2025 (5)

• Durka, W., Michalski, S.G., Höfner, J., Bucharova, A., Kolář, F., Müller, C.M., Oberprieler, C., Šemberová, K., Bauer, M., Bernt, M., Bleeker, W., Brändel, S., Bucher, S.F., Eibes, P.M., Ewald, M., Goldberg, R., Grant, K., Haider, S., Harpke, A., Haun, F., Kaufmann, R., Korell, L., Kunzmann, D., Lauterbach, D., Leib, S., Lenzewski, N., Loritz, H., Madaj, A.-M., Mainz, A.K., Meinecke, P., Mertens, H., Meyer, H.M., Musche, M., Ristow, M., Rosche, C., Roscher, C., Rutte, D., Schacherer, A., Schmidt, W., Schmoldt, J., Schneider, S., Schwarz, J.-H., Skowronek, S., Socher, S.A., Stanik, N., Twerski, A., Weiß, K., Weiß, M., Wille, A., Zehm, A., Zidorn, C., the RegioDiv Consortium, (2025):
  Assessment of genetic diversity among seed transfer zones for multiple grassland plant species across Germany
  Basic Appl. Ecol. 84 , 50 - 60
  10.1016/j.baae.2024.11.004
• Massei, R., Busch, W., Serrano-Solano, B., Bernt, M., Scholz, S., Nicolay, E.K., Bohring, H., Bumberger, J. (2025):
  High-content screening (HCS) workflows for FAIR image data management with OMERO
  Sci. Rep. 15 , art. 16236
  10.1038/s41598-025-00720-0
• Nasr, E., Pechlivanis, N., Strepis, N., Amato, P., Bernt, M., Bhardwaj, A., Blankenberg, D., Brites, D., Cumbo, F., Do, K.T., Ferrari, E., Griffin, T.J., Grüning, B., Hiltemann, S., Hyde, C.J., Jagtap, P., Mehta, S., Métris, K.L., Momin, S., Nelson, T.M., Oba, A., Pavloudi, C., Péguilhan, R., Price, G.R., Psomopoulos, F., Rosic, N., Schatz, M.C., Schiml, V.C., Siguret, C., Soranzo, N., Stubbs, A., van Heusden, P., Vohra, M., microGalaxy Community, Zierep, P., Batut, B. (2025):
  Microbiology Galaxy Lab: The first community-driven gateway for reproducible and FAIR analysis of microbial data
  bioRxiv
  10.1101/2024.12.23.629682
• Saraiva, J.P., Borim Corrêa, F., Bernt, M., Ghanem, N., Nieto, E., Brizola Toscan, R., Wick, L.Y., Chatzinotas, A. (2025):
  PHI: Prophage-Host Interaction toolkit for automated prediction and comprehensive profiling of prophages and their hosts via Galaxy
  bioRxiv
  10.64898/2025.12.02.691814
• Schor, J., Scheibe, P., Bernt, M., Hackermüller, J. (2025):
  deepFPlearn - AI for predicting chemical-effect associations at the chemical universe level
  Version: v1.2 Zenodo
  10.5281/zenodo.13329413

2024 (7)

• Abueg, L.A.L., Afgan, E., Allart, O., Awan, A.H., Bacon, W.A., Baker, D., Bassetti, M., Batut, B., Bernt, M., Zoabi, R., et al., The Galaxy Community (2024):
  The Galaxy platform for accessible, reproducible, and collaborative data analyses: 2024 update
  Nucleic Acids Res. 52 (W1), W83 - W94
  10.1093/nar/gkae410
• Batut, B., Bacon, W., Zierep, P., Bernt, M., Soranzo, N., Gustafsson, J. (2024):
  Galaxy CoDex for finding tools, workflows, and training [version 1]
  Galaxy Community Conference 2024
  F1000Research 13
  F1000 Research Ltd, London, 705 (slides)
  10.7490/f1000research.1119764.1
• Batut, B., Bernt, M., Hojat Ansari, M., Kalaš, M., Klemm, P., Libouban, R., Nasr, E., Rioualen, C., Thang, W.C., Zoabi, R., Zierep, P. (2024):
  How to improve the annotation of Galaxy resources? Outcomes of an online hackathon for improving the annotation of Galaxy resources for microbial data resources
  BioHackrXiv Preprints
  10.37044/osf.io/s7tru
• Fiedler, L., Bernt, M., Middendorf, M. (2024):
  DeGeCI 1.1: a web platform for gene annotation of mitochondrial genomes
  Bioinform. Adv. 4 (1), vbae072
  10.1093/bioadv/vbae072
• Hartmann, T., Middendorf, M., Bernt, M. (2024):
  Genome rearrangement analysis: Cut and join genome rearrangements and gene cluster preserving approaches
  In: Setubal, J.C., Stadler, P.F., Stoye, J. (eds.)
  Comparative genomics: Methods and protocols
  Methods in Molecular Biology 2802
  Springer Nature, p. 215 - 245
  10.1007/978-1-0716-3838-5_9
• Ozerova, I., Fallmann, J., Mörl, M., Bernt, M., Prohaska, S.J., Stadler, P.F. (2024):
  Aberrant mitochondrial tRNA genes appear frequently in animal evolution
  Genome Biol. Evol. 16 (11), evae232
  10.1093/gbe/evae232
• Pfeuffer, J., Bielow, C., Wein, S., Jeong, K., Netz, E., Walter, A., Alka, O., Nilse, L., Colaianni, P.D., McCloskey, D., Kim, J., Rosenberger, G., Bichmann, L., Walzer, M., Veit, J., Boudaud, B., Bernt, M., Patikas, N., Pilz, M., Startek, M.P., Kutuzova, S., Heumos, L., Charkow, J., Sing, J.C., Feroz, A., Siraj, A., Weisser, H., Dijkstra, T.M.H., Perez-Riverol, Y., Röst, H., Kohlbacher, O., Sachsenberg, T. (2024):
  OpenMS 3 enables reproducible analysis of large-scale mass spectrometry data
  Nat. Methods 21 (3), 365 - 367
  10.1038/s41592-024-02197-7

2023 (7)

• Bray, S., Chilton, J., Bernt, M., Soranzo, N., van den Beek, M., Batut, B., Rasche, H., Čech, M., Cock, P.J.A., Grüning, B., Nekrutenko, A. (2023):
  The Planemo toolkit for developing, deploying, and executing scientific data analyses in Galaxy and beyond
  Genome Res. 33 , 261 - 268
  10.1101/gr.276963.122
• Fiedler, L., Bernt, M., Middendorf, M., Stadler, P.F. (2023):
  Detecting gene breakpoints in noisy genome sequences using position-annotated colored de-Bruijn graphs
  BMC Bioinformatics 24 , art. 235
  10.1186/s12859-023-05371-4
• Fiedler, L., Middendorf, M., Bernt, M. (2023):
  Fully automated annotation of mitochondrial genomes using a cluster-based approach with de Bruijn graphs
  Front. Genet. 14 , art. 1250907
  10.3389/fgene.2023.1250907
• Mehta, S., Bernt, M., Chambers, M., Fahrner, M., Föll, M.C., Gruening, B., Horro, C., Johnson, J.E., Loux, V., Rajczewski, A.T., Schilling, O., Vandenbrouck, Y., Gustafsson, O.J.R., Thang, W.C.M., Hyde, C., Price, G., Jagtap, P.D., Griffin, T.J. (2023):
  A Galaxy of informatics resources for MS-based proteomics
  Expert Rev. Proteomics 20 (11), 251 - 266
  10.1080/14789450.2023.2265062
• Schor, J., Scheibe, P., Soulios, K., Bernt, M. (2023):
  deepFPlearn +: enhancing toxicity prediction across the chemical universe using graph neural networks
  Version: v2.0 Zenodo
  10.5281/zenodo.13329443
• Soulios, K., Scheibe, P., Bernt, M., Hackermüller, J., Schor, J. (2023):
  deepFPlearn+
  Zenodo
  10.5281/zenodo.8146252
• Soulios, K., Scheibe, P., Bernt, M., Hackermüller, J., Schor, J. (2023):
  deepFPlearn⁺: enhancing toxicity prediction across the chemical universe using graph neural networks
  Bioinformatics 39 (12), btad713
  10.1093/bioinformatics/btad713

2022 (4)

• Fahrner, M., Föll, M.C., Grüning, B.A., Bernt, M., Röst, H., Schilling, O. (2022):
  Democratizing data-independent acquisition proteomics analysis on public cloud infrastructures via the Galaxy framework
  GigaScience 11 , giac005
  10.1093/gigascience/giac005
• Ostrovsky, A.E., Mahmoud, A., Lonie, A., Syme, A., Fouilloux, A., Bretaudeau, A., Nekrutenko, A., Kumar, A., Eschenlauer, A.C., DeSanto, A.D., Guerler, A., Serrano-Solano, B., Batut, B., Grüning, B.A., Langhorst, B.W., Carr, B., Blankenberg, D., Goecks, J., Bernt, M., Schatz, M.C., et al., The Galaxy Community (2022):
  The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2022 update
  Nucleic Acids Res. 50 (W1), W345 - W351
  10.1093/nar/gkac247
• Schor, J., Scheibe, P., Bernt, M., Busch, W., Lai, C., Hackermüller, J. (2022):
  AI for predicting chemical-effect associations at the chemical universe level — deepFPlearn
  Brief. Bioinform. 23 (5), bbac257
  10.1093/bib/bbac257
• VijayKrishna, N., Joshi, J., Coraor, N., Hillman-Jackson, J., Bouvier, D., van den Beek, M., Eguinoa, I., Coppens, F., Davis, J., Stolarczyk, M., Sheffield, N.C., Gladman, S., Cuccuru, G., Grüning, B., Soranzo, N., Rasche, H., Langhorst, B.W., Bernt, M., Fornika, D., de Lima Morais, D.A., Barrette, M., van Heusden, P., Petrillo, M., Puertas-Gallardo, A., Patak, A., Hotz, H.-R., Blankenberg, D. (2022):
  Expanding the Galaxy’s reference data
  Bioinform. Adv. 2 (1), vbac030
  10.1093/bioadv/vbac030

2019 (3)

• Donath, A., Jühling, F., Al-Arab, M., Bernhart, S.H., Reinhardt, F., Stadler, P.F., Middendorf, M., Bernt, M. (2019):
  Improved annotation of protein-coding genes boundaries in metazoan mitochondrial genomes
  Nucleic Acids Res. 47 (20), 10543 - 10552
  10.1093/nar/gkz833
• Hartmann, T., Bernt, M., Middendorf, M. (2019):
  An exact algorithm for sorting by weighted preserving genome rearrangements
  IEEE-ACM Trans. Comput. Biol. Bioinform. 16 (1), 52 - 62
  10.1109/TCBB.2018.2831661
• Li, Y., Kocot, K.M., Tassia, M.G., Cannon, J.T., Bernt, M., Halanych, K.M. (2019):
  Mitogenomics reveals a novel genetic code in Hemichordata
  Genome Biol. Evol. 11 (1), 29 - 40
  10.1093/gbe/evy254

2018 (1)

• Hartmann, T., Bernt, M., Middendorf, M. (2018):
  EqualTDRL: illustrating equivalent tandem duplication random loss rearrangements
  BMC Bioinformatics 19 , art. 192
  10.1186/s12859-018-2170-x

2017 (1)

• Al Arab, M., Bernt, M., Höner zu Siederdissen, C., Tout, K., Stadler, P.F. (2017):
  Partially local three-way alignments and the sequence signatures of mitochondrial genome rearrangements
  Algorithms Mol. Biol. 12 , art. 22
  10.1186/s13015-017-0113-0