Most recent publications

  • 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.
  • 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.
  • Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLOS One Walker*, B., Abeel*, T., Shea, T., Priest, M., Abouelliel, A., Sakthikumar, S., Cuomo, C., Zeng, Q., Wortman, J., Young, S., Earl, A. [PubMed]
  • Evolution of invasion in a diverse set of Fusobacterium species. mBio 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. [PubMed]


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 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.

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