The NNF Center for Protein Research

  1. Published

    Analytical utility of mass spectral binning in proteomic experiments by SPectral Immonium Ion Detection (SPIID)

    Kelstrup, C. D., Freese, C., Heck, A. J. R., Olsen, Jesper Velgaard & Nielsen, Michael Lund, 3 Jun 2014, In : Molecular & Cellular Proteomics. 13, 8, p. 1914-1924 11 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  2. Published

    Limits for resolving isobaric tandem mass tag reporter ions using phase constrained spectrum deconvolution

    Kelstrup, C. D., Aizikov, K., Batth, Tanveer Singh, Kreutzman, A., Grinfeld, D., Lange, O., Mourad, D., Makarov, A. A. & Olsen, Jesper Velgaard, 2018, In : Journal of Proteome Research. 17, 11, p. 4008-4016 9 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  3. Published

    Reduced Hsp70 and Glutamine in Pediatric Severe Malaria Anemia: Role of Hemozoin in Suppressing Hsp70 and NF-κB activation

    Kempaiah, P., Dokladny, K., Karim, Z., Raballah, E., Ong'echa, J. M., Moseley, Pope Lloyd & Perkins, D. J., 2016, In : Molecular Medicine. 22, p. 570-584 15 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  4. Published

    OTULIN antagonizes LUBAC signaling by specifically hydrolyzing met1-linked polyubiquitin

    Keusekotten, K., Elliott, P. R., Kulathu, Y., Wauer, T., Hospenthal, M. K., Komander, D., Glockner, L., Krappmann, D., Fiil, B. K., Damgaard, R. B., Gyrd-Hansen, M. & Hofmann, K., 6 Jun 2013, In : Cell. 153, 6, p. 1312-1326 15 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  5. Published

    Transfection of small RNAs globally perturbs gene regulation by endogenous microRNAs

    Khan, A. A., Betel, D., Miller, M. L., Sander, C., Leslie, C. S. & Marks, D. S., 2009, In : Nature Biotechnology. 27, 6, p. 549-55 6 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  6. Published

    Purification, characterization and crystallization of the human 80S ribosome

    Khatter, H., Myasnikov, A. G., Mastio, L., Billas, I. M. L., Birck, C., Stella, Stefano & Klaholz, B. P., 1 Jan 2014, In : Nucleic Acids Research. 42, 6

    Research output: Contribution to journalJournal articleResearchpeer-review

  7. Published

    Utilisation of antibody microarrays for the selection of specific and informative antibodies from recombinant library binders of unknown quality

    Kibat, J., Schirrmann, T., Knape, M. J., Helmsing, S., Meier, D., Hust, M., Schröder, C., Bertinetti, D., Winter, G., Pardes, K., Funk, M., Lages Lino Vala, A., Giese, N., Herberg, F. W., Dübel, S. & Hoheisel, J. D., Sep 2016, In : New Biotechnology. 33, 5A, p. 574-581 8 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  8. Published

    Evolution reveals a glutathione-dependent mechanism of 3-hydroxypropionic acid tolerance

    Kildegaard, K. R., Hallström, B. M., Blicher, T. H., Sonnenschein, N., Jensen, N. B., Sherstyk, S., Harrison, S. J., Maury, J., Herrgård, M. J., Juncker, A. S., Forster, J., Nielsen, J. & Borodina, I., Sep 2014, In : Metabolic Engineering. 26C, p. 57-66 10 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  9. Published

    Disruption of Ca2+i Homeostasis and Connexin 43 Hemichannel Function in the Right Ventricle Precedes Overt Arrhythmogenic Cardiomyopathy in Plakophilin-2-Deficient Mice

    Kim, J., Perez-Hernandez, M., Alvarado, F. J., Maurya, S. R., Montnach, J., Yin, Y., Zhang, M., Lin, X., Vasquez, C., Heguy, A., Liang, F., Woo, S., Morley, G. E., Rothenberg, E., Lundby, Alicia, Valdivia, H. H., Cerrone, M. & Delmar, M., 2019, In : Circulation. 140, 12, p. 1015-1030

    Research output: Contribution to journalJournal articleResearchpeer-review

  10. Published

    Development of Computational Methods for Cancer Research: Strategies for closing the feedback loop in omics workflows

    Kirik, U., 2015, Lund University Publications.

    Research output: Book/ReportPh.D. thesisResearch

  11. Published

    Multimodel pathway enrichment methods for functional evaluation of expression regulation

    Kirik, U., Cifani, P., Albrekt, A., Lindstedt, M., Heyden, A. & Levander, F., 4 May 2012, In : Journal of Proteome Research. 11, 5, p. 2955-67 13 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  12. Published

    Improving Peptide-Spectrum Matching by Fragmentation Prediction Using Hidden Markov Models

    Kirik, U., Refsgaard, J. C. & Jensen, Lars Juhl, 2019, In : Journal of Proteome Research. 18, 6, p. 2385-2396

    Research output: Contribution to journalJournal articleResearchpeer-review

  13. Published

    The impact of the protein interactome on the syntenic structure of mammalian genomes

    Kirk, I. K., Weinhold, N., Brunak, Søren & Belling, Kirstine G, 2017, In : PLOS ONE. 12, 9, 14 p., e0179112.

    Research output: Contribution to journalJournal articleResearchpeer-review

  14. Published

    Chromosome-wise Protein Interaction Patterns and Their Impact on Functional Implications of Large-Scale Genomic Aberrations

    Kirk, I. K., Weinhold, N., Belling, Kirstine G, Skakkebæk, Niels Erik, Jensen, T. S., Leffers, H., Juul, Anders & Brunak, Søren, 22 Mar 2017, In : Cell Systems. 4, 3, 11 p., 357-364.e3.

    Research output: Contribution to journalJournal articleResearchpeer-review

  15. Published

    Linking glycemic dysregulation in diabetes to symptoms, comorbidities, and genetics through EHR data mining

    Kirk, I. K., Simon, C., Banasik, Karina, Holm, Peter Christoffer, Haue, Amalie Dahl, Jensen, P. B., Jensen, Lars Juhl, Leal Rodriguez, Cristina, Pedersen, M. K., Eriksson, Robert, Andersen, H. U., Almdal, Thomas Peter, Bork-Jensen, J., Grarup, Niels, Borch-Johnsen, K., Pedersen, Oluf Borbye, Pociot, Flemming, Hansen, Torben, Bergholdt, R., Rossing, Peter & Brunak, Søren, 2019, In : eLife. 8, 19 p., e44941.

    Research output: Contribution to journalJournal articleResearchpeer-review

  16. Published

    Transcriptome analysis in patients with temporal lobe epilepsy

    Kjær, C., Barzaghi, G., Bak, Lasse Kristoffer, Goetze, Jens P. , Yde, C. W., Woldbye, David Paul Drucker, Pinborg, Lars Hageman & Jensen, Lars Juhl, 2019, In : Brain. 142, 10, p. 49-64 16 p., e55.

    Research output: Contribution to journalLetterResearchpeer-review

  17. Published

    Cetuximab Resistance in Squamous Carcinomas of the Upper Aerodigestive Tract Is Driven by Receptor Tyrosine Kinase Plasticity: Potential for mAb Mixtures

    Kjær, I., Lindsted, T., Fröhlich, C., Olsen, Jesper Velgaard, Horak, I. D., Kragh, M. & Pedersen, M. W., Jul 2016, In : Molecular Cancer Therapeutics. 15, 7, p. 1614-1626 13 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  18. Published

    Interaction of RECQ4 and MCM10 is important for efficient DNA replication origin firing in human cells

    Kliszczak, M., Sedlackova, H., Pitchai, G. P., Streicher, W. W., Krejci, L. & Hickson, Ian David, 1 Dec 2015, In : OncoTarget. 6, 38, p. 40464-79 16 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  19. Published

    Comparative Study of Different Methods for the Prediction of Drug-Polymer Solubility

    Knopp, M. M., Tajber, L., Tian, Y., Olesen, N. E., Jones, D. S., Kozyra, A., Löbmann, Korbinian, Paluch, K., Brennan, C. M., Holm, R., Healy, A. M., Andrews, G. P. & Rades, Thomas, 8 Sep 2015, In : Molecular Pharmaceutics. 12, 9, p. 3408-19 12 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  20. Published

    ERG promotes the maintenance of hematopoietic stem cells by restricting their differentiation

    Knudsen, K. J., Rehn, Matilda Carolina, Hasemann, M. S., Rapin, N. P. J., Bagger, F. O., Ohlsson, E. K., Willer, A., Frank, Anne-Katrine, Søndergaard, Elisabeth, Jendholm, L. J., Thorén, L. A. M., Lee, J., Rak, J., Theilgaard-Mønch, Kim & Porse, Bo Torben, 2015, In : Genes & Development. 29, p. 1915-1929 15 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  21. Published

    Migraine polygenic risk score associates with efficacy of migraine-specific drugs

    Kogelman, L. J. A., Esserlind, A., Christensen, A. F., Awasthi, S., Ripke, S., Ingason, A., Davidsson, O. B., Erikstrup, C., Hjalgrim, H., Ullum, Henrik, Olesen, Jes, Hansen, Thomas Folkmann, Gudbjartsson, D., Gastafsson, O., Stefansson, K., Stefansson, H., Porsteinsdottir, U., Andersen, S., Banasik, Karina, Brunak, Søren, Buil, A., Burgdorf, K., Gregor, J., Jennum, Poul, Nielsen, K. R., Nyegaard, M., Paarup, H. M., Pedersen, O. B., Sørensen, E., Werge, Thomas, Anttila, V., Artto, V., Belin, A. C., de Boer, I., Boomsma, D. I., Borte, S., Chasman, D. I., Cherkas, L., Cormand, B., Cuenca-Leon, E., Davey-Smith, G., Dichgans, M., van Duijn, C., Esko, T., Ferrari, M., Frants, R. R., Freilinger, T., Furlotte, N., Gormley, P., Griffiths, L., Hamalainen, E., Hiekkala, M., Ikram, M. A., Jarvelin, M., Kajanne, R., Kallela, M., Kaprio, J., Kaunisto, M., Kubisch, C., Kurki, M., Kurth, T., Launer, L., Lehtimaki, T., Lessel, D., Ligthart, L., Litterman, N., van den Maagdenberg, A., Macaya, A., Malik, R., Mangino, M., McMahon, G., Muller-Myhsok, B., Neale, B. M., Northover, C., Nyholt, D. R., Palotie, A., Palta, P., Pedersen, L., Pedersen, N., Posthuma, D., Pozo-Rosich, P., Pressman, A., Raitakari, O., Schurks, M., Sintas, C., Steinberg, S., Strachan, D., Terwindt, G., Vila-Pueyo, M., Wessman, M., Winsvold, B. S., Zhao, H. & Zwart, J., 2019, In : Neurology: Genetics. 5, 6, 12 p., e364.

    Research output: Contribution to journalJournal articleResearchpeer-review

  22. Published

    Comparing migraine with and without aura to healthy controls using RNA sequencing

    Kogelman, L. J. A., Falkenberg, K., Halldorsson, G. H., Poulsen, L. U., Worm, J., Ingason, A., Stefansson, H., Stefansson, K., Hansen, Thomas Folkmann & Olesen, Jes, 2019, In : Cephalalgia. 39, 11, p. 1435-1444

    Research output: Contribution to journalJournal articleResearchpeer-review

  23. Published

    Discovery of biomarkers for glycaemic deterioration before and after the onset of type 2 diabetes: descriptive characteristics of the epidemiological studies within the IMI DIRECT Consortium

    Koivula, R. W., Forgie, I. M., Kurbasic, A., Viñuela, A., Heggie, A., Giordano, G. N., Hansen, Tue Haldor, Hudson, M., Koopman, A. D. M., Rutters, F., Siloaho, M., Allin, Kristine Højgaard, Brage, S., Brorsson, C. A., Dawed, A. Y., De Masi, F., Groves, C. J., Kokkola, T., Mahajan, A., Perry, M. H., Rauh, S. P., Ridderstråle, M., Teare, H. J. A., Thomas, E. L., Tura, A., Vestergaard, Henrik, White, T., Adamski, J., Bell, J. D., Beulens, J. W., Brunak, Søren, Dermitzakis, E. T., Froguel, P., Frost, G., Gupta, R., Hansen, Torben, Hattersley, A., Jablonka, B., Kaye, J., Laakso, M., McDonald, T. J., Pedersen, Oluf Borbye, Schwenk, J. M., Pavo, I., Mari, A., McCarthy, M. I., Ruetten, H., Walker, M., Pearson, E., Franks, P. W. & IMI-DIRECT consortium, I. C., 2019, In : Diabetologia. 62, 9, p. 1601-1615

    Research output: Contribution to journalJournal articleResearchpeer-review

  24. Published

    Heterologous expression and purification of an active human TRPV3 ion channel

    Kol, S., Braun, C. S., Thiel, G., Doyle, D. A., Sundström, M., Gourdon, Pontus Emanuel & Nissen, P., 1 Dec 2013, In : The F E B S Journal (Online). 280, 23, p. 6010-6021 12 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  25. Published

    Alterations of the interactome of Bcl-2 proteins in breast cancer at the transcriptional, mutational and structural level

    Konig, S. M., Rissler, V., Terkelsen, T., Lambrughi, M. & Papaleo, Elena, 2019, In : P L o S One. 15, 12, 28 p., e1007485.

    Research output: Contribution to journalJournal articleResearchpeer-review

  26. Published

    Proceedings of the EuBIC Winter School 2019

    Kopczynski, D., Bittremieux, W., Bouyssié, D., Dorfer, V., Locard-Paulet, Marie, Van Puyvelde, B., Schwämmle, V., Soggiu, A., Willems, S. & Uszkoreit, J., 2019, In : EuPA Open Proteomics. 22-23, p. 4-7 4 p.

    Research output: Contribution to journalConference articleResearchpeer-review

  27. Published

    Dynamics of the Eukaryotic Replicative Helicase at Lagging-Strand Protein Barriers Support the Steric Exclusion Model

    Kose, H. B., Larsen, Nicolai Balle, Duxin, Julien & Yardimci, H., 2019, In : Cell Reports. 26, 8, p. 2113-2125.e6 19 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  28. Published

    A secretory system for bacterial production of high-profile protein targets

    Kotzsch, A., Vernet, E., Hammarström, M., Berthelsen, J., Weigelt, J., Gräslund, S. & Sundström, M., 2011, In : Protein Science. 20, 3, p. 597-609 13 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  29. Published

    A substrate-optimized electrophoretic mobility shift assay for ADAM12

    Kotzsch, A., Skovgaard, T., Buus, U., Andersen, S., Devkota, K. & Berthelsen, J., 1 May 2014, In : Analytical Biochemistry. 452, p. 34-42 9 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  30. Published

    Facilitating the use of large-scale biological data and tools in the era of translational bioinformatics

    Kouskoumvekaki, I., Shublaq, N. & Brunak, Søren, 1 Aug 2013, In : Briefings in Bioinformatics. 11 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  31. Published

    On the hunt for the alternate host of Hemileia vastatrix

    Koutouleas, Tina, Jørgensen, Hans Jørgen Lyngs, Jensen, Birgit, Lillesø, Jens-Peter Barnekow, Junge, A. & Ræbild, Anders, 2019, In : Ecology and Evolution. 9, 23, p. 13619-13631 13 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  32. Published

    Catching Lipid Droplet Contacts by Proteomics

    Krahmer, N. & Mann, Matthias, 2019, In : Contact. 2, p. 1-8 8 p.

    Research output: Contribution to journalReviewResearchpeer-review

  33. Published

    Organellar Proteomics and Phospho-Proteomics Reveal Subcellular Reorganization in Diet-Induced Hepatic Steatosis

    Krahmer, N., Najafi, B., Schueder, F., Quagliarini, F., Steger, M., Seitz, S., Kasper, R., Salinas, F., Cox, J., Uhlenhaut, N. H., Walther, T. C., Jungmann, R., Zeigerer, A., Borner, G. H. H. & Mann, Matthias, 2018, In : Developmental Cell. 47, 2, p. 205-221.E7

    Research output: Contribution to journalJournal articleResearchpeer-review

  34. Published

    ChemProt-3.0: a global chemical biology diseases mapping

    Kringelum, J. V., Kjærulff, S. K., Brunak, Søren, Lund, O., Oprea, T. I. & Taboureau, Olivier Thierry, 2016, In : Database. 2016, 7 p., bav123.

    Research output: Contribution to journalJournal articleResearchpeer-review

  35. Published

    Ibuprofen alters human testicular physiology to produce a state of compensated hypogonadism

    Kristensen, D. M., Desdoits-Lethimonier, C., Mackey, Abigail, Dalgaard, M. D., De Masi, F., Munkbøl, C. H., Styrishave, Bjarne, Antignac, J., Le Bizec, B., Platel, C., Hay-Schmidt, Anders, Jensen, T. K., Lesné, L., Mazaud-Guittot, S., Kristiansen, Karsten, Brunak, Søren, Kjær, Michael, Juul, Anders & Jégou, B., 2018, In : Proceedings of the National Academy of Sciences of the United States of America. 115, 4, p. e715-e724 10 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  36. Published

    Serological assessment of neutrophil elastase activity on elastin during lung ECM remodeling

    Kristensen, J. H., Karsdal, M. A., Sand, J. M. B., Willumsen, N., Diefenbach, C., Svensson, B., Hägglund, Per Mårten & Oersnes-Leeming, D. J., 3 May 2015, In : BMC Pulmonary Medicine. 15, 1, 53.

    Research output: Contribution to journalJournal articleResearchpeer-review

  37. Published

    The role of extracellular matrix quality in pulmonary fibrosis

    Kristensen, J. H., Karsdal, M. A., Genovese, F., Johnson, S., Svensson, B., Jacobsen, S., Hägglund, Per Mårten & Leeming, D. J., 14 Apr 2014, In : Respiration. 88, 6, p. 487-499 13 p.

    Research output: Contribution to journalReviewResearchpeer-review

  38. Published

    miRNAs in Human Subcutaneous Adipose Tissue: Effects of Weight Loss Induced by Hypocaloric Diet and Exercise

    Kristensen, M. M., Davidsen, P. K., Vigelso, A., Hansen, C. N., Jensen, Lars Juhl, Jessen, N., Bruun, Jens Meldgaard, Dela, Flemming & Helge, Jørn Wulff, Mar 2017, In : Obesity. 25, 3, p. 572-580 9 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  39. Published

    Cellular Barcoding Links B-1a B Cell Potential to a Fetal Hematopoietic Stem Cell State at the Single-Cell Level

    Kristiansen, T. A., Jaensson Gyllenbäck, E., Zriwil, A., Björklund, T., Daniel, J. A., Sitnicka, E., Soneji, S., Bryder, D. & Yuan, J., 16 Aug 2016, In : Immunity. 45, 2, p. 346-57 12 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  40. Published

    Revision of the Classical Dopamine D2 Agonist Pharmacophore Based on an Integrated Medicinal Chemistry, Homology Modelling and Computational Docking Approach

    Krogsgaard-Larsen, N., Harpsøe, Kasper, Kehler, J., Christoffersen, C. T., Brøsen, P. & Balle, T., 24 Jul 2014, In : Neurochemical Research. 39, 10, p. 1997-2007 12 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  41. Published

    Actin homolog MreB and RNA polymerase interact and are both required for chromosome segregation in Escherichia coli

    Kruse, Thomas, Blagoev, B., Løbner-Olesen, Anders, Wachi, M., Sasaki, K., Iwai, N., Mann, Matthias & Gerdes, K., 1 Jan 2006, In : Genes & Development. 20, 1, p. 113-124 12 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  42. Published

    Dysfunctional MreB inhibits chromosome segregation in Escherichia coli

    Kruse, Thomas, Møller-Jensen, J., Løbner-Olesen, Anders & Gerdes, K., 1 Oct 2003, In : E M B O Journal. 22, 19, p. 5283-92 10 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  43. Published

    The Ebola Virus Nucleoprotein Recruits the Host PP2A-B56 Phosphatase to Activate Transcriptional Support Activity of VP30

    Kruse, Thomas, Biedenkopf, N., Hertz, Emil Peter Thrane, Dietzel, E., Stalmann, G., López-Méndez, B., Davey, N. E., Nilsson, Jakob & Becker, S., 4 Jan 2018, In : Molecular Cell. 69, 1, p. 136-145 10 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  44. Published

    A direct role of Mad1 in the spindle assembly checkpoint beyond Mad2 kinetochore recruitment

    Kruse, Thomas, Larsen, M. S. Y., Sedgwick, G. G., Sigurdsson, J. O., Streicher, W., Olsen, Jesper Velgaard & Nilsson, Jakob, 29 Jan 2014, In : E M B O Reports. 15, p. 282-290

    Research output: Contribution to journalJournal articleResearchpeer-review

  45. Published

    Direct binding between BubR1 and B56-PP2A phosphatase complexes regulate mitotic progression

    Kruse, Thomas, Zhang, G., Larsen, M. S. Y., Lischetti, T., Streicher, W., Nielsen, T. K., Bjørn, S. P. & Nilsson, Jakob, 23 Jan 2013, In : Journal of Cell Science. 126, p. 1086-1092 7 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  46. Accepted/In press

    Mechanisms of site-specific dephosphorylation and kinase opposition imposed by PP2A regulatory subunits

    Kruse, Thomas, Gnosa, Sebastian Peter, Nasa, I., Garvanska, Dimitriya Hristoforova, bmk286, bmk286, Nguyen, H., Samsøe-Petersen, Jacob, Lopez-Mendez, B., Hertz, Emil Peter Thrane, Schwarz, J., Pena, H. S., Nikodemus, Denise, Kveiborg, Marie, Kettenbach, A. N. & Nilsson, Jakob, 1 Jan 2020, (Accepted/In press) In : EMBO Journal. p. 1-18 e103695.

    Research output: Contribution to journalJournal articleResearchpeer-review

  47. Published

    Compass: A hybrid method for clinical and biobank data mining

    Krysiak-Baltyn, K., Nordahl Petersen, T., Audouze, K. M. L., Jørgensen, N., Ängquist, Lars & Brunak, Søren, Feb 2014, In : Journal of Biomedical Informatics. 47, p. 160-170

    Research output: Contribution to journalJournal articleResearchpeer-review

  48. Published

    Large-scale prediction of drug-target relationships

    Kuhn, M., Campillos, M., González, P., Jensen, Lars Juhl & Bork, P., 2008, In : F E B S Letters. 582, 8, p. 1283-90 8 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  49. Published

    STITCH 2: an interaction network database for small molecules and proteins

    Kuhn, M., Szklarczyk, D., Franceschini, A., Campillos, M., von Mering, C., Jensen, Lars Juhl, Beyer, A. & Bork, P., 2010, In : Nucleic Acids Research. 38, Database issue, p. D552-6

    Research output: Contribution to journalJournal articleResearchpeer-review

  50. Published

    A side effect resource to capture phenotypic effects of drugs

    Kuhn, M., Campillos, M., Letunic, I., Jensen, Lars Juhl & Bork, P., 1 Jan 2010, In : Molecular Systems Biology. 6, p. 343

    Research output: Contribution to journalJournal articleResearchpeer-review

  51. Published

    STITCH 4: integration of protein-chemical interactions with user data

    Kuhn, M., Szklarczyk, D. M., Pletscher-Frankild, S., Blicher, T. H., von Mering, C., Jensen, Lars Juhl & Bork, P., 28 Nov 2013, In : Nucleic Acids Research. 42, D1, p. D401-D407 7 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  52. Published

    Systematic identification of proteins that elicit drug side effects

    Kuhn, M., Al Banchaabouchi, M., Campillos, M., Jensen, Lars Juhl, Gross, C., Gavin, A. & Bork, P., 30 Apr 2013, In : Molecular Systems Biology. 9, p. 663 9 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  53. Published

    The SIDER database of drugs and side effects

    Kuhn, M., Letunic, I., Jensen, Lars Juhl & Bork, P., 4 Jan 2016, In : Nucleic Acids Research. 44, p. D1075-9

    Research output: Contribution to journalJournal articleResearchpeer-review

  54. Published

    STITCH 3: zooming in on protein-chemical interactions

    Kuhn, M., Szklarczyk, D., Franceschini, A., von Mering, C., Jensen, Lars Juhl & Bork, P., 2012, In : Nucleic Acids Research. 40, Database issue, p. D876-80

    Research output: Contribution to journalJournal articleResearchpeer-review

  55. Published

    Loss-less Nano-fractionator for High Sensitivity, High Coverage Proteomics

    Kulak, N. A., Geyer, P. E. & Mann, Matthias, Apr 2017, In : Molecular and Cellular Proteomics. 16, 4, p. 694-705 12 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  56. Published

    Incorporating symptom data in longitudinal disease trajectories for more detailed patient stratification

    Lademann, M., zmw894, zmw894, Boeck Jensen, A. & Brunak, Søren, 2019, In : International Journal of Medical Informatics. 129, p. 107-113 7 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  57. Published

    Variability in the incidence of miRNAs and genes in fragile sites and the role of repeats and CpG islands in the distribution of genetic material

    Laganà, A., Russo, Francesco, Sismeiro, C., Giugno, R., Pulvirenti, A. & Ferro, A., 11 Aug 2010, In : PLoS ONE. 5, 6, e11166.

    Research output: Contribution to journalJournal articleResearchpeer-review

  58. Published

    Computational design of artificial RNA molecules for gene regulation

    Laganà, A., Veneziano, D., Russo, Francesco, Pulvirenti, A., Giugno, R., Croce, C. M. & Ferro, A., 10 Jan 2015, RNA Bioinformatics. Springer New York LLC, p. 393-412 20 p.

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

  59. Published

    Extracellular circulating viral microRNAs: Current knowledge and perspectives

    Laganà, A., Russo, Francesco, Veneziano, D., Bella, S. D., Giugno, R., Pulvirenti, A., Croce, C. M. & Ferro, A., 11 Sep 2013, In : Frontiers in Genetics. 4, JUN, Article 120.

    Research output: Contribution to journalReviewResearchpeer-review

  60. Published

    MiR-EdiTar: A database of predicted A-to-I edited miRNA target sites

    Laganà, A., Paone, A., Veneziano, D., Cascione, L., Gasparini, P., Carasi, S., Russo, Francesco, Nigita, G., MacCa, V., Giugno, R., Pulvirenti, A., Shasha, D., Ferro, A. & Croce, C. M., 1 Dec 2012, In : Bioinformatics. 28, 23, p. 3166-3168 3 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  61. Published

    Computational design of artificial RNA molecules for gene regulation

    Laganà, A., Veneziano, D., Russo, Francesco, Pulvirenti, A., Giugno, R., Croce, C. M. & Ferro, A., 1 Jan 2015, In : Methods in Molecular Biology. 1269, p. 393-410 18 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  62. Published

    Prediction of human targets for viral-encoded microRNAs by thermodynamics and empirical constraints

    Laganá, A., Forte, S., Russo, Francesco, Giugno, R., Pulvirenti, A. & Ferro, A., 2010, In : Journal of RNAi and Gene Silencing.

    Research output: Contribution to journalJournal articleResearchpeer-review

  63. Published

    Myosin binding protein H-like (MYBPHL): a promising biomarker to predict atrial damage

    Lahm, H., Dressen, M., Beck, N., Doppler, S., Deutsch, M., Matsushima, S., Neb, I., Koenig, K. C., Sideris, K., Voss, S., Eschenbach, L., Puluca, N., Deisenhofer, I., Doll, S., Holdenrieder, S., Mann, Matthias, Lange, R. & Krane, M., 2019, In : Scientific Reports. 9, 8 p., 9986.

    Research output: Contribution to journalJournal articleResearchpeer-review

  64. Published

    Expression, purification, crystallization and preliminary X-ray diffraction analysis of the dihydroorotase domain of human CAD

    Lallous, N., Grande-García, A., Molina, Rafael & Ramón-Maiques, S., 1 Nov 2012, In : Acta Crystallographica Section F: Structural Biology Communications. 68, Pt 11, p. 1341-5 5 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  65. Published

    Advancing cell biology through proteomics in space and time (PROSPECTS)

    Lamond, A. I., Uhlen, M., Horning, S., Makarov, A., Robinson, C. V., Serrano, L., Hartl, F. U., Baumeister, W., Werenskiold, A. K., Mann, Matthias, Andersen, J. S., Vorm, O., Linial, M. & Aebersold, R., 1 Mar 2012, In : Molecular & Cellular Proteomics. 11, 3, 12 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  66. Published

    High-affinity DNA binding sites for H-NS provide a molecular basis for selective silencing within proteobacterial genomes

    Lang, B., Blot, N., Bouffartigues, E., Buckle, M., Geertz, M., Gualerzi, C. O., Mavathur, R., Muskhelishvili, G., Pon, C. L., Rimsky, S., Stella, Stefano, Babu, M. M. & Travers, A., 1 Sep 2007, In : Nucleic Acids Research. 35, 18, p. 6330-6337 8 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  67. Published

    The NBS1-Treacle complex controls ribosomal RNA transcription in response to DNA damage

    Larsen, D. H., Hari, F., Clapperton, J. A., Gwerder, M., Gutsche, K., Altmeyer, M., Jungmichel, S., Toledo Lazaro, Luis Ignacio, Fink, D., Rask, M., Grøfte, M., Lukas, Claudia, Nielsen, Michael Lund, Smerdon, S. J., Lukas, Jiri & Stucki, M., Aug 2014, In : Nature Cell Biology. 16, 8, p. 792-803 12 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  68. Published

    Suppression of water as a nucleophile in Candida antarctica lipase B catalysis

    Larsen, M. W., Zielinska, D. F., Martinelle, M., Hidalgo, A., Jensen, Lars Juhl, Bornscheuer, U. T. & Hult, K., 12 Apr 2010, In : ChemBioChem. 11, 6, p. 796-801 6 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  69. Published

    Replication-Coupled DNA-Protein Crosslink Repair by SPRTN and the Proteasome in Xenopus Egg Extracts

    Larsen, Nicolai Balle, Gao, A. O., Sparks, J. L., Gallina, Irene, Wu, R. A., Mann, Matthias, Räschle, M., Walter, J. C. & Duxin, Julien, 2019, In : Molecular Cell. 73, 3, p. 574-588.e7 23 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  70. Published

    Proteome-wide analysis of arginine monomethylation reveals widespread occurrence in human cells

    Buch-Larsen, Sara Charlotte, Sylvestersen, K. B., Mund, Andreas, Lyon, D., Mullari, Meeli, Vistrup-Parry, Maria, Daniel, J. A., Jensen, Lars Juhl & Nielsen, Michael Lund, 30 Aug 2016, In : Science signaling. 9, 443, 14 p., rs9.

    Research output: Contribution to journalJournal articleResearchpeer-review

  71. Published

    Proteome-Wide Identification of In Vivo ADP-Ribose Acceptor Sites by Liquid Chromatography-Tandem Mass Spectrometry

    Buch-Larsen, Sara Charlotte, Leutert, M., Bilan, V., Martello, R., Jungmichel, S., Young, C., Hottiger, M. O. & Nielsen, Michael Lund, 2017, Poly(ADP-Ribose) Polymerase. Tulin, A. V. (ed.). Humana Press, Vol. 1608. p. 149-162 14 p. (Methods in molecular biology (Clifton, N.J.)).

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

  72. Published

    Systems-wide Analysis of Serine ADP-Ribosylation Reveals Widespread Occurrence and Site-Specific Overlap with Phosphorylation

    Buch-Larsen, Sara Charlotte, Hendriks, Ivo Alexander, Lyon, D., Jensen, Lars Juhl & Nielsen, Michael Lund, 2018, In : Cell Reports. 24, 9, p. 2493-2505

    Research output: Contribution to journalJournal articleResearchpeer-review

  73. Published

    Human chitotriosidase CHIT1 cross reacts with mammalian-like substrates

    Larsen, T., Yoshimura, Y., Voldborg, B. G. R., Cazzamali, G., Bovin, N. V., Westerlind, U., Palcic, M. M. & Leisner, Jørgen, 2014, In : F E B S Letters. 588, 5, p. 746-751 6 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  74. Published

    Discovery of a selective catalytic p300/CBP inhibitor that targets lineage-specific tumours

    Lasko, L. M., Jakob, C. G., Edalji, R. P., Qiu, W., Montgomery, D., Digiammarino, E. L., Hansen, T. M., Risi, R. M., Frey, R., Manaves, V., Shaw, B., Algire, M., Hessler, P., Lam, L. T., Uziel, T., Faivre, E., Ferguson, D., Buchanan, F. G., Martin, R. L., Torrent, M., Chiang, G. G., Karukurichi, K., Langston, J. W., Weinert, B. T., Choudhary, Chuna Ram, de Vries, P., Van Drie, J. H., McElligott, D., Kesicki, E., Marmorstein, R., Sun, C., Cole, P. A., Rosenberg, S. H., Michaelides, M. R., Lai, A. & Bromberg, K. D., 5 Oct 2017, In : Nature. 550, 7674, p. 128-132 5 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  75. Published

    Barley peroxidase isozymes. Expression and post-translational modification in mature seeds as identified by two-dimensional gel electrophoresis and mass spectrometry

    Laugesen, S., Bak-Jensen, K. S., Hägglund, Per Mårten, Henriksen, A., Finnie, C., Svensson, B. & Roepstorff, P., 1 Dec 2007, In : International Journal of Mass Spectrometry. 268, 2-3, p. 244-253 10 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  76. Published

    Analysis of Continuous Glucose Monitoring in Pregnant Women With Diabetes: Distinct Temporal Patterns of Glucose Associated With Large-for-Gestational-Age Infants

    Law, G. R., Ellison, G. T. H., Secher, A. L., Damm, Peter, Mathiesen, Elisabeth, Temple, R., Murphy, H. R. & Scott, E. M., Jul 2015, In : Diabetes Care. 38, 7, p. 1319-25 7 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  77. Published

    Functional intersection of ATM and DNA-dependent protein kinase catalytic subunit in coding end joining during V(D)J recombination

    Lee, B., Gapud, E. J., Zhang, S., Dorsett, Y., Bredemeyer, A., George, R., Callen, E., Daniel, J. A., Osipovich, O., Oltz, E. M., Bassing, C. H., Nussenzweig, A., Lees-Miller, S., Hammel, M., Chen, B. P. C. & Sleckman, B. P., Sep 2013, In : Molecular and Cellular Biology. 33, 18, p. 3568-79 12 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  78. Published

    Tousled-like kinases stabilize replication forks and show synthetic lethality with checkpoint and PARP inhibitors

    Lee, S., Segura-Bayona, S., Villamor-Payà, M., Saredi, G., Todd, Matthew, Attolini, C. S., Chang, T., Stracker, T. H. & Groth, Anja, 2018, In : Science Advances. 4, 8, p. 1-14 14 p., eaat4985.

    Research output: Contribution to journalJournal articleResearchpeer-review

  79. Published

    Novel serological neo-epitope markers of extracellular matrix proteins for the detection of portal hypertension

    Leeming, D. J., Karsdal, M. A., Byrjalsen, I., Bendtsen, Flemming, Trebicka, J., Nielsen, Michael Lund, Christiansen, C., Møller, Søren & Krag, A., 2013, In : Alimentary Pharmacology and Therapeutics. 38, 9, p. 1086-1096 11 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  80. Published

    Adverse outcome pathways: opportunities, limitations and open questions

    Leist, M., Ghallab, A., Graepel, R., Marchan, R., Hassan, R., Bennekou, S. H., Limonciel, A., Vinken, M., Schildknecht, S., Waldmann, T., Danen, E., van Ravenzwaay, B., Kamp, H., Gardner, I., Godoy, P., Bois, F. Y., Braeuning, A., Reif, R., Oesch, F., Drasdo, D., Höhme, S., Schwarz, M., Hartung, T., Braunbeck, T., Beltman, J., Vrieling, H., Sanz, F., Forsby, A., Gadaleta, D., Fisher, C., Kelm, J., Fluri, D., Ecker, G., Zdrazil, B., Terron, A., Jennings, P., van der Burg, B., Dooley, S., Meijer, A. H., Willighagen, E., Martens, M., Evelo, C., Mombelli, E., Taboureau, Olivier Thierry, Mantovani, A., Hardy, B., Koch, B., Escher, S., van Thriel, C., Cadenas, C., Kroese, D., van de Water, B. & Hengstler, J. G., Nov 2017, In : Archives of Toxicology. 91, 11, p. 3477-3505 29 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  81. Published

    Top-Down and Intact Protein Mass Spectrometry Data Visualization for Proteoform Analysis Using VisioProt-MS

    Lesne, J., Bousquet, M., Marcoux, J. & Locard-Paulet, Marie, 2019, In : Bioinformatics and Biology Insights. 13, 6 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  82. Published

    Ibuprofen is deleterious for the development of first trimester human fetal ovary ex vivo

    Leverrier-Penna, S., Mitchell, R. T., Becker, E., Lecante, L., Ben Maamar, M., Homer, N., Lavoue, V., Kristensen, D. M., Dejucq-Rainsford, N., Jegou, B. & Mazaud-Guittot, S., 2018, In : Human Reproduction. 33, 3, p. 482-493

    Research output: Contribution to journalJournal articleResearchpeer-review

  83. Published

    ALKBH4-dependent demethylation of actin regulates actomyosin dynamics

    Li, M., Shi, Y., Niu, Y., Wu, Y., Huang, C., Jin, K., Lv, Y., Danielsen, J. M. R., Yang, Y., Nilsen, A., Fusser, M., Olofsson, M., Klungland, A., Ding, Y., Dong, M., Fu, Y., He, C., Liu, B. & Xu, X., 14 May 2013, In : Nature Communications. 4, 13 p., 1832.

    Research output: Contribution to journalJournal articleResearchpeer-review

  84. Published

    A scored human protein-protein interaction network to catalyze genomic interpretation

    Li, T., Wernersson, R., Hansen, R. B., Horn, H., Mercer, J., Slodkowicz, G., Workman, C. T., Rigina, O., Rapacki, K., Stærfeldt, H. H., Brunak, Søren, Jensen, T. S. & Hansen, K. L., Jan 2017, In : Nature Methods. 14, 1, p. 61–64

    Research output: Contribution to journalLetterResearchpeer-review

  85. Published

    Heavy metal exposure causes changes in the metabolic health-associated gut microbiome and metabolites

    Li, X., Brejnrod, A. D., Ernst, M., Rykær, M., Herschend, J., Olsen, N. M. C., Dorrestein, P. C., Rensing, C. & Sørensen, Søren Johannes, 2019, In : Environment International. 126, p. 454-467 14 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  86. Published

    Phosphorylation of the yeast γ-tubulin Tub4 regulates microtubule function

    Lin, T., Gombos, L., Neuner, A., Sebastian, D., Olsen, Jesper Velgaard, Hrle, A., Benda, C. & Schiebel, E., 2011, In : P L o S One. 6, 5, p. e19700

    Research output: Contribution to journalJournal articleResearchpeer-review

  87. Published

    Drug target ontology to classify and integrate drug discovery data

    Lin, Y., Mehta, S., Küçük-McGinty, H., Turner, J. P., Vidovic, D., Forlin, M., Koleti, A., Nguyen, D., Jensen, Lars Juhl, Guha, R., Mathias, S. L., Ursu, O., Stathias, V., Duan, J., Nabizadeh, N., Chung, C., Mader, C., Visser, U., Yang, J. J., Bologa, C. G., Oprea, T. I. & Schürer, S. C., 9 Nov 2017, In : Journal of Biomedical Semantics. 8, 1, 16 p., 50.

    Research output: Contribution to journalJournal articleResearchpeer-review

  88. Published

    Quantitative proteomics and single-nucleus transcriptomics of the sinus node elucidates the foundation of cardiac pacemaking

    Linscheid, N., Logantha, S. J. R. J., Poulsen, C., Zhang, S., Schrölkamp, Maren, Egerod, Kristoffer Lihme, Thompson, J. J., Kitmitto, A., Galli, G., Humphries, M. J., Zhang, H., Pers, Tune H, Olsen, Jesper Velgaard, Boyett, M. & Lundby, Alicia, 2019, In : Nature Communications. 10, 19 p., 2889.

    Research output: Contribution to journalJournal articleResearchpeer-review

  89. Published

    The internal Cdc20 binding site in BubR1 facilitates both spindle assembly checkpoint signalling and silencing

    Lischetti, T., Zhang, G., Sedgwick, G. G., Bolanos-Garcia, V. M. & Nilsson, Jakob, Dec 2014, In : Nature Communications. 5, p. 1-12 12 p., 5563.

    Research output: Contribution to journalJournal articleResearchpeer-review

  90. Published

    Regulation of mitotic progression by the spindle assembly checkpoint

    Lischetti, T. & Nilsson, Jakob, 1 Jan 2015, In : Molecular & Cellular Oncology. 2, 1, p. e970484

    Research output: Contribution to journalJournal articleResearchpeer-review

  91. Published

    Evidence that OGG1 glycosylase protects neurons against oxidative DNA damage and cell death under ischemic conditions

    Liu, D., Croteau, D. L., Souza-Pinto, N., Pitta, M., Tian, J., Wu, C., Jiang, H., Mustafa, K., Keijzers, Guido, Bohr, Vilhelm & Mattson, M. P., Feb 2011, In : Journal of Cerebral Blood Flow and Metabolism. 31, 2, p. 680-692 13 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  92. Published

    In vivo brain GPCR signaling elucidated by phosphoproteomics

    Liu, J. J., Sharma, K., Zangrandi, L., Chen, C., Humphrey, S. J., Chiu, Y., Spetea, M., Liu-Chen, L., Schwarzer, C. & Mann, Matthias, 2018, In : Science (New York, N.Y.). 360, 6395, p. 1-11

    Research output: Contribution to journalJournal articleResearchpeer-review

  93. Published

    Comparing 22 Popular Phosphoproteomics Pipelines for Peptide Identification and Site Localization

    Locard-Paulet, Marie, Bouyssié, D., Froment, C., Burlet-Schiltz, O. & Jensen, Lars Juhl, 6 Mar 2020, In : Journal of Proteome Research. 19, 3, p. 1338-1345 8 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  94. Published

    Congenital diaphragmatic hernia interval on chromosome 8p23.1 characterized by genetics and protein interaction networks

    Longoni, M., Hansen, K. L., Russell, M. K., Loscertales, M., Abdul-Rahman, O. A., Baynam, G., Bleyl, S. B., Brady, P. D., Breckpot, J., Chen, C. P., Devriendt, K., Gillessen-Kaesbach, G., Grix, A. W., Rope, A. F., Shimokawa, O., Strauss, B., Wieczorek, D., Zackai, E. H., Coletti, C. M., Maalouf, F. I., Noonan, K. M., Park, J. H., Tracy, A. A., Lee, C., Donahoe, P. K. & Pober, B. R., Dec 2012, In : American Journal of Medical Genetics. Part A. 158A, 12, p. 3148-58 11 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  95. Published

    Progressive resistance training in head and neck cancer patients undergoing concomitant chemoradiotherapy

    Lonkvist, C. K., Vinther, A., Zerahn, B., Rosenbom, E., Deshmukh, Atul Shahaji, Hojman, P. & Gehl, Julie, Oct 2017, In : Laryngoscope Investigative Otolaryngology. 2, 5, p. 295-306 12 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  96. Published

    Comparison of global gene expression profiles of microdissected human foetal Leydig cells with their normal and hyperplastic adult equivalents

    Lottrup, G., Belling, Kirstine G, Leffers, H., Nielsen, J. E., Dalgaard, M. D., Juul, Anders, Skakkebæk, Niels Erik, Brunak, Søren & Meyts, E. R., 1 May 2017, In : Molecular Human Reproduction. 23, 5, p. 339-354 16 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  97. Published

    Distinct signatures of lung cancer types: aberrant mucin O-glycosylation and compromised immune response

    Lucchetta, M., da Piedade, I., Mounir, M., Vabistsevits, M., Terkelsen, T. & Papaleo, Elena, 2019, In : BMC Cancer. 19, 824.

    Research output: Contribution to journalJournal articleResearchpeer-review

  98. Published

    A new non-catalytic role for ubiquitin ligase RNF8 in unfolding higher-order chromatin structure

    Luijsterburg, M. S., Acs, K., Ackermann, L., Wiegant, W. W., Bekker-Jensen, Simon Holst, Larsen, D. H., Khanna, K. K., van Attikum, H., Mailand, Niels & Dantuma, N. P., 2012, In : E M B O Journal. 31, 11, p. 2511-27 17 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  99. Published

    53BP1 nuclear bodies form around DNA lesions generated by mitotic transmission of chromosomes under replication stress

    Lukas, Claudia, Savic, V., Bekker-Jensen, Simon Holst, Doil, C., Neumann, B., Pedersen, R. S., Grøfte, M., Chan, K. L., Hickson, Ian David, Bartek, J. & Lukas, Jiri, 1 Mar 2011, In : Nature Cell Biology. 13, 3, p. 243-53 11 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  100. Published

    Shielding broken DNA for a quick fix

    Lukas, Jiri & Lukas, Claudia, 8 Feb 2013, In : Science. 339, 6120, p. 652-653 2 p.

    Research output: Contribution to journalReviewResearchpeer-review

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