Publications

Peer-reviewed artikler

Lennartsson, C., Kyriakidou, P., Nielsen, M. L., Olsen, J. V., Cox, J. & Hendriks, I. A. (2026). Improved peptide search for identification of SUMO and sequence-based modifications, in MaxSBM. Molecular & Cellular Proteomics : MCP, Artikel 101589. Advance online publication. https://doi.org/10.1016/j.mcpro.2026.101589

Groslambert, J., Buch-Larsen, S. C., Hendriks, I. A., Kurzbauer, R., Elsborg, J. D., Chatrin, C., Agnew, T., Henfrey, C., Tellier, M., Prokhorova, E., Hoang, S. M., Barosso-Gonzalez, J., O’Sullivan, R. J., Clausen, T., Nielsen, M. L. & Ahel, I. (2026). PARG regulates the proteasomal degradation of TARG1. Cell Reports, 45(1), Artikel 116789. https://doi.org/10.1016/j.celrep.2025.116789

Cho, H., Nielsen, M. L. & Olsen, J. V. (2026). Quantitative proteomics and phosphoproteomics reveal glucocorticoid stimulation of TLR and Rho GTPase signaling in neutrophil-like cells. Genome Biology, 27(1), Artikel 77. https://doi.org/10.1186/s13059-026-03985-4

Bone, R. A., Lowndes, M. P., Raineri, S., R Riveiro, A., Lundregan, S. L., Dall, M., Sulek, K., Romero, J. A. H., Malzard, L., Koigi, S., Heckenbach, I. J., Solis-Mezarino, V., Völker-Albert, M., Vasilopoulou, C. G., Meier, F., Trusina, A., Mann, M., L Nielsen, M., Treebak, J. T. & Brickman, J. M. (2025). Altering metabolism programs cell identity via NAD⁺-dependent deacetylation. EMBO Journal, 44(11), 3056-3084. https://doi.org/10.1038/s44318-025-00417-0

Sellés-Baiget, S., Ambjørn, S. M., Carli, A., Hendriks, I. A., Gallina, I., Davey, N. E., Benedict, B., Zarantonello, A., Gadi, S. A., Meeusen, B., Hertz, E. P. T., Slappendel, L., Semlow, D., Sturla, S., Nielsen, M. L., Nilsson, J., Miller, T. C. R. & Duxin, J. P. (2025). Catalytic and noncatalytic functions of DNA polymerase κ in translesion DNA synthesis. Nature Structural and Molecular Biology, 32(2), 300–314. Artikel 15125. https://doi.org/10.1038/s41594-024-01395-3

Ingham, A., de Vega, I. A., Morlot, L., Gittens, W., Hendriks, I. A., Kakulidis, E. S., Freire, R., Davey, N. E., Duxin, J. P., Lund Nielsen, M. & Mailand, N. (2025). CRAMP1-dependent histone H1 biogenesis is essential for topoisomerase II inhibitor tolerance. Molecular Cell, 85(13), 2487-2502. https://doi.org/10.1016/j.molcel.2025.04.006

Anagho-Mattanovich, M., Anagho-Mattanovich, H. A., Argemi-Muntadas, L., Nielsen, M. L., Gao, Q. & Moritz, T. (2025). Multi-omics analysis of thermogenic lipolysis in brown adipocytes. iScience, 28(9), Artikel 113382. https://doi.org/10.1016/j.isci.2025.113382

Anagho-Mattanovich, H. A., Mullari, M., Anagho-Mattanovich, M., Cho, H., Pedersen, A. K., Palasca, O., Olsen, J. V., Locard-Paulet, M. & Nielsen, M. L. (2025). Multi-omics Characterization of Acquired Olaparib Resistance in BRCA1 and BRCA2 Mutant Breast Cancer Cell Lines. Molecular and Cellular Proteomics, 24(8), Artikel 101034. https://doi.org/10.1016/j.mcpro.2025.101034

Elsborg, J. D., Munk, S. H. N., Adelantado-Rubio, A., Pék, R., Fábian, Z., Imburchia, V., Zentout, S., Hendriks, I. A., Buch-Larsen, S. C., Smith, R., Bartek, J., Duxin, J. P., Huet, S., Maya-Mendoza, A. & Nielsen, M. L. (2025). PARP1 auto-modification promotes faithful Okazaki fragment processing and limits replication fork speed. Molecular Cell, 85(19), 3562-3575.e10. https://doi.org/10.1016/j.molcel.2025.09.006

Gadi, S. A., Hendriks, I. A., Nielsen, C. F., Popova, P., Hickson, I. D., Nielsen, M. L. & Toledo, L. (2025). Quantitative Chromatin Protein Dynamics During Replication Origin Firing in Human Cells. Molecular and Cellular Proteomics, 24(3), Artikel 100915. https://doi.org/10.1016/j.mcpro.2025.100915

Marín-Arraiza, L., Roa-Eguiara, A., Pape, T., Sofos, N., Hendriks, I. A., Lund Nielsen, M., Steiner-Rebrova, E. M. & Taylor, N. M. I. (2025). Structural characterization of an extracellular contractile injection system from Photorhabdus luminescens in extended and contracted states. Nature Communications, 16(1), Artikel 9327. https://doi.org/10.1038/s41467-025-64377-z

Hu, H., Popp, P. F., Hughes, T. C. D., Roa-Eguiara, A., Rutbeek, N. R., Martin, F. J. O., Hendriks, I. A., Payne, L. J., Yan, Y., Humolli, D., Klein-Sousa, V., Songailiene, I., Wang, Y., Nielsen, M. L., Berry, R. M., Harms, A., Erhardt, M., Jackson, S. A. & Taylor, N. M. I. (2025). Structure and mechanism of the Zorya anti-phage defence system. Nature, 639(8056), 1093-1101. https://doi.org/10.1038/s41586-024-08493-8

Goffeney, A., Hendriks, I. A., Morel, V., Loe-Mie, Y., Charon, F., Nielsen, M. L., Cossec, J. C., Noordermeer, D., Seeler, J. S. & Dejean, A. (2025). SUMO operates from a unique long tandem repeat to keep innate immunity in check. Nucleic Acids Research, 53(14), Artikel gkaf750. https://doi.org/10.1093/nar/gkaf750

Anagho, H. A., Mullari, M., Prósz, A. G., Buch-Larsen, S. C., Cho, H., Locard-Paulet, M., Szallasi, Z. & Nielsen, M. L. (2024). ADP-ribosylome analysis reveals homogeneous DNA-damage-induced serine ADP-ribosylation across wild-type and BRCA-mutant breast cancer cell lines. Cell Reports, 43(7), Artikel 114433. https://doi.org/10.1016/j.celrep.2024.114433

Rebak, A. S., Hendriks, I. A., Elsborg, J. D., Buch-Larsen, S. C., Nielsen, C. H., Terslev, L., Kirsch, R., Damgaard, D., Doncheva, N. T., Lennartsson, C., Rykær, M., Jensen, L. J., Christophorou, M. A. & Nielsen, M. L. (2024). A quantitative and site-specific atlas of the citrullinome reveals widespread existence of citrullination and insights into PADI4 substrates. Nature Structural and Molecular Biology, 31(6), 977–995. https://doi.org/10.1038/s41594-024-01214-9

Liu, J. C. Y., Ackermann, L., Hoffmann, S., Gál, Z., Hendriks, I. A., Jain, C., Morlot, L., Tatham, M. H., McLelland, G. L., Hay, R. T., Nielsen, M. L., Brummelkamp, T., Haahr, P. & Mailand, N. (2024). Concerted SUMO-targeted ubiquitin ligase activities of TOPORS and RNF4 are essential for stress management and cell proliferation. Nature Structural and Molecular Biology, 31(9), 1355-1367. https://doi.org/10.1038/s41594-024-01294-7

Balachandra, V., Shrestha, R. L., Hammond, C. M., Lin, S., Hendriks, I. A., Sethi, S. C., Chen, L., Sevilla, S., Caplen, N. J., Chari, R., Karpova, T. S., McKinnon, K., Todd, M. A. M., Koparde, V., Cheng, K. C. C., Nielsen, M. L., Groth, A. & Basrai, M. A. (2024). DNAJC9 prevents CENP-A mislocalization and chromosomal instability by maintaining the fidelity of histone supply chains. EMBO Journal, 43(11), 2166-2197. https://doi.org/10.1038/s44318-024-00093-6

Anagho, H. A., Mullari, M., Prósz, A. G., Buch-Larsen, S. C., Cho, H., Locard-Paulet, M., Szallasi, Z. & Nielsen, M. L. (2024). Erratum: ADP-ribosylome analysis reveals homogeneous DNA-damage-induced serine ADP-ribosylation across wild-type and BRCA-mutant breast cancer cell lines (Cell Reports (2024) 43(7), (S2211124724007629), (10.1016/j.celrep.2024.114433)). Cell Reports, 43(8), Artikel 114603. https://doi.org/10.1016/j.celrep.2024.114603

Coulson-Gilmer, C., Littler, S., Barnes, B. M., Brady, R. M., Anagho, H. A., Pillay, N., Dey, M., Macmorland, W., Bronder, D., Nelson, L., Tighe, A., Lin, W. H., Morgan, R. D., Unwin, R. D., Nielsen, M. L., McGrail, J. C. & Taylor, S. S. (2024). Intrinsic PARG inhibitor sensitivity is mimicked by TIMELESS haploinsufficiency and rescued by nucleoside supplementation. NAR Cancer, 6(3), Artikel zcae030. https://doi.org/10.1093/narcan/zcae030

Kar, P., Chatrin, C., Đukić, N., Suyari, O., Schuller, M., Zhu, K., Prokhorova, E., Bigot, N., Ahel, J., Elsborg, J. D., Nielsen, M. L., Clausen, T., Huet, S., Niepel, M., Sanyal, S., Ahel, D., Smith, R. & Ahel, I. (2024). PARP14 and PARP9/DTX3L regulate interferon-induced ADP-ribosylation. EMBO Journal, 43(14), 2929-2953. https://doi.org/10.1038/s44318-024-00126-0

Fábián, Z., Kakulidis, E. S., Hendriks, I. A., Kühbacher, U., Larsen, N. B., Oliva-Santiago, M., Wang, J., Leng, X., Dirac-Svejstrup, A. B., Svejstrup, J. Q., Nielsen, M. L., Caldecott, K. & Duxin, J. P. (2024). PARP1-dependent DNA-protein crosslink repair. Nature Communications, 15(1), Artikel 6641. https://doi.org/10.1038/s41467-024-50912-x

Carabias, A., Camara-Wilpert, S., Mestre, M. R., Lopéz-Méndez, B., Hendriks, I. A., Zhao, R., Pape, T., Fuglsang, A., Luk, S. H. C., Nielsen, M. L., Pinilla-Redondo, R. & Montoya, G. (2024). Retron-Eco1 assembles NAD⁺-hydrolyzing filaments that provide immunity against bacteriophages. Molecular Cell, 84(11), 2185-2202.e12. https://doi.org/10.1016/j.molcel.2024.05.001

Condezo, Y. B., Sainz-Urruela, R., Gomez, L. H., Salas-Lloret, D., Felipe-Medina, N., Bradley, R., Wolff, I. D., Tanis, S., Barbero, J. L., Sánchez-Martín, M., de Rooij, D., Hendriks, I. A., Nielsen, M. L., Gonzalez-Prieto, R., Cohen, P. E., Pendas, A. M. & Llano, E. (2024). RNF212B E3 ligase is essential for crossover designation and maturation during male and female meiosis in the mouse. Proceedings of the National Academy of Sciences of the United States of America, 121(25), Artikel e2320995121. https://doi.org/10.1073/pnas.2320995121

Mirsanaye, A. S., Hoffmann, S., Weisser, M., Mund, A., Lopez Mendez, B., Typas, D., van den Boom, J., Benedict, B., Hendriks, I. A., Nielsen, M. L., Meyer, H., Duxin, J. P., Montoya, G. & Mailand, N. (2024). VCF1 is a p97/VCP cofactor promoting recognition of ubiquitylated p97-UFD1-NPL4 substrates. Nature Communications, 15(1), Artikel 2459. https://doi.org/10.1038/s41467-024-46760-4

Mullari, M., Fossat, N., Skotte, N. H., Asenjo-Martinez, A., Humphreys, D. T., Bukh, J., Kirkeby, A., Scheel, T. K. H. & Nielsen, M. L. (2023). Characterising the RNA-binding protein atlas of the mammalian brain uncovers RBM5 misregulation in mouse models of Huntington’s disease. Nature Communications, 14(1), Artikel 4348. https://doi.org/10.1038/s41467-023-39936-x

Anagho, H. A., Elsborg, J. D., Hendriks, I. A., Buch-Larsen, S. C. & Nielsen, M. L. (2023). Characterizing ADP-Ribosylation Sites Using Af1521 Enrichment Coupled to ETD-Based Mass Spectrometry. I Methods in Molecular Biology (s. 251-270). Humana Press. https://doi.org/10.1007/978-1-0716-2891-1_15

Rebak, A. S., Hendriks, I. A. & Nielsen, M. L. (2023). Characterizing citrullination by mass spectrometry-based proteomics. Philosophical Transactions of the Royal Society B: Biological Sciences, 378(1890), Artikel 20220237. https://doi.org/10.1098/rstb.2022.0237

Carraro, M., Hendriks, I. A., Hammond, C. M., Solis-Mezarino, V., Völker-Albert, M., Elsborg, J. D., Weisser, M. B., Spanos, C., Montoya, G., Rappsilber, J., Imhof, A., Nielsen, M. L. & Groth, A. (2023). DAXX adds a de novo H3.3K9me3 deposition pathway to the histone chaperone network. Molecular Cell, 83(7), 1075-1092.e9. https://doi.org/10.1016/j.molcel.2023.02.009

Đukić, N., Strømland, Ø., Elsborg, J. D., Munnur, D., Zhu, K., Schuller, M., Chatrin, C., Kar, P., Duma, L., Suyari, O., Rack, J. G. M., Baretić, D., Crudgington, D. R. K., Groslambert, J., Fowler, G., Wijngaarden, S., Prokhorova, E., Rehwinkel, J., Schüler, H. ... Ahel, I. (2023). PARP14 is a PARP with both ADP-ribosyl transferase and hydrolase activities. Science Advances, 9(37), Artikel eadi2687. https://doi.org/10.1126/sciadv.adi2687

Colding-Christensen, C. S., Kakulidis, E. S., Arroyo-Gomez, J., Hendriks, I. A., Arkinson, C., Fábián, Z., Gambus, A., Mailand, N., Duxin, J. P. & Nielsen, M. L. (2023). Profiling ubiquitin signalling with UBIMAX reveals DNA damage- and SCF^β-Trcp1-dependent ubiquitylation of the actin-organizing protein Dbn1. Nature Communications, 14(1), Artikel 8293. https://doi.org/10.1038/s41467-023-43873-0

Richards, F., Llorca-Cardenosa, M. J., Langton, J., Buch-Larsen, S. C., Shamkhi, N. F., Sharma, A. B., Nielsen, M. L. & Lakin, N. D. (2023). Regulation of Rad52-dependent replication fork recovery through serine ADP-ribosylation of PolD3. Nature Communications, 14(1), Artikel 4310. https://doi.org/10.1038/s41467-023-40071-w

Fontana, P., Buch-Larsen, S. C., Suyari, O., Smith, R., Suskiewicz, M. J., Schützenhofer, K., Ariza, A., Rack, J. G. M., Nielsen, M. L. & Ahel, I. (2023). Serine ADP-ribosylation in Drosophila provides insights into the evolution of reversible ADP-ribosylation signalling. Nature Communications, 14(1), Artikel 3200. https://doi.org/10.1038/s41467-023-38793-y

Hertz, E. P. T., Vega, I. A. D., Kruse, T., Wang, Y., Hendriks, I. A., Bizard, A. H., Eugui-Anta, A., Hay, R. T., Nielsen, M. L., Nilsson, J., Hickson, I. D. & Mailand, N. (2023). The SUMO–NIP45 pathway processes toxic DNA catenanes to prevent mitotic failure. Nature Structural and Molecular Biology, 30(9), 1303-1313. https://doi.org/10.1038/s41594-023-01045-0

Cossec, J. C., Traboulsi, T., Sart, S., Loe-Mie, Y., Guthmann, M., Hendriks, I. A., Theurillat, I., Nielsen, M. L., Torres-Padilla, M. E., Baroud, C. N. & Dejean, A. (2023). Transient suppression of SUMOylation in embryonic stem cells generates embryo-like structures. Cell Reports, 42(4), Artikel 112380. https://doi.org/10.1016/j.celrep.2023.112380

Lüscher, B., Ahel, I., Altmeyer, M., Ashworth, A., Bai, P., Chang, P., Cohen, M., Corda, D., Dantzer, F., Daugherty, M. D., Dawson, T. M., Dawson, V. L., Deindl, S., Fehr, A. R., Feijs, K. L. H., Filippov, D. V., Gagné, J. P., Grimaldi, G., Guettler, S. ... Ziegler, M. (2022). ADP-ribosyltransferases, an update on function and nomenclature. FEBS journal, 289(23), 7399-7410. https://doi.org/10.1111/febs.16142

Schubert, L., Hendriks, I. A., Hertz, E. P. T., Wu, W., Sellés-Baiget, S., Hoffmann, S., Viswalingam, K. S., Gallina, I., Pentakota, S., Benedict, B., Johansen, J., Apelt, K., Luijsterburg, M. S., Rasmussen, S., Lisby, M., Liu, Y., Nielsen, M. L., Mailand, N. & Duxin, J. P. (2022). SCAI promotes error-free repair of DNA interstrand crosslinks via the Fanconi anemia pathway. EMBO Reports, 23(4), Artikel e53639. https://doi.org/10.15252/embr.202153639

Zhao, X., Hendriks, I. A., Le Gras, S., Ye, T., Ramos-Alonso, L., Nguea P, A., Lien, G. F., Ghasemi, F., Klungland, A., Jost, B., Enserink, J. M., Nielsen, M. L. & Chymkowitch, P. (2022). Waves of sumoylation support transcription dynamics during adipocyte differentiation. Nucleic Acids Research, 50(3), 1351-1369. https://doi.org/10.1093/nar/gkac027

Martín Monreal, M. T., Rebak, A. S., Massarenti, L., Mondal, S., Šenolt, L., Ødum, N., Nielsen, M. L., Thompson, P. R., Nielsen, C. H. & Damgaard, D. (2021). Applicability of Small-Molecule Inhibitors in the Study of Peptidyl Arginine Deiminase 2 (PAD2) and PAD4. Frontiers in Immunology, 12, Artikel 716250. https://doi.org/10.3389/fimmu.2021.716250

Rodriguez, K. M., Buch-Larsen, S. C., Kirby, I. T., Siordia, I. R., Hutin, D., Rasmussen, M., Grant, D. M., David, L. L., Matthews, J., Nielsen, M. L. & Cohen, M. S. (2021). Chemical genetics and proteome-wide site mapping reveal cysteine MARylation by PARP-7 on immune-relevant protein targets. eLife, 10, 1-94. Artikel e60480. https://doi.org/10.7554/eLife.60480

Hammond, C. M., Bao, H., Hendriks, I. A., Carraro, M., García-Nieto, A., Liu, Y., Reverón-Gómez, N., Spanos, C., Chen, L., Rappsilber, J., Nielsen, M. L., Patel, D. J., Huang, H. & Groth, A. (2021). DNAJC9 integrates heat shock molecular chaperones into the histone chaperone network. Molecular Cell, 81(12), 2533-2548. https://doi.org/10.1016/j.molcel.2021.03.041

Liu, C., Wu, T., Shu, X., Li, S. T., Wang, D. R., Wang, N., Zhou, R., Yang, H., Jiang, H., Hendriks, I. A., Gong, P., Zhang, L., Nielsen, M. L., Li, K., Wang, L. & Yang, B. (2021). Identification of Protein Direct Interactome with Genetic Code Expansion and Search Engine OpenUaa. Advanced Biology, 5(3), Artikel 2000308. https://doi.org/10.1002/adbi.202000308

Hendriks, I. A., Akimov, V., Blagoev, B. & Nielsen, M. L. (2021). MaxQuant. Live Enables Enhanced Selectivity and Identification of Peptides Modified by Endogenous SUMO and Ubiquitin. Journal of Proteome Research, 20(4), 2042-2055. https://doi.org/10.1021/acs.jproteome.0c00892

Liu, J. C. Y., Kühbacher, U., Larsen, N. B., Borgermann, N., Garvanska, D. H., Hendriks, I. A., Ackermann, L., Haahr, P., Gallina, I., Guérillon, C., Branigan, E., Hay, R. T., Azuma, Y., Nielsen, M. L., Duxin, J. P. & Mailand, N. (2021). Mechanism and function of DNA replication-independent DNA-protein crosslink repair via the SUMO-RNF4 pathway. EMBO Journal, 40(18), Artikel e107413. https://doi.org/10.15252/embj.2020107413

Prokhorova, E., Zobel, F., Smith, R., Zentout, S., Gibbs-Seymour, I., Schützenhofer, K., Peters, A., Groslambert, J., Zorzini, V., Agnew, T., Brognard, J., Nielsen, M. L., Ahel, D., Huet, S., Suskiewicz, M. J. & Ahel, I. (2021). Serine-linked PARP1 auto-modification controls PARP inhibitor response. Nature Communications, 12(1), Artikel 4055. https://doi.org/10.1038/s41467-021-24361-9

Vistrup-Parry, M., Chen, X., Johansen, T. L., Bach, S., Buch-Larsen, S. C., Bartling, C. R. O., Ma, C., Clemmensen, L. S., Nielsen, M. L., Zhang, M. & Stromgaard, K. (2021). Site-specific phosphorylation of PSD-95 dynamically regulates the postsynaptic density as observed by phase separation. iScience, 24(11), Artikel 103268. https://doi.org/10.1016/j.isci.2021.103268

Buch-Larsen, S. C., Rebak, A. K. L. F. S., Hendriks, I. A. & Nielsen, M. L. (2021). Temporal and site-specific adp-ribosylation dynamics upon different genotoxic stresses. Cells, 10(11), Artikel 2927. https://doi.org/10.3390/cells10112927

Hendriks, I. A., Buch-Larsen, S. C., Prokhorova, E., Elsborg, J. D., Rebak, A. K. L. F. S., Zhu, K., Ahel, D., Lukas, C., Ahel, I. & Nielsen, M. L. (2021). The regulatory landscape of the human HPF1-and ARH3-dependent ADP-ribosylome. Nature Communications, 12(1), Artikel 5893. https://doi.org/10.1038/s41467-021-26172-4

Gallina, I., Hendriks, I. A., Hoffmann, S., Larsen, N. B., Johansen, J., Colding-Christensen, C. S., Schubert, L., Sellés-Baiget, S., Fábián, Z., Kühbacher, U., Gao, A. O., Räschle, M., Rasmussen, S., Nielsen, M. L., Mailand, N. & Duxin, J. P. (2021). The ubiquitin ligase RFWD3 is required for translesion DNA synthesis. Molecular Cell, 81(3), 442-458.e9. https://doi.org/10.1016/j.molcel.2020.11.029

Prokhorova, E., Agnew, T., Wondisford, A. R., Tellier, M., Kaminski, N., Beijer, D., Holder, J., Groslambert, J., Suskiewicz, M. J., Zhu, K., Reber, J. M., Krassnig, S. C., Palazzo, L., Murphy, S., Nielsen, M. L., Mangerich, A., Ahel, D., Baets, J., O'Sullivan, R. J. & Ahel, I. (2021). Unrestrained poly-ADP-ribosylation provides insights into chromatin regulation and human disease. Molecular Cell, 81(12), 2640-2655.e8. https://doi.org/10.1016/j.molcel.2021.04.028

Theurillat, I., Hendriks, I. A., Cossec, J. C., Andrieux, A., Nielsen, M. L. & Dejean, A. (2020). Erratum: Extensive SUMO Modification of Repressive Chromatin Factors Distinguishes Pluripotent from Somatic Cells (Cell Reports (2020) 32(11), (S2211124720311359), (10.1016/j.celrep.2020.108146)). Cell Reports, 33(1), Artikel 108251. https://doi.org/10.1016/j.celrep.2020.108251

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