Peer-reviewed articles

Publications from the department

Journal covers made by researchers from our department

Peer-reviewed publications at MBG - 2025

Sort by: Date | Author | Title

Christiansen, M. P. V. & Hammer, B. (2025). Gradient-based grand canonical optimization enabled by graph neural networks with fractional atomic existence. Machine Learning: Science and Technology, 6(4), Article 045049. https://doi.org/10.1088/2632-2153/ae1bf6

FinnGen (2025). Complex genetic effects linked to plasma protein abundance in the UK Biobank. Nature Communications. Advance online publication. https://doi.org/10.1038/s41467-025-67235-0

Jensen, E. G., Jakobsen, T. S., Schnabolk, G., Wilson, K., Rask-Pedersen, M., Jensen, N., Andersen, G. R., Thiel, S., Aagaard, L., Rohrer, B., Askou, A. L. & Corydon, T. J. (2025). Nanobody-based gene therapy targeting complement component C3 reduces choroidal neovascularization in mice. Molecular Therapy Methods and Clinical Development, 33(4), Article 101620. https://doi.org/10.1016/j.omtm.2025.101620

Tsitsikli, M., Simonsen, B., Luu, T. B., Larsen, M. M., Andersen, C. G., Gysel, K., Lironi, D., Krönauer, C., Rübsam, H., Hansen, S. B., Bærentsen, R., Wulff, J. L., Johansen, S. H., Sezer, G., Stougaard, J., Andersen, K. R. & Radutoiu, S. (2025). Two residues reprogram immunity receptors for nitrogen-fixing symbiosis. Nature, 648(8093), 443-450. https://doi.org/10.1038/s41586-025-09696-3

Otzen, D. E., Gamon, L. F., Hägglund, P., Nielsen, J., Pedersen, J. N., Nybo, T., Nowak, J. S., Amstrup, S. K., Pirhaghi, M. & Davies, M. J. (2025). Nitrated products formed on α-synuclein are preferentially incorporated into oligomers but excluded from fibrils: A mechanism for accumulation of neurotoxic species. Biochimica et Biophysica Acta - Proteins and Proteomics, 1874(2), 141118. Advance online publication. https://doi.org/10.1016/j.bbapap.2025.141118

McLain, A., Saffie-Siebert, S. R., Nielsen, N. S., Patterson, B., Scavenius, C., Enghild, J. J., Marshall, J., Baran-Rachwalska, P., Welsh, M., Sutera, F. M., Moore, L., Willoughby, C., Nesbit, M. A. & Moore, T. (2025). Topical mutant allele-specific siRNA delivery for treatment of Meesmann epithelial corneal dystrophy and elucidation of disease biomarkers. Journal of Controlled Release, 388, Article 114315. https://doi.org/10.1016/j.jconrel.2025.114315

Peña-Díaz, S., Jiang, Y., Zhang, Z., Daugberg, A., Ferreira, P., López Hernández, M., Mittal, C., Ramos, M. J., Pedersen, J. S., Dueholm, M. K. D., Qin, C., Wang, H. & Otzen, D. E. (2025). The Importance of Being Imperfect: Structure and Function of Bacterial Amyloid. Advanced Science, e17090. Advance online publication. https://doi.org/10.1002/advs.202517090

Chrenková, A., Nashier, P., Madsen, C. L., Singh, M., Nielsen, J., Otzen, D. E., Enghild, J. J., Macek, B., Skjerning, R. B. & Brodersen, D. E. (2025). Homologous HipA-like kinases are controlled by internal translational initiation and genetic organisation. FEBS Letters. Advance online publication. https://doi.org/10.1002/1873-3468.70234

Ismail, S., Kubíková, J., Maichel, M., Andersen, P. & Jeske, M. (2025). Probing direct interactions between nuclear proteins in cells with nxReLo. Proceedings of the National Academy of Sciences of the United States of America, 122(48), Article e2518711122. https://doi.org/10.1073/pnas.2518711122

Kawamura, Y. K., Ozonov, E. A., Papasaikas, P., Kondo, T., Nguyen, N. V., Stadler, M. B., Smallwood, S. A., Koseki, H. & Peters, A. H. F. M. (2025). Preventing CpG hypermethylation in oocytes safeguards mouse development. Developmental Cell, 60(23), 3285-3303.e9. https://doi.org/10.1016/j.devcel.2025.08.005

Situ, K., Duan, H., Godin, S. K., Yang, J., McCloskey, G. Q., Naeem, B., Gillis, M. K., Zeb, M. H., Salhotra, S., Rawal, P., Patel, N., Mouliere, S. K., Chen, J., Békési, A., Pálinkás, H. L., Venkatesan, S., Green, A. M., Birkbak, N. J., Vértessy, B. G. ... Pathania, S. (2025). BRCA2 deficiency and replication stress drive APOBEC3-Mediated genomic instability. Nature Communications, 16(1), Article 9544. https://doi.org/10.1038/s41467-025-64578-6

García-Rodríguez, J. L., Korsgaard, U., Vissing, S. M., Paasch, T. P., Semenova, M., Vendelbo, S. L., Jensby, E. F., Williams, H. L., Salachan, P. V., Brandt, C. B., Hanimann, J., Lin, L., Zlobec, I., Sørensen, K. D., Kjems, J., Hager, H. & Kristensen, L. S. (2025). Cancer-associated fibroblasts shape the formation of budding cancer cells at the invasive front of human colorectal cancer. Communications Biology, 8(1), Article 1345. https://doi.org/10.1038/s42003-025-08799-x

Shyrokova, L., Egorov, A. A., Cole, A., Duque-Pedraza, J. J., Tyagi, A., Ernits, K., Mets, T., Kurata, T., Juozapaitis, J., Yang, A. L. J., Ibarra Chavez, R., Graversgaard Henriksen, F. O., Lassen, S., Atkinson, G. C., Hauryliuk, V. & Johansson, M. J. O. (2025). Characterization of five environmental phages infecting Escherichia coli K-12 isolated during a phage biology training course. Microbiology Spectrum, 13(12), Article e0227425. https://doi.org/10.1128/spectrum.02274-25

Zhang, S., Ma, J., Riera Belles, M., Besenbacher, S., Niskanen, J. E., Salokorpi, N., Hundi, S., Hytönen, M. K., Zhou, T., Li, G.-M., Ostrander, E. A., Schierup, M. H., Lohi, H. & Wang, G.-D. (2025). Determinants of de novo mutations in extended pedigrees of 43 dog breeds. Genome Biology, 26(1), Article 305. https://doi.org/10.1186/s13059-025-03804-2

Zhang, T., Bär, J., Risberg, L., Gómez Mejia, A., Hammar, H., Löffler, S., Otzen, D. E., Andreasen, M., Meyer, R. L., Melican, K., Zinkernagel, A. S. & Richter-Dahlfors, A. (2025). Dynamic visualization of extracellular matrix components in S. aureus colony biofilms reveals functional amyloids leading to the formation of cap-like structures. Biofilm, 10, Article 100318. https://doi.org/10.1016/j.bioflm.2025.100318

Garde, C., Pavlidis, M. A., Garces, P., Lange, E. J., Ramarathinam, S. H., Sokač, M., Pandey, K., Faridi, P., Ahrenfeldt, J., Chung, S., Friis, S., Kleine-Kohlbrecher, D., Birkbak, N. J., Kringelum, J. V., Rønø, B., Purcell, A. W. & Trolle, T. (2025). Endogenous viral elements constitute a complementary source of antigens for personalized cancer vaccines. NPJ vaccines, 10(1), Article 54. https://doi.org/10.1038/s41541-025-01107-y

Rasmussen, C. L. M., Frederiksen, S. F., Heegaard, C. W., Thomsen, M. S., Hede, E., Laczek, B., Körbelin, J., Wüstner, D., Thomsen, L. B., Schwaninger, M., Jensen, O. N., Moos, T. & Burkhart, A. (2025). Endothelial and neuronal engagement by AAV-BR1 gene therapy alleviates neurological symptoms and lipid deposition in a mouse model of Niemann-Pick type C2. Fluids and Barriers of the CNS, 22(1), Article 13. https://doi.org/10.1186/s12987-025-00621-4

Qin, Q., Wei, P., Usman, S., Ahamefule, C. S., Jin, C., Wang, B., Yan, K., van Aalten, D. M. F. & Fang, W. (2025). Gfa1 (glutamine fructose-6-phosphate aminotransferase) is essential for Aspergillus fumigatus growth and virulence. BMC Biology, 23(1), Article 80. https://doi.org/10.1186/s12915-025-02184-0

Gómez-Repollés, A., Villa-Rodríguez, E., Blahovska, Z., Ferguson, S. & Radutoiu, S. (2025). High-quality genome assemblies of 152 root commensal bacteria from the model legume Lotus japonicus. Scientific Data, 12(1), Article 1793. https://doi.org/10.1038/s41597-025-06078-2

Porsborg, P. S., Charmouh, A. P., Singh, V. K., Winge, S. B., Hvilsom, C., Oroperv, C., Hansen, L. T., Berner, J. A., Pelizzola, M., Laurentino, S., Neuhaus, N., Hobolth, A., Bataillon, T., Besenbacher, S., Almstrup, K. & Schierup, M. H. (2025). Long-read sequencing of primate testis and human sperm allows identification of recombination events in individuals. Nature Communications, 16(1), Article 10337. https://doi.org/10.1038/s41467-025-65248-3

Morin, M., Yin, W., MacLean, H., Devlin, B., Reichenberg, A., Swan, S. H., Buxbaum, J. D., Schendel, D., Persson, M., Laursen, T. M., Kolevzon, A., Grove, J., Klei, L., Roeder, K. & Sandin, S. (2025). Maternal body mass index in early pregnancy and autism in offspring: a population-based cohort study in Sweden and Denmark. BMC Medicine, 23(1), Article 620. https://doi.org/10.1186/s12916-025-04487-z

Hjelholt, A. J., Gholipourshahraki, T., Bai, Z., Shrestha, M., Kjolby, M., Sørensen, P. & Rohde, P. D. (2025). mLeveraging genetic correlations to prioritize drug groups for repurposing in type 2 diabetes. Pharmacogenomics Journal, 25(6), Article 33. https://doi.org/10.1038/s41397-025-00392-z

Hansen, S. B., Bartual, S. G., Yuan, H., Raimi, O. G., Gorelik, A., Ferenbach, A. T., Lytje, K., Pedersen, J. S., Drace, T., Boesen, T. & van Aalten, D. M. F. (2025). Multi-domain O-GlcNAcase structures reveal allosteric regulatory mechanisms. Nature Communications, 16(1), Article 8828. https://doi.org/10.1038/s41467-025-63893-2

Bryzek, D., Gasiorek, A., Kowalczyk, D., Santocki, M., Ciaston, I., Dobosz, E., Kolaczkowska, E., Kjøge, K., Kantyka, T., Lech, M., Potempa, B., Enghild, J. J., Potempa, J. & Koziel, J. (2025). Non-classical neutrophil extracellular traps induced by PAR2-signaling proteases. Cell Death & Disease, 16(1), Article 109. https://doi.org/10.1038/s41419-025-07428-z

Wimberley, T., Plana-Ripoll, O., Pedersen, C. B., Pedersen, M. G., Dreier, J. W., Christensen, J., Horsdal, H. T., Astrup, A., Thompson, W. K., Helenius, D., McGrath, J. J., Wray, N. R., Petersen, L. V., Vilhjálmsson, B., Mortensen, P. B. & Agerbo, E. (2025). Population-representative inference for primary and secondary outcomes in extended case-cohort designs. Discover public health, 22(1), Article 599. https://doi.org/10.1186/s12982-025-00888-w

Gobet, A., Moissonnier, L., Zarkadas, E., Magnard, S., Bettler, E., Martin, J., Terreux, R., Schoehn, G., Orelle, C., Jault, J. M., Falson, P. & Chaptal, V. (2025). Rhodamine6G and Hœchst33342 narrow BmrA conformational spectrum for a more efficient use of ATP. Nature Communications, 16(1), Article 1745. https://doi.org/10.1038/s41467-025-56849-z

Thorsen, T. S., Kulkarni, Y., Sykes, D. A., Bøggild, A., Drace, T., Hompluem, P., Iliopoulos-Tsoutsouvas, C., Nikas, S. P., Daver, H., Makriyannis, A., Nissen, P., Gajhede, M., Veprintsev, D. B., Boesen, T., Kastrup, J. S. & Gloriam, D. E. (2025). Structural basis of THC analog activity at the Cannabinoid 1 receptor. Nature Communications, 16(1), Article 486. https://doi.org/10.1038/s41467-024-55808-4

Wang, X., Nursyifa, C., Aninta, S. G., Garcia-Erill, G., Bertola, L. D., Khan, A., Kuja, J., Hanghøj, K., Meisner, J., Bøggild, T., Bradshaw, C. J. A., Al-Chaer, A., Persada, A. P., Priyono, D. S., Tribudi, Y. A., Sudrajad, P., Gaina, C. D., Jiang, Y., Lenstra, J. A. ... Heller, R. (2025). The genetic diversity of Indonesian cattle has been shaped by multiple introductions and adaptive introgression. Nature Communications, 16(1), Article 8192. https://doi.org/10.1038/s41467-025-62692-z

Waligórska, I., Żak, K. M., Mikrut, N., Budziaszek, J., Medviediev, V., Bielecka, E., Kantyka, T., Kozieł, J., Thøgersen, I. B., Enghild, J. J., Grudnik, P., Potempa, J. & Książek, M. (2025). Periodontopathogens degrade angiotensin I from the human renin-angiotensin system through surface-attached proteases. Scientific Reports. Advance online publication. https://doi.org/10.1038/s41598-025-27891-0

Gobet, A. & Flygaard, R. K. (2025). CDP-alcohol phosphotransferases: Structures and function of highly diverse sub-classes within a protein family. Journal of Structural Biology, 217(4), Article 108266. https://doi.org/10.1016/j.jsb.2025.108266

Novosylna, O., Shalak, V., Dąbrowska, K., Patmanidis, I., Lozhko, D., Bondarchuk, T., Schiøtt, B., Pedersen, J. S., Knudsen, C. R., Nissen, P., Dadlez, M. & Negrutskii, B. (2025). Dynamics and structural features of the eEF1A1 and eEF1A2 paralogs. Nucleic Acids Research, 53(21), Article gkaf1177. https://doi.org/10.1093/nar/gkaf1177

Jiang, Y. & Kjems, J. (2025). RNA denaturation underlies circular RNA separation. Nucleic Acids Research, 53(21), Article gkaf1160. https://doi.org/10.1093/nar/gkaf1160

Yu, X., Liu, C. D., Shen, S., Kim, E. S., Liu, Z., Zhang, H., Sun, N., Liu, Y., Martensen, P. M., Huang, Y. & Guo, H. (2025). Interferon alpha-inducible protein 27 (IFI27) inhibits hepatitis B virus (HBV) transcription through downregulating cellular transcription factor C/EBPα. Journal of Virology, 99(11), e0150925. https://doi.org/10.1128/jvi.01509-25

Jansen, S. A. H., Dreyer, L. S. A., van Basten, J., Yao, Y., Otzen, D. E., de Greef, T. F. A., Knowles, T. P. J., Meijer, E. W. & Erkamp, N. A. (2025). PhaseXplorer Creates High-Dimensional Phase Diagrams with Closed-Loop Active Learning. ACS Nano, 19(45), 38981-38989. https://doi.org/10.1021/acsnano.5c07268

Demontis, D., Duan, J., Hsu, Y.-H. H., Pintacuda, G., Grove, J., Nielsen, T. T., Thirstrup, J., Martorana, M., Botts, T., Satterstrom, F. K., Bybjerg-Grauholm, J., Tsai, J. H. Y., Glerup, S., Hoogman, M., Buitelaar, J., Klein, M., Ziegler, G. C., Jacob, C., Grimm, O. ... Børglum, A. D. (2025). Rare genetic variants confer a high risk of ADHD and implicate neuronal biology. Nature. Advance online publication. https://doi.org/10.1038/s41586-025-09702-8

Talay, A., Belikov, A. V., To, P. K. P., Alfatemi, H. H., Alon, U., Deelen, J., Ewald, C. Y., Gems, D., Gorbunova, V., Gruber, J., Hägg, S., Hemming, J., Horvath, S., Kaya, A., Lewis, C. J., Maier, A. B., Marinova, M. B., Pawelec, G., Peleg, S. ... de Magalhães, J. P. (2025). Open problems in ageing science: a roadmap for biogerontology. GeroScience. Advance online publication. https://doi.org/10.1007/s11357-025-01964-4

Bærentsen, R. L., Kronborg, K., Brodersen, D. E. & Zhang, Y. E. (2025). Catalytic mechanism and differential alarmone regulation of a conserved stringent nucleosidase. Structure. Advance online publication. https://doi.org/10.1016/j.str.2025.10.012

Gabs, E., Aalto-Setälä, E., Välisaari, A., Malinen, A. M., Jensen, T. H., McLaughlin, S. H., Passmore, L. A. & Turtola, M. (2025). A kinetic ruler controls mRNA poly(A) tail length. Genes & Development, 39(21-22), 1377-1394. https://doi.org/10.1101/gad.352912.125