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Research Output

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.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
File
2 Citations (Scopus)
90 Downloads (Pure)

Computational Methods for Strain-Level Microbial Detection in Colony and Metagenome Sequencing Data

Anyansi, C., Straub, T. J., Manson, A. L., Earl, A. M. & Abeel, T., 2020, In : Frontiers in Microbiology. 11, p. 1-17 17 p., 1925.

Research output: Contribution to journalReview articleScientificpeer-review

Open Access
File
1 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.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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10 Downloads (Pure)

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.

Research output: Contribution to journalArticleScientificpeer-review

File
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.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
File
1 Citation (Scopus)
27 Downloads (Pure)

Deciphering drug resistance in Mycobacterium tuberculosis using whole-genome sequencing: Progress, promise, and challenges

Cohen, K. A., Manson, A. L., Desjardins, C. A., Abeel, T. & Earl, A. M., 2019, In : Genome Medicine. 11, 1, p. 1-18 18 p., 45.

Research output: Contribution to journalReview articleScientificpeer-review

Open Access
File
5 Citations (Scopus)
53 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.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
File
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.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
File
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.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
File
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.

Research output: Contribution to journalArticleScientificpeer-review

File
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.

Research output: Contribution to journalArticleScientificpeer-review

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

Reply to Lee and Howden

Manson, A. L., Abeel, T., Galagan, J., Chandrabose Sundaramurthi, J., Shanmugam, S. K., Palaniyandi, K., Narayanan, S., Swaminathan, S. & Earl, A. M., 2018, In : Clinical Infectious Diseases. 66, 1, p. 160-161 2 p.

Research output: Contribution to journalComment/Letter to the editorScientific

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.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
File
3 Citations (Scopus)
45 Downloads (Pure)
2017

Evolution of laboratory-made S. cerevisiae x S. eubayanus hybrid to investigate the domestication of S. pastorianus

Gorter de Vries, A., van Aalst, A., Jansen, L., Christensen, L. H., van den Broek, M., Salazar, A., Brouwers, N., Abeel, T., Pronk, J. & Daran, J. M., 2017.

Research output: Contribution to conferencePosterProfessional

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.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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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.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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30 Citations (Scopus)
64 Downloads (Pure)

Targeted chromosome copy number engineering in aneuploid lager-brewing yeast

Gorter de Vries, A., Knibbe, E., van Roosmalen, R., el Masoudi, A., Salazar, A., van den Broek, M., Brouwers, N., Pronk, J., Abeel, T. & Daran, J. M., 2017.

Research output: Contribution to conferencePosterProfessional

The Diaspora of Multidrug-Resistant Tuberculosis: Whole-Genome Analysis of Globally Migrant MDR Clades

Cohen, K. A., Manson, A., Abeel, T., Desjardins, C., Birren, B. & Earl, A. M., 2017, p. 1-1. 1 p.

Research output: Contribution to conferenceAbstractScientific

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.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
File
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)

Karyollele specific expression in Agaricus Bisporus

Gehrmann, T., Pelkmans, J. F., Wösten, H. A. B., Ohm, R., Sonnenberg, A., Baars, J. J. P., Reinders, M. & Abeel, T., 2016. 1 p.

Research output: Contribution to conferencePosterScientific

Open Access
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9 Downloads (Pure)

Whole Genome Analysis of 5,310 Globally Diverse Mycobacterium Tuberculosis Isolates Reveals Consistent Ordering in the Emergence of Drug Resistance

Cohen, KA., Manson McGuire, A., Abeel, T., Desjardins, C. A., Pym, AS. & Earl, A. M., 2016, p. 1-1. 1 p.

Research output: Contribution to conferenceAbstractScientific

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

Detecting mixed Mycobacterium tuberculosis infection and differences in drug susceptibility with WGS data

Keo, A. & Abeel, T., Dec 2015. 1 p.

Research output: Contribution to conferencePosterScientific

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)
2012

Semantically linking molecular entities in literature through entity relationships

Landeghem, S., Bjorne, J., Abeel, TEPMF., De Baets, B., Salakoski, T. & van de Peer, Y., 2012, Proceedings of the BioNLP shared task 2011. Kim, JD., Nguyen, N., Wang, Y., Tsujii, JI., Takagi, T. & Yonezawa, A. (eds.). London: BioMed Central, p. 1-9 9 p. (BMC Bioinformatics; vol. 13).

Research output: Chapter in Book/Conference proceedings/Edited volumeConference contributionScientificpeer-review

Open Access
11 Citations (Scopus)