D. Calderon Franco, R.G. Sarelse, S. Christou, M. Pronk, Mark C.M. van Loosdrecht, T.E.P.M.F. Abeel, D.G. Weissbrodt (2022), Metagenomic profiling and transfer dynamics of antibiotic resistance determinants in a full-scale granular sludge wastewater treatment plant, In Water Research Volume 219.

S. Pillay, D. Calderon Franco, A. Urhan, T.E.P.M.F. Abeel (2022), Metagenomic-based surveillance systems for antibiotic resistance in non-clinical settings, In Frontiers in Microbiology Volume 13.

Lucas R. van Dijk, Bruce J. Walker, Timothy J. Straub, Colin J. Worby, Alexandra Grote, Henry L. Schreiber, Christine Anyansi, Amy J. Pickering, Scott J. Hultgren, Abigail L. Manson, Thomas Abeel, Ashlee M. Earl (2022), StrainGE: a toolkit to track and characterize low-abundance strains in complex microbial communities, In Genome biology Volume 23.

A. Urhan, T.E.P.M.F. Abeel (2021), A comparative study of pan-genome methods for microbial organisms: Acinetobacter baumannii pan-genome reveals structural variation in antimicrobial resistance-carrying plasmids, In Microbial Genomics Volume 7.

Aysun Urhan, Thomas Abeel (2021), Emergence of novel SARS-CoV-2 variants in the Netherlands, In Scientific Reports Volume 11.

Alex N. Salazar, Franklin L. Nobrega, Christine Anyansi, Cristian Aparicio-Maldonado, Ana Rita Costa, Anna C. Haagsma, Anwar Hiralal, Ahmed Mahfouz, Rebecca E. McKenzie, Teunke van Rossum, Stan J.J. Brouns, Thomas Abeel (2020), An educational guide for nanopore sequencing in the classroom, In PLoS Computational Biology Volume 16 p.e1007314.

Christine Anyansi, Timothy J. Straub, Abigail L. Manson, Ashlee M. Earl, Thomas Abeel (2020), Computational Methods for Strain-Level Microbial Detection in Colony and Metagenome Sequencing Data, In Frontiers in Microbiology p.1-17.

Francine J. Boonekamp, Sofiia Dashko, Donna Duiker, Thies Gehrmann, Marcel van den Broek, Maxime den Ridder, Martin Pabst, Vincent Robert, Thomas Abeel, Eline D. Postma, Jean Marc Daran, Pascale Daran-Lapujade (2020), Design and Experimental Evaluation of a Minimal, Innocuous Watermarking Strategy to Distinguish Near-Identical DNA and RNA Sequences, In ACS Synthetic Biology Volume 9 p.1361-1375.

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.