Lucas R. van Dijk, Abigail L. Manson , Ashlee M. Earl, Kiran V. Garimella, Thomas Abeel (2025), Fast and exact gap-affine partial order alignment with POASTA, In Bioinformatics Volume 41.

Nina Roothans, Martin Pabst, Menno van Diemen, Claudia Herrera Mexicano, Marcel Zandvoort, Thomas Abeel, Mark C.M. van Loosdrecht, Michele Laureni (2025), Long-term multi-meta-omics resolves the ecophysiological controls of seasonal N2O emissions during wastewater treatment, In Nature Water Volume 3 p.590-604.

Stephanie Pillay, Ramin Shirali Hossein Zade, Paul van Lent, David Calderón-Franco, Thomas Abeel (2025), Metagenomic analysis of antibiotic resistance across the wastewater process, In Heliyon Volume 11.

Nina Roothans, Minke Gabriëls, Thomas Abeel, Martin Pabst, Mark C.M. van Loosdrecht, Michele Laureni (2024), Aerobic denitrification as an N₂O source from microbial communities, In ISME Journal Volume 18.

C. Peng, Mahdi Ghanbari, Ali May, T.E.P.M.F. Abeel (2024), Effects of antibiotic growth promoter and its natural alternative on poultry cecum ecosystem: an integrated analysis of gut microbiota and host expression, In Frontiers in Microbiology Volume 15.

Julia A. Schwartzman, Francois Lebreton, Rauf Salamzade, Terrance Shea, Melissa J. Martin, Katharina Schaufler, Aysun Urhan, Thomas Abeel, Ilana L.B.C. Camargo, More Authors (2024), Global diversity of enterococci and description of 18 previously unknown species, In Proceedings of the National Academy of Sciences of the United States of America Volume 121.

Erin Noel Jordan, Ramin Shirali Hossein Zade, Stephanie Pillay, Paul van Lent, Thomas Abeel, Oliver Kayser (2024), Integrated omics of Saccharomyces cerevisiae CENPK2-1C reveals pleiotropic drug resistance and lipidomic adaptations to cannabidiol, In npj systems biology and applications Volume 10.

Aysun Urhan, Bianca-Maria Cosma, Ashlee M. Earl, Abigail L. Manson, Thomas Abeel (2024), SAFPred: Synteny-aware gene function prediction for bacteria using protein embeddings, In Bioinformatics Volume 40.

Junhan Wen, Camiel R. Verschoor, Chengming Feng, Irina Mona Epure, Thomas Abeel, Mathijs De Weerdt (2024), The Growing Strawberries Dataset: Tracking Multiple Objects with Biological Development over an Extended Period, In Proceedings - 2024 IEEE Winter Conference on Applications of Computer Vision, WACV 2024 p.7089-7099.

D. Calderon Franco, Mark C.M. van Loosdrecht, T.E.P.M.F. Abeel, D.G. Weissbrodt (2023), Catch me if you can: capturing microbial community transformation by extracellular DNA using Hi-C sequencing, In Antonie van Leeuwenhoek, International Journal of General and Molecular Microbiology Volume 116 p.667-685.