Most recent publications

  • 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]
  • 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.
  • 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]
  • Normalizing alternate representations of large sequence variants across multiple bacterial genomes. BMC Bioinformatics Salazar, A., Earl, A., Desjardins, C., Abeel, T.

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