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2020

An educational guide for nanopore sequencing in the classroom

Salazar, A. N., Nobrega, F. L., Anyansi, C., Aparicio-Maldonado, C., Costa, A. R., Haagsma, A. C., Hiralal, A., Mahfouz, A., McKenzie, R. E., van Rossum, T., Brouns, S. J. J. & Abeel, T., 2020, In : PLoS Computational Biology. 16, 1, p. e1007314 7 p., e1007314.

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2 Citations (Scopus)
90 Downloads (Pure)

Design and Experimental Evaluation of a Minimal, Innocuous Watermarking Strategy to Distinguish Near-Identical DNA and RNA Sequences

Boonekamp, F. J., Dashko, S., Duiker, D., Gehrmann, T., van den Broek, M., den Ridder, M., Pabst, M., Robert, V., Abeel, T., Postma, E. D., Daran, J. M. & Daran-Lapujade, P., 2020, In : ACS Synthetic Biology. 9, 6, p. 1361-1375 15 p.

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QuantTB- A method to classify mixed Mycobacterium tuberculosis infections within whole genome sequencing data

Anyansi, C., Keo, A., Walker, B. J., Straub, T. J., Manson, A. L., Earl, A. M. & Abeel, T., 28 Jan 2020, In : BMC Genomics. 21, 1, 80.

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1 Citation (Scopus)
33 Downloads (Pure)

Spatially distinct physiology of Bacteroides fragilis within the proximal colon of gnotobiotic mice

Donaldson, G. P., Chou, W. C., Manson, A. L., Rogov, P., Abeel, T., Bochicchio, J., Ciulla, D., Melnikov, A., Ernst, P. B. & More Authors, 2020, In : Nature Microbiology. 5, 5, p. 746-756 11 p.

Research output: Contribution to journalArticleScientificpeer-review

1 Citation (Scopus)
2019

Chromosome level assembly and comparative genome analysis confirm lager-brewing yeasts originated from a single hybridization

Salazar, A. N., Gorter De Vries, A. R., Van Den Broek, M., Brouwers, N., de la Torre Cortes, P., Kuijpers, N. G. A., Daran, J. M. G. & Abeel, T., 2019, In : BMC Genomics. 20, 1, p. 1-18 18 p., 916.

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1 Citation (Scopus)
27 Downloads (Pure)

Extensive global movement of multidrug-resistant M. tuberculosis strains revealed by whole-genome analysis

Cohen, K. A., Manson, A. L., Abeel, T., Desjardins, C. A., Chapman, S. B., Hoffner, S., Birren, B. W. & Earl, A. M., 2019, In : Thorax. 74, 9, p. 882-889 8 p.

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6 Citations (Scopus)
62 Downloads (Pure)

Laboratory Evolution of a Saccharomyces cerevisiae × S. eubayanus Hybrid Under Simulated Lager-Brewing Conditions

Gorter de Vries, A., Voskamp, M., van Aalst, A., Kristensen, L. H., Jansen, L., Salazar, A., van den Broek, M., Brouwers, N., Abeel, T., Pronk, J. & Daran, J. M., 2019, In : Frontiers in Genetics. 10, 18 p., 242.

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9 Citations (Scopus)
92 Downloads (Pure)
2018

Approximate, simultaneous comparison of microbial genome architectures via syntenic anchoring of quiver representations

Salazar, A. N. & Abeel, T., 2018, In : Bioinformatics. 34, 17, p. i732-i742 11 p.

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1 Citation (Scopus)
30 Downloads (Pure)

Nucleus-specific expression in the multinuclear mushroom-forming fungus Agaricus bisporus reveals different nuclear regulatory programs

Gehrmann, T., Pelkmans, J. F., Ohm, R. A., Vos, A. M., Sonnenberg, A. S. M., Baars, J. J. P., Wösten, H. A. B., Reinders, M. J. T. & Abeel, T., 24 Apr 2018, In : Proceedings of the National Academy of Sciences of the United States of America. 115, 17, p. 4429-4434 6 p.

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12 Citations (Scopus)
32 Downloads (Pure)

Patterns of conservation and diversification in the fungal polarization network

Diepeveen, E. T., Gehrmann, T., Abeel, T., Pourquié, V. & Laan, L., 2018, In : Genome Biology and Evolution. 10, 7, p. 1765-1782 18 p.

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Open Access
3 Citations (Scopus)
8 Downloads (Pure)

SynerClust: A highly scalable, synteny-aware orthologue clustering tool

Georgescu, C., Manson McGuire, A. L., Griggs, A. D., Desjardins, C. A., Pironti, A., Wapinski, I., Abeel, T., Haas, B. J. & Earl, A. M., 2018, In : Microbial Genomics. 4, 11, p. 1-7 7 p.

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3 Citations (Scopus)
45 Downloads (Pure)
2017

Genomic analysis of globally diverse Mycobacterium tuberculosis strains provides insights into the emergence and spread of multidrug resistance

Manson, A. L., Cohen, K. A., Abeel, T., Desjardins, C. A., Armstrong, D. T., Barry III, C. E., Brand, J., Chapman, S. B., Cho, S-N., Gabrielian, A., Salazar, A. & More Authors, 2017, In : Nature Genetics. 49, 3, p. 395-402 8 p.

Research output: Contribution to journalArticleScientificpeer-review

91 Citations (Scopus)

Mycobacterium tuberculosis Whole Genome Sequences From Southern India Suggest Novel Resistance Mechanisms and the Need for Region-Specific Diagnostics

Manson, A. L., Abeel, T., Galagan, J. E., Chandrabose Sundaramurthi, J., Salazar, A., Gehrmann, T., Shanmugam, S. K., Palaniyandi, K., Narayanan, S., Swaminathan, S. & Earl, A. M., 2017, In : Clinical Infectious Diseases. 64, 11, p. 1494-1501 8 p.

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3 Citations (Scopus)
12 Downloads (Pure)

Nanopore sequencing enables near-complete de novo assembly of Saccharomyces cerevisiae reference strain CEN.PK113-7D

Salazar, A. N., Gorter de Vries, A. R., van den Broek, M., Wijsman, M., De La Torre Cortes, P., Brickwedde, A., Brouwers, N., Daran, J. M. G. & Abeel, T., 2017, In : FEMS Yeast Research. 17, 7, p. 1-11 11 p.

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30 Citations (Scopus)
64 Downloads (Pure)
2016

Computational pan-genomics: Status, promises and challenges

Marschall, T., Marz, M., Abeel, TEPMF., Dijkstra, L., Dutilh, B. E., Ghaffaari, A., Kersey, P., Kloosterman, W. P., de Ridder, J., Wessels, L. & More Authors, 2016, In : Briefings in Bioinformatics. p. 1-18 18 p.

Research output: Contribution to journalArticleScientificpeer-review

2 Citations (Scopus)

Draft Genome Sequences of Two Extensively Drug-Resistant Strains of Mycobacterium tuberculosis Belonging to the Euro-American S Lineage

Malinga, L. A., Abeel, TEPMF., Desjardins, C. A., Dlamini, T. C., Cassell, G., Chapman, S. B., Birren, B. W., Earl, A. M. & van der Walt, M., 2016, In : Genome Announcements. 4, 2, p. 1-2 2 p.

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1 Citation (Scopus)

Genomic and functional analyses of Mycobacterium tuberculosis strains implicate ald in D-cycloserine resistance

Desjardins, C. A., Cohen, K. A., Munsamy, V., Abeel, T., Maharaj, K., Walker, B. J., Shea, T. P., Almeida, D. V., Manson, A. L., Salazar, A. & More Authors, 2016, In : Nature Genetics. 48, 5, p. 544-551 8 p.

Research output: Contribution to journalArticleScientificpeer-review

76 Citations (Scopus)

Whole Genome Sequencing of Mycobacterium africanum Strains from Mali Provides Insights into the Mechanisms of Geographic Restriction

Winglee, K., Manson McGuire, A., Maiga, M., Abeel, TEPMF., Shea, T., Desjardins, C. A., Diarra, B., Baya, B., Sanogo, M., Diallo, S., Earl, A. M. & Bishai, W. R., 11 Jan 2016, In : PLoS Neglected Tropical Diseases (Online). 10, 1, p. 1-28 28 p.

Research output: Contribution to journalArticleScientificpeer-review

25 Citations (Scopus)
2015

Evolution of extensively drug-resistant tuberculosis over four decades: Whole genome sequencing and dating analysis of mycobacterium tuberculosis isolates from KwaZulu-Natal

Cohen, KA., Abeel, TEPMF., Manson McGuire, A., Desjardins, CA., Munsamy, V., Shea, TP., Walker, BJ., Bantubani, N., Almeida, DV., Alvarado, L., Chapman, SB., Mvelase, NR., Duffy, EY., Fitzgerald, MG., Govender, P., Gujja, S., Hamilton, S., Howarth, C., Larimer, JD., Maharaj, K. & 13 others, Pearson, MD., Priest, ME., Zeng, Q., Padayatchi, N., Grosset, J., Young, SK., Wortman, J., Mlisana, KP., O'Donnel, MR., Birren, BW., Bishai, WR., Pym, AS. & Earl, AM., 2015, In : PLoS Medicine (Print). 12, 9, p. 1-22 22 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
127 Citations (Scopus)

Molecular antecedents and timing of XDR emergence revealed by whole genome sequencing of mycobacterium tuberculosis in KwaZulu-Natal, South Africa

Cohen, KA., Abeel, TEPMF., Manson McGuire, A., Desjardins, CA., Munsamy, V., Pym, AS. & Earl, AM., 2015, In : American Journal of Respiratory and Critical Care Medicine.

Research output: Contribution to journalArticleScientificpeer-review

Open Access

Normalizing alternate representations of large sequence variants across multiple bacterial genome

Salazar, A., Earl, A., Desjardins, C. & Abeel, TEPMF., 2015, In : BMC Bioinformatics. 16, p. 1-2 2 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access

Populations of latent mycobacterium tuberculosis lack a cell wall: Isolation, visualization, and whole-genome characterization

Akbar Velayati, A., Abeel, TEPMF., Shea, T., Konstantinovich Zhavnerko, G., Birren, B., Cassell, GH., Earl, AM., Hoffner, S. & Farnia, P., 2015, In : International Journal of Mycobacteriology (online). 5, 1, p. 66-73 8 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
15 Citations (Scopus)
2014

Soft skills: An important asset acquired from organizing regional student group activities

de Ridder, J., Meysman, P., Oluwagbemi, O. & Abeel, TEPMF., 2014, In : PLoS Computational Biology (Print). 10, 7, p. 1-3 3 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
6 Citations (Scopus)
2013

Don't wear your new shoes (yet): Taking the right steps to become a successful principal investigator

de Ridder, J., Abeel, TEPMF., Michaut, M., Satagopam, VP. & Gehlenborg, N., 2013, In : PLoS ONE. 9, 1, p. 1-3 3 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
2 Citations (Scopus)