Publications – University of Copenhagen

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Centre for Epigenetics > Publications

Centre for Epigenetics Publications

 

2015

Vandamme J, Sidoli S, Mariani L, Friis C, Christensen J, Helin K, Jensen ON, Salcini AE. H3K23me2 is a new heterochromatic mark in Caenorhabditis elegans. Nucleic Acids Res. 2015 Nov 16;43(20):9694-710. doi: 10.1093/nar/gkv1063. (PR, OA)

Kim SH, Joshi K, Ezhilarasan R, Myers TR, Siu J, Gu C, Nakano-Okuno M, Taylor D, Minata M, Sulman EP, Lee J, Bhat KP, Salcini AE, Nakano I. EZH2 protects glioma stem cells from radiation-induced cell death in a MELK/FOXM1-dependent manner. Stem Cell Reports. 2015 Feb 10;4(2):226-38. doi: 10.1016/j.stemcr.2014.12.006.  (PR, CO, OA)

Tvardovskiy A, Wrzesinski K, Sidoli S, Fey SJ, Rogowska-Wrzesinska A, Jensen ON. Top-down and Middle-down Protein Analysis Reveals that Intact and Clipped Human Histones Differ in Post-translational Modification Patterns. Mol Cell Proteomics. 2015 Dec;14(12):3142-53. doi: 10.1074/mcp.M115.048975. Epub 2015 Sep 30. (PR)

Wu X, Bekker-Jensen IH, Christensen J, Rasmussen KD, Sidoli S, Qi Y, Kong Y, Wang X, Cui Y, Xiao Z, Xu G, Williams K, Rappsilber J, Sønderby CK, Winther O, Jensen ON, Helin K. Tumor suppressor ASXL1 is essential for the activation of INK4B expression in response to oncogene activity and anti-proliferative signals. Cell Res. 2015 Nov;25(11):1205-18. doi: 10.1038/cr.2015.121. Epub 2015 Oct 16. (PR, CO)

Lund RR, Leth-Larsen R, Caterino TD, Terp MG, Nissen J, Lænkholm AV, Jensen ON, Ditzel HJ. NADH-Cytochrome b5 Reductase 3 Promotes Colonization and Metastasis Formation and Is a Prognostic Marker of Disease-Free and Overall Survival in Estrogen Receptor-Negative Breast Cancer. Mol Cell Proteomics. 2015 Nov;14(11):2988-99. doi: 10.1074/mcp.M115.050385. Epub 2015 Sep 8. (PR)

Belda-Ferre P, Williamson J, Simón-Soro Á, Artacho A, Jensen ON, Mira A. The human oral metaproteome reveals potential biomarkers for caries disease. Proteomics. 2015 Oct;15(20):3497-507. doi: 10.1002/pmic.201400600. Epub 2015 Sep 22. (PR, CO)

de Bang TC, Petersen J, Pedas PR, Rogowska-Wrzesinska A, Jensen ON, Schjoerring JK, Jensen PE, Thelen JJ, Husted S. A laser ablation ICP-MS based method for multiplexed immunoblot analysis: applications to manganese-dependent protein dynamics of photosystem II in barley (Hordeum vulgare L.). Plant J. 2015 Aug;83(3):555-65. doi: 10.1111/tpj.12906. (PR, CO)

Such-Sanmartín G, Bache N, Bosch J, Gutiérrez-Gallego R, Segura J, Jensen ON. Detection and differentiation of 22 kDa and 20 kDa Growth Hormone proteoforms in human plasma by LC-MS/MS. Biochim Biophys Acta. 2015 Apr;1854(4):284-90. doi: 10.1016/j.bbapap.2014.12.022. Epub 2014 Dec 30. (PR, CO)

Casanovas A, Sprenger RR, Tarasov K, Ruckerbauer DE, Hannibal-Bach HK, Zanghellini J, Jensen ON, Ejsing CS. Quantitative analysis of proteome and lipidome dynamics reveals functional regulation of global lipid metabolism. Chem Biol. 2015 Mar 19;22(3):412-25. doi: 10.1016/j.chembiol.2015.02.007.  (PR, CO)

Alabert C, Barth TK, Reverón-Gómez N, Sidoli S, Schmidt A, Jensen ON, Imhof A, Groth A. Two distinct modes for propagation of histone PTMs across the cell cycle. Genes Dev. 2015 Mar 15;29(6):585-90. doi: 10.1101/gad.256354.114.  (PR, OA, CO)

Huang H, Strømme CB, Saredi G, Hödl M, Strandsby A, González-Aguilera C, Chen S, Groth A, Patel DJ. A unique binding mode enables MCM2 to chaperone histones H3-H4 at replication forks. Nat Struct Mol Biol. 2015 Aug;22(8):618-26. doi: 10.1038/nsmb.3055. Epub 2015 Jul 13. (PR, CO, OA)

Gallina I, Colding C, Henriksen P, Beli P, Nakamura K, Offman J, Mathiasen DP, Silva S, Hoffmann E, Groth A, Choudhary C, Lisby M. Nat Commun. 2015 Mar 30;6:6533. doi: 10.1038/ncomms7533. Cmr1/WDR76 defines a nuclear genotoxic stress body linking genome integrity and protein quality control. (PR, CO, OA)

Such-Sanmartín G, Bache N, Callesen AK, Rogowska-Wrzesinska A, Jensen ON. Targeted mass spectrometry analysis of the proteins IGF1, IGF2, IBP2, IBP3 and A2GL by blood protein precipitation. J Proteomics. 2015 Jan 15;113:29-37. doi: 10.1016/j.jprot.2014.09.013. Epub 2014 Sep 30.

Zub KA, Sousa MM, Sarno A, Sharma A, Demirovic A, Rao S, Young C, Aas PA, Ericsson I, Sundan A, Jensen ON, Slupphaug G. Modulation of cell metabolic pathways and oxidative stress signaling contribute to acquired melphalan resistance in multiple myeloma cells. PLoS One. 2015 Mar 13;10(3):e0119857. doi: 10.1371/journal.pone.0119857. eCollection 2015. (CO, OA)

Veit Schwämmle, Thiago Verano-Braga, and Peter Roepstorff. Computational and statistical methods for high-throughput analysis of post-translational modifications of proteins. J Proteomics 129, 3–15 (2015). doi: 10.1016/j.jprot.2015.07.016

Cruickshank VA, Sroczynska P, Sankar A, Miyagi S, Rundsten CF, Johansen JV, Helin K. PLoS One. 2015 Nov 16;10(11):e0142806. doi: 10.1371/journal.pone.0142806. eCollection 2015. SWI/SNF Subunits SMARCA4, SMARCD2 and DPF2 Collaborate in MLL-Rearranged Leukaemia Maintenance. (PR, OA)

Ptaschinski C, Mukherjee S, Moore ML, Albert M, Helin K, Kunkel SL, Lukacs NW.PLoS Pathog. 2015 Jun17;11(6):e1004978.doi:10.1371/journal.ppat.1004978. eCollection 2015 Jun. RSV-Induced H3K4 Demethylase KDM5B Leads to Regulation of Dendritic Cell-Derived Innate Cytokines and Exacerbates Pathogenesis In Vivo. (PR, CO, OA)

Fork C, Gu L, Hitzel J, Josipovic I, Hu J, SzeKa Wong M, Ponomareva Y, Albert M, Schmitz SU, Uchida S, Fleming I, Helin K, Steinhilber D, Leisegang MS, Brandes RP. Arterioscler Thromb Vasc Biol. 2015 Jul;35(7):1645-52. doi: 10.1161/ATVBAHA.115.305561. Epigenetic Regulation of Angiogenesis by JARID1B-Induced Repression of HOXA5. (PR, CO)

Rasmussen KD, Helin K. Nat Immunol. 2015 Jun;16(6):592-4. doi: 10.1038/ni.3176. TET1: an epigenetic guardian of lymphomagenesis.

Montes M, Nielsen MM, Maglieri G, Jacobsen A, Højfeldt J, Agrawal-Singh S, Hansen K, Helin K, van de Werken HJ, Pedersen JS, Lund AH. Nat Commun. 2015 Apr 24;6:6967. doi: 10.1038/ncomms7967. The lncRNA MIR31HG regulates p16(INK4A) expression to modulate senescence. (PR, CO, OA)

Rasmussen KD, Jia G, Johansen JV, Pedersen MT, Rapin N, Bagger FO, Porse BT, Bernard OA, Christensen J, Helin K. Genes Dev. 2015 May 1;29(9):910-22. doi: 10.1101/gad.260174.115. Loss of TET2 in hematopoietic cells leads to DNA hypermethylation of active enhancers and induction of leukemogenesis. (PR, CO, OA)

Ueda T, Nagamachi A, Takubo K, Yamasaki N, Matsui H, Kanai A, Nakata Y, Ikeda K, Konuma T, Oda H, Wolff L, Honda Z, Wu X, Helin K, Iwama A, Suda T, Inaba T, Honda H. Blood. 2015 May 28;125(22):3437-46. doi: 10.1182/blood-2014-03-562694. Fbxl10 overexpression in murine hematopoietic stem cells induces leukemia involving metabolic activation and upregulation of Nsg2. (PR, CO)

Stewart MH, Albert M, Sroczynska P, Cruickshank VA, Guo Y, Rossi DJ, Helin K, Enver T. Blood. 2015 Mar 26;125(13):2075-8. doi: 10.1182/blood-2014-08-596734. The histone demethylase Jarid1b is required for hematopoietic stem cell self-renewal in mice. (PR, CO)

Funa NS, Schachter KA, Lerdrup M, Ekberg J, Hess K, Dietrich N, Honoré C, Hansen K, Semb H.Cell Stem Cell. 2015 Jun 4;16(6):639-52. doi: 10.1016/j.stem.2015.03.008. β-Catenin Regulates Primitive Streak Induction through Collaborative Interactions with SMAD2/SMAD3 and OCT4. (PR, CO) 

2014

Alabert C, Bukowski-Wills J-C, Lee S-P, Kustatscher G, Nakamura K, de Lima Alves F, Menard P, Mejlvang J, Rappsilber J, Groth A (2014). Nascent chromatin capture proteomics determines chromatin dynamics during DNA replication and identifies unknown fork components. Nature Cell Biology, 16(3):281-93. doi: 10.1038/ncb2918 (PR, CO, OA)

Carvalho AS, Ribeiro H, Voabil P, Penque D, Jensen ON, Molina H, Matthiesen R (2014). Global mass spectrometry and transcriptomics array based drug profiling provides novel insight into glucosamine induced ER stress. Mol Cell Proteomics pii: mcp.M113.034363. doi: 10.1074/mcp.M113.034363. (PR,CO)

Christensen LL, Holm A, Rantala J, Kallioniemi O, Rasmussen MH, Ostenfeld MS, Dagnaes-Hansen F, Oster B, Schepeler T, Tobiasen H, Thorsen K, Sieber OM, Gibbs P, Lamy P, Hansen TF, Jakobsen A, Riising EM, Helin K, Lubinski J, Hagemann-Madsen R, Laurberg S, Orntoft TF, Andersen CL (2014). Functional Screening Identifies miRNAs Influencing Apoptosis and Proliferation in Colorectal Cancer. PloS one 9(6):e96767.  doi: 10.1371/journal.pone.0096767 (PR,CO, OA)

De Raedt T, Beert E, Pasmant E, Luscan A, Brems H, Ortonne N, Helin K, Hornick JL, Mautner V, Kehrer-Sawatzki H, Clapp W, Bradner J, Vidaud M, Upadhyaya M, Legius E, Cichowski K (2014). PRC2 loss amplifies Ras-driven transcription and confers sensitivity to BRD4-based therapies. Nature 514(7521):247-51. doi: 10.1038/nature13561. (PR ,CO)

Damkjaer M, Jensen PH, Schwämmle V, Sprenger RR, Jacobsen IA, Jensen ON, Bie P (2014). Selective renal vasoconstriction, exaggerated natriuresis and excretion rates of exosomic proteins in essential hypertension. Acta Physiol (Oxf) 212(1):106-18. doi: 10.1111/apha.12345. (PR, CO)

Dikopoltsev E, Foltyn VN, Zehl M, Jensen ON, Mori H, Radzishevsky I, Wolosker H (2014). FBXO22 Protein Is Required for Optimal Synthesis of the N-Methyl-d-Aspartate (NMDA) Receptor Coagonist d-Serine. J Biol Chem. 289(49):33904-15. doi: 10.1074/jbc.M114.618405. (PR, CO)

Falkenby LG, Such-Sanmartín G, Larsen MR, Vorm O, Bache N, Jensen ON (2014). Integrated Solid-Phase Extraction-Capillary Liquid Chromatography (speLC) Interfaced to ESI-MS/MS for Fast Characterization and Quantification of Protein and Proteomes. J Proteome Res. 13(12):6169-75. doi: 10.1021/pr5008575. (PR, CO)

Feyder M, Södersten E, Santini E, Vialou V, LaPlant Q, Watts EL, Spigolon G, Hansen K, Caboche J, Nestler EJ, Fisone G (2014). A Role for Mitogen- and Stress-Activated Kinase 1 in L-DOPA-Induced Dyskinesia and ∆FosB Expression. Biological Psychiatry pii: S0006-3223(14)00552-6. doi: 10.1016/j.biopsych.2014.07.019 (PR,CO)

Gingold H, Tehler D, Christoffersen NR, Nielsen MM, Asmar F, Kooistra SM, Christophersen NS, Christensen LL, Borre M, Sørensen KD, Andersen LD, Andersen CL, Hulleman E, Wurdinger T, Ralfkiær E, Helin K, Grønbæk K, Orntoft T, Waszak SM, Dahan O, Pedersen JS, Lund AH, Pilpel Y (2014). A dual program for translation regulation in cellular proliferation and differentiation. Cell 158(6):1281-92. doi: 10.1016/j.cell.2014.08.011 (PR,CO)

Heinemann B, Nielsen JM, Hudlebusch HR, Lee, MJ, Larsen DV, Boesen T, Labelle M, Gerlach L-O, Birk P, Helin K (2014). Inhibition of demethylases by GSK-J1/J4. Nature, 514(7520):E1-2. doi: 10.1038/nature13688 (PR, CO)

Klimovskaia IM, Young C, Strømme CB, Menard P, Jasencakova Z, Mejlvang J, Ask K, Ploug M, Nielsen ML, Jensen ON, Groth A (2014). Tousled-like kinases phosphorylate Asf1 to promote histone supply during DNA replication. Nature Communications, 5:3394. doi: 10.1038/ncomms4394 (PR, CO, OA)

Kooistra SM, Rudkjær LC, Lees MJ, Steinhauer C, Johansen JV, Helin K (2014). A Screen Identifies the Oncogenic Micro-RNA miR-378a-5p as a Negative Regulator of Oncogene-Induced Senescence. PloS one 9(3):e91034. doi: 10.1371/journal.pone.0091034 (PR, OA)

Langlois T, da Costa Reis Monte Mor B, Lenglet G, Droin N, Marty C, Le Couédic J-P, Almire C, Auger N, Mercher T, Delhommeau F, Christensen JA, Helin K, Debili N, Fuks F, Bernard OA, Solary E, Vainchenker W, Plo I (2014). TET2 deficiency inhibits mesoderm and hematopoietic differentiation in human embryonic stem cells. Stem Cells 32(8):2084-97. doi: 10.1002/stem.1718 (PR, CO)

Laugesen A, Helin K (2014). Chromatin Repressive Complexes in Stem Cells, Development, and Cancer. Cell Stem Cell 14(6)735-51. doi: 10.1016/j.stem.2014.05.006 (PR)

Liu Y, Carlsson R, Comabella M, Wang J, Kosicki MK, Carrion B, Hasan M, Wu X, Montalban X, Dziegiel MH, Sellebjerg F, Sørensen PS, Helin K, Navikas S (2014). FoxA1 directs the lineage and immunosuppressive properties of a novel regulatory T cell population in EAE and MS. Nature Medicine 20(3):272-82. doi: 10.1038/nm.3485 (PR, CO)

Mejlvang J, Feng Y, Alabert C, Neelsen KJ, Jasencakova Z, Zhao X, Lees M, Sandelin A, Pasero P, Lopes M, Groth A (2014). New histone supply regulates replication fork speed and PCNA unloading. Journal of Cell Biology 204(1):29-43. doi: 10.1083/jcb.201305017 (PR, CO, OA)

Méndez-García C, Mesa V, Sprenger RR, Richter M, Diez MS, Solano J, Bargiela R, Golyshina OV, Manteca Á, Ramos JL, Gallego JR, Llorente I, Martins dos Santos VA, Jensen ON, Peláez AI, Sánchez J, Ferrer M (2014). Microbial stratification in low pH oxic and suboxic macroscopic growths along an acid mine drainage. ISME J 8(6):1259-74. doi: 10.1038/ismej.2013.242. (PR, CO, AO)

Palmowski P, Rogowska-Wrzesinska A, Williamson J, Beck HC, Mikkelsen JD, Hansen HH, Jensen ON (2014). Acute phencyclidine treatment induces extensive and distinct protein phosphorylation in rat frontal cortex. J Proteome Res 13(3):1578-92. doi: 10.1021/pr4010794. (PR, CO)

Pedersen MT, Agger K, Laugesen A, Johansen JV, Cloos PAC, Christensen JA, Helin K (2014). The Demethylase JMJD2C Localizes to H3K4me3 Positive Transcription Start Sites and Is Dispensable for Embryonic Development. Molecular and Cellular Biology 34(6):1031-45. doi: 10.1128/MCB.00864-13 (PR, OA)

Piunti A, Rossi A, Cerutti A, Albert M, Jammula S, Scelfo A, Cedrone L, Fragola G, Pålsson LE, Koseki H, Testa G, Casola S, Helin K, d'Adda di Fagagna F, Pasini D (2014). Polycomb proteins control proliferation and transformation independently of cell cycle checkpoints by regulating DNA replication. Nature Communications, 5:3649. doi: 10.1038/ncomms4649 (PR, CO, OA)

Riising EM, Vacher-Comet I, Leblanc BO, Wu X, Johansen JV, Helin K (2014). Gene Silencing Triggers Polycomb Repressive Complex 2 Recruitment to CpG Islands Genome Wide. Molecular Cell 55(3):347-60. doi: 10.1016/j.molcel.2014.06.005 (PR)

da Rocha ST, Boeva V, Escamilla-Del-Arenal M, Ancelin K, Granier C, Matias NR, Sanulli S, Chow J, Schulz E, Picard C, Kaneko S, Helin K, Reinberg D, Stewart AF, Wutz A, Margueron R, Heard E (2014). Jarid2 Is Implicated in the Initial Xist-Induced Targeting of PRC2 to the Inactive X Chromosome. Molecular Cell 53(2):301-16. doi: 10.1016/j.molcel.01.002 (PR, CO, OA)

Salvato F, Havelund JF, Chen M, Rao RS, Rogowska-Wrzesinska A, Jensen ON, Gang DR, Thelen JJ, Møller IM (2104). The potato tuber mitochondrial proteome. Plant Physiol 164(2):637-53. doi: 10.1104/pp.113.229054. (PR, CO, OA)

Schwämmle V, Aspalter CM, Sidoli S, Jensen ON (2014). Large Scale Analysis of Co-existing Post-translational Modifications in Histone Tails Reveals Global Fine Structure of Cross-talk. Mol Cell Proteomics 13(7):1855-65. doi: 10.1074/mcp.O113.036335. (PR)

Sidoli S, Schwämmle V, Ruminowicz C, Hansen TA, Wu X, Helin K, Jensen ON (2014). Middle-down hybrid chromatography/tandem mass spectrometry workflow for characterization of combinatorial post-translational modifications in histones. Proteomics 14(19):2200-11. doi: 10.1002/pmic.201400084 (PR)  

Siersbæk R, Rabiee A, Nielsen R, Sidoli S, Traynor S, Loft A, La Cour Poulsen L, Rogowska-Wrzesinska A, Jensen ON, Mandrup S (2014). Transcription factor cooperativity in early adipogenic hotspots and super-enhancers. Cell Rep 7(5):1443-55. doi: 10.1016/j.celrep.2014.04.042. (PR, CO, OA)

Siersbæk R, Baek S, Rabiee A, Nielsen R, Traynor S, Clark N, Sandelin A, Jensen ON, Sung MH, Hager GL, Mandrup S (2014). Molecular architecture of transcription factor hotspots in early adipogenesis. Cell Rep 7(5):1434-42. doi: 10.1016/j.celrep.2014.04.043. (PR, CO, OA)

Sroczynska P, Cruickshank VA, Bukowski JP, Miyagi S, Bagger FO, Walfridsson J, Schuster MB, Porse B, Helin K (2014). shRNA screening identifies JMJD1C as being required for leukemia maintenance. Blood. 2014 Mar 20;123(12):1870-82. doi: 10.1182/blood-2013-08-522094. (PR, CO, OA)

Such-Sanmartín G, Bache N, Callesen AK, Rogowska-Wrzesinska A, Jensen ON (2014). Targeted mass spectrometry analysis of the proteins IGF1, IGF2, IBP2, IBP3 and A2GL by blood protein precipitation. J Proteomics 113:29-37. (PR, CO) doi: 10.1016/j.bbapap.2014.12.022. (PR,CO)

Such-Sanmartín G, Ventura-Espejo E, Jensen ON (2014). Depletion of abundant plasma proteins by poly(N-isopropylacrylamide-acrylic acid) hydrogel particles. Anal Chem 86(3):1543-50. doi: 10.1021/ac403749j. (PR, CO)

Such-Sanmartín G, Sidoli S, Ventura-Espejo E, Jensen ON (2014). KYSS: mass spectrometry data quality assessment for protein analysis and large-scale proteomics. Biochem Biophys Res Commun 445(4):702-7. doi: 10.1016/j.bbrc.2014.01.066. (PR, CO)

Södersten E, Feyder M, Lerdrup, M Rodrigues Gomes AL, Kryh H, Spigolon G, Caboche J, Fisone G, Hansen K (2014). Dopamine signaling leads to loss of Polycomb repression and aberrant gene activation in experimental parkinsonism. P L o S Genetics 10(9):e1004574. doi: 10.1371/journal.pgen.1004574 (PR, CO, OA)

Vacher-Comet I, Helin K (2014). Revolution in the Polycomb hierarchy. Nat Struct Mol Biol. 21(7):573-5. doi: 10.1038/nsmb.2848 (PR)

Vondriska TM, Jensen ON (2014). Proteomics in chromatin biology and epigenetics. Proteomics 14(19):2105-8. doi: 10.1002/pmic.201470143 (PR, CO)

Wang WQ, Ye JQ, Rogowska-Wrzesinska A, Wojdyla KI, Jensen ON, Møller IM, Song SQ (2014). Proteomic comparison between maturation drying and prematurely imposed drying of Zea mays seeds reveals a potential role of maturation drying in preparing proteins for seed germination, seedling vigor, and pathogen resistance. J Proteome Res 13(2):606-26. doi: 10.1021/pr4007574. (PR, CO)

Williams K, Christensen J, Rappsilber J, Nielsen AL, Johansen JV, Helin K (2014). The Histone Lysine Demethylase JMJD3/KDM6B Is Recruited to p53 Bound Promoters and Enhancer Elements in a p53 Dependent Manner. PloS one 9( 5):e96545. doi: 10.1371/journal.pone.0096545 (PR,CO, OA)

Zhao X, Bak S, Pedersen AJ, Jensen ON, Højlund K (2014). Insulin increases phosphorylation of mitochondrial proteins in human skeletal muscle in vivo. J Proteome Res 13(5):2359-69. doi: 10.1021/pr401163t. (PR, CO)

Zhao X, Sidoli S, Wang L, Wang W, Guo L, Jensen ON, Zheng L (2014). Comparative proteomic analysis of histone post-translational modifications upon ischemia/reperfusion-induced retinal injury. J Proteome Res 13(4):2175-86. doi: 10.1021/pr500040a. (PR, CO) 

2013

Albert M, Schmitz SU, Kooistra SM, Malatesta M, Morales Torres C, Rekling JC, Johansen JV, Abarrategui I, Helin K (2013). The Histone Demethylase Jarid1b Ensures Faithful Mouse Development by Protecting Developmental Genes from Aberrant H3K4me3. PLoS Genet 9(4):e1003461. (PR, OA)

Arteaga MF, Mikesch JH, Qiu J, Christensen J, Helin K, Kogan SC, Dong S, So CW (2013). The Histone Demethylase PHF8 Governs Retinoic Acid Response in Acute Promyelocytic Leukemia. Cancer Cell. 18;23(3):376-89. (PR, CO)

Asmar F, Punj V, Christensen J, Pedersen MT, Pedersen A, Nielsen AB, Hother C, Ralfkiaer U, Brown P, Ralfkiaer E, Helin K, Grønbæk K (2013). Genome-wide profiling identifies a DNA methylation signature that associates with TET2 mutations in diffuse large B-cell lymphoma. Haematologica  98(12):1912-20. (PR, CO)

Bak S, León IR, Jensen ON, Højlund K (2013). Tissue specific phosphorylation of mitochondrial proteins isolated from rat liver, heart muscle, and skeletal muscle. Journal of Proteome Research. 12(10):4327-39. (PR, CO)

Ballabeni A, Zamponi R, Moore JK, Helin K, Kirschner MW (2013). Geminin deploys multiple mechanisms to regulate Cdt1 before cell division thus ensuring the proper execution of DNA replication. Proc Natl Acad Sci USA 110(30):E2848-53. (PR, CO)

Bender S, Tang Y, Lindroth AM, Hovestadt V, Jones DT, Kool M, Zapatka M, Northcott PA, Sturm D, Wang W, Radlwimmer B, Højfeldt JW, Truffaux N, Castel D, Schubert S, Ryzhova M, Seker-Cin H, Gronych J, Johann PD, Stark S, Meyer J, Milde T, Schuhmann M, Ebinger M, Monoranu CM, Ponnuswami A, Chen S, Jones C, Witt O, Collins VP, von Deimling A, Jabado N, Puget S, Grill J, Helin K, Korshunov A, Lichter P, Monje M, Plass C, Cho YJ, Pfister SM (2013). Reduced H3K27me3 and DNA Hypomethylation Are Major Drivers of Gene Expression in K27M Mutant Pediatric High-Grade Gliomas. Cancer Cell 24(5):660-72. (PR, CO)

Busch A, Petersen J, Webber-Birungi MT, Powikrowska M, Lassen LMM, Naumann-Busch B, Nielsen AZ, Ye J, Boekema EJ, Jensen ON, Lunde C, Jensen PE. (2013). Composition and structure of photosystem I in the moss Physcomitrella patens. J Exp Bot 64(10):2689-2699. (PR, CO)

Di Croce L, Helin K (2013). Transcriptional regulation by Polycomb group proteins. Nat Struct Mol Biol 20(10):1147-55. (PR)

Egan CM, Nyman U, Skotte J, Streubel G, Turner S, O'Connell DJ, Rraklli V, Dolan MJ, Chadderton N, Hansen K, Farrar GJ, Helin K, Holmberg J, Bracken AP (2013). CHD5 is required for neurogenesis and has a dual role in facilitating gene expression and polycomb gene repression. Dev Cell 26(3):223-36. (PR, CO)

Grassilli E, Narloch R, Federzoni E, Ianzano L, Pisano F, Giovannoni R, Romano G, Masiero L, Leone BE, Bonin S, Donada M, Stanta G, Helin K, Lavitrano M (2013). Inhibition of GSK3B Bypass Drug Resistance of p53-Null Colon Carcinomas by Enabling Necroptosis in Response to Chemotherapy. Clin Cancer Res 19(14):3820-31. (PR, CO)

Halcsik E, Forni MF, Fujita A, Verano-Braga T, Jensen ON, Sogayar MC (2013). New insights in osteogenic differentiation revealed by mass spectrometric assessment of phosphorylated substrates in murine skin mesenchymal cells. B M C Cell Biology 14(47). (PR, CO)

Hattori N, Niwa T, Kimura K, Helin K, Ushijima T (2013). Visualization of multivalent histone modification in a single cell reveals highly concerted epigenetic changes on differentiation of embryonic stem cells. Nucleic Acids Res 41(15):7231-9. (PR, CO)

Helin K, Dhanak D. Chromatin proteins and modifications as drug targets. Nature. 2013 Oct 24;502(7472):480-8. (PR)

Højfeldt JW, Agger K, Helin K (2013). Histone lysine demethylases as targets for anticancer therapy. Nat Rev Drug Discov 12(12):917-30. (PR)

Jensen PH, Mysling S, Højrup P, Jensen ON (2013). Glycopeptide Enrichment for MALDI-TOF Mass Spectrometry Analysis by Hydrophilic Interaction Liquid Chromatography Solid Phase Extraction (HILIC SPE). Methods Mol Biol 951;131-144. (PR)

 Jung HR, Sidoli S, Haldbo SN, Sprenger RR, Schwämmle V, Pasini D, Helin K, Jensen ON (2013). Precision mapping of co-existing modifications in histone H3 tails from embryonic stem cells by ETD-MS/MS. Anal Chem 85(17):8232-9. (PR)

Klauke K, Radulović V, Broekhuis M, Weersing E, Zwart E, Olthof S, Ritsema M,  Bruggeman S, Wu X, Helin K, Bystrykh L, de Haan G (2013). Polycomb Cbx family members mediate the balance between haematopoietic stem cell self-renewal and differentiation. Nat Cell Biol 15(4):353-62. (PR, CO)

Leon IR, Schwämmle V, Jensen ON, Sprenger RR (2013). Quantitative assessment of in-solution digestion efficiency identifies optimal protocols for unbiased protein analysis: Quantitative assessment of protein digestion protocols. Mol Cell Proteomics 12(10):2992-3005. (PR)

Malatesta M, Steinhauer C, Mohammad F, Pandey DP, Squartrito M, Helin K (2013). Histone acetyltransferase PCAF is required for Hedgehog-Gli-dependent transcription and cancer cell proliferation. Cancer Res 73(20):6323-33. (PR)

Mejlvang J, Feng Y, Alabert C, Neelsen KJ, Jasencakova Z, Zhao X, Lees M, Sandelin A, Pasero P, Lopes M, Groth A (2013). Nucleosome Assembly Regulates Replication Fork Speed and PCNA unloading. Epub Dec. 30, 2013. (PR)

Morales Torres C, Laugesen A, Helin K (2013). Utx Is Required for Proper Induction of Ectoderm and Mesoderm during Differentiation of Embryonic Stem Cells. PLoS One. 2013;8(4):e60020. (PR, OA)

Musacchio A, Helin K (2013). Cell cycle, differentiation and disease. Curr Opin Cell Biol 25(6):673-5. (PR)

Petersen J, Rogowska-Wrzesinska A, Jensen ON (2013). Functional proteomics of barley and barley chloroplasts – strategies, methods and perspectives. Front Plant Sci 4:52. (PR)

Reales-Calderón JA, Sylvester M, Strijbis K, Jensen ON, Nombela C, Molero G, Gil C (2013). Candida albicans induces pro-inflammatory and anti-apoptotic signals in macrophages as revealed by quantitative proteomics and phosphoproteomics. J Proteomics 91:106-135. (PR, CO)

Repetto D, Aramu S, Boeri Erba E, Sharma N, Grasso S, Russo I, Jensen ON, Cabodi S, Turco E, Di Stefano P, Defilippi P (2013). Mapping of p140Cap phosphorylation sites: the EPLYA and EGLYA motifs have a key role in tyrosine phosphorylation and Csk binding, and are substrates of the Abl kinase. PLoS One 8(1):e54931. (PR, CO, OA)

de la Rica L, Rodríguez-Ubreva J, García M, Islam AB, Urquiza JM, Hernando H, Christensen J, Helin K, Gómez-Vaquero C, Ballestar E (2013). PU.1 target genes undergo Tet2-coupled demethylation and DNMT3b-mediated methylation in monocyte-to-osteoclast differentiation. Genome Biol 14(9):R99. (PR, CO)

Schoofs T, Rohde C, Hebestreit K, Klein H, Göllner H, Schulze I, Lerdrup M, Dietrich N, Agrawal-Singh S, Witten A, Stoll M, Lengfelder E, Hofmann W, Schlenke P, Büchner T, Hansen K, Berdel WE, Rosenbauer F, Dugas M and Müller-Tidow C (2013). DNA methylation changes are a late event in Acute Promyelocytic Leukemia and coincide with loss of transcription factor binding. Blood 121(1):178-87. (PR, CO)

Schwämmle V, Jensen ON. A Computational Model for Histone Mark Propagation Reproduces the Distribution of Heterochromatin in Different Human Cell Types. PLoS One 2013;8:e73818. (PR, OA)

Schwämmle V, León IR, Jensen ON. Assessment and improvement of statistical tools for comparative proteomics analysis of sparse data sets with few experimental replicates. J Proteome Res 12(9):3874-3883. (PR)

Terp MG, Lund RR, Jensen ON, Leth-Larsen R, Ditzel HJ (2013). Identification of markers associated with highly aggressive metastatic phenotypes using quantitative comparative proteomics. Cancer Genomics Proteomics 9(5):265-73. (PR, CO)

Tsushima H, Malabarba MG, Confalonieri S, Senic-Matuglia F, Verhoef LG, Bartocci C, D'Ario G, Cocito A, Di Fiore PP, Salcini AE (2013). A snapshot of the physical and functional wiring of the eps15 homology domain network in the nematode. PLoS One 8(2):e56383. (PR, OA)

Vandamme J, Salcini AE (2013). Catalytic-independent roles of UTX-1in C. elegans development. Worm 2(2):e22188. (PR)

Vella P, Scelfo A, Jammula S, Chiacchiera F, Williams K, Cuomo A, Roberto A, Christensen J, Bonaldi T, Helin K, Pasini D (2013). Tet Proteins Connect the O-Linked N-acetylglucosamine Transferase Ogt to Chromatin in Embryonic Stem Cells. Mol Cell 49(4):645-56. 24. (PR, CO)

Williamson JC, Scheipers P, Schwämmle V, Zibert JR, Beck HC, Jensen ON (2013). A proteomics approach to the identification of biomarkers for psoriasis utilising keratome biopsy. J Proteomics 94:176-185. (PR)

Wrzesinski K, León IR, Kulej K, Sprenger RR, Bjørdal B, Christiansen BJ, Berge RK, N Jensen O, Rogowska-Wrzesinska A (2013). Proteomics identifies molecular networks affected by tetradecylthioacetic acid and fish oil supplemented diets. J Proteomics 84:61-77. (PR, CO)

Wu X, Johansen JV, Helin K (2013). Fbxl10/Kdm2b Recruits Polycomb Repressive Complex 1 to CpG Islands and Regulates H2A Ubiquitylation. Mol Cell 49(6):1134-46. (PR) 

2012

Adams D, Altucci L, Antonarakis SE, Ballesteros J, Beck S, Bird A, Bock C, Boehm B, Campo E, Caricasole A, Dahl F, Dermitzakis ET, Enver T, Esteller M, Estivill X, Ferguson-Smith A, Fitzgibbon J, Flicek P, Giehl C, Graf T, Grosveld F, Guigo R, Gut I, Helin K, Jarvius J, Küppers R, Lehrach H, Lengauer T, Lernmark Å, Leslie D, Loeffler M, Macintyre E, Mai A, Martens JH, Minucci S, Ouwehand WH, Pelicci PG, Pendeville H, Porse B, Rakyan V, Reik W, Schrappe M, Schübeler D, Seifert M, Siebert R, Simmons D, Soranzo N, Spicuglia S, Stratton M, Stunnenberg HG, Tanay A, Torrents D, Valencia A, Vellenga E, Vingron M, Walter J, Willcocks S (2012). BLUEPRINT to decode the epigenetic signature written in blood. Nat Biotechnol 30(3):224-6. (PR, CO)

Agrawal-Singh S, Isken F, Agelopoulos K, Klein HU, Thoennissen NH, Koehler G, Hascher A, Bäumer N, Berdel WE, Thiede C, Ehninger G, Becker A, Schlenke P, Wang Y, McClelland M, Krug U, Koschmieder S, Büchner T, Yu DY, Singh SV, Hansen K, Serve H, Dugas M, Müller-Tidow C (2012). Genome-wide analysis of histone H3 acetylation patterns in AML identifies PRDX2 as an epigenetically silenced tumor suppressor gene. Blood. 119(10):2346-57. (PR, CO)

Alabert C, Groth A (2012). Chromatin replication and epigenome maintenance. Nat Rev Mol Cell Biol 13(3):153-67. Review. (PR)

Amon S, Trelle MB, Jensen ON, Jørgensen TJ (2012). Spatially resolved protein hydrogen exchange measured by subzero-cooled chip-based nanoelectrospray ionization tandem mass spectrometry. Anal Chem. 84(10):4467-73. (PR, CO)

Ask K, Jasencakova Z, Menard P, Feng Y, Almouzni G, Groth A (2012). Codanin-1, mutated in the anaemic disease CDAI, regulates Asf1 function in S-phase histone supply. EMBO J 31(8):2013-23 (PR)

Beck H, Nähse-Kumpf V, Yoo Larsen MS, O'Hanlon KA, Patzke S, Holmberg C, Mejlvang J, Groth A, Nielsen O, Syljuåsen RG, Sørensen CS (2012). CDK suppression by WEE1 kinase protects the genome through control of replication initiation and nucleotide consumption. Mol Cell Biol 32(20):4226-36. (PR,CO)

Bisgaard CF, Bak S, Christensen T, Jensen ON, Enghild JJ, Wiborg O (2012). Vesicular signalling and immune modulation as hedonic fingerprints: proteomic profiling in the chronic mild stress depression model. J Psychopharmacol. 26(12):1569-83. (PR, CO)

Boulay G, Dubuissez M, Van Rechem C, Forget A, Helin K, Ayrault O, Leprince D (2012). Hypermethylated in cancer 1 (HIC1) recruits polycomb repressive complex 2 (PRC2) to a subset of its target genes through interaction with human polycomb-like (hPCL) proteins. J Biol Chem. 287(13):10509-24. (PR, CO)

Dietrich N, Lerdrup M, Landt E, Agrawal-Singh S, Bak M, Tommerup N, Rappsilber J, Södersten E, Hansen K (2012). REST-Mediated Recruitment of Polycomb Repressor Complexes in Mammalian Cells. PLoS Genet 8(3):e1002494. (PR, CO)

Galli GG, Honnens de Lichtenberg K, Carrara M, Hans W, Wuelling M, Mentz B, Multhaupt HA, Fog CK, Jensen KT, Rappsilber J, Vortkamp A, Coulton L, Fuchs H, Gailus-Durner V, Hrabě de Angelis M, Calogero RA, Couchman JR, Lund AH (2012). Prdm5 regulates collagen gene transcription by association with RNA polymerase II in developing bone. PLoS Genetics 8(5):e1002711 (PR, OA)

Gregersen LH, Jacobsen A, Frankel LB, Wen J, Krogh A, Lund AH (2012). microRNA-143 down-regulates Hexokinase 2 in colon cancer cells. BMC Cancer. 12(1):232 (PR)

Hansen TA, Sylvester M, Jensen ON, Kjeldsen F (2012). Automated and high confidence protein phosphorylation site localization using complementary collision-activated dissociation and electron transfer dissociation tandem mass spectrometry. Anal Chem 84(22):9694-9. (PR, CO)

Henningsen K, Palmfeldt J, Christiansen S, Baiges I, Bak S, Jensen ON, Gregersen N, Wiborg O (2012). Candidate hippocampal biomarkers of susceptibility and resilience to stress in a rat model of depression. Mol Cell Proteomics 11(7):M111.016428. (PR, CO)

Jeker LT, Zhou X, Gershberg K, de Kouchkovsky D, Morar MM, Stadthagen G, Lund AH, Bluestone JA (2012). microRNA 10a Marks Regulatory T cells. PLoS ONE 7(5): e36684. (PR, CO, OA)

Kallin EM, Rodríguez-Ubreva J, Christensen J, Cimmino L, Aifantis I, Helin K, Ballestar E, Graf T (2012). Tet2 Facilitates the Derepression of Myeloid Target Genes during CEBPα-Induced Transdifferentiation of Pre-B Cells. Mol Cell 48(2):266-76. (PR, CO)

Kooistra SM, Helin K (2012). Molecular mechanisms and potential functions of histone demethylases. Nat Rev Mol Cell Biol 13(5):297-311. Review. (PR)

Kristensen LH, Nielsen AL, Helgstrand C, Lees M, Cloos P, Kastrup JS, Helin K, Olsen L, Gajhede M (2012). Studies of H3K4me3 demethylation by KDM5B/Jarid1B/PLU1 reveals strong substrate recognition in vitro and identifies 2,4-pyridine-dicarboxylic acid as an in vitro and in cell inhibitor. FEBS J 279(11):1905-14. (PR, CO)

Krogager TP, Nielsen LV, Bak S, Young C, Ferreri C, Jensen ON, Højrup P, Thoma V, Thøgersen IB, Enghild JJ (2012). Identification of a potential biomarker panel for the intake of the common dietary trans fat elaidic acid (trans∆9-C18:1). J Proteomics 75(9):2685-96. (PR, CO)

Lee SB, Jasencakova Z, Groth A (2012). H3K56me1 marks a spot for PCNA. Mol Cell 46(1):1-2. (PR)

Leth-Larsen R, Terp MG, Christensen AG, Elias D, Kühlwein T, Jensen ON, Petersen OW, Ditzel HJ (2012). Functional heterogeneity within the CD44 high human breast cancer stem cell-like compartment reveals a gene signature predictive of distant metastasis. Mol Med 18:1109-21. (PR, CO)

Lund RR, Terp MG, Laenkholm AV, Jensen ON, Leth-Larsen R, Ditzel HJ (2012). Quantitative proteomics of primary tumors with varying metastatic capabilities using stable isotope-labeled proteins of multiple histogenic origins. Proteomics 12(13):2139-48. (PR, CO)

Leucci E, Zriwil A, Gregersen LH, Jensen KT, Obad S, Bellan C, Leoncini L, Kauppinen S, Lund AH (2012). Inhibition of miR-9 targets HuR and DICER1 and impairs Hodgkin Lymphoma tumor outgrowth in vivo. Oncogene 31(49):5081-9 (PR)

Le Bihan MC, Bigot A, Jensen SS, Dennis JL, Rogowska-Wrzesinska A, Lainé J, Gache V, Furling D, Jensen ON, Voit T, Mouly V, Coulton GR, Butler-Browne G (2012). In-depth analysis of the secretome identifies three major independent secretory pathways in differentiating human myoblasts. J Proteomics 77:344-56. (PR, CO)

Louarn S, Nawrocki A, Edelenbos M, Jensen DF, Jensen ON, Collinge DB, Jensen  B (2012). The influence of the fungal pathogen Mycocentrospora acerina on the proteome and polyacetylenes and 6-methoxymellein in organic and conventionally cultivated  carrots (Daucus carota) during post-harvest storage. J Proteomics 75(3):962-77. (PR, CO)

Nielsen AL, Kristensen LH, Stephansen KB, Kristensen JB, Helgstrand C, Lees M, Cloos P, Helin K, Gajhede M, Olsen L (2012). Identification of catechols as histone-lysine demethylase inhibitors. FEBS Lett 586(8):1190-4. (PR, CO)

Ngara R, Ndimba R, Borch-Jensen J, Jensen ON, Ndimba B (2012). Identification and profiling of salinity stress-responsive proteins in Sorghum bicolor seedlings. J Proteomics 75(13):4139-50. (PR, CO)

Riising EM, Helin K (2012). A new role for the polycomb group protein Ezh1 in promoting transcription. Mol Cell 45(2):145-6. (PR)

Rudashevskaya EL, Ye J, Jensen ON, Fuglsang AT, Palmgren MG (2012). Phosphosite mapping of P-type plasma membrane H+-ATPase in homologous and heterologous environments. J Biol Chem 287(7):4904-13. (PR, CO)

Schepeler T, Holm A, Halvey P, Nordentoft I, Lamy P, Riising EM, Christensen LL, Thorsen K, Liebler DC, Helin K, Orntoft TF, Andersen CL (2012). Attenuation of the beta-catenin/TCF4 complex in colorectal cancer cells induces several growth-suppressive microRNAs that target cancer promoting genes. Oncogene 31(22):2750-60. (PR, CO)

Sidoli S, Cheng L, Jensen ON (2012). Proteomics in chromatin biology and epigenetics: Elucidation of post-translational modifications of histone proteins by mass spectrometry. J Proteomics 75(12):3419-33. (PR)

Terp MG, Lund RR, Jensen ON, Leth-Larsen R, Ditzel HJ (2012). Identification of markers associated with highly aggressive metastatic phenotypes using quantitative comparative proteomics. Cancer Genomics Proteomics 9(5):265-73. (PR, CO)

Tóth K, Stratil TF, Madsen EB, Ye J, Popp C, Antolín-Llovera M, Grossmann C, Jensen ON, Schüssler A, Parniske M, Ott T (2012). Functional domain analysis of the Remorin protein LjSYMREM1 in Lotus japonicus. PLoS One 7(1):e30817. (PR, CO, OA)

Vandamme J, Lettier G, Sidoli S, Di Schiavi E, Nørregaard Jensen O, Salcini AE (2012). The C. elegans H3K27 demethylase UTX-1 is essential for normal development, independent of its enzymatic activity. PLoS Genet 8(5):e1002647. (PR, OA)

 2011

Andersen DC, Kortesidis A, Zannettino ACW, Kratchmarova I, Chen L, Jensen ON et al (2011). Development of novel monoclonal antibodies that define differentiation stages of human stromal (mesenchymal) stem cells. Mol Cell 32(2):133-42. (PR, CO)

Anderton JA, Bose S, Vockerodt M, Vrzalikova K, Wei W, Kuo M, Helin K, Christensen J, Rowe M, Murray PG, Woodman CB (2011). The H3K27me3 demethylase, KDM6B, is induced by Epstein-Barr virus and over-expressed in Hodgkin's Lymphoma. Oncogene. 30(17):2037-43. (PR, CO)

Bilgin M, Markgraf DF, Duchoslav E, Knudsen J, Jensen ON, de Kroon AIPM et al. Quantitative profiling of PE, MMPE, DMPE, and PC lipid species by multiple precursor ion scanning: A tool for monitoring PE metabolism. Biochimica et Biophysica Acta. 1811(12):1081-1089. (PR, CO)

Bou Kheir T, Futoma-Kazmierczak E, Jacobsen A, Krogh A, Bardram L, Hother C, Grønbæk K, Federspiel B, Lund AH, Friis-Hansen L (2011). miR-449 inhibits cell proliferation and is down-regulated in gastric cancer. Mol Cancer 10:29. (Review, CO)

Chen F, Pruett-Miller SM, Huang Y, Gjoka M, Duda K, Taunton J, Collingwood TN, Frödin M, Davis GD (2011). High frequency genome editing using ssDNA oligos and zinc finger nucleases. Nature Methods 8:753-5. (PR, CO)

Dong L, Zhang X, Fu X, Zhang X, Gao X, Zhu M, Wang X, Yang Z, Jensen ON, Saarikettu J, Yao Z, Silvennoinen O, Yang J (2011). PTB-associated splicing factor (PSF) functions as a repressor of STAT6-mediated Ig epsilon gene transcription by recruitment of HDAC1. J Biol Chem 286(5):3451-9. (PR, CO)

Frankel LB, Wen J, Lees M, Høyer-Hansen M, Farkas T, Krogh A, Jäättelä M, Lund AH (2011). microRNA-101 is a potent inhibitor of autophagy. EMBO Journal 30(22):4628-41. doi: 10.1038/emboj.2011.331. (PR, CO)

Hansson J, Panchaud A, Favre L, Bosco N, Mansourian R, Benyacoub J, Blum S, Jensen ON, Kussmann M (2011). Time-resolved quantitative proteome analysis of in vivo intestinal development. Mol Cell Proteomics 10(3):M110.005231. (PR, CO)

Hua Y, Duan S, Murmann AE, Larsen N, Kjems J, Lund AH, Peter ME (2011). miRConnect: Identifying Effector Genes of miRNAs and miRNA Families in Cancer Cells. PLoS One (6)10:e26521. (PR, CO, OA)

Hudlebusch HR, Santoni-Rugiu E, Simon R, Ralfskiær E, Rossing HH, Johansen JV, Jorgensen M, Sauter G, Helin K (2011). The histone methyltransferase and putative oncoprotein MMSET is overexpressed in a large variety of human tumors. Clin Cancer Res. 17(9):2919-33. (PR, CO)

Hudlebusch H R, Skotte J, Santoni-Rugiu E, Zimling ZG, Lees MJ, Simon R, Sauter G, Rota R, De Ioris MA, Quarto M, Johansen JV, Jorgensen M, Rechnitzer C, Maroun LL, Schrøder H, Petersen BL, Helin K (2011). MMSET is highly expressed and associated with aggressiveness in neuroblastoma. Cancer Research 71(12):4226-35. (PR, CO)

Jørgensen S, Eskildsen M, Fugger K, Hansen L, Larsen MS, Kousholt AN, Syljuåsen RG, Trelle MB, Jensen ON, Helin K, Sørensen CS (2011). SET8 is degraded via PCNA-coupled CRL4(CDT2) ubiquitylation in S phase and after UV irradiation. J Cell Biol 192(1):43-54. (PR, CO)

Koronakis V, Hume PJ, Humphreys D, Liu T, Hørning O, Jensen ON et al (2011). WAVE regulatory complex activation by cooperating GTPases Arf and Rac1. National Academy of Sciences, Proceedings 108(35):14449-54. (PR, CO)

Lohse B, Kristensen JL, Kristensen LH, Agger K, Helin K, Gajhede M, Clausen RP (2011). Inhibitors of histone demethylases. Bioorganic & Medicinal Chemistry Lett. 19(12):3625-36. (Review, CO)

Lohse B, Nielsen AL, Kristensen JBL, Helgstrand C, Cloos PAC, Olsen L, Gajhede M, Clausen RP, Kristensen JL (2011). Targeting histone lysine demethylases by truncating the histone 3 tail to obtain selective substrate-based inhibitors. Angewandte Chemie (International Edition) (50)39:9100-03. (PR, CO)

Madsen EB, Antolín-Llovera M, Grossmann C, Ye J, Vieweg S, Broghammer A, Krusell L, Radutoiu S, Jensen ON, Stougaard J, Parniske M (2011). Autophosphorylation is essential for the in vivo function of the Lotus japonicus Nod factor receptor 1 and receptor-mediated signalling in cooperation with Nod factor receptor 5. Plant Journal 65(3):404-17.

Manteca A, Ye J, Sánchez J, Jensen ON (2011). Phosphoproteome analysis of streptomyces development reveals extensive protein phosphorylation accompanying bacterial differentiation. Journal of Proteome Research 10(12):5481-92. (PR, CO)

Nawrocki A, Thorup-Kristensen K, Jensen ON (2011). Quantitative proteomics by 2DE and MALDI MS/MS uncover the effects of organic and conventional cropping methods on vegetable products. Journal of proteomics 74(12):2810-25. (PR)

Rosenqvist H, Ye J, Jensen ON (2011). Analytical strategies in mass spectrometry-based phosphoproteomics. Methods in Molecular Biology 753:183-213. (PR)

Rudashevskaya EL, Ye J, Jensen ON, Fuglsang AT, Palmgren MG (2011). Phosphosite mapping of the P-type plasma membrane H+-ATPase in homologous and heterologous environments. J Biol Chem. 2011 Dec 15. [Epub ahead of print] (PR, CO)

Scavenius C, Sanggaard KW, Nikolajsen CL, Bak S, Valnickova Z, Thøgersen IB, Jensen ON, Højrup P, Enghild JJ (2011). Human inter-α-inhibitor is a substrate for factor XIIIa and tissue transglutaminase. Biochim Biophys Acta 1814(12):1624-30. (PR, CO)

Schepeler T, Holm A, Halvey P, Nordentoft I, Lamy P, Riising EM, Christensen LL, Thorsen K, Liebler DC, Helin K, Orntoft TF, Andersen CL (2011). Attenuation of the beta-catenin/TCF4 complex in colorectal cancer cells induces several growth-suppressive microRNAs that target cancer promoting genes. Oncogene. 2011 Oct 3. doi: 10.1038/onc.2011.453. [Epub ahead of print] (PR, CO) 

Schmitz SU, Albert M, Malatesta M, Morey L, Johansen JV, Bak M, Tommerup N, Abarrategui I, Helin K (2011). Jarid1b targets genes regulating development and is involved in neural differentiation. EMBO J 30(22):4586-600. (PR, CO)

Sonne-Schmidt CS, Sanggaard KW, Nikolajsen CL, Bak S, Valnickova Z, Thøgersen I, Jensen ON et al (2011). Human inter-α-inhibitor is a substrate for factor XIIIa and tissue transglutaminase. Biochimica et Biophysica Acta 1814(12):1624-30. (PR, CO)

Stojic L, Jasencakova Z, Prezioso C, Stützer A, Bodega B, Pasini D, Klingberg R, Mozzetta C, Margueron R, Puri PL, Schwarzer D, Helin K, Fischle W, Orlando V (2011). Chromatin regulated interchange between polycomb repressive complex 2 (PRC2)-Ezh2 and PRC2-Ezh1 complexes controls myogenin activation in skeletal muscle cells. Epigenetics Chromatin. 2011 Sep 5;4:16. (PR, CO)

Tehler D, Høyland-Kroghsbo, NM, Lund AH (2011). The miR-10 microRNA precursor family. RNA Biology. 8, 5. (PR, CO)

Thingholm TE, Bak S, Beck-Nielsen H, Jensen ON, Gaster M (2011). Characterization of human myotubes from type 2 diabetic and non-diabetic subjects using complementary quantitative mass spectrometric methods (2011). Molecular and Cellular Proteomics 10(9):M110.006650. (PR, CO)

Ungureanu D, Wu J, Pekkala T, Niranjan Y, Young C, Jensen ON et al (2011). The pseudokinase domain of JAK2 is a dual-specificity protein kinase that negatively regulates cytokine signaling. Nature Structural and Molecular Biology 18(9):971-6. (PR, CO)

Viticchiè G, Lena AM, Latina A, Formosa A, Gregersen LH, Lund AH, Bernardini S, Mauriello A, Miano R, Spagnoli LG, Knight RA, Candi E, Melino G (2011). MiR-203 controls proliferation, migration and invasive potential of prostate cancer cell lines. Cell Cycle. (10)7:1121-31. (PR, CO)

Williams K, Christensen J, Helin K (2011). DNA methylation: TET proteins-guardians of CpG islands? EMBO Rep. 13(1):28-35. doi: 10.1038/embor.2011.233. (PR)

 Williams K, Christensen J, Pedersen MT, Johansen JV, Cloos PAC, Rappsilber J, Helin K (2011). TET1 and hydroxymethylcytosine in transcription and DNA methylation fidelity. Nature (473)7347:343-8. (PR, CO)

2010

Agrawal-Singh S, Koschmieder S, Gelsing S, Stocking C, Stehling M, Thiede C, Thoennissen NH, Köhler G, Valk PJ, Delwel R, Mills K, Bäumer N, Tickenbrock L, Hansen K, Berdel WE, Müller-Tidow C, Serve H (2010). Pim2 cooperates with PML-RARalpha to induce acute myeloid leukemia in a bone marrow transplantation model. Blood 115(22):4507-16. (PR, CO)

Albert M and Helin K (2010). Histone methyl transferases in cancer. Seminars in Cell and Develop Biol 21(2):209-20. (PR)

BouKheir T, Lund AH (2010). Epigenetic dynamics across the cell cycle. Essays Biochem 48(1):107-20. (PR)

Christophersen NS and Helin K (2010). Epigenetic control of embryonic stem cell fate. J Exp Med 207(11):2287-95. (PR).

Foltyn VN, Zehl M, Dikopoltsev E, Jensen ON, Wolosker H (2010). Phosphorylation of mouse serine racemase regulates D-serine synthesis. FEBS letters 584(13):2937-41. (PR, CO)

von Freyend SJ, Rosenqvist H, Fink A, Melzer IM, Clos J, Jensen ON, Wiese M (2010). LmxMPK4, an essential mitogen-activated protein kinase of Leishmania mexicana is phosphorylated and activated by the STE7-like protein kinase LmxMKK5. Int J Parasitol. 40(8):969-78. (PR, CO)

Gehani SS, Agrawal-Singh S, Dietrich N, Christophersen NS, Helin K, Hansen K (2010). Polycomb group protein displacement and gene activation through MSK-dependent H3K27me3S28 phosphorylation. Mol Cell 39(6):886-900. (PR)

Gregersen LH, Jacobsen AB, Frankel LB, Wen J, Krogh A, Lund AH (2010). MicroRNA-145 targets YES and STAT1 in colon cancer cells. PLoS One 5(1):e8836. (PR, CO, OA)

Jung HR, Pasini D, Helin K, Jensen ON (2010) Quantitative mass spectrometry of histone H3.2 and H3.3 in Suz12 deficient mouse ES cells reveals distinct, dynamic post-translational modifications at K27 and K36. Mol Cell Proteomics 9:838-50. (PR)

Kleine-Kohlbrecher D, Christensen J, Vandamme J, Abarrategui I, Bak M, Tommerup N, Shi X, Gozani O, Rappsilber J, Salcini AE and Helin K (2010). A functional link between the histone demethylase PHF8 and the transcription factor ZNF711 in X-linked mental retardation. Mol Cell 38(2):165-78. (PR, CO)

Kondo A, Thaysen-Andersen M, Hjernø K, Jensen ON (2010). Characterization of sialylated and fucosylated glycopeptides of beta2-glycoprotein I by a combination of HILIC LC and MALDI MS/MS. J Sep Sci 33(6-7):891-902. (PR)

Kool J, Uren AG, Martins CP, Sie D, de Ridder J, Turner G, van Uitert M, Matentzoglu K, Lagcher W, Krimpenfort P, Gadiot J, Pritchard C, Lenz J, Lund AH, Jonkers J, Rogers J, Adams DJ, Wessels L, Berns A, van Lohuizen M (2010). Insertional mutagenesis in mice deficient for p15Ink4b, p16Ink4a, p21Cip1, and p27Kip1 reveals cancer gene interactions and correlations with tumor phenotypes. Cancer Res 70(2):520-31. (PR, CO)

Leeb M, Pasini D, Novatchkova M, Jaritz M, Helin K, Wutz A (2010). Polycomb complexes act redundantly to repress genomic repeats and genes. Genes Dev 24(3):265-76. (PR, CO)

Lund AH (2010). miR-10 in development and cancer. Cell Death Differ 17(2):209-14. (PR)

Manteca A, Jung HR, Schwämmle V, Jensen ON, Sanchez J (2010). Quantitative Proteome Analysis of Streptomyces coelicolor Nonsporulating Liquid Cultures Demonstrates a Complex Differentiation Process Comparable to That Occurring in Sporulating Solid Cultures. J Proteome Res 9(9):4801-11. (PR, CO)

Manteca A, Sanchez J, Jung HR, Schwämmle V, Jensen ON (2010). Quantitative proteomic analysis of Streptomyces coelicolor development demonstrates that onset of secondary metabolism coincides with hyphae differentiation. Mol Cell Proteomics 9(7):1423-36. (PR, CO)

Morey L, Helin K (2010). Polycomb group protein-mediated transcriptional repression. Trends Biochem 35:323-32. (PR)

Negishi M, Saraya A, Mochizuki S, Helin K, Koseki H, and Iwama A (2010). A novel zinc finger protein Zfp277 mediates transcriptional repression of the Ink4a/Arf locus through polycomb repressive complex 1. PlosOne, 5, el 2373. (PR, CO, OA)

Pasini D, Cloos PA, Walfridsson J, Olsson L, Bukowski JP, Johansen JV, Bak M, Tommerup N, Rappsilber J, Helin K (2010). JARID2 regulates binding of the Polycomb repressive complex 2 to target genes in ES cells. Nature 464:306-10. (PR, CO)

Pasini D, Malatesta M, Jung HR, Walfridsson J, Willer A, Olsson L, Skotte J, Wutz A, Porse B, Jensen ON, Helin K (2010). Characterization of an antagonistic switch between Histone H3 lysine 27 methylation and acetylation in the transcriptional regulation of Polycomb group target genes. Nucleic Acids Res 38:4958-69. (PR, CO)

Pedersen MT, Helin K (2010). Histone demethylases in development and disease. Trends in Cell Biology 20(11):662-71. (PR)

Porse BT, Petersen OW, Helin K. [Basic stem cell biology and cancer] (2010). Ugeskr Laeger 172(38):2600-3. In Danish.

Rand KD, Zehl M, Jensen ON, Jørgensen TJ (2010). Loss of ammonia during electron-transfer dissociation of deuterated peptides as an inherent gauge of gas-phase hydrogen scrambling. Anal Chem. 2010 Dec 1;82(23):9755-62. (PR, CO)

Roepstorff P, Jensen ON (2010). Analysis of post-translationally modified proteins in proteomics. Functional Proteomics: Principles and practical applications. Edit. P. Ping, Humana Press.

Schubert S, Knoch K-P, Ouwendijk J, Mohammed S, Bodrov Y, Jäger M, Altkrüger A, Wegbrod C, Adams ME, Kim Y, Froehner SC, Jensen ON, Kalaidzidis Y, Solimena M (2010). b2-Syntrophin is a Cdk5 Substrate that Restrains the Motility of Insulin Secretory Granules. PLOS One 23:5(9):e12929. (PR, CO, OA)

Schwämmle V, Jensen ON (2010). A simple and fast method to determine the parameters for fuzzy c-means cluster analysis. Bioinformatics  26(22):2841-8. (PR, CO)

Sprenger RR, Jensen ON (2010). Proteomics and the dynamic plasma membrane: Quo Vadis? Proteomics10(22)3997-4011. (PR)

Sørensen CS, Melixetian M, Klein DK, Helin K (2010). NEK11: linking CHK1 and CDC25A in DNA damage checkpoint signaling. Cell Cycle 9(3):450-5. (PR)

Ye J, Zhang X, Young C, Zhao X, Hao Q, Cheng L, Jensen ON (2010). Optimized IMAC-IMAC protocol for phosphopeptide recovery from complex biological samples. J Proteome Res. 2;9(7):3561-73.  (PR, CO)

 Ytterberg AJ, Jensen ON (2010). Modification-specific proteomics in plant biology. J Proteomics 73(11):2249-66. (PR, CO)

 Zhao X, Leon IR, Bak S, Mogensen M, Wrzesinski K, Hojlund K, Jensen ON. Phosphoproteome analysis of functional mitochondria isolated from resting human muscle reveals extensive phosphory­lation of inner membrane protein complexes and enzymes. Mol Cell Proteomics 10(1):M110.000299.

 Ørom UA, Lund AH (2010). Experimental identification of microRNA targets. Gene 451(1-2):1-5. (PR)

2009

 Agger K, Cloos  PAC, Rudkjaer L, Williams K, Andersen G, Christensen J, Helin K (2009). The H3K27me3 demethylase JMJD3 contributes to the activation of the INK4A-ARF locus in response to oncogene- and stress-induced senescence. Genes Dev 23(10):1171-6. (PR)

Balan L, Foltyn VN, Zehl M, Dumin E, Dikopoltsev E, Knoh D, Ohno Y, Kihara A, Jensen ON, Radzishevsky IS, Wolosker H (2009). Feedback inactivation of D-serine synthesis by NMDA receptor-elicited translocation of serine racemase to the membrane. Proceedings of the National Academy of Science of the United States of America 106(18):7589-94.

Ballabeni A, Zamponi R, Caprara G, Melixetian M, Bossi S, Masiero L, Helin K (2009). Human CDT1 associates with CDC7 and recruits CDC45 to chromatin during S phase. J Biol Chem 284(5):3028-36. (PR, CO)

Barends S, Zehl M, Bialek S, de Waal E, Traag BA, Willemse J, Jensen ON, Vijgenboom E, van Wezel GP (2009). Transfer-messenger RNA controls the translation of cell-cycle and stress proteins in Streptomyces. EMBO Rep. 11(2):119-25.

Boccalatte FE, Voena C, Riganti C, Bosia A, D’Amico L, Riera L, Cheng M, Ruggeri B, Jensen ON, Goss VL, Lee K, Nardone J, Rush J, Polakiewicz RD, Comb MJ, Chiarle R, Inghirami G (2009). The enzymatic activity of 5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase (ATIC) is enhanced by NPM-ALK: new insights in ALK-mediated pathogenesis and the treatment of ALCL. Blood 8(3):2776-90. (PR, CO)

Bracken AP, Helin K (2009). Polycomb group proteins: navigators of lineage pathways led astray in cancer. Nat Rev Cancer 9(11):773-84. (PR, CO)

Callesen AK, Madsen JS, Vach W, Kruse TA, Mogensen O, Jensen ON (2009). Serum protein profiling by solid phase extraction and mass spectrometry: A future diagnostics tool? Proteomics 9(6):1428-41. (PR)

Callesen AK, Madsen JS, Iachina M, Vach W, Kruse TA, Jensen ON, Mogensen O (2009). Serum peptin/protein profiling by mass spectrometry provides diagnostic information independently of CA125 in women with an ovarian tumor. Cancer Biomark. 6(2):73-82. (PR)

Calvano C, Jensen ON, Zambonin C (2009). Selective extraction of phospholipids from dairy products by micro-solid phase extraction based on titanium dioxide microcolumns followed by MALDI-TOF-MS analysis. Analytical and Bioanalytical Chemistry 394(5):1453-61. (PR, CO)

Caprara G, Zamponi R, Melixetian M, Helin K (2009). Isolation and characterization of DUSP11, a novel p53 target gene. J Cell Mol Med 13(8B):2158-70. (PR, CO)

Ciró M, Prosperini E, Quarto M, Grazini U, Walfridsson J, McBlane F, Nucifero P, Pacchiana G, Capra M, Christensen J, Helin K (2009). ATAD2 is a novel cofactor for MYC, overexpressed and amplified in aggressive tumors. Cancer Res 69(21): 8491-8. (PR, CO)

Christoffersen NR, Shalgi R, Frankel LB, Leucci E, Lees M, Klausen M, Pilpel Y, Nielsen FC, Oren M, Lund AH (2009). p53-independent upregulation of miR-34a during oncogene-induced senescence represses MYC. Cell Death and Differ 17(2):235-45. (PR, CO)

Dettori R, Sonzogni S, Meyer  L, Lopez-Garcia LA, Morrice NA, Zeuzem S, Engel M, Piiper A, Neimanis S, Frödin M, Biondi RM (2009). Regulation of the interaction between protein kinase C-related protein kinase 2 (PRK2) and its upstream kinase, 3-phosphoinositide-dependent protein kinase 1 (PDK1). J Biol Chem 284(44)30318-27. (PR, CO)

Doehn U, Hauge C, Frank SR, Jensen CAJ, Duda K, Nielsen JV, Cohen MS, Johansen JV, Winther BR, Lund LR, Winther O, Taunton J, Hansen SH, Frödin M (2009). RSK is a principal effector of the RAS-ERK pathway for eliciting a coordinate promotile/invasive gene program and phenotype in epithelial cells. Mol Cell 35(4):511-22. (PR, CO)

Hansen K, Helin K (2009). Epigenetic inheritance through self-recruitment of the polycomb repressive complex 2. Epigenetics 4(3):133-8. (PR)

Hulleman E, Quarto M, Vernell R, Masserdotti G, Colli E, Kros JM, Levi D, Gaetani P, Tunici P, Finocchiaro G, Baena RR, Capra M, Helin K (2009). A role for the transcription factor HEY1 in glioblastoma. J Cell Mol Med 13(1):136-46. (PR, CO)

Hynek R, Svensson B, Jensen ON, Barkholt V, Finnie C (2009). The plasma membrane proteome of germinating barley embryos. Proteomics 9(14):3787-94. (PR, CO)

Jenal M, Trinh E, Britschgi C, Britschgi A, Roh V, Vorburger SA, Tobler A, Leprince D, Fey MF, Helin K, Tschan MP (2009). The tumor suppressor gene hypermethylated in cancer 1 is transcriptionally regulated by E2F1. Mol Cancer Res 7(6):916-22. (PR, CO)

Kondo A, Miyamoto T, Yonekawa O, Giessing A, Østerlund EC, Jensen ON (2009). Glycopeptide profiling of beta-2-glycoprotein I by mass spectrometry reveals attenuated sialylation in patients with antiphospholipid syndrome. Journal of Proteomics 73(1):123-33. (PR, CO)

Leth-Larsen R, Lund R, Hansen HV, Laenkholm A, Tarin D, Jensen ON, Ditzel H (2009). Metastasis-related plasma membrane proteins of human breast cancer cells identified by comparative quantitative mass spectrometry. Molecular and Cellular Proteomics 8(6):1436-49. (PR, CO)

Lund R, Leth-Larsen R, Jensen ON, Ditzel HJ (2009). Efficient Isolation and Quantitative Proteomic Analysis of Cancer Cell Plasma Membrane Proteins for Identification of Metastasis-Associated Cell Surface Markers. Journal of Proteome Research 8(6):3078–90. (PR, CO)

Melixetian M, Klein DK, Sørensen CS, Helin K (2009). NEK11 regulates CDC25A degradation and the IR-induced G2/M checkpoint. Nat Cell Biol 11(10):1247-53. (PR, CO)

Nienhuijs MEL, Poulsen K, van der Zande M, Briest A, Merkx MAW, Stoelinga PJW, Jensen ON, Jansen JA, Walboomers XF (2009). Analytical assessment of the osteoinductive material COL-LOSSE, Journal of Biomedical Materials Research. Part B: Applied Biomaterials 89B(2):300-5. (PR, CO)

Rand KD, Zehl M, Jensen ON, Jørgensen TJD (2009). Protein hydrogen exchange measured at single-residue resolution by electron transfer dissociation mass spectrometry. Analytical Chemistry 81(14):5577-84. (PR)

Salcedo-Amaya AM, van Driel MA, Alako BT, Trelle MB, van den Elzen AMG, Cohen AM, Janssen-Megens EM, van de Vegte-Bolmer M, Selzer RR, Iniguez AL, Green RD, Sauerwein RW, Jensen ON, Stunnenberg, HG 2009, ‘Dynamic histone H3 epigenome marking during the intraerythrocytic cycle of Plasmodium falciparum’, Proceedings of the National Academy of Science of the United States of America 106(24):9655-60. (PR, CO)

Stulemeijer IJE, Joosten MHAJ, Jensen ON (2009). Quantitative Phosphoproteomics of Tomato Mounting a Hypersensitive Response Reveals a Swift Suppression of Photosynthetic Activity and a Differential Role for Hsp90 Isoforms. Journal of Proteome Research 8(3):1168-82. (PR, CO)

Svenningsen P, Bistrup C, Friis UG, Bertog M, Haerteis S, Krueger B, Stubbe J, Jensen ON, Thiesson HC, Uhrenholt TR, Jespersen B, Jensen BL, Korbmacher C, Skøtt O (2009). Plasmin in Nephrotic Urine Activates the Epithelial Sodium Channel. Journal of the American Society of Nephrology 20(2):299-310. (PR, CO)

Thingholm TE, Jensen ON, Larsen MR (2009). Analytical strategies for phosphoproteomics. Proteomics 9(6):1451-68. (PR, CO)

Thingholm TE, Jensen ON, Larsen MR (2009). Enrichment and characterization of phosphopeptides by immobilized metal affinity chromatography (IMAC) and mass spectrometry. Methods Mol Biol. 527:47-56 xi. (PR, CO)

Thingholm TE, Jensen ON, Larsen MR (2009). Enrichment and separation of mono- and multiply phosphorylated peptides using sequential elution from IMAC prior to mass spectrometric analysis. Methods Mol Biol. 527:67-78, xi. (PR, CO)

Trelle MB, Salcedo-Amaya AM, Cohen A, Stunneberg HG, Jensen ON (2009). Global histone analysis by mass spectrometry reveals a high content of acetylated lysine residues in the malaria parasite Plasmodium falciparum. Journal of Proteome Research 8(7):3439-50. (PR)

Uren AG, Mikkers H, Kool J, van der Weyden L, Lund AH, Wilson CH, Rance R, Jonkers J, van Lohuizen M, Berns A, Adams DJ (2009). A high-throughput splinkerette-PCR method for the isolation and sequencing of retroviral insertion sites. Nat Protoc. 4(5):789-98. (PR, CO)

Zhao Y, Jensen ON (2009). Modification-specific proteomics: strategies for characterization of post-translational modifications using enrichment techniques. Proteomics 9(20):4632-41. (PR, CO) 

2008

Agger K, Christensen J, Cloos PA, Helin K (2008). The emerging functions of histone demethylases. Curr Opin Genet Dev. 18(2):159-68. (PR)

Britschgi A, Trinh E, Rizzi M, Jenal M, Ress A, Tobler A, Fey MF, Helin K, Tschan MP (2008). DAPK2 is a novel E2F1/KLF6 target gene involved in their proapoptotic function. Oncogene 27(43):5706-16. (PR, CO)

Cloos PA, Christensen J, Agger K, Helin K (2008). Erasing the methyl mark: histone demethylases at the center of cellular differentiation and disease. Genes Dev. 22(9):1115-40. (PR)

Hansen KH, Bracken AP, Pasini D, Dietrich N, Gehani SS, Monrad A, Rappsilber J, Lerdrup M, Helin K (2008). A model for transmission of the H3K27me3 epigenetic mark. Nat Cell Biol. 10(11):1291-300. (PR, CO)

Herranz N, Pasini D, Díaz VM, Francí C, Gutierrez A, Dave N, Escrivà M, Hernandez-Muñoz I, Di Croce L, Helin K, García de Herreros A, Peiró S (2008). Polycomb complex 2 is required for E-cadherin repression by the Snail1 transcription factor. Mol Cell Biol. 28(15):4772-81. (PR, CO)

Hørning OB, Kjeldsen F, Theodorsen S, Vorm O, Jensen ON (2008). Isocratic Solid Phase Extraction-Liquid Chromatography (SPE-LC) Interfaced to High-Performance Tandem Mass Spectrometry for Rapid Protein Identification. J Proteome Res. 7(8):3159-67. (PR)

Kjeldsen F, Hørning OB, Jensen SS, Giessing AM, Jensen ON (2008). Towards Liquid Chromatography Time-Scale Peptide Sequencing and Characterization of Post-Translational Modifications in the Negative-Ion Mode Using Electron Detachment Dissociation Tandem Mass Spectrometry. J Am Soc Mass Spectrom. 19(8):1156-62. (PR)

Lindroth AM, Park YJ, McLean CM, Dokshin GA, Persson JM, Herman H, Pasini D, Miró X, Donohoe ME, Lee JT, Helin K, Soloway PD (2008). Antagonism between DNA and H3K27 methylation at the imprinted Rasgrf1 locus. PLoS Genet. 4(8):e1000145. (PR, CO, OA)

Mathivanan S, Ahmed M, Ahn NG, Alexandre H, Amanchy R, Andrews PC, Bader JS, Balgley BM, Bantscheff M, Bennett KL, Björling E, Blagoev B, Bose R, Brahmachari SK, Burlingame AS, Bustelo XR, Cagney G, Cantin GT, Cardasis HL, Celis JE, Chaerkady R, Chu F, Cole PA, Costello CE, Cotter RJ, Crockett D, DeLany JP, De Marzo AM, DeSouza LV, Deutsch EW, Dransfield E, Drewes G, Droit A, Dunn MJ, Elenitoba-Johnson K, Ewing RM, Van Eyk J, Faca V, Falkner J, Fang X, Fenselau C, Figeys D, Gagné P, Gelfi C, Gevaert K, Gimble JM, Gnad F, Goel R, Gromov P, Hanash SM, Hancock WS, Harsha HC, Hart G, Hays F, He F, Hebbar P, Helsens K, Herme­king H, Hide W, Hjernø K, Hochstrasser DF, Hofmann O, Horn DM, Hruban RH, Ibarrola N, James P, Jensen ON, Jensen PH, Jung P, Kandasamy K, Kheterpal I, Kikuno RF, Korf U, Körner R, Kuster B, Kwon MS, Lee HJ, Lee YJ, Lefevre M, Lehvaslaiho M, Lescuyer P, Levander F, Lim MS, Löbke C, Loo JA, Mann M, Martens L, Martinez-Heredia J, McComb M, McRed­mond J, Mehrle A, Menon R, Miller CA, Mischak H, Mohan SS, Mohmood R, Molina H, Moran MF, Morgan JD, Moritz R, Morzel M, Muddiman DC, Nalli A, Navarro JD, Neubert TA, Ohara O, Oliva R, Omenn GS, Oyama M, Paik YK, Pennington K, Pepperkok R, Periaswamy B, Petricoin EF, Poirier GG, Prasad TS, Purvine SO, Rahiman BA, Ramachan­dran P, Ramachandra YL, Rice RH, Rick J, Ronnholm RH, Salonen J, Sanchez JC, Sayd T, Seshi B, Shankari K, Sheng SJ, Shetty V, Shivakumar K, Simpson RJ, Sirdesh­mukh R, Siu KW, Smith JC, Smith RD, States DJ, Sugano S, Sullivan M, Superti-Furga G, Takatalo M, Thongboonkerd V, Trinidad JC, Uhlen M, Vandekerckhove J, Vasilescu J, Veenstra TD, Vidal-Taboada JM, Vihinen M, Wait R, Wang X, Wiemann S, Wu B, Xu T, Yates JR, Zhong J, Zhou M, Zhu Y, Zurbig P, Pandey A (2008). Human Proteinpedia enables sharing of human protein data. Nat Biotechnol. 26(2):164-167. (PR, CO)

Pasini D, Bracken AP, Agger K, Christensen J, Hansen K, Cloos PA, Helin K (2008). Regulation of Stem Cell Differentiation by Histone Methyltransferases and Demethylases. Cold Spring Harb Symp Quant Biol. 73:253-63. (PR)

Pasini D, Hansen KH, Christensen J, Agger K, Cloos PA, Helin K (2008). Coordinated regulation of transcriptional repression by the RBP2 H3K4 demethylase and Polycomb-Repressive Complex 2. Genes Dev. 22(10):1345-55. (PR)

Riising EM, Boggio R, Chiocca S, Helin K, Pasini D (2008). The polycomb repressive complex 2 is a potential target of SUMO modifications. PLoS ONE. 3(7):e2704. (PR, CO, OA)

Thingholm TE, Jensen ON, Robinson P, Larsen MR (2008). SIMAC (sequential elution from IMAC), a phosphoproteomics strategy for the rapid separation of monophosphorylated from multiply phosphorylated peptides. Mol Cell Proteomics. 7(4):661-71. (PR)

Thingholm TE, Larsen MR, Ingrell CR, Kassem M, Jensen ON (2008). TiO2-Based Phosphoproteomic Analysis of the Plasma Membrane and the Effects of Phosphatase Inhibitor Treatment. J Proteome Res. 7(8):3304-13. (PR)

Trelle MB, Jensen ON (2008). Utility of immonium ions for assignment of epsilon-N-acetyllysine-containing peptides by tandem mass spectrometry. Anal Chem. 80(9):3422-30. (PR)

Ørom UA, Nielsen FC, Lund AH (2008). MicroRNA-10a binds the 5’UTR of ribosomal protein mRNAs and enhances their translation. Mol Cell 30(4):460-71. (PR, CO) 

2007

Agger K, Christensen J, Cloos PA, Pasini D, Rose S, Rappsilber J, Issaeva I, Canaani E, Salsini AE and Helin K (2007). UTX and JMJD3 are H3K27 demethylases involved in HOX gene regulation and development. Nature 449(7163):731-4. (PR, CO)

Albar JP, Corthals GL, Gil C, James P, Jensen ON, Palagi PM, Penque D (2007). Promoting Proteomics Knowledge on Europe:report on the Activities of the EuPA Education Committee 2006-2007. Proteomics Suppl 1:90-4. (PR, CO)

Banuelos S, Omaetxebarria MJ, Ramos I, Laesen MR, Arregi I, Jensen ON, Arizmendi JM, Prado A, Muga A (2007). Phosphorylation of both nucleaoplasmin domains is required for activity. J Biol Chem 282(29):21213-21. (PR, CO)

Basu U, Gyrd-Hansen M, Baby SM, Lozynska O, Krag TOB, Jensen CJ, Frodin M, Khurena TS (2007). Heregulin-induced epigenetic regulation of the Utrophin-A promoter, FEBS Letters 581(22)4153-8. (PR, CO)

Bracken AP, Kleine-Kohlbrecher D, Dietrich N, Pasini D, Gargiulo G, Beekman C, Theilgaard- Monch K, Minucci S, Porse BT, Marine JC, Hansen KH and Helin K (2007). The Polycomb group proteins bind thoughout the INK4A-ARF locus and are dissociated in senescent cells. Genes Dev 21(5):535-40. (PR, CO)

Christoffersen NR, Silahtaroglu A, Orom UA, Kauppinen S, Lund AH (2007). miR-200b mediates post-transcriptional repression of ZFHX1B. RNA 13:1172-8. (PR, CO)

Christensen J, Agger K, Cloos P, Pasini D, Sennels L, Rappsilber J, Hansen KH, Salsini AE and Helin K (2007). RBP2 belongs to family of demethylases specific for tri- and di-methylated lysine 4 on Histone 3. Cell 128(6):1063-76. (PR, CO)

Chuankhayan P, Rimlumduan T, Tantanuch W, Mothong N, Kongsaeree PT, Metheenukul P, Svasti J, Jensen ON, Cairns JR (2007). Functional and structural differences between isoflavonoid beta-glycosidases from Dalbergia sp. Arch Biochem Biophys. 468(2) 205-16. (PR, CO)

el Arroyo AG, Messaoudi SE, Clark PA, James M, Stott F, Bracken A, Helin K, and Peters G (2007). E2F-dependent induction of p14ARF during cell cycle re-entry in human T cells. Cell Cycle 6(21):2697-2705. (PR, CO)

Dietrich N, Bracken AP, Trinh E, Schjerling CK, Koseki H, Rappsilber J, Helin K, and Hansen KH (2007). Bypass of senescence by the Polycomb group protein CBX8 throuh direct binding to the INK4A-ARF locus. EMBO Journal 26(6):1637-48. (PR, CO).

Duran MC, Boeri-Erba E, Mohammed S, Martin-Ventura JL, Egido J, Vivanco F, Jensen ON (2007). Characterization of HSP27 phosphorylation sites in human atherosclerotic plaque secretome. Metods Mol Biol 357:151-63. (PR, CO)

Duran MC, Martin-Ventura JL, Mas S, Barderas MG, Darde VM, Jensen ON, Egido J, Vivanco F (2007). Characterization of the human atheroma plaque secretome by proteomic analysis. Methods Mol Biol. 357: 141-50. (PR, CO)

Duran MC, Martin-Ventura Jl, Mohammed S, Barderas MG, Blanco-Colio LM, Mas S, Moral V, Otega L, Tunon J, Jensen ON, Vivanco F, Egido J (2007). Atorvastatin modulates the profile of proteins released by human atherosclerotic plaques. Eur J Pharmacol. 562(1-2): 119-29. (PR, CO)

Erba EB, Matgiesen R, Bunkenborg J, Schulze WX, Stefano PD, Cabodi S, Tarone G, Delfilippi P, Jensen ON (2007). Quantitation of Multisite EGF Receptor Phosphorylation Using Mass Spectrometry and a Novel Normalization Approach. J Proteome Res 6(7): 2768-85. (PR, CO)

Fog CK, Jensen KT, Lund AH, Kunder S, Quintanilla-Martinez L, Schmidt J, Wang B, Wabl M, Pedersen FS (2007). Impairment of alternative splice sites defining a novel gammaretroviral exon within gag modifies the oncogenic properties of Akv murine leukemia virus. Retrovirology. 2007 Jul 6;4:46. (PR, CO)

Frankel LB, Christoffersen NR, Jacobsen A, Lindow M, Krogh A, Lund AH (2007). Programmed cell death 4 (PDCD4) is an important functional target of the microRNA miR in breast cancer cells. J Biol Chem.283: 1026-33. (PR, CO)

Hagen L, Kavli B, Sousa MM, Torseth K, Liabakk NB, Sundheim O, Pena-diaz J, Otterlei M, Hørning O, Jensen ON, Krokan HE, Slupphaugh G(2007). Cell cycle-apecific UNG2 phosphory­lations regulate protein turnover, activity and association with RPA. EMBO J. 27(1) 51-61. (PR, CO)

Hagglund P, Matthiesen R, Elortza F, Hojrup P, Roepstorff P, Jensen ON, Bunkenborg J(2007). An enzymatic deglycosylation scheme enabling indentification of core fucosylated N-glycans and O-glycosylation site mapping of human plasma proteins. J Proteome Res. 6(8) 3021-31. (PR)

Hauge C, Antal TL, Hirschberg D, Doehn U, Thorup K, Idrissova L, Hansen K, Jensen ON, Jørgensen TJD, Biondi RM and Frodin M(2007). Two C-terminal phosphorylation sites cooperate to activate AGC kinases via the hydrophobic motif. EMBO J. 26(9)2251-61. (PR, CO)

Hørning O, Theodorsen S, Vorm, O, Jensen ON (2007). Solid phase extraction-liquid chromatography (SPE-LC) interface for automated peptide separation and identification by tandem mass spectrometry. Int. J. Mass Spectrom. 268(2-3) 147-57.

Jensen ON, Heck AJR, Hillenkamp F (2007). Peter Roepstorff, a brief biography. Int J Mass Spectrom. 268, 2-3.

Jørgensen S, Elvers I, Trelle MB, Menzel T, Eskildsen M, Jensen ON, Helleday T, Helin K, Sørensen CS (2007). The histone methyltransferase SET8 is required for S-phase progression. Jounal of Cell Biol 179(7):1337-45. (PR, CO)

Kedde M, Strasser MJ, Boldajiipour B, Vrielink JA, Slanchev K, le Sage C, Nagel R, Voorhoeve PM, van Duijse J, Ørom UA, Lund AH, Perrakis A, Raz E, Agami R (2007). RNA-Binding Protein Dnd 1 Inhibits MicroRNA Access to Target mRNA. Cell 131:1273-86. (PR, CO)

Kjeldsen F, Giessing AM, Ingrell CR, Jensen ON (2007). Peptide Sequincing and Characterization of Post-Translational Modifications by Enhanced ion-Charging and Liquid Cromatography Electron-Transfer Dissociation Tandem Mass Spectrometry. Anal Chem. 79(24)9243-52. (PR)

Kleinnijenhuis AJ, Kjeldsen F, Kallipolitis B, Haselmann KF, Jensen ON (2007). Analysis of Histidine Phosphorylation Using Tandem MS and Ion-Electron Reactions. Anal Chem. 79(19)7450-6. (PR)

Omaetxebarria MJ, Elortza F, Rodriguez-Suarez E, Aloria K, Arizmendi JM, Jensen ON, Matthiesen R(2007). Computional approach for identification and characterization of GPI-anchored peptides in proteomics experiments. Proteomics. 7(12):1951-60. (PR, CO)

Pasini D, Bracken AP, Hansen JB, Capillo M and Helin K (2007). The Polycomb group protein Suz12 is required for embryonic stem cell differentiation. Mol Cel Biol 27(10):3769-79. (PR, CO)

Qiao H, Di Stefano L, Tian C, Li Y-Y, Qian X-P, Pang X-W, Li Y, McNutt MA, Helin K, Zhang Y, Chen W-F (2007). Human TFDP3, a novel DP protein inhibits DNA binding and transactivation by E2F. J Biol Chem 282(1):454-66. (PR, CO)

Sachon, E, Nielsen, PF, Jensen ON (2007). Characterization of N-palmitoylated human growth homone by in situ liquid extraction and MALDI tandem mass spectrometry. J Mass Spectrom 42(6):724-34. (PR)

Sorensen AB, Lund AH, Kunder S, Quintanilla-Martinez L, Schmidt J, Wang B, Wabl M, Pedersen FS (2007). Impairment of alternative splice sites defining a novel gammaretroviral exon within gag modifies the oncogenic properties of Akv murine leukemia virua. Retrovirology 4:46. (PR, CO)

Trelle, M.B, and Jensen, ON (2007). Proteomics in histone research and epigenetics. Expert Rev. Proteomics 4(4)491-503. (PR)

Villa R, Pasini D, Gutierrez A, Morey L, Occhionorelli M, Vire E, Nomdedeu JF, Jenuwein T, Pelicci PG, Minucci S, Fuks F, Helin K, Di Croce L (2007). Role of the Polycomb repressive complex 2 in acute promyelocytic leukemia. Cancer Cell 11(6):513-25. (PR, CO)

Voena C, Conte C, Ambrogio C, Boeri Erba E, Boccalatte F, Mohammed S, Jensen ON, Palestro G, Inghirami G, Chiarle R (2007). The tysine phosphatase Shp2 interacts with NPM-ALK and regulates anaplastic lymphoma cell growth and migration. Cancer Res. 67(9):4278-86. (PR, CO)

Yang J, Valineva T, Hong J, Bu T, Yao Z, Jensen ON, Frilander MJ, Silvennoinen O (2007). Transcriptional co-activator protein p100 interacts with snRNP proteins and facilitates the assembly of the spliceosome. Nucleic Acids Res. 35(13):4485-94. (PR, CO)

Zhang X, Ye J, Jensen ON, Roepstorff P (2007). Highly efficient phosphopeptide enrichment by calcium phosphate precipitation combined with subsequent serial immobilized metal ion affinity chromatography (IMAC) enrichment. Mol Cell Proteomics. 6 (11) 2032-42. (PR)

Ørum, UA, Lund AH (2007). Isolation of microRNA targets using biotinylated synthetic microRNAs. Methods 43:162-5. (PR)

 

PhD theses

 

Epigenetic regulation of stem cell fate: Elucidating the role of histone modifications and DNA methylation during the generation of pancreatic lineages from human embryonic stem cells. Jesper Due Jensen 2015.

Characterization of the Jumonji domain containing proteins JMJD1B and JMJD1C. John-Paul Bukowski 2014.

 Investigating the biological functions of TET2 and 5-hydroxymethylcytosine - Loss of TET2 in DNA methylation and Acute Myeloid Leukemia - A screen for 5-hydroxymethylcytosine binding proteins. Guangshuai Jia 2014.

shRNA screens identify epigenetic factors as potential therapeutic targets in leukaemia. Adam Cruickshank 2014.

Identification and characterization of new proteins involved in chromatin replication. Arsenios Vlassis 2014.

Interdependence of multiple post-translational modifications. Jia Dai 2014.

Characterization of novel factors and mechanisms involved in chromatin replication. Yunpeng Feng 2013.

Characterization of combinatorial histone marks by middle-down mass spectrometry. Simone Sidoli 2013.

Codanin-1, a new Asf1 binding partner regulating histone dynamics. Katrine Ask 2013

Zbtb48 facilitates Polycomb recruitment at CpG islands and modulates PRC2 activity in mouse embryonic stem cells. Eskild M Landt 2013.

Regulation of the Asf1 histone chaperone by Tousled-like kinases. Ilnaz Kamalyukova 2012.

Tales of Chromatin – Characterization of histone methyltransferase MMSET in neuroblastoma, and initial characterization of the CXXC proteins CXXC5 and CXXC4. Julie Skotte 2012.

Development and use of small molecule kinase inhibitors to study the biological roles of RSK and MSK. Katarzyna Duda 2012.

Modification of chromatin structure: Characterisation of the DNA hydroxylases Tet1 and Tet2, and the histone lysine demethylase JMJD3. Kristine Williams 2011.

The Histone Demethylase Jarid1b in Embryonic Stem Cells, Differentiation and Development. Sandra U Schmitz 2011.

Charting the human cell cycle epigenome – Elucidating mechanisms involved in microRNA turnover and microRNA deregulation in gastric cancer. Tony Bou Kheir 2011.

Modifying chromatin marks - characterization of the histone demethylase JMJD2C and the DNA Hydroxylase TET1. Marianne T Pedersen 2011.

Molecular mechanisms underlying oncogene-induced senescence. Lise Rudkjær 2011.

Polycomb group protein displacement and gene activation through MSK-dependent H3K27me3S28 phosphorylation. Simmi Gehani 2011.

Application of magnetic beads technology to functional phospho-proteomics – deciphering signaling to chromatin. Lei Cheng 2011.

The Activity-dependent neuroprotective protein is a transcriptional repressor interacting with HP1 and the chromatin remodeller CHD4. Astrid Monrad 2010.

Characterization of histone proteins using mass spectrometry. Hye R Jung 2010.

Characterization of the MMSET gene involved in multiple myeloma. Heidi Hudlebusch 2010.

Regulation of RSK and other AGC kinases. Claus Juel Jensen 2010.

Identification and characterization of the novel tumor suppressor PRDM11. Cathrine KF Tonnesen 2009.

Mechanisms for regulation of the kinase activity of the AGC kinases RSK and MSK. Camilla Hauge 2009.

Identification and characterization of miRNA target interactions. Ulf LA Ørom 2008.

Identification and quantitation of multisite histone modifications by MS. Morten B Trelle 2008.

 miRNA and cancer. Nanna R Christoffersen 2008.

Regulation of cell proliferation and target gene repression by the Polycomb group protein CBX8. Nikolaj Dietrich 2008.