D. Calderon Franco, Mark C.M. van Loosdrecht, T.E.P.M.F. Abeel, D.G. Weissbrodt (2020), Free-floating extracellular DNA: systematic profiling of mobile genetic elements and antibiotic resistance from wastewater, In Water Research Volume 189.

Christine Anyansi, D.L. Keo, Bruce J. Walker, Timothy J. Straub, Abigail L. Manson, Ashlee M. Earl, Thomas Abeel (2020), QuantTB- A method to classify mixed Mycobacterium tuberculosis infections within whole genome sequencing data, In BMC Genomics Volume 21.

Gregory P. Donaldson, Wen Chi Chou, Abigail L. Manson, Peter Rogov, Thomas Abeel, James Bochicchio, Dawn Ciulla, Alexandre Melnikov, Peter B. Ernst, More Authors (2020), Spatially distinct physiology of Bacteroides fragilis within the proximal colon of gnotobiotic mice, In Nature Reviews Microbiology Volume 5 p.746-756.

Alex N. Salazar, Arthur R. Gorter De Vries, Marcel Van Den Broek, Nick Brouwers, Pilar de la Torre Cortes, Niels G.A. Kuijpers, Jean Marc G. Daran, Thomas Abeel (2019), Chromosome level assembly and comparative genome analysis confirm lager-brewing yeasts originated from a single hybridization, In BMC Genomics Volume 20 p.1-18.

Keira A. Cohen, Abigail L. Manson, Christopher A. Desjardins, Thomas Abeel, Ashlee M. Earl (2019), Deciphering drug resistance in Mycobacterium tuberculosis using whole-genome sequencing: Progress, promise, and challenges, In Genome Medicine p.1-18.

Keira A. Cohen, Abigail L. Manson, Thomas Abeel, Christopher A. Desjardins, Sinead B. Chapman, Sven Hoffner, Bruce W. Birren, Ashlee M. Earl (2019), Extensive global movement of multidrug-resistant M. tuberculosis strains revealed by whole-genome analysis, In Thorax Volume 74 p.882-889.

Arthur Gorter de Vries, Maaike Voskamp, Aafke van Aalst, L.H. Kristensen, Liset Jansen, Alex Salazar, Marcel van den Broek, Nick Brouwers, Thomas Abeel, Jack Pronk, Jean Marc Daran (2019), Laboratory Evolution of a Saccharomyces cerevisiae × S. eubayanus Hybrid Under Simulated Lager-Brewing Conditions, In Frontiers in Genetics Volume 10.

Alex N. Salazar, Thomas Abeel (2018), Approximate, simultaneous comparison of microbial genome architectures via syntenic anchoring of quiver representations, In Bioinformatics Volume 34 p.i732-i742.

Thies Gehrmann, Jordi F. Pelkmans, Robin A. Ohm, Aurin M. Vos, Anton S.M. Sonnenberg, Johan J.P. Baars, Han A.B. Wösten, Marcel J.T. Reinders, Thomas Abeel (2018), Nucleus-specific expression in the multinuclear mushroom-forming fungus Agaricus bisporus reveals different nuclear regulatory programs, In Proceedings of the National Academy of Sciences of the United States of America Volume 115 p.4429-4434.

Eveline T. Diepeveen, Thies Gehrmann, Thomas Abeel, Valérie Pourquié, Liedewij Laan (2018), Patterns of conservation and diversification in the fungal polarization network, In Genome Biology and Evolution Volume 10 p.1765-1782.