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Selected recent publications

2020

Immunoelectron microscopy and mass spectrometry for classification of amyloid deposits. Abildgaard, N, Rojek, AM, Møller, HEH, Palstrøm, NB, Nyvold, CG, Rasmussen, LM, Toftmann, CT, Beck, HC, Marcussen, N. Amyloid, 27, 59-66, 2020.

Shliaha PV, Gorshkov V, Kovalchuk SI, Schwammle V, Baird MA, Shvartsburg AA, Jensen ON. Middle-Down Proteomic Analyses with Ion Mobility Separations of Endogenous Isomeric Proteoforms. Anal Chem. 2020.

Barrio-Hernandez I, Jafari A, Rigbolt KTG, Hallenborg P, Sanchez-Quiles V, Skovrind I, Akimov V, Kratchmarova I, Dengjel J, Kassem M, Blagoev B. (2020) Phosphoproteomic profiling reveals a defined genetic program for osteoblastic lineage commitment of human bone marrow–derived stromal stem cells. Genome Res. 30(1): 127-37.

Ægidius HM, Veidal SS, Feigh M, Hallenborg P, Puglia M, Pers TH, Vrang N, Jelsing J, Kornum BR, Blagoev B, Rigbolt KTG. (2020) Multi-omics characterization of a diet-induced obese model of non-alcoholic steatohepatitis. Sci Rep. 10(1): 1148.

Kang T, Boland BB, Jensen P, Alarcon C, Nawrocki A, Grimsby JS, Rhodes CJ, Larsen MR. Characterization of signaling pathways associated with pancreatic β-cell adaptive flexibility in compensation of obesity-linked diabetes in db/db mice. Re-submitted to molecular and cellular proteomics, February 2020.

Bekker-Jensen DB, Martinez-Val A, Steigerwald S, Rüther PL, Fort KL, Arrey TN, Harder A, Makarov AA, Olsen JV. A Compact Quadrupole-Orbitrap Mass Spectrometer with FAIMS Interface Improves Proteome Coverage in Short LC Gradients. Mol Cell Proteomics. 2020 Feb 12. pii: mcp.TIR119.001906. doi: 10.1074/mcp.TIR119.001906.

Bekker-Jensen DB, Bernhardt OA, Hogrebe A, Martinez-Val A, Verbeke L, Gandhi T, Kelstrup CD, Reiter L, Olsen JV. Rapid and site-specific deep phosphoproteome profiling by data-independent acquisition without the need for spectral libraries. Nat Commun. 2020 Feb 7;11(1):787. doi: 10.1038/s41467-020-14609-1.

2019

Kang T, Boland BB, Alarcon C, Grimsby JS, Rhodes CJ, Larsen MR. Proteomic Analysis of Restored Insulin Production and Trafficking in Obese Diabetic Mouse Pancreatic Islets Following Euglycemia. J Proteome Res. 2019, 18(9):3245-3258.

Sabino, F., Egli, F. E., Savickas, S., Holstein, J., Kaspar, D., Rollmann, M., . . . auf dem Keller, U. (2018) Comparative Degradomics of Porcine and Human Wound Exudates Unravels Biomarker Candidates for Assessment of Wound Healing Progression in Trauma Patients. J. Invest. Dermatol. 138, 413-422.

Seltmann, K., *Meyer, M., Sulcova, J., Kockmann, T., Wehkamp, U., Weidinger, S., . . #auf dem Keller U,. #Werner, S. (2018) Humidity-regulated CLCA2 protects the epidermis from hyperosmotic stress. Sci. Transl. Med. 10.

Stender, E.G.P, C.D. Andersen, F. Fredslund, J. Holck, A. Solberg, D. Teze, G.H.J. Peters, B.E. Christensen, F.L. Aachmann, D.H. Welner & B. Svensson: Structural and functional aspects of mannuronic acid–specific PL6 alginate lyase from the human gut microbe Bacteroides cellulosilyticus. J. Biol. Chem. 294, 17915-17930 (2019).

Janeček, Š., F. Mareček, E.A. MacGregor & B. Svensson: Starch-binding domains as CBM families – history, occurrence, structure, function and evolution. Biotechnol. Advanc. 37, art. No. 107431 (2019)

Lundby A, Franciosa G, Emdal KB, Refsgaard JC, Gnosa SP, Bekker-Jensen DB, Secher A, Maurya SR, Paul I, Mendez BL, Kelstrup CD, Francavilla C, Kveiborg M, Montoya G, Jensen LJ, Olsen JV. Oncogenic Mutations Rewire Signaling Pathways by Switching Protein Recruitment to Phosphotyrosine Sites. Cell. 2019 Oct 3;179(2):543-560.e26. doi: 10.1016/j.cell.2019.09.008.

Cappellini E, Welker F, Pandolfi L, Ramos-Madrigal J, Samodova D, Rüther PL, Fotakis AK, Lyon D, Moreno-Mayar JV, Bukhsianidze M, Rakownikow Jersie-Christensen R, Mackie M, Ginolhac A, Ferring R, Tappen M, Palkopoulou E, Dickinson MR, Stafford TW Jr, Chan YL, Götherström A, Nathan SKSS, Heintzman PD, Kapp JD, Kirillova I, Moodley Y, Agusti J, Kahlke RD, Kiladze G, Martínez-Navarro B, Liu S, Sandoval Velasco M, Sinding MS, Kelstrup CD, Allentoft ME, Orlando L, Penkman K, Shapiro B, Rook L, Dalén L, Gilbert MTP, Olsen JV*, Lordkipanidze D, Willerslev E*. Early Pleistocene enamel proteome from Dmanisi resolves Stephanorhinus phylogeny. Nature. 2019 Oct;574(7776):103-107. doi: 10.1038/s41586-019-1555-y.

M. Alexeeva, M.N. Moen, K. Grøsvik, A.N. Tesfahun, X.M. Xu, I. Muruzábal-Lecumberri, K.M. Olsen, A. Rasmussen, P. Ruoff, F. Kirpekar, A. Klungland & S. Bjelland (2019). Excision of uracil from DNA by hSMUG1 includes strand incision and processing. Nucleic Acids Res. 47, 779-793.

C. Enroth, L.D. Poulsen, S. Iversen, F. Kirpekar, A. Albrechtsen, J. Vinther (2019). Detection of internal N7-methylguanosine (m7G) RNA modifications by mutational profiling sequencing. Nucleic Acids Res. 47, e126 (doi: 10.1093/nar/gkz736).

Radzisheuskaya A, Shliaha PV, Grinev V, Lorenzini E, Kovalchuk S, Shlyueva D, Gorshkov V, Hendrickson RC, Jensen ON, Helin K. PRMT5 methylome profiling uncovers a direct link to splicing regulation in acute myeloid leukemia. Nat Struct Mol Biol. 2019.

Kovalchuk SI, Jensen ON, Rogowska-Wrzesinska A. FlashPack: Fast and Simple Preparation of Ultrahigh-performance Capillary Columns for LC-MS. Mol Cell Proteomics. 2019;18(2):383-90.

2018

Kang T, Jensen P, Solovyeva V, Brewer JR, Larsen MR. Dynamic changes in the protein localization in the nuclear environment in pancreatic β-cell after brief glucose stimulation. J Proteome Res. 2018, 17(4):1664-1676.

Kang T, Jensen P, Huang H, Christensen GL, Billestrup N and Larsen MR. Characterization of the molecular mechanisms underlying Glucose Stimulated Insulin Secretion from freshly isolated pancreatic β-cells using PTMomics. Mol Cell Proteomics. 2018, 17(1):95-110.

Aebersold R et al. How many human proteoforms are there? Nat Chem Biol. 2018 Feb 14;14(3):206-214. Preliminary investigations of proteome alterations in non-affected arterial tissue from patients with abdominal aortic aneurysms. Kidholm, CL, Beck, HC, Madsen, JB, Lindholt, JS, Rasmussen, LM Plos One, 13 (2), e0192957, 2018.

Abdominal aortic aneurysms growth is associated with high concentrations of plasma proteins in the intraluminal thrombus and diseases arterial tissue – a proteome study. Behr-Rasmussen, C, Lindholt, JS, .,Halekoh, U, Stubbe, J, Jensen, PS, Rasmussen, LM, Beck HC. Arterioscl Thromb Vasc Biol, 38(9): 2254-2267, 2018

Proteomic discovery and validation of the confounding effect of heparin administration on the analysis of candidate cardiovascular biomarkers. Beck HC, Jensen, LO, Gils C, Ilondo AMM, Frydland, M, Hassager, C, Møller-Helgestad, OK, Møller JE, Rasmussen LM. Clin Chem, 64 (19), 1474-1484, 2018

Celebioglu, H.U. & B. Svensson: Dietary nutrients, proteomes, and adhesion of probiotic lactobacilli to mucin and host epithelial cells. Microorganisms 6, art. no. 6 (2018).

Larsen SC, Hendriks IA, Lyon D, Jensen LJ, Nielsen ML. Systems-wide Analysis of Serine ADP-Ribosylation Reveals Widespread Occurrence and Site-Specific Overlap with Phosphorylation. Cell Rep. 2018 Aug 28;24(9):2493-2505.e4. doi: 10.1016/j.celrep.2018.07.083.

Hendriks IA, Lyon D, Su D, Skotte NH, Daniel JA, Jensen LJ, Nielsen ML. Site-specific characterization of endogenous SUMOylation across species and organs. Nat Commun. 2018 Jun 25;9(1):2456. doi: 10.1038/s41467-018-04957-4.

F. Kirpekar, L.H. Hansen, J. Mundus, S. Tryggedsson, P. Teixeira dos Santos, E. Ntokou & B. Vester (2018). Mapping of ribosomal 23S ribosomal RNA modifications in Clostridium sporogenes. RNA Biol. 15, 1060-1070.

Akimov V, Barrio-Hernandez I, Hansen SVF, Hallenborg P, Pedersen AK, Bekker-Jensen DB, Puglia M, Christensen SDK, Vanselow JT, Nielsen MM, Kratchmarova I, Kelstrup CD, Olsen JV, Blagoev B. (2018) UbiSite approach for comprehensive mapping of lysine and N-terminal ubiquitination sites. Nature Struct Mol Biol. 25(7): 631-40.

Akimov V, Olsen LCB, Hansen SVF, Barrio-Hernandez I, Puglia M, Jensen SS, Solov’yov IA, Kratchmarova I, Blagoev B. (2018) StUbEx PLUS-A Modified Stable Tagged Ubiquitin Exchange System for Peptide Level Purification and In-Depth Mapping of Ubiquitination Sites. J Proteome Res. 17(1): 296-304.

Hojfeldt JW, Laugesen A, Willumsen BM, Damhofer H, Hedehus L, Tvardovskiy A, Mohammad F, Jensen ON, Helin K. Accurate H3K27 methylation can be established de novo by SUZ12-directed PRC2. Nat Struct Mol Biol. 2018;25(3):225-32.

Bergauer K, Fernandez-Guerra A, Garcia JAL, Sprenger RR, Stepanauskas R, Pachiadaki MG, Jensen ON, Herndl GJ. Organic matter processing by microbial communities throughout the Atlantic water column as revealed by metaproteomics. Proc Natl Acad Sci U S A. 2018;115(3):E400-E8.

Weissmann S, Cloos PA, Sidoli S, Jensen ON, Pollard S, Helin K. The Tumor Suppressor CIC Directly Regulates MAPK Pathway Genes via Histone Deacetylation. Cancer Res. 2018;78(15):4114-25.

Schwammle V, Jensen ON. VSClust: feature-based variance-sensitive clustering of omics data. Bioinformatics. 2018;34(17):2965-72.

Shliaha PV, Gibb S, Gorshkov V, Jespersen MS, Andersen GR, Bailey D, Schwartz J, Eliuk S, Schwammle V, Jensen ON. Maximizing Sequence Coverage in Top-Down Proteomics By Automated Multimodal Gas-Phase Protein Fragmentation. Anal Chem. 2018;90(21):12519-26.

2017

Herschend, J., Z.B.V. Damholt, A.M. Marquard, B. Svensson, S.J. Sørensen, P. Hägglund & M. Burmølle: A meta-proteomics approach to study the interspecies interactions affecting microbial biofilm development in a model community. Sci. Rep. 7, art. no. 16483 (2017).

Celebioglu, H.U. & B. Svensson: Exo- and surface proteomes of the probiotic bacterium Lactobacillus acidophilus NCFM. Proteomics 17, art. no. 1700019 (2017)

Hendriks IA, Lyon D, Young C, Jensen LJ, Vertegaal AC, Nielsen ML. Site-specific mapping of the human SUMO proteome reveals co-modification with phosphorylation. Nat Struct Mol Biol. 2017 Mar;24(3):325-336. doi: 10.1038/nsmb.3366.

Bekker-Jensen DB, Kelstrup CD, Batth TS, Larsen SC, Haldrup C, Bramsen JB, Sørensen KD, Høyer S, Ørntoft TF, Andersen CL, Nielsen ML, Olsen JV. An Optimized Shotgun Strategy for the Rapid Generation of Comprehensive Human Proteomes. Cell Syst. 2017 Jun 28;4(6):587-599.e4. doi: 10.1016/j.cels.2017.05.009.

Bllaci L, Torsetnes SB, Wierzbicka C, Shinde S, Sellergren B, Rogowska-Wrzesinska A, Jensen ON. Phosphotyrosine Biased Enrichment of Tryptic Peptides from Cancer Cells by Combining pY-MIP and TiO2 Affinity Resins. Anal Chem. 2017;89(21):11332-40.

Mohammad F, Weissmann S, Leblanc B, Pandey DP, Hojfeldt JW, Comet I, Zheng C, Johansen JV, Rapin N, Porse BT, Tvardovskiy A, Jensen ON, Olaciregui NG, Lavarino C, Sunol M, de Torres C, Mora J, Carcaboso AM, Helin K. EZH2 is a potential therapeutic target for H3K27M-mutant pediatric gliomas. Nat Med. 2017;23(4):483-92.

Shliaha PV, Baird MA, Nielsen MM, Gorshkov V, Bowman AP, Kaszycki JL, Jensen ON, Shvartsburg AA. Characterization of Complete Histone Tail Proteoforms Using Differential Ion Mobility Spectrometry. Anal Chem. 2017;89(10):5461-6.

Tvardovskiy A, Schwammle V, Kempf SJ, Rogowska-Wrzesinska A, Jensen ON. Accumulation of histone variant H3.3 with age is associated with profound changes in the histone methylation landscape. Nucleic Acids Res. 2017;45(16):9272-89.

Sanchez-Quiles V, Akimov V, Osinalde N, Francavilla C, Puglia M, Barrio-Hernandez I, Kratchmarova I, Olsen JV, Blagoev B. (2017) Cylindromatosis Tumor Suppressor Protein (CYLD) Deubiquitinase is Necessary for Proper Ubiquitination and Degradation of the Epidermal Growth Factor Receptor. Mol Cell Proteomics. 16(8): 1433-46.

2016

Martello R, Leutert M, Jungmichel S, Bilan V, Larsen SC, Young C, Hottiger MO, Nielsen ML. Proteome-wide identification of the endogenous ADP-ribosylome of mammalian cells and tissue. Nat Commun. 2016 Sep 30;7:12917. doi: 10.1038/ncomms12917.

Larsen SC, Sylvestersen KB, Mund A, Lyon D, Mullari M, Madsen MV, Daniel JA, Jensen LJ, Nielsen ML. Proteome-wide analysis of arginine monomethylation reveals widespread occurrence in human cells. Sci Signal. 2016 Aug 30;9(443):rs9. doi: 10.1126/scisignal.aaf7329.

J. Mundus, K.F. Flyvbjerg & F. Kirpekar (2016). Identification of the methyltransferase targeting C2499 in Deinococcus radiodurans 23S ribosomal RNA. Extremophiles 20, 91-99.

2015

H. Li, M.I. Rasmussen, M.R. Larsen, Y. Guo, C. Jers, G. Palmisano, J.D. Mikkelsen & F. Kirpekar (2015). Automated N-glycan profiling of a mutant Trypanosomas rangeli sialidase, expressed in Pichia pastoris, using tandem mass spectrometry and bioinformatics. Glycobiology 25, 1350-1361.

Quantitative Proteome Analysis Reveals Increased Content of Basement Membrane Proteins in Arteries from Patients with Type 2 Diabetes and Lower Levels among Metformin Users. Preil, SAR, Kristensen, LP, Beck, HC, Jensen, PS, Nielsen, PS, Steiniche, T, Bjørling-Poulsen, M, Larsen, MR, Hansen, ML, Rasmussen, LM. Circulation; Cardiovasc Gen, 8, 727-35, 2015