Most recent publications

All publications

  • Evidence for highly variable, region-specific patterns of T-cell epitope mutations accumulating in Mycobacterium tuberculosis strains. Frontiers in Immunology Ramaiah, A., Nayak, S., Rakshit, S., Manson, K., Shanmugam, S., Abeel, T., Sundaramurthi, J., Narayanan, S., Jesuraj, A., Dâ??Souza, G., Hoegen, P., Ottenhoff, T., Earl, A., Swaminathan, S., Vyakarnam, A.
  • Approximate, simultaneous comparison of microbial genome architectures via syntenic anchoring of quiver representations. Bioinformatics Salazar, A., Abeel, T. [PubMed] [PMC]
  • Patterns of conservation and diversification in the fungal polarization network. Genome biology and evolution Diepeveen, E., Gehrmann, T., Pourquié, V., Abeel, T., Laan, L. [PubMed]
  • Nucleus-specific expression in the multinuclear mushroom-forming fungus Agaricus bisporus reveals different nuclear regulatory programs. PNAS Gehrmann, T., Pelkmans, J., Ohm, R., Vos, A., Sonnenberg, A., Baars, J., Wösten, H., Reinders, M., Abeel, T. [PubMed]
  • SynerClust: a highly scalable, synteny-aware ortholog clustering tool. Microbial Genomics Georgescu, C., Manson, A., Griggs, A., Desjardins, C., Pironti, A., Wapinski, I., Regev, A., Abeel, T., Haas, B., Earl, A. [PubMed]
  • Nanopore sequencing enables near-complete de novo assembly of Saccharomyces cerevisiae reference strain CEN. PK113-7D. FEMS Yeast Research Salazar, A., Vries, A., Broek, M., Wijsman, M., Cortés, P., Brickwedde, A., Brouwers, N., Daran, J., Abeel, T. [PubMed]
  • Mycobacterium tuberculosis Whole Genome Sequences From Southern India Suggest Novel Resistance Mechanisms and the Need for Region-Specific Diagnostics. Clinical Infectious Diseases Manson, A., Abeel, T., Galagan, J., Sundaramurthi, J., Salazar, A., Gehrmann, T., Shanmugam, S., Palaniyandi, K., Narayanan, S., Swaminathan, S., Earl, A. [PubMed]
  • 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]