., Quiñones, M., Abeel, T., Chapman, S., Tartakovsky, M., Gabrielian, A., Hoffner, S., Skrahin, A., Birren, B., Rosenthal, A., Skrahina, A., Earl, A. 2017. Whole genome sequencing of Mycobacterium tuberculosis provides insight into the evolution and genetic composition of drug-resistant tuberculosis in Belarus. Journal of Clinical Microbiology. 55 (2): 457-469
42) Manson, A., Cohen, K., Abeel, T., Desjardins, C., Armstrong, D., Barry III, C., Brand, J., Chapman, S., Cho, S., Gabrielian, A., Gomez, J., Jodals, A., Joloba, M., Jureen, P., Lee, J., Malinga, L., Maiga, M., Nordenberg, D., Noroc, E., Romancenco, E., Salazar, A., Ssengooba, W., Velayati, A., Winglee, K., Zalutskaya, A., Via, L., Cassell, G., Dorman, S., Ellner, J., Farnia, P., Galagan, J., Rosenthal, A., Crudu, V., Homorodean, D., Hsueh, P., Narayanan, S., Pym, A., Skrahina, A., Swaminathan, S., Walt, M., Alland, D., Bishai, W., Cohen, T., Hoffner, S., Birren, B., Earl, A., TBResist Global Genome Consortium, . 2017. Genomic analysis of globally diverse Mycobacterium tuberculosis strains provides insights into the emergence and spread of multidrug resistance. Nature Genetics. in press
41) Gehrmann, T., Pelkmans, J., Lugones, L., Wösten, H., Abeel, T., Reinders, M. 2016. Schizophyllum commune has an extensive and functional alternative splicing repertoire.. Nature Scientific Reports. 633640
40) Desjardins, C., Cohen, K., Munsamy, V., Abeel, T., Maharaj, K., Walker, B., Shea, T., Almeida, D., Manson, A., Salazar, A., Padayatchi, N., O'Donnell, M., Mlisana, K., Wortman, J., Birren, B., Grosset, J., Earl, A., Pym, A. 2016. Genomic and functional analyses of Mycobacterium tuberculosis strains implicate ald in d-cycloserine resistance. Nature Genetics. 201 (6): 544–551
39) Malinga, L., Abeel, T., Desjardins, C., Dlamini, T., Cassell, G., Chapman, S., Birren, B., Earl, A., Walt, M. 2016. Draft genome sequences of two extensively drug-resistant strains of Mycobacterium tuberculosis belonging to the Euro-American S lineage. Genome announcements. 4 (2): e01771-15
38) Marschall, T., Marz, M., Abeel, T., Dijkstra, L., Dutilh, B., Ghaffaari, A., Kersey, P., Kloosterman, W., Makinen, V., Novak, A., Paten, B., Porubsky, D., RIVALS, E., Alkan, C., Baaijens, J., Bakker, P., Boeva, V., Chiaromonte, F., Chikhi, R., Ciccarelli, F., Cijvat, R., Datema, E., Duijn, C., Eichler, E., Ernst, C., Eskin, E., Garrison, E., El-Kebir, M., Klau, G., Korbel, J., Lameijer, E., Langmead, B., Martin, M., Medvedev, P., Mu, J., Neerincx, P., Ouwens, K., Peterlongo, P., Nadia, P., Rahmann, S., Raphael, B., Reinert, K., Ridder, D., Ridder, J., Schlesner, M., Schulz-Trieglaff, O., Sanders, A., Sheikhizadeh, S., Shneider, C., Smit, S., Valenzuela, D., Wang, J., Wessels, L., Zhang, Y., Guryev, V., Vandin, F., Ye, K., Schoenhuth, A. 2016. Computational pan-Genomics: Status, Promises and Challenges. Briefings in bioinformatics. bbw089
37) Velayati, A., Abeel, T., Shea, T., Zhavnerko, G., Birren, B., Cassell, G., Earl, A., Hoffner, S., Farnia, P. 2016. Populations of latent Mycobacterium tuberculosis lack a cell wall: Isolation, visualization, and whole-genome characterization. International Journal of Mycobacteriology. 5 (1): 66-73
36) Winglee, K., Manson, M., Maiga, M., Abeel, T., Shea, T., Desjardins, C., Diarra, B., Baya, B., Sanogo, M., Diallo, S., Earl, A., Bishai, W. 2016. Whole Genome Sequencing of Mycobacterium africanum Strains from Mali Provides Insights into the Mechanisms of Geographic Restriction.. PLOS Neglected Tropical Diseases. 10 (1): e0004332-e0004332
35) Cohen, K., Abeel, T., McGuire, A., Desjardins, C., Munsamy, V., Shea, T., Walker, B., Bantubani, N., Almeida, D., Alvarado, L., Chapman, S., Mvelase, N., Duffy, E., Fitzgerald, M., Govender, P., Gujja, S., Hamilton, S., Howarth, C., Larimer, J., Maharaj, K., Pearson, M., Priest, M., Zeng, Q., Padayatchi, N., Grosset, J., Young, S., Wortman, J., Mlisana, K., O’Donnell, M., Birren, B., Bishai, W., Pym, A., Earl, A. 2015. Evolution of extensively drug-resistant tuberculosis over four decades revealed by whole genome sequencing of Mycobacterium tuberculosis from KwaZulu-Natal, South Africa. International Journal of Mycobacteriology. 424-25
34) Abeel, T., Manson McGuire, A., Desjardins, C., Munsamy, V., Pym, A., Earl, A., Cohen, K. 2015. Molecular Antecedents And Timing Of Xdr Emergence Revealed By Whole Genome Sequencing Of Mycobacterium Tuberculosis In Kwazulu-Natal, South Africa. Am J Respir Crit Care Med. 191A2181
33) Cohen*, K., Abeel*, T., Manson McGuire, A., Desjardins, C., Munsamy, V., Shea, T., Walker, B., Bantubani, N., Almeida, D., Alvarado, L., Chapman, S., Mvelase, N., Duffy, E., Fitzgerald, M., Govender, P., Gujja, S., Hamilton, S., Howarth, C., Larimer, J., Maharaj, K., Pearson, M., Priest, M., Zeng, Q., Padayatchi, N., Grosset, J., Young, S., Wortman, J., Mlisana, K., O'Donnell, M., Birren, B., Bishai, W., Pym+, A., Earl+, A. 2015. Evolution of extensively drug-resistant tuberculosis over four decades: whole genome sequencing and dating analysis of Mycobacterium tuberculosis isolates from KwaZulu-Natal. PLOS Medicine. 12 (9): e1001880
32) Williams, O., Abeel, T., Casali, N., Cohen, K., Pym, A., Mungall, S., Desjardins, C., Banerjee, A., Drobniewski, F., Earl, A., Cooke, G. 2015. Fatal Nosocomial MDR TB Identified through Routine Genetic Analysis and Whole-Genome Sequencing. Emerging Infectious Diseases. 21 (6): 1082-1084
31) Salazar, A., Earl, A., Desjardins, C., Abeel, T. 2015. Normalizing alternate representations of large sequence variants across multiple bacterial genomes. BMC Bioinformatics. 16 (2): A8
30) Walker*, B., Abeel*, T., Shea, T., Priest, M., Abouelliel, A., Sakthikumar, S., Cuomo, C., Zeng, Q., Wortman, J., Young, S., Earl, A. 2014. Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLOS One. 9 (11): e112963
29) Mishra, T., Parra, G., Abeel, T. 2014. The Upside of Failure: How Regional Student Groups Learn from Their Mistakes. PLOS Computational Biology. 10 (8): e1003768
28) de Ridder, J., Meysman, P., Oluwagbemi, O., Abeel, T. 2014. Soft skills: An Important Asset Acquired from Organizing Regional Student Group Activities. PLOS Computational Biology. 10 (7): e1003708
27) Manson McGuire, A., Cochrane, K., Griggs, A., Haas, B., Abeel, T., Zeng, Q., Nice, J., MacDonald, H., Birren, B., Berger, B., Allen-Vercoe, E., Earl, A. 2014. Evolution of invasion in a diverse set of Fusobacterium species. mBio. 5 (6): e01864
26) Gomes, A., Abeel, T., Peterson, M., Lyubetskaya, A., Carvalho, L., Galagan, J. 2014. Decoding ChIP-seq peaks with a double-binding signal refines binding peaks to single-nucleotide and predicts cooperative interaction. Genome Research. 241686-1697
25) Vercruyssen, L., Verkest, A., Gonzalez, N., Heyndrickx, K., Eeckhout, D., Han, S., Jégu, T., Archacki, R., Van Leene, J., Andriankaja, M., De Bodt, S., Abeel, T., Coppens, F., Dhondt, S., De Milde, L., Vermeersch, M., Maleux, K., Gevaert, K., Jerzmanowski, A., Benhamed, M., Wagner, D., Vandepoele, K., De Jaeger, G., Inzé, D. 2014. ANGUSTIFOLIA 3 binds SWI/SNF chromatin remodeling complexes to regulate transcription during Arabidopsis leaf development. Plant Cell. 26 (3): 210-229
24) Verkest, A., Abeel, T., Heyndrickx, K., Van Leene, J., Lanz, C., Van De Slijke, E., De Winne, N., Eeckhout, D., Persiau, G., Van Breusegem, F., Inzé, D., Vandepoele, K., De Jaeger, G. 2014. Tandem chromatin affinity purification (TChAP) in Arabidopsis cell suspension cultures improves the identification of transcription factor target genes . Plant Physiology. 164 (3): 1122-1133
23) Szczepinska, T., Iwasaki, W., Abeel, T. 2013. The spirit of competition: to win or not to win. PLOS Computational Biology. e1003413
22) Shanmugam, A., Macintyre, G., Michaut, M., Abeel, T. 2013. Ten Simple Rules for Starting a Regional Student Group. PLOS Computational Biology. 9 (11): e1003340
21) Macintyre, G., Michaut, M., Abeel, T. 2013. The Regional Student Group Program of the ISCB Student Council: Stories from the Road. PLOS Computational Biology. 9 (9): e1003241
20) Bateman, A., Kelso, J., Mietchen, D., Macintyre, G., Di Domenico, T., Abeel, T., Logan, D., Radivojac, P., Rost, B. 2013. ISCB Computational Biology Wikipedia Competition. PLOS Computational Biology. 9 (9): e1003242
19) 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. 499 (7457): 178–183
18) 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
17) 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
16) 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

14) Machine learning methods for genotype-phenotype association in bacterial genomes (contributed)
ISMB 2013, 21/07/2013, Berlin, Germany
13) Presenting your science visually (invited)
9th ISCB Student Council Symposium, 20/07/2013, Berlin, Germany
12) Visualizing the next generation of sequencing data with GenomeView (contributed)
14th Annual Bioinformatics Open Source Conference (BOSC 2013), 19/07/2013, Berlin, Germany
11) Visualizing the next generation of sequencing data with GenomeView (invited)
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
9) Visualizing HTS and comparative data with GenomeView (invited)
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
7) Visualizing NGS data with GenomeView (invited)
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
5) ProSOM: Core promoter prediction based on unsupervised clustering of DNA physical profiles (contributed)
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
3) Generic core promoter prediction (invited)
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,
1) The structure of the promoter unravelled (contributed)
Benelux Bioinformatics Conference, 17/10/2006-18/10/2006, Wageningen, the Netherlands

Proceedings

11) Cohen, K., Abeel, T., McGuire, A., Desjardins, C., Munsamy, V., Shea, T., Walker, B., Bantubani, N., Almeida, D., Alvarado, L., Chapman, S., Mvelase, N., Duffy, E., Fitzgerald, M., Govender, P., Gujja, S., Hamilton, S., Howarth, C., Larimer, J., Maharaj, K., Pearson, M., Priest, M., Zeng, Q. 2015. Evolution of extensively drug-resistant tuberculosis over four decades revealed by whole genome sequencing of Mycobacterium tuberculosis from KwaZulu-Natal, South Africa. Proceedings of International Journal of Mycobacteriology. International Journal of Mycobacteriology. 24-25. volume 4
10) Abeel, T., Manson McGuire, A., Desjardins, C., Munsamy, V., Pym, A., Earl, A., Cohen, K. 2015. Molecular Antecedents And Timing Of XDR Emergence Revealed By Whole Genome Sequencing Of Mycobacterium Tuberculosis In Kwazulu-Natal, South Africa. Proceedings of Am J Respir Crit Care Med. Am J Respir Crit Care Med. A2181. volume 191
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


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