Publications

Peer-reviewed articles

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), Article 108251. https://doi.org/10.1016/j.celrep.2020.108251

Theurillat, I., Hendriks, I. A., Cossec, J. C., Andrieux, A., Nielsen, M. L. & Dejean, A. (2020). Extensive SUMO Modification of Repressive Chromatin Factors Distinguishes Pluripotent from Somatic Cells. Cell Reports, 32(11), Article 108146. https://doi.org/10.1016/j.celrep.2020.108146

Buch-Larsen, S. C., Hendriks, I. A., Lodge, J. M., Rykær, M., Furtwängler, B., Shishkova, E., Westphall, M. S., Coon, J. J. & Nielsen, M. L. (2020). Mapping Physiological ADP-Ribosylation Using Activated Ion Electron Transfer Dissociation. Cell Reports, 32(12), Article 108176. https://doi.org/10.1016/j.celrep.2020.108176

Guérillon, C., Smedegaard, S., Hendriks, I. A., Nielsen, M. L. & Mailand, N. (2020). Multisite SUMOylation restrains DNA polymerase η interactions with DNA damage sites. Journal of Biological Chemistry, 295, 8350-8362. https://doi.org/10.1074/jbc.RA120.013780

Mooser, C., Symeonidou, I. E., Leimbacher, P. A., Ribeiro, A., Shorrocks, A. M. K., Jungmichel, S., Larsen, S. C., Knechtle, K., Jasrotia, A., Zurbriggen, D., Jeanrenaud, A., Leikauf, C., Fink, D., Nielsen, M. L., Blackford, A. N. & Stucki, M. (2020). Treacle controls the nucleolar response to rDNA breaks via TOPBP1 recruitment and ATR activation. Nature Communications, 11(1), Article 123. https://doi.org/10.1038/s41467-019-13981-x

Hendriks, I. A., Larsen, S. C. & Nielsen, M. L. (2019). An advanced strategy for comprehensive profiling of ADP-ribosylation sites using mass spectrometry-based proteomics. Molecular and Cellular Proteomics, 18(5), 1010-1024. https://doi.org/10.1074/mcp.TIR119.001315

Wiese, M., Bannister, A. J., Basu, S., Boucher, W., Wohlfahrt, K., Christophorou, M. A., Nielsen, M. L., Klenerman, D., Laue, E. D. & Kouzarides, T. (2019). Citrullination of HP1γ chromodomain affects association with chromatin. Epigenetics and Chromatin, 12(1), Article 21. https://doi.org/10.1186/s13072-019-0265-x

Samudyata, Amaral, P. P., Engström, P. G., Robson, S. C., Nielsen, M. L., Kouzarides, T. & Castelo-Branco, G. (2019). Interaction of Sox2 with RNA binding proteins in mouse embryonic stem cells. Experimental Cell Research, 381(1), 129-138. https://doi.org/10.1016/j.yexcr.2019.05.006

Falcão, A. M., Meijer, M., Scaglione, A., Rinwa, P., Agirre, E., Liang, J., Larsen, S. C., Heskol, A., Frawley, R., Klingener, M., Varas-Godoy, M., Raposo, A. A. S. F., Ernfors, P., Castro, D. S., Nielsen, M. L., Casaccia, P. & Castelo-Branco, G. (2019). PAD2-Mediated Citrullination Contributes to Efficient Oligodendrocyte Differentiation and Myelination. Cell Reports, 27(4), 1090-1102.e10. https://doi.org/10.1016/j.celrep.2019.03.108

Taylor, R., Long, J., Yoon, J. W., Childs, R., Sylvestersen, K. B., Nielsen, M. L., Leong, K. F., Iannaccone, S., Walterhouse, D. O., Robbins, D. J. & Iannaccone, P. (2019). Regulation of GLI1 by cis DNA elements and epigenetic marks. DNA Repair, 79, 10-21. https://doi.org/10.1016/j.dnarep.2019.04.011

Borgermann, N., Ackermann, L., Schwertman, P., Hendriks, I. A., Thijssen, K., Liu, J. C. Y., Lans, H., Nielsen, M. L. & Mailand, N. (2019). SUMOylation promotes protective responses to DNA-protein crosslinks. EMBO Journal, 38(8), Article e101496. https://doi.org/10.15252/embj.2019101496

Hou, W., Nemitz, S., Schopper, S., Nielsen, M. L., Kessels, M. M. & Qualmann, B. (2018). Arginine Methylation by PRMT2 Controls the Functions of the Actin Nucleator Cobl. Developmental Cell, 45(2), 262-275.e8. https://doi.org/10.1016/j.devcel.2018.03.007

Skotte, N. H., Andersen, J. V., Santos, A., Aldana, B. I., Willert, C. W., Nørremølle, A., Waagepetersen, H. S. & Nielsen, M. L. (2018). Integrative Characterization of the R6/2 Mouse Model of Huntington's Disease Reveals Dysfunctional Astrocyte Metabolism. Cell Reports, 23(7), 2211-2224. https://doi.org/10.1016/j.celrep.2018.04.052

Hendriks, I. A., Lyon, D., Su, D., Skotte, N. H., Daniel, J. A., Jensen, L. J. & Nielsen, M. L. (2018). Site-specific characterization of endogenous SUMOylation across species and organs. Nature Communications, 9, 1-17. Article 2456. https://doi.org/10.1038/s41467-018-04957-4

Larsen, S. C., Hendriks, I. A., Lyon, D., Jensen, L. J. & Nielsen, M. L. (2018). Systems-wide Analysis of Serine ADP-Ribosylation Reveals Widespread Occurrence and Site-Specific Overlap with Phosphorylation. Cell Reports, 24(9), 2493-2505.e4. https://doi.org/10.1016/j.celrep.2018.07.083

Bekker-Jensen, D. B., Kelstrup, C. D., Batth, T. S., Larsen, S. C., Haldrup, C., Bramsen, J. B., Sørensen, K. D., Høyer, S., Ørntoft, T. F., Andersen, C. L., Nielsen, M. L. & Olsen, J. V. (2017). An Optimized Shotgun Strategy for the Rapid Generation of Comprehensive Human Proteomes. Cell Systems, 4(6), 587-599.e4. https://doi.org/10.1016/j.cels.2017.05.009

Zhang, G., Kruse, T., López-Méndez, B., Sylvestersen, K. B., Garvanska, D. H., Schopper, S., Nielsen, M. L. & Nilsson, J. (2017). Bub1 positions Mad1 close to KNL1 MELT repeats to promote checkpoint signalling. Nature Communications, 8, Article 15822. https://doi.org/10.1038/ncomms15822

Falcao, A., Meijer, M., Rinwa, P., Cummings, T., Varas, M., Liang, J., Casaccia, P., Christophorou, M., Nielsen, M. L., Ernfors, P. & Castelo-Branco, G. (2017). Citrullination modulates oligodendrocyte differentiation. Glia, 65(S1), E389.

Young, C., Podtelejnikov, A. V. & Nielsen, M. L. (2017). Improved Reversed Phase Chromatography of Hydrophilic Peptides from Spatial and Temporal Changes in Column Temperature. Journal of Proteome Research, 16(6), 2307-2317. https://doi.org/10.1021/acs.jproteome.6b01055

Larsen, S. C., Leutert, M., Bilan, V., Martello, R., Jungmichel, S., Young, C., Hottiger, M. O. & Nielsen, M. L. (2017). Proteome-Wide Identification of In Vivo ADP-Ribose Acceptor Sites by Liquid Chromatography-Tandem Mass Spectrometry. In A. V. Tulin (Ed.), Poly(ADP-Ribose) Polymerase (Vol. 1608, pp. 149-162). Humana Press. https://doi.org/10.1007/978-1-4939-6993-7_11

Hendriks, I. A., Lyon, D., Young, C., Jensen, L. J., Vertegaal, A. C. O. & Nielsen, M. L. (2017). Site-specific mapping of the human SUMO proteome reveals co-modification with phosphorylation. Nature Structural and Molecular Biology, 24(3), 325-336. https://doi.org/10.1038/nsmb.3366

Mullari, M., Lyon, D., Jensen, L. J. & Nielsen, M. L. (2017). Specifying RNA-Binding Regions in Proteins by Peptide Cross-Linking and Affinity Purification. Journal of Proteome Research, 16(8), 2762-2772. https://doi.org/10.1021/acs.jproteome.7b00042

Larsen, S. C., Sylvestersen, K. B., Mund, A., Lyon, D., Mullari, M., Madsen, M. V., Daniel, J. A., Jensen, L. J. & Nielsen, M. L. (2016). Proteome-wide analysis of arginine monomethylation reveals widespread occurrence in human cells. Science Signaling, 9(443), Article rs9. https://doi.org/10.1126/scisignal.aaf7329

Martello, R., Leutert, M., Jungmichel, S., Bilan, V., Larsen, S. C., Young, C., Hottiger, M. O. & Nielsen, M. L. (2016). Proteome-wide identification of the endogenous ADP-ribosylome of mammalian cells and tissue. Nature Communications, 7, Article 12917. https://doi.org/10.1038/ncomms12917

Mathiassen, S. G., Larsen, I. B., Poulsen, E. G., Madsen, C. T., Papaleo, E., Lindorff-Larsen, K., Kragelund, B. B., Nielsen, M. L., Kriegenburg, F. & Hartmann-Petersen, R. (2015). A two-step protein quality control pathway for a misfolded DJ-1 variant in fission yeast. The Journal of Biological Chemistry, 290(34), 21141-21153. https://doi.org/10.1074/jbc.M115.662312

Madsen, C. T., Sylvestersen, K. B., Young, C., Larsen, S. C., Poulsen, J. W., Andersen, M. A., Palmqvist, E. A., Hey-Mogensen, M., Jensen, P. B., Treebak, J. T., Lisby, M. & Nielsen, M. L. (2015). Biotin starvation causes mitochondrial protein hyperacetylation and partial rescue by the SIRT3-like deacetylase Hst4p. Nature Communications, 6, Article 7726. https://doi.org/10.1038/ncomms8726

Lundgaard, I., Li, B., Xie, L., Kang, H., Sanggaard, S., Haswell, J. D. R., Sun, W., Goldman, S., Blekot, S., Nielsen, M., Takano, T., Deane, R. & Nedergaard, M. (2015). Direct neuronal glucose uptake Heralds activity-dependent increases in cerebral metabolism. Nature Communications, 6, Article 6807. https://doi.org/10.1038/ncomms7807

Christensen, M. H., Nielsen, M. L. & Kohlmeier, K. A. (2015). Electrophysiological changes in laterodorsal tegmental neurons associated with prenatal nicotine exposure: Implications for heightened susceptibility to addict to drugs of abuse. Journal of Developmental Origins of Health and Disease, 6(3), 182-200. https://doi.org/10.1017/S204017441400049X

Sylvestersen, K. B. & Nielsen, M. L. (2015). Large-scale identification of the arginine methylome by mass spectrometry. Current Protocols in Protein Science, 2015, 24.7.1-24.7.17. https://doi.org/10.1002/0471140864.ps2407s82

Altmeyer, M., Neelsen, K. J., Teloni, F., Pozdnyakova, I., Pellegrino, S., Grøfte, M., Rask, M.-B. D., Streicher, W., Jungmichel, S., Nielsen, M. L. & Lukas, J. (2015). Liquid demixing of intrinsically disordered proteins is seeded by poly(ADP-ribose). Nature Communications, 6, 1-12. Article 8088. https://doi.org/10.1038/ncomms9088

Kelstrup, C. D., Frese, C., Heck, A. J. R., Olsen, J. V. & Nielsen, M. L. (2014). Analytical utility of mass spectral binning in proteomic experiments by SPectral Immonium Ion Detection (SPIID). Molecular and Cellular Proteomics, 13(8), 1914-1924. https://doi.org/10.1074/mcp.O113.035915

Christophorou, M. A., Castelo-Branco, G., Halley-Stott, R. P., Oliveira, C. S., Loos, R., Radzisheuskaya, A., Mowen, K. A., Bertone, P., Silva, J. C. R., Zernicka-Goetz, M., Nielsen, M. L., Gurdon, J. B. & Kouzarides, T. (2014). Citrullination regulates pluripotency and histone H1 binding to chromatin. Nature, 507(7490), 104-108. https://doi.org/10.1038/nature12942

Tessarz, P., Santos-Rosa, H., Robson, S. C., Sylvestersen, K. B., Nelson, C. J., Nielsen, M. L. & Kouzarides, T. (2014). Glutamine methylation in histone H2A is an RNA-polymerase-I-dedicated modification. Nature, 505(7484), 564-568. https://doi.org/10.1038/nature12819

Andresen, C. A., Smedegaard, S., Sylvestersen, K. B., Svensson, C., Iglesias-Gato, D., Cazzamali, G., Nielsen, T. K., Nielsen, M. L. & Flores Morales, A. (2014). Protein Interaction Screening for the Ankyrin Repeats and Suppressor of Cytokine Signaling (SOCS) Box (ASB) Family Identify Asb11 as a Novel Endoplasmic Reticulum Resident Ubiquitin Ligase. The Journal of Biological Chemistry, 289(4), 2043-2054. https://doi.org/10.1074/jbc.M113.534602

Sylvestersen, K. B., Horn, H., Jungmichel, S., Jensen, L. J. & Nielsen, M. L. (2014). Proteomic analysis of arginine methylation sites in human cells reveals dynamic regulation during transcriptional arrest. Molecular and Cellular Proteomics, 13(8), 2072-2088. https://doi.org/10.1074/mcp.O113.032748

Jungmichel, S., Sylvestersen, K. B., Choudhary, C. R., Nguyen, S., Mann, M. & Nielsen, M. L. (2014). Specificity and commonality of the phosphoinositide-binding proteome analyzed by quantitative mass spectrometry. Cell Reports, 6(3), 578-91. https://doi.org/10.1016/j.celrep.2013.12.038

Larsen, D. H., Hari, F., Clapperton, J. A., Gwerder, M., Gutsche, K., Altmeyer, M., Jungmichel, S., Toledo, L. I., Fink, D., Rask, M. B., Grøfte, M., Lukas, C., Nielsen, M. L., Smerdon, S. J., Lukas, J. & Stucki, M. (2014). The NBS1-Treacle complex controls ribosomal RNA transcription in response to DNA damage. Nature Cell Biology, 16(8), 792-803. https://doi.org/10.1038/ncb3007

Klimovskaia, I. M., Young, C., Strømme, C. B., Menard, P., Jasencakova, Z., Mejlvang, J., Ask, K., Ploug, M., Nielsen, M. L., Jensen, O. N. & Groth, A. (2014). Tousled-like kinases phosphorylate Asf1 to promote histone supply during DNA replication. Nature Communications, 5, Article 3394. https://doi.org/10.1038/ncomms4394

Sylvestersen, K. B., Young, C. & Nielsen, M. L. (2013). Advances in characterizing ubiquitylation sites by mass spectrometry. Current Opinion in Chemical Biology, 17(1), 49-58. https://doi.org/10.1016/j.cbpa.2012.12.009

Villumsen, B. H., Danielsen, J. R., Povlsen, L., Sylvestersen, K. B., Merdes, A., Beli, P., Yang, Y.-G., Choudhary, C. R., Nielsen, M. L., Mailand, N. & Bekker-Jensen, S. (2013). A new cellular stress response that triggers centriolar satellite reorganization and ciliogenesis. EMBO Journal, 32(23), 3029-3040. https://doi.org/10.1038/emboj.2013.223

Cepeda, D., Ng, H. F., Sharifi, H. R., Mahmoudi, S., Cerrato, V. S., Fredlund, E., Magnusson, K., Nilsson, H., Malyukova, A., Rantala, J., Klevebring, D., Viñals, F., Bhaskaran, N., Zakaria, S. M., Rahmanto, A. S., Grotegut, S., Nielsen, M. L., Szigyarto, C. A. K., Sun, D. ... Sangfelt, O. (2013). CDK-mediated activation of the SCF^FBXO28 ubiquitin ligase promotes MYC-driven transcription and tumourigenesis and predicts poor survival in breast cancer. EMBO Molecular Medicine, 5(7), 999-1018. https://doi.org/10.1002/emmm.201202341

Martin, MH., Nielsen, MB., Madsen, IE., Petersen, SM., Lange, T. & Rugulies, R. (2013). Effectiveness of a coordinated and tailored return-to-work intervention for sickness absence beneficiaries with mental health problems. Journal of Occupational Rehabilitation, 23(4), 621-30.

Leeming, D. J., Karsdal, M. A., Byrjalsen, I., Bendtsen, F., Trebicka, J., Nielsen, M. J., Christiansen, C., Møller, S. & Krag, A. (2013). Novel serological neo-epitope markers of extracellular matrix proteins for the detection of portal hypertension. Alimentary Pharmacology and Therapeutics, 38(9), 1086-1096. https://doi.org/10.1111/apt.12484

Jungmichel, S., Rosenthal, F., Altmeyer, M., Lukas, J., Hottiger, M. O. & Nielsen, M. L. (2013). Proteome-wide identification of poly(ADP-Ribosyl)ation targets in different genotoxic stress responses. Molecular Cell, 52(2), 272-285. https://doi.org/10.1016/j.molcel.2013.08.026

Bentin, T. & Nielsen, M. L. (2013). RNA-DNA sequence differences spell genetic code ambiguities. Artificial DNA, 2(3), 69-70.

Poulsen, J. W., Madsen, C. T., Young, C., Poulsen, F. M. & Nielsen, M. L. (2013). Using guanidine-hydrochloride for fast and efficient protein digestion and single-step affinity-purification mass spectrometry. Journal of proteome Research, 12(2), 1020-1030. https://doi.org/10.1021/pr300883y

Poulsen, J. W., Madsen, C. T., Young, C., Kelstrup, C. D., Grell, H. C., Henriksen, P., Juhl-Jensen, L. & Nielsen, M. L. (2012). Comprehensive profiling of proteome changes upon sequential deletion of deubiquitylating enzymes. Journal of Proteomics, 75(13), 3886-3897. https://doi.org/10.1016/j.jprot.2012.04.055

Kelstrup, C. D., Young, C., Lavallee, R., Nielsen, M. L. & Olsen, J. V. (2012). Optimized Fast and Sensitive Acquisition Methods for Shotgun Proteomics on a Quadrupole Orbitrap Mass Spectrometer. Journal of Proteome Research, 3487-3497. https://doi.org/10.1021/pr3000249

Frogne, T., Sylvestersen, K. B., Kubicek, S., Nielsen, M. L. & Hecksher-Sørensen, J. (2012). Pdx1 is post-translationally modified in vivo and serine 61 is the principal site of phosphorylation. PLoS One, 7(4), Article e35233. https://doi.org/10.1371/journal.pone.0035233

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Revised 11.05.2026