The NNF Center for Protein Research

  1. Published

    Proteomics Reveals Global Regulation of Protein SUMOylation by ATM and ATR Kinases during Replication Stress

    Munk, S., Sigurðsson, J. O., Xiao, Z., Batth, Tanveer Singh, Franciosa, Giulia, von Stechow, L., Lopez-Contreras, Andres, Vertegaal, A. C. O. & Olsen, Jesper Velgaard, 2017, In : Cell Reports. 21, 2, p. 546-558 13 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  2. Published

    Systems Analysis for Interpretation of Phosphoproteomics Data

    Munk, S., Refsgaard, J. C. & Olsen, Jesper Velgaard, 2016, Phospho-Proteomics: Methods and Protocols. Stechow, L. V. (ed.). Springer, Vol. 1355. p. 341-60 20 p. (Methods in molecular biology (Clifton, N.J.)).

    Research output: Chapter in Book/Report/Conference proceedingBook chapterResearchpeer-review

  3. Published

    Single muscle fiber proteomics reveals unexpected mitochondrial specialization

    Murgia, M., Nagaraj, N., Deshmukh, Atul Shahaji, Zeiler, M., Cancellara, P., Moretti, I., Reggiani, C., Schiaffino, S. & Mann, Matthias, 1 Mar 2015, In : E M B O Reports. 16, 3, p. 387-95 9 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  4. Published

    Proteomics of Cytochrome c Oxidase-Negative versus -Positive Muscle Fiber Sections in Mitochondrial Myopathy

    Murgia, M., Tan, J., Geyer, P. E., Doll, S., Mann, Matthias & Klopstock, T., 2019, In : Cell Reports. 29, 12, p. 3825-3834 15 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  5. Published

    Pharmacological characterization and modeling of the binding sites of novel 1,3-bis(pyridinylethynyl)benzenes as metabotropic glutamate receptor 5-selective negative allosteric modulators

    Mølck, C., Harpsøe, Kasper, Gloriam, David E., Clausen, Rasmus Prætorius, Madsen, Ulf, Pedersen, L., Jimenez, H. N., Nielsen, S. M., Mathiesen, Jesper M. & Bräuner-Osborne, Hans, 2012, In : Molecular Pharmacology. 82, 5, p. 929-37 9 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  6. Published

    mGluR5: Exploration of Orthosteric and Allosteric Ligand Binding Pockets and Their Applications to Drug Discovery

    Mølck, C., Harpsøe, Kasper, Gloriam, David E., Mathiesen, Jesper M., Nielsen, S. M. & Bräuner-Osborne, Hans, Oct 2014, In : Neurochemical Research. 39, 10, p. 1862-1875 14 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  7. Published

    Association studies of genetic scores of serum vitamin B12 and folate levels with symptoms of depression and anxiety in two danish population studies

    Møllehave, L. T., Skaaby, T., Simonsen, K. S., Thuesen, B. H., Mortensen, Erik Lykke, Sandholt, C. H., Pedersen, Oluf Borbye, Grarup, Niels, Hansen, Torben & Linneberg, Allan René, 2017, In : European Journal of Clinical Nutrition. 71, p. 1054-1060 7 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  8. Published

    Small Angle X-Ray Scattering Studies of Mitochondrial Glutaminase C Reveal Extended Flexible Regions, and Link Oligomeric State with Enzyme Activity

    Møller, M., Nielsen, S. S., Ramachandran, S., Li, Y., Tria, G., Streicher, W., Petoukhov, M. V., Cerione, R. A., Gillilan, R. E. & Vestergaard, Bente, 30 Sep 2013, In : P L o S One. 8, 9, e74783.

    Research output: Contribution to journalJournal articleResearchpeer-review

  9. Published

    Protein-driven inference of miRNA-disease associations

    Mørk, S., Pletscher-Frankild, S., Palleja, A., Gorodkin, Jan & Jensen, Lars Juhl, 2014, In : Bioinformatics (Oxford, England). 30, 3, p. 392-397 6 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  10. Published

    A RIPK2 inhibitor delays NOD signalling events yet prevents inflammatory cytokine production

    Nachbur, U., Stafford, C. A., Bankovacki, A., Zhan, Y., Lindqvist, L. M., Fiil, B. K., Khakham, Y., Ko, H., Sandow, J. J., Falk, H., Holien, J. K., Chau, D., Hildebrand, J., Vince, J. E., Sharp, P. P., Webb, A. I., Jackman, K. A., Mühlen, S., Kennedy, C. L., Lowes, K. N., Murphy, J. M., Gyrd-Hansen, M., Parker, M. W., Hartland, E. L., Lew, A. M., Huang, D. C. S., Lessene, G. & Silke, J., 17 Mar 2015, In : Nature Communications. 6, 13 p., 6442.

    Research output: Contribution to journalJournal articleResearchpeer-review

  11. Published

    Correction to Feasibility of Large-Scale Phosphoproteomics with Higher Energy Collisional Dissociation Fragmentation

    Nagaraj, N., D'Souza, R. C. J., Cox, J., Olsen, Jesper Velgaard & Mann, Matthias, 2012, In : Journal of Proteome Research.

    Research output: Contribution to journalJournal articleResearchpeer-review

  12. Published

    Feasibility of large-scale phosphoproteomics with higher energy collisional dissociation fragmentation

    Nagaraj, N., D'Souza, R. C. J., Cox, J., Olsen, Jesper Velgaard & Mann, M., 3 Dec 2010, In : Journal of Proteome Research. 9, 12, p. 6786-94 9 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  13. Published

    Functions and mechanisms of non-histone protein acetylation

    Narita, Takeo, Weinert, B. T. & Choudhary, Chuna Ram, 2019, In : Nature Reviews. Molecular Cell Biology. 20, p. 156-174 19 p.

    Research output: Contribution to journalReviewResearchpeer-review

  14. Published

    Plant redox proteomics

    Navrot, N., Finnie, C., Svensson, B. & Hägglund, Per Mårten, 12 Aug 2011, In : Journal of Proteomics. 74, 8, p. 1450-1462 13 p.

    Research output: Contribution to journalReviewResearchpeer-review

  15. Published

    A redox-dependent dimerization switch regulates activity and tolerance for reactive oxygen species of barley seed glutathione peroxidase

    Navrot, N., Skjoldager, N., Bunkenborg, J., Svensson, B. & Hägglund, Per Mårten, 1 May 2015, In : Plant Physiology and Biochemistry. 90, p. 58-63 6 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  16. Published

    Effects of 2 weeks lower limb immobilization and two separate rehabilitation regimens on gastrocnemius muscle protein turnover signaling and normalization genes

    Nedergaard, A., Jespersen, J. G., Pingel, Jessica, Christensen, B., Sroczynski, N., Langberg, Henning, Kjær, Michael & Schjerling, P., 28 Mar 2012, In : BMC Research Notes. 5, 1, p. 166 1 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  17. Published

    Pharos: Collating protein information to shed light on the druggable genome

    Nguyen, D., Mathias, S., Bologa, C., Brunak, Søren, Fernandez, N., Gaulton, A., Hersey, A., Holmes, J., Jensen, Lars Juhl, Karlsson, A., Liu, G., Ma'ayan, A., Mandava, G., Mani, S., Mehta, S., Overington, J., Patel, J., Rouillard, A. D., Schürer, S., Sheils, T., Simeonov, A., Sklar, L. A., Southall, N., Ursu, O., Vidovic, D., Waller, A., Yang, J., Jadhav, A., Oprea, T. I. & Guha, R., Jan 2017, In : Nucleic Acids Research. 45, D1, p. D995–D1002

    Research output: Contribution to journalJournal articleResearchpeer-review

  18. Published

    Assessment and Challenges of Ligand Docking into Comparative Models of G-Protein Coupled Receptors

    Nguyen, E. D., Meiler, J., Norn, Christoffer & Frimurer, Thomas Michael, 2 Jul 2013, In : PLOS ONE. 8, 7, p. e67302 19 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  19. Published

    A Small Molecule Inhibitor of the BLM Helicase Modulates Chromosome Stability in Human Cells

    Nguyen, G. H., Dexheimer, T. S., Rosenthal, A. S., Chu, W. K., Singh, D. K., Mosedale, G., Bachrati, C. Z., Schultz, L., Sakurai, M., Savitsky, P., Abu, M., McHugh, P. J., Bohr, Vilhelm, Harris, C. C., Jadhav, A., Gileadi, O., Maloney, D. J., Simeonov, A. & Hickson, Ian David, 24 Jan 2013, In : Chemistry & Biology. 20, 1, p. 55-62 8 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  20. Published

    Deubiquitylating enzyme USP9x regulates hippo pathway activity by controlling angiomotin protein turnover

    Nguyen, T. H., Andrejeva, D., Gupta, R., Choudhary, Chuna Ram, Hong, X., Eichhorn, P. J., Loya, Anand Chainsukh & Cohen, S. M., 29 Mar 2016, In : Cell Discovery. 2, 13 p., 16001.

    Research output: Contribution to journalJournal articleResearchpeer-review

  21. Published

    Antimicrobial resistance: Monitoring the quantities of antimicrobials used in husbandry

    Nicholls, T., Acar, J., Anthony, F., Franklin, A., Gupta, R., Tamura, Y., Thompson, S., Threlfall, E. J., Vose, D., Van Vuuren, M., White, D. G., Wegener, H. C. & Costarrica, M. L., 1 Jan 2001, In : OIE Revue Scientifique et Technique. 20, 3, p. 841-847 7 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  22. Published

    Selective use of corifollitropin for controlled ovarian stimulation for IVF in patients with low anti-Müllerian hormone

    Nielsen, Anna Pors, Korsholm, A., Lemmen, J. G., Lykke-Sylvest, Randi, Sopa, N. & Andersen, Anders Nyboe, 18 Feb 2016, In : Gynecological Endocrinology. 32, 8, p. 625–628 4 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  23. Published

    Survival prediction in intensive-care units based on aggregation of long-term disease history and acute physiology: a retrospective study of the Danish National Patient Registry and electronic patient records

    Nielsen, Annelaura Bach, Thorsen-Meyer, Hans-Christian, Belling, Kirstine G, Nielsen, Anna Pors, Thomas, C. E., Chmura, Piotr Jaroslaw, Lademann, M., Moseley, Pope Lloyd, Heimann, M., Dybdahl, L., Spangsege, L., Hulsen, P., Perner, Anders & Brunak, Søren, 2019, In : The Lancet Digital Health. 1, 2, p. e78-e89 12 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  24. Published

    PICH promotes sister chromatid disjunction and co-operates with topoisomerase II in mitosis

    Nielsen, Christian Thomas Friberg, Huttner, D., Bizard, Anna Helene, Hirano, S., Li, T., Palmai-Pallag, T., Bjerregaard, V. A., Liu, Ying, Nigg, E. A., Wang, L. H. & Hickson, Ian David, 2015, In : Nature Communications. 6, 15 p., 8962.

    Research output: Contribution to journalJournal articleResearchpeer-review

  25. Published

    A Brief History of Protein Sorting Prediction

    Nielsen, H., Tsirigos, Konstantinos, Brunak, Søren & von Heijne, G., 2019, In : The Protein Journal. 38, 3, p. 200-216 17 p.

    Research output: Contribution to journalReviewResearchpeer-review

  26. E-pub ahead of print

    Predictors of weight loss after bariatric surgery - a cross-disciplinary approach combining physiological, social, and psychological measures

    Nielsen, Mette Søndergaard, Christensen, B. J., Schmidt, J. B., Tækker, L., Holm, Lotte, Lunn, Susanne, Ritz, Christian, Albrechtsen, Nicolai Jacob Wewer, Holst, Jens Juul, Schnurr, Theresia Maria, Hansen, Torben, le Roux, C. W., Lund, Thomas Bøker, Floyd, A. K. & Sjödin, Anders Mikael, 23 Apr 2020, In : International Journal of Obesity.

    Research output: Contribution to journalJournal articleResearchpeer-review

  27. Published

    Non-tropical sprue. Malignant diseases and mortality rate

    Nielsen, Ole Haagen, Jacobsen, O., Pedersen, E. R., Rasmussen, Simon, Petri, M., Laulund, S. & Jarnum, S., Jan 1985, In : Scandinavian Journal of Gastroenterology. 20, 1, p. 13-8 6 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  28. Published

    Calcium absorption and acceptance of low-lactose milk among children with primary lactase deficiency

    Nielsen, Ole Haagen, Schiøtz, P. O., Rasmussen, Simon & Krasilnikoff, P. A., Mar 1984, In : Journal of Pediatric Gastroenterology and Nutrition. 3, 2, p. 219-23 5 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  29. Published

    Can sequestering of mitotic spindle proteins cause aneuploidy? (Comment on DOI 10.1002/bies.201400175)

    Nilsson, Jakob, Mar 2015, In : BioEssays. 37, 3, p. 234 1 p.

    Research output: Contribution to journalComment/debateResearchpeer-review

  30. Published

    Bub1/BubR1: swiss army knives at kinetochores

    Nilsson, Jakob, 11 Aug 2015, In : Cell Cycle. 14, 9, p. 2999-3000 2 p.

    Research output: Contribution to journalEditorialResearchpeer-review

  31. Published

    Protein phosphatases in the regulation of mitosis

    Nilsson, Jakob, 2019, In : The Journal of Cell Biology. 218, 2, 15 p., 395.

    Research output: Contribution to journalReviewResearchpeer-review

  32. Published

    Mps1-Ndc80: one interaction to rule them all

    Nilsson, Jakob, 10 Jun 2015, In : OncoTarget. 6, 19, p. 16822–16823 2 p.

    Research output: Contribution to journalEditorialResearchpeer-review

  33. Published

    Cdc20 control of cell fate during prolonged mitotic arrest: do Cdc20 protein levels affect cell fate in response to antimitotic compounds?

    Nilsson, Jakob, 2011, In : BioEssays. 33, 12, p. 903-9 7 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  34. Published

    Looping in on Ndc80 - how does a protein loop at the kinetochore control chromosome segregation?

    Nilsson, Jakob, Dec 2012, In : BioEssays. 34, 12, p. 1070-7 8 p.

    Research output: Contribution to journalReviewResearchpeer-review

  35. Published

    Herpes Simplex Virus Type 1 infection is associated with suicidal behavior and first registered psychiatric diagnosis in a healthy population

    Nissen, J., Trabjerg, B., Pedersen, M. G., Banasik, Karina, Pedersen, Ole Birger Vesterager, Sørensen, E., Nielsen, K. R., Erikstrup, C., Petersen, M. S., Paarup, H. M., Bruun-Rasmussen, P., Westergaard, David, Hansen, Thomas Folkmann, Pedersen, C. B., Werge, Thomas, Torrey, F., Hjalgrim, H., Mortensen, P. B., Yolken, R., Brunak, Søren, Ullum, Henrik & Burgdorf, K. S., Oct 2019, In : Psychoneuroendocrinology. 108, p. 150-154

    Research output: Contribution to journalJournal articleResearchpeer-review

  36. Published

    Constructing a cell-type resolved human liver proteome atlas: THU-034

    Niu, Lili, Geyer, P. & Mann, Matthias, 2018, In : Journal of Hepatology. 68, p. S138-S139

    Research output: Contribution to journalConference abstract in journalResearchpeer-review

  37. Published

    Proteomics in the Study of Liver Diseases

    Niu, Lili, Geyer, P. E. & Mann, Matthias, 2018, The Human Gut-Liver-Axis in Health and Disease. Krag, A. & Hansen, T. (eds.). Springer, p. 165-193

    Research output: Chapter in Book/Report/Conference proceedingBook chapterResearchpeer-review

  38. Published

    Quick and clean: Cracking sentences encoded in E. coli by LC-MS/MS, de novo sequencing, and dictionary search

    Niu, Lili & Mann, Matthias, 2019, In : EuPA Open Proteomics. 22-23, p. 30-35 6 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  39. Published

    Plasma proteome profiling discovers novel proteins associated with non-alcoholic fatty liver disease

    Niu, Lili, Geyer, P. E., Albrechtsen, Nicolai Jacob Wewer, Gluud, Lise Lotte, Santos Delgado, Alberto, Doll, S., Treit, P. V., Holst, Jens Juul, Knop, Filip Krag, Vilsbøll, Tina, Junker, A., Sachs, S., Stemmer, K., Müller, T. D., Tschöp, M. H., Hofmann, S. M. & Mann, Matthias, 2019, In : Molecular Systems Biology. 15, 16 p., e8793.

    Research output: Contribution to journalJournal articleResearchpeer-review

  40. Published

    Roadmap for a precision-medicine initiative in the Nordic region

    Njølstad, P. R., Andreassen, O. A., Brunak, Søren, Børglum, A. D., Dillner, J., Esko, T., Franks, P. W., Freimer, N., Groop, L., Heimer, H., Hougaard, D. M., Hovig, E., Hveem, K., Jalanko, A., Kaprio, J., Knudsen, G. P., Melbye, Mads, Metspalu, A., Mortensen, P. B., Palmgren, J., Palotie, A., Reed, W., Stefánsson, H., Stitziel, N. O., Sullivan, P. F., Thorsteinsdóttir, U., Vaudel, M., Vuorio, E., Werge, Thomas, Stoltenberg, C. & Stefánsson, K., 2019, In : Nature Genetics. 51, p. 924-930

    Research output: Contribution to journalComment/debateResearch

  41. Published

    Metallopeptidase Inhibitor 1 (TIMP-1) promotes receptor tyrosine kinase c-Kit signaling in colorectal cancer

    Nordgaard, Cathrine, Doll, S., Matos, A. L. D. S. A., Høeberg, M., Kazi, J. U., Friis, S., Stenvang, Jan, Rönnstrand, L., Mann, Matthias & Moreira, José, 2019, In : Molecular Oncology. 13, 12, p. 2646-2662

    Research output: Contribution to journalJournal articleResearchpeer-review

  42. Published

    Mutation-Guided Unbiased Modeling of the Fat Sensor GPR119 for High-Yield Agonist Screening.

    Norn, Christoffer, Pedersen, Maria Hauge, Engelstoft, M. S., Kim, S. H., Lehmann, J., Jones, R. M., Schwartz, Thue W. & Frimurer, Thomas Michael, 2015, In : Structure. 23, 12, p. 2377-2386 10 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  43. Published

    The forebrain synaptic transcriptome is organized by clocks but its proteome is driven by sleep

    Noya, S. B., Colameo, D., Brüning, F., Spinnler, A., Mircsof, D., Opitz, L., Mann, Matthias, Tyagarajan, S. K., Robles, M. S. & Brown, S. A., 2019, In : Science. 366, 6462, eaav2642 .

    Research output: Contribution to journalJournal articleResearchpeer-review

  44. Published

    Immunity and mental illness: findings from a Danish population-based immunogenetic study of seven psychiatric and neurodevelopmental disorders

    Nudel, R., Benros, M. E., Krebs, M. D., Allesøe, R. L., Lemvigh, C. K., Bybjerg-Grauholm, J., Børglum, A. D., Daly, M. J., Nordentoft, Merete, Mors, O., Hougaard, D. M., Mortensen, P. B., Buil, A., Werge, Thomas, Rasmussen, Simon & Thompson, W. K., 2019, In : European Journal of Human Genetics. 27, p. 1445-1455

    Research output: Contribution to journalJournal articleResearchpeer-review

  45. Published

    Reflect: a practical approach to web semantics

    O'Donoghue, S. I., Horn, H., Pafilisa, E., Haag, S., Kuhn, M., Satagopam, V. P., Schneider, R. & Jensen, Lars Juhl, Jul 2010, In : Journal of Web Semantics. 8, 2-3, p. 182-189

    Research output: Contribution to journalJournal articleResearchpeer-review

  46. Published

    Stabilization of chromatin topology safeguards genome integrity

    Ochs, F., Karemore, Gopal, Miron, E., Brown, J., Sedlackova, Hana, Rask, M., Lampe, M., Buckle, V., Schermelleh, L., Lukas, Jiri & Lukas, Claudia, 2019, In : Nature. 574, 7779, p. 571-574 4 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  47. Published

    53BP1 fosters fidelity of homology-directed DNA repair

    Ochs, F., Somyajit, Kumar, Altmeyer, M., Rask, M. D., Lukas, Jiri & Lukas, Claudia, Aug 2016, In : Nature Structural and Molecular Biology. 23, 8, p. 714-21 8 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  48. Published

    UBL5 is essential for pre-mRNA splicing and sister chromatid cohesion in human cells

    Oka, Y., Varmark, H., Vitting-Seerup, Kristoffer, Beli, P., Waage, J. E., Hakobyan, A., Mistrik, M., Choudhary, Chuna Ram, Rohde, M., Bekker-Jensen, Simon Holst & Mailand, Niels, 2014, In : E M B O Reports. 15, 9, p. 956-964 9 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  49. Published

    Ubiquitin-like protein UBL5 promotes the functional integrity of the Fanconi anemia pathway

    Oka, Y., Bekker-Jensen, Simon Holst & Mailand, Niels, 9 Apr 2015, In : E M B O Journal. 34, p. 1385-1398

    Research output: Contribution to journalJournal articleResearchpeer-review

  50. Published

    Persons who have never had a headache. Socio-demographic characteristics

    Olofsson, I. A., Erikstrup, C., Sørensen, E., Paarup, H. M., Mathiasen, H. P., Hjalmgrim, H., Banasik, Karina, Nielsen, K. R., Burgdorf, K. S., Pedersen, Ole Birger Vesterager, Ullum, Henrik, Olesen, Jes & Hansen, Thomas Folkmann, 2019, In : Cephalalgia. 39, 1, suppl., p. 88-89 1 p.

    Research output: Contribution to journalConference abstract in journalResearchpeer-review

  51. Published

    Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis

    Olsen, Jesper Velgaard, Vermeulen, M., Santamaria, A., Kumar, C., Miller, M. L., Jensen, Lars Juhl, Gnad, F., Cox, J., Jensen, T. S., Nigg, E. A., Brunak, Søren & Mann, Matthias, 2010, In : Science Signaling. 3, 104, p. ra3 15 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  52. Published

    Status of large-scale analysis of post-translational modifications by mass spectrometry

    Olsen, Jesper Velgaard & Mann, Matthias, 1 Nov 2013, In : Molecular & Cellular Proteomics. 12, p. 3444-52

    Research output: Contribution to journalJournal articleResearchpeer-review

  53. Published

    Effective representation and storage of mass spectrometry-based proteomic data sets for the scientific community

    Olsen, Jesper Velgaard & Mann, Matthias, 1 Jan 2011, In : Science Signaling. 4, 160, p. pe7

    Research output: Contribution to journalJournal articleResearchpeer-review

  54. Published

    A computational method for identification of vaccine targets from protein regions of conserved human leukocyte antigen binding

    Olsen, L. R., Simon, C., Kudahl, U. J., Bagger, F. O., Winther, Ole, Reinherz, E. L., Zhang, G. L. & Brusic, V., 2015, In : B M C Medical Genomics. 8, Suppl 4, 6 p., 5.

    Research output: Contribution to journalJournal articleResearchpeer-review

  55. Published

    Evaluation of candidate biomarkers to predict cancer cell sensitivity or resistance to PARP-1 inhibitor treatment

    Oplustilova, L., Wolanin, K., Bartkova, J., Lukas, Jiri, Bartek, J., Lau, A., O'Connor, M. J., Mistrik, M., Korinkova, G., Simkova, D., Bouchal, J. & Lenobel, R., 15 Oct 2012, In : Cell Cycle. 11, 20, p. 3837-3850 14 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  56. Published

    Unexplored therapeutic opportunities in the human genome

    Oprea, T. I., Bologa, C. G., Brunak, Søren, Campbell, A., Gan, G. N., Gaulton, A., Gomez, S. M., Guha, R., Hersey, A., Holmes, J., Jadhav, A., Jensen, Lars Juhl, Johnson, G. L., Karlson, A., Leach, A. R., Ma'ayan, A., Malovannaya, A., Mani, S., Mathias, S. L., McManus, M. T., Meehan, T. F., von Mering, C., Muthas, D., Nguyen, D., Overington, J. P., Papadatos, G., Qin, J., Reich, C., Roth, B. L., Schürer, S. C., Simeonov, A., Sklar, L. A., Southall, N., Tomita, S., Tudose, I., Ursu, O., Vidovic, D., Waller, A., Westergaard, David, Yang, J. J. & Zahoránszky-Köhalmi, G., 2018, In : Nature Reviews. Drug Discovery. 17, 5, p. 317-332 16 p.

    Research output: Contribution to journalReviewResearchpeer-review

  57. Published

    Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse

    Orlando, Ludovic Antoine Alexandre, Ginolhac, A., Zhang, G., Froese, D., Albrechtsen, Anders, Stiller, M., Schubert, M., Cappellini, Enrico, Petersen, Bent, Moltke, Ida, Johnson, P. L. F., Fumagalli, M., Mouatt, J. T. V., Raghavan, M., Korneliussen, Thorfinn Sand, Malaspinas, A. S., Vogt, J., Szklarczyk, D. M., Kelstrup, C., Vinther, J., Dolocan, A., Stenderup, J., Velazquez, A. M. V., Cahill, J., Rasmussen, M., Wang, X., Min, J., Zazula, G. D., Seguin-Orlando, A., Mortensen, C., Magnussen, K., Thompson, J. F., Weinstock, J., Gregersen, K., Røed, K. H., Eisenmann, V., Rubin, C. J., Miller, D. C., Antczak, D. F., Bertelsen, M. F., Brunak, S., Al-Rasheid, K. A. S., Ryder, O., Andersson, L., Mundy, J., Krogh, Anders, Gilbert, M Thomas P, Kjær, Kurt H., Sicheritz-Pontén, T., Jensen, Lars Juhl, Olsen, Jesper Velgaard, Hofreiter, M., Nielsen, R., Shapiro, B., Wang, Jun & Willerslev, Eske, 4 Jul 2013, In : Nature. 499, 7456, p. 74-78 5 p.

    Research output: Contribution to journalLetterResearchpeer-review

  58. Published

    In Silico Systems Pharmacology to Assess Drug's Therapeutic and Toxic Effects

    Aguayo Orozco, Alejandro, Audouze, K., Brunak, Søren & Taboureau, Olivier Thierry, 2016, In : Current Pharmaceutical Design. 22, 46, p. 6895-6902 8 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  59. Published

    Elevated levels of soluble urokinase receptor in serum from mycobacteria infected patients: still looking for a marker of treatment efficacy

    Ostrowski, Sisse Rye, Ravn, P., Hoyer-Hansen, G., Ullum, Henrik & Andersen, A. B., 2006, Elevated levels of soluble urokinase receptor in serum from mycobacteria infected patients. Vol. 38. p. 1028-32 5 p. (Scandinavian Journal of Infectious Diseases. Supplementum).

    Research output: Chapter in Book/Report/Conference proceedingBook chapterResearchpeer-review

  60. Published

    EXTRACT: interactive extraction of environment metadata and term suggestion for metagenomic sample annotation

    Pafilis, E., Buttigieg, P. L., Ferrell, B., Pereira, E., Schnetzer, J., Arvanitidis, C. & Jensen, Lars Juhl, 2016, In : Database. 2016, 7 p., baw005.

    Research output: Contribution to journalJournal articleResearchpeer-review

  61. Published

    The SPECIES and ORGANISMS Resources for Fast and Accurate Identification of Taxonomic Names in Text

    Pafilis, E., Pletscher-Frankild, S., Fanini, L., Faulwetter, S., Pavloudi, C., Vasileiadou, A., Arvanitidis, C. & Jensen, Lars Juhl, 18 Jun 2013, In : PloS one. 8, 6, p. e65390

    Research output: Contribution to journalJournal articleResearchpeer-review

  62. Published

    Reflect: augmented browsing for the life scientist

    Pafilis, E., O'Donoghue, S. I., Jensen, Lars Juhl, Horn, H., Kuhn, M., Brown, N. P. & Schneider, R., 2009, In : Nature Biotechnology. 27, 6, p. 508-10 2 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  63. Published

    ENVIRONMENTS and EOL: identification of Environment Ontology terms in text and the annotation of the Encyclopedia of Life

    Pafilis, E., Pletscher-Frankild, S., Schnetzer, J., Fanini, L., Faulwetter, S., Pavloudi, C., Vasileiadou, K., Leary, P., Hammock, J., Schulz, K., Parr, C. S., Arvanitidis, C. & Jensen, Lars Juhl, 2015, In : Bioinformatics. 31, 11, p. 1872-1874

    Research output: Contribution to journalJournal articleResearchpeer-review

  64. Published

    TISSUES 2.0: an integrative web resource on mammalian tissue expression

    Palasca, O., Santos Delgado, Alberto, Stolte, C., Gorodkin, Jan & Jensen, Lars Juhl, 2018, In : Database. 2018, 1, p. 1-12

    Research output: Contribution to journalJournal articleResearchpeer-review

  65. Published

    Roux-en-Y gastric bypass surgery of morbidly obese patients induces swift and persistent changes of the individual gut microbiota

    Palleja, A., Kashani, A., Allin, Kristine Højgaard, Nielsen, Trine, Zhang, C., Li, Y., Brach, Thorsten, Liang, S., Feng, Q., Jørgensen, N. B., Bojsen-Møller, K. N., Dirksen, C., Burgdorf, K. S., Holst, Jens Juul, Madsbad, Sten, Wang, Jun, Pedersen, Oluf Borbye, Hansen, Torben & Arumugam, Mani, 2016, In : Genome Medicine. 8, 13 p., 67.

    Research output: Contribution to journalJournal articleResearchpeer-review

  66. Published

    HOODS: finding context-specific neighborhoods of proteins, chemicals and diseases

    Palleja, A. & Jensen, Lars Juhl, 2015, In : PeerJ. 3, p. 1-10 10 p., e1057.

    Research output: Contribution to journalJournal articleResearchpeer-review

  67. Published

    Recovery of gut microbiota of healthy adults following antibiotic exposure

    Palleja, A., Mikkelsen, K. H., Forslund, S. K., Kashani, A., Allin, Kristine Højgaard, Nielsen, Trine, Hansen, Tue Haldor, Liang, S., Feng, Q., Zhang, C., Pyl, P. T., Coelho, L. P., Yang, H., Wang, J., Typas, A., Nielsen, M. F., Nielsen, H. B., Bork, P., Wang, Jun, Vilsbøll, Tina, Hansen, Torben, Knop, Filip Krag, Arumugam, Mani & Pedersen, Oluf Borbye, Nov 2018, In : Nature Microbiology. 3, 11, p. 1255-1265 11 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  68. Published

    DistiLD Database: diseases and traits in linkage disequilibrium blocks

    Palleja, A., Horn, H., Eliasson, S. & Jensen, Lars Juhl, 2012, In : Nucleic Acids Research. 40, Database issue, p. D1036-40

    Research output: Contribution to journalJournal articleResearchpeer-review

  69. Published

    Global effects of kinase inhibitors on signaling networks revealed by quantitative phosphoproteomics

    Pan, C., Olsen, Jesper Velgaard, Daub, H. & Mann, Matthias, 2009, In : Molecular and Cellular Proteomics. 8, 12, p. 2796-808 12 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  70. E-pub ahead of print

    Predicting protein-RNA interaction amino acids using random forest based on submodularity subset selection

    Pan, X., Zhu, L., Fan, Y. & Yan, J., 13 Nov 2014, In : Computational Biology and Chemistry. 53PB, p. 324-330 7 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  71. Published

    Inferring disease-associated long non-coding RNAs using genome - wide tissue expression profiles

    Pan, X., Jensen, Lars Juhl & Gorodkin, Jan, 2019, In : Bioinformatics. 35, 9, p. 1494-1502 9 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  72. Published

    OUGENE: a disease associated over-expressed and under-expressed gene database

    Pan, X. & Shen, H., 2016, In : Science Bulletin. 61, 10, p. 752-754 3 p.

    Research output: Contribution to journalLetterResearchpeer-review

  73. Published

    Genome-wide identification of clusters of predicted microRNA binding sites as microRNA sponge candidates

    Pan, X., Wenzel, Anne, Jensen, Lars Juhl & Gorodkin, Jan, 2018, In : PLoS ONE. 13, 8, 15 p., e0202369.

    Research output: Contribution to journalJournal articleResearchpeer-review

  74. Published

    WebCircRNA: Classifying the Circular RNA Potential of Coding and Noncoding RNA.

    Pan, X., Xiong, K., Anthon, Christian, Hyttel, Poul, Freude, Kristine, Jensen, Lars Juhl & Gorodkin, Jan, 6 Nov 2018, In : Genes. 9, 11, 11 p., 536.

    Research output: Contribution to journalJournal articleResearchpeer-review

  75. Published

    ImmunoGrid, an integrative environment for large-scale simulation of the immune system for vaccine discovery, design and optimization

    Pappalardo, F., Halling-Brown, M. D., Rapin, N., Zhang, P., Alemani, D., Emerson, A., Paci, P., Duroux, L. P., Pennisi, M., Palladini, A., Miotto, O., Churchill, D., Rossi, E., Shepherd, A. J., Moss, D. S., Castiglione, F., Bernaschi, M., Lefranc, M., Brunak, Søren, Motta, S., Lollini, P., Basford, K. E. & Brusic, V., 2009, In : Briefings in Bioinformatics. 10, 3, p. 330-40 11 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  76. Published

    A thermophilic ionic liquid-tolerant cellulase cocktail for the production of cellulosic biofuels

    Park, J. I., Steen, E. J., Burd, H., Evans, S. S., Redding-Johnson, A. M., Batth, Tanveer Singh, Benke, P. I., D'haeseleer, P., Sun, N., Sale, K. L., Keasling, J. D., Lee, T. S., Petzold, C. J., Mukhopadhyay, A., Singer, S. W., Simmons, B. A. & Gladden, J. M., 2012, In : PLoS ONE. 7, 5, p. e37010

    Research output: Contribution to journalJournal articleResearchpeer-review

  77. Published

    BioStar: an online question & answer resource for the bioinformatics community

    Parnell, L. D., Lindenbaum, P., Shameer, K., Dall'Olio, G. M., Swan, D. C., Jensen, Lars Juhl, Cockell, S. J., Pedersen, B. S., Mangan, M. E., Miller, C. A. & Albert, I., 2011, In : P L o S Computational Biology (Online). 7, 10, p. e1002216

    Research output: Contribution to journalJournal articleResearchpeer-review

  78. Published

    Assessment of the analgesic dipyrone as a possible (anti) androgenic endocrine disruptor

    Passoni, M. T., Kristensen, Maja Nørgaard, Morais, R. N., Woitkowiak, C., Boareto, A. C., da Silva Amaral, B. A., Grechi, N., Dalsenter, P. R., Munkboel, C. H., Styrishave, Bjarne, Kristensen, D. M., Gomes, C., van Ravenzwaay, B. & Martino-Andrade, A. J., 15 Mar 2018, In : Toxicology Letters. 285, p. 139-147

    Research output: Contribution to journalJournal articleResearchpeer-review

  79. Published

    CRISPR-Cas12a: functional overview and applications

    Paul, Bijoya & Montoya, Guillermo, 2020, In : Biomedical Journal. 43, 1, p. 8-17

    Research output: Contribution to journalReviewResearchpeer-review

  80. Published

    The ubiquitin ligase Cullin5SOCS2 regulates NDR1/STK38 stability and NF-κB transactivation

    Paul, I., Batth, Tanveer Singh, Iglesias Gato, Diego, Al-Araimi, A., Al-Haddabi, I., Alkharusi, A., Norstedt, G., Olsen, Jesper Velgaard, Zadjali, F. & Flores-Morales, A., 2017, In : Scientific Reports. 7, 14 p., 42800.

    Research output: Contribution to journalJournal articleResearchpeer-review

  81. Published

    Impact of microRNA-130a on the neutrophil proteome

    Pedersen, C. C., Refsgaard, J. C., Østergaard, Ole, Jensen, Lars Juhl, Heegaard, N. H. H., Borregaard, N. & Cowland, J. B., 25 Nov 2015, In : B M C Immunology. 16, 10 p., 70.

    Research output: Contribution to journalJournal articleResearchpeer-review

  82. Published

    Pancreatic Islet Protein Complexes and Their Dysregulation in Type 2 Diabetes

    Pedersen, Helle Krogh, Gudmundsdottir, V. & Brunak, Søren, 2017, In : Frontiers in Genetics. 8, 43.

    Research output: Contribution to journalJournal articleResearchpeer-review

  83. Published

    Ranking factors involved in diabetes remission after bariatric surgery using machine-learning integrating clinical and genomic biomarkers

    Pedersen, Helle Krogh, Gudmundsdottir, V., Pedersen, M. K., Brorsson, C., Brunak, Søren & Gupta, R., 2016, In : npj Genomic Medicine. 1, 16035.

    Research output: Contribution to journalJournal articleResearchpeer-review

  84. Published

    A computational framework to integrate high-throughput "-omics" datasets for the identification of potential mechanistic links

    Pedersen, Helle Krogh, Forslund, S. K., Gudmundsdottir, V., Petersen, A. Ø., Hildebrand, F., Hyötyläinen, T., Nielsen, Trine, Hansen, Torben, Bork, P., Ehrlich, S. D., Brunak, Søren, Oresic, M., Pedersen, Oluf Borbye & Nielsen, H. B., 2018, In : Nature Protocols. 13, 12, p. 2781-2800 20 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  85. Published

    Human gut microbes impact host serum metabolome and insulin sensitivity

    Pedersen, H. K., Gudmundsdottir, V., Nielsen, H. B., Hyotylainen, T., Nielsen, Trine, Jensen, Benjamin Anderschou Holbech, Forslund, K., Hildebrand, F., Prifti, E., Falony, G., Le Chatelier, E., Levenez, F., Doré, J., Mattila, I., Plichta, D. R., Pöhö, P., Hellgren, L. I., Arumugam, Mani, Sunagawa, S., Vieira-Silva, S., Jørgensen, T., Holm, J. B., Trošt, K., Kristiansen, Karsten, Brix, Susanne, Raes, J., Wang, Jun, Hansen, Torben, Bork, P., Brunak, Søren, Oresic, M., Ehrlich, S. D., Pedersen, Oluf Borbye & MetaHIT Consortium, M. C., 2016, In : Nature. 535, 7612, p. 376-381 6 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  86. Published

    Continual removal of H3K9 promoter methylation by Jmjd2 demethylases is vital for ESC self-renewal and early development

    Pedersen, Marianne Terndrup, Kooistra, S. M., Radzisheuskaya, Aliaksandra, Laugesen, Anne, Johansen, Jens Vilstrup, Hayward, D. G., Nilsson, Jakob, Agger, Karl & Helin, Kristian, 15 Jul 2016, In : E M B O Journal. 35, 14, p. 1550-64 15 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  87. Published

    Profiling DNA damage response following mitotic perturbations

    Pedersen, R. S., Karemore, Gopal, Gudjonsson, T., Rask, M., Neumann, B., Hériché, J., Pepperkok, R., Ellenberg, J., Gerlich, D. W., Lukas, Jiri & Lukas, Claudia, 15 Dec 2016, In : Nature Communications. 7, 12 p., 13887.

    Research output: Contribution to journalJournal articleResearchpeer-review

  88. Published

    Systematic Analysis of the Crosstalk between Mitosis and DNA Damage by a Live Cell siRNA Screen

    Pedersen, R. S., 2014, Faculty of Science, University of Copenhagen. 143 p.

    Research output: Book/ReportPh.D. thesisResearch

  89. Published

    TopBP1 is required at mitosis to reduce transmission of DNA damage to G1 daughter cells

    Pedersen, R. T., Kruse, Thomas, Nilsson, Jakob, Østergaard, Vibe Hallundbæk & Lisby, Michael, 2015, In : Journal of Cell Biology. 210, 4, p. 565-582 18 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  90. Published

    MetaRanker 2.0: a web server for prioritization of genetic variation data

    Pers, T. H., Dworzynski, P., Thomas, C. E., Hansen, K. L. & Brunak, Søren, 1 Jul 2013, In : Nucleic Acids Research. 41, W1, p. W104-W108

    Research output: Contribution to journalJournal articleResearchpeer-review

  91. Published

    Meta-analysis of heterogeneous data sources for genome-scale identification of risk genes in complex phenotypes

    Pers, Tune H, Hansen, N. T., Hansen, K. L., Koefoed, P., Dworzynski, P., Miller, M. L., Flint, T. J., Mellerup, Erling Thyge, Dam, Henrik, Andreassen, O. A., Djurovic, S., Melle, I., Børglum, A. D., Werge, Thomas, Purcell, S., Ferreira, M. A., Kouskoumvekaki, I., Workman, C., Hansen, Torben, Mors, O. & Brunak, Søren, 11 Apr 2011, In : Genetic Epidemiology. 35, 5, p. 318-332 5 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  92. Published

    B-lymphoid tyrosine kinase (Blk) is an oncogene and a potential target for therapy with Dasatinib in cutaneous T-cell lymphoma (CTCL)

    Petersen, David Leander, Krejsgaard, Thorbjørn Frej, Berthelsen, J., Fredholm, S., Willerslev-Olsen, Andreas, Sibbesen, N. A., Bonefeld, Charlotte Menne, Andersen, M. H., Francavilla, C., Olsen, Jesper Velgaard, Hu, T., Zhang, M., Wasik, M. A., Geisler, Carsten, Woetmann, Anders & Ødum, Niels, 12 Jun 2014, In : Leukemia. 28, p. 2109-12 4 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  93. Published
  94. Published

    Functional Differences between Synaptic Mitochondria from the Striatum and the Cerebral Cortex

    Petersen, M. H., Willert, C. W., Andersen, Jens Velde, Waagepetersen, Helle S., Skotte, Niels Henning & Nørremølle, Anne, May 2019, In : Neuroscience. 406, p. 432-443 12 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  95. Published

    SignalP 4.0: discriminating signal peptides from transmembrane regions

    Petersen, T. N., Brunak, Søren, von Heijne, G. & Nielsen, H., 2011, In : Nature Methods. 8, 10, p. 785-6 2 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  96. Published

    MCM2 promotes symmetric inheritance of modified histones during DNA replication

    Petryk, N., Dalby, M., Wenger, Alice, Stromme, C. B., Strandsby, A., Andersson, Robin & Groth, Anja, 2018, In : Science. 361, 6409, p. 1389-1392 3 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  97. Published

    KIT(D816V) Induces SRC-Mediated Tyrosine Phosphorylation of MITF and Altered Transcription Program in Melanoma

    Phung, B., Kazi, J. U., Lundby, Alicia, Bergsteinsdottir, K., Sun, J., Goding, C. R., Jönsson, G., Olsen, Jesper Velgaard, Steingrímsson, E. & Rönnstrand, L., 2017, In : Molecular cancer research : MCR. 15, 9, p. 1265-1274 10 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  98. Published

    Mte1 interacts with Mph1 and promotes crossover recombination and telomere maintenance

    Pinela da Silva, S. C., Altmannova, V., Luke-Glaser, S., Henriksen, P., Gallina, Irene, Yang, X., Choudhary, Chuna Ram, Luke, B., Krejci, L. & Lisby, Michael, 2016, In : Genes & Development. 30, 6, p. 700-717 18 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  99. Published

    Global phosphoproteome profiling reveals unanticipated networks responsive to cisplatin treatment of embryonic stem cells

    Pines, A., Kelstrup, C. D., Vrouwe, M. G., Puigvert, J. C., Typas, D., Misovic, B., de Groot, A., von Stechow, L., van de Water, B., Danen, E. H. J., Vrieling, H., Mullenders, L. H. F. & Olsen, Jesper Velgaard, 2011, In : Molecular and Cellular Biology. 31, 24, p. 4964-77 14 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  100. Published

    The human methyltransferase ZCCHC4 catalyses N6-methyladenosine modification of 28S ribosomal RNA

    Pinto, R., Vågbø, C. B., Jakobsson, Magnus Erik, Kim, Y., Baltissen, M. P., O'Donohue, M., Guzmán, U. H., Małecki, J. M., Wu, J., Kirpekar, F., Olsen, Jesper Velgaard, Gleizes, P., Vermeulen, M., Leidel, S. A., Slupphaug, G. & Falnes, P. Ø., 24 Jan 2020, In : Nucleic Acids Research. 48, 2, p. 830-846 17 p.

    Research output: Contribution to journalJournal articleResearchpeer-review