Most recent publications

  • Genomic analysis of globally diverse Mycobacterium tuberculosis strains provides insights into the emergence and spread of multidrug resistance. Nature Genetics 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, . [PubMed]
  • Whole genome sequencing of Mycobacterium tuberculosis provides insight into the evolution and genetic composition of drug-resistant tuberculosis in Belarus. Journal of Clinical Microbiology 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. [PubMed]
  • Computational pan-Genomics: Status, Promises and Challenges. Briefings in bioinformatics 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. [PubMed]
  • Schizophyllum commune has an extensive and functional alternative splicing repertoire.. Nature Scientific Reports Gehrmann, T., Pelkmans, J., Lugones, L., Wösten, H., Abeel*, T., Reinders*, M. [PubMed]
  • Genomic and functional analyses of Mycobacterium tuberculosis strains implicate ald in d-cycloserine resistance. Nature Genetics 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. [PubMed]
  • Draft genome sequences of two extensively drug-resistant strains of Mycobacterium tuberculosis belonging to the Euro-American S lineage. Genome announcements Malinga, L., Abeel, T., Desjardins, C., Dlamini, T., Cassell, G., Chapman, S., Birren, B., Earl, A., Walt, M. [PubMed]
  • Populations of latent Mycobacterium tuberculosis lack a cell wall: Isolation, visualization, and whole-genome characterization. International Journal of Mycobacteriology Velayati, A., Abeel, T., Shea, T., Zhavnerko, G., Birren, B., Cassell, G., Earl, A., Hoffner, S., Farnia, P. [PubMed]
  • Whole Genome Sequencing of Mycobacterium africanum Strains from Mali Provides Insights into the Mechanisms of Geographic Restriction.. PLOS Neglected Tropical Diseases Winglee, K., Manson, M., Maiga, M., Abeel, T., Shea, T., Desjardins, C., Diarra, B., Baya, B., Sanogo, M., Diallo, S., Earl, A., Bishai, W. [PubMed]
  • Evolution of extensively drug-resistant tuberculosis over four decades: whole genome sequencing and dating analysis of Mycobacterium tuberculosis isolates from KwaZulu-Natal. PLOS Medicine 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. [PubMed]
  • Fatal Nosocomial MDR TB Identified through Routine Genetic Analysis and Whole-Genome Sequencing. Emerging Infectious Diseases Williams, O., Abeel, T., Casali, N., Cohen, K., Pym, A., Mungall, S., Desjardins, C., Banerjee, A., Drobniewski, F., Earl, A., Cooke, G. [PubMed]

Lab software projects

GenomeView

GenomeView logo

GenomeView is a next-generation stand-alone genome browser and editor initiated in the BSB group at VIB and currently developed at Broad Institute. It provides interactive visualization of sequences, annotation, multiple alignments, syntenic mappings, short read alignments and more. Many standard file formats are supported and new functionality can be added using a plugin system.

Java-ML

Java-ML logo Java-ML is a collection of machine learning algorithms with a common interface for each type of algorithms. The library is aimed at software engineers and programmers, so no GUI, but clear interfaces. It provides reference implementations for algorithms described in the scientific literature, it has well documented source code and provides plenty of code samples and tutorials.

Other projects