The NNF Center for Protein Research

  1. 2019
  2. 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

  3. Published

    FoxK1 and FoxK2 in insulin regulation of cellular and mitochondrial metabolism

    Sakaguchi, M., Cai, W., Wang, C., Cederquist, C. T., Damasio, M., Homan, E. P., Batista, T., Ramirez, A. K., Gupta, M. K., Steger, M., Albrechtsen, Nicolai Jacob Wewer, Singh, S. K., Araki, E., Mann, M., Enerbäck, S. & Kahn, C. R., 5 Apr 2019, In : Nature Communications. 10, 1, 17 p., 1582.

    Research output: Contribution to journalJournal articleResearchpeer-review

  4. Published

    Molecular dynamics-guided discovery of an ago-allosteric modulator for GPR40/FFAR1

    Lückmann, Michael, Trauelsen, Mette, Bentsen, Marie Aare, Nissen, Tinne Amalie Damgaard, Martins, J., Fallah, Z., Nygaard, Mads Mørup, Papaleo, Elena, Lindorff-Larsen, Kresten, Schwartz, Thue W. & Frimurer, Thomas Michael, 2 Apr 2019, In : Proceedings of the National Academy of Sciences of the United States of America. 116, 14, p. 7123-7128

    Research output: Contribution to journalJournal articleResearchpeer-review

  5. Published

    Palaeoproteomic analysis of Early Pleistocene Gigantopithecus blacki

    Welker, Frido, Ramos Madrigal, Jazmin, Wang, W., Kuhlwilm, M., Montero, M. D. M., Demeter, Fabrice, Lalueza-Fox, C., Marques-Bonet, T., Olsen, Jesper Velgaard & Cappellini, Enrico, Mar 2019, In : American Journal of Physical Anthropology. 168, suppl. 68, p. 265-266

    Research output: Contribution to journalConference abstract in journalResearchpeer-review

  6. Published

    Acetylation of intrinsically disordered regions regulates phase separation

    Saito, M., Hess, D., Eglinger, J., Fritsch, A. W., Kreysing, M., Weinert, B. T., Choudhary, Chuna Ram & Matthias, P., Jan 2019, In : Nature Chemical Biology. 15, 1, p. 51-61

    Research output: Contribution to journalJournal articleResearchpeer-review

  7. Published

    53BP1 nuclear bodies enforce replication timing at under-replicated DNA to limit heritable DNA damage

    Spies, Julian, Lukas, Claudia, Somyajit, Kumar, Rask, M., Lukas, Jiri & Neelsen, K. J., 2019, In : Nature Cell Biology. 21, p. 487-497

    Research output: Contribution to journalJournal articleResearchpeer-review

  8. Published
  9. 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

  10. Published

    A Consensus Binding Motif for the PP4 Protein Phosphatase

    Ueki, Yumi, Kruse, Thomas, Weisser, Melanie, Sundell, G. N., Larsen, M. S. Y., Mendez, B. L., Jenkins, N. P., Garvanska, Dimitriya Hristoforova, Cressey, L., Zhang, G., Davey, N., Montoya, Guillermo, Ivarsson, Y., Kettenbach, A. N. & Nilsson, Jakob, 2019, In : Molecular Cell. 76, 6, p. 953-964.e6

    Research output: Contribution to journalJournal articleResearchpeer-review

  11. Published

    A Guide to Dictionary-Based Text Mining

    Cook, H. V. & Jensen, Lars Juhl, 2019, Bioinformatics and Drug Discovery. Larson, R. S. & Oprea, T. I. (eds.). 3 ed. Humana Press, Vol. 1939. p. 73-89 17 p. (Methods in Molecular Biology).

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

  12. Published

    A chromatin-based signalling mechanism directs the switch from mutagenic to error-free repair of DNA double strand breaks

    Bartke, T. & Groth, Anja, 2019, In : Molecular & Cellular Oncology. 6, 4, 3 p., 1605820.

    Research output: Contribution to journalJournal articleResearchpeer-review

  13. Published

    A generic deep convolutional neural network framework for prediction of receptor–ligand interactions - NetPhosPan: application to kinase phosphorylation prediction

    Fenoy, E., Izarzugaza, J. M. G., Jurtz, V., Brunak, Søren & Nielsen, M., 2019, In : Bioinformatics. 35, 7, p. 1098-1107

    Research output: Contribution to journalJournal articleResearchpeer-review

  14. Published

    A large size-selective DNA nanopore with sensing applications

    Thomsen, R. P., Malle, Mette Galsgaard, Okholm, A. H., Krishnan, S., Bohr, Søren Schmidt-Rasmussen, Sørensen, R. S., Ries, O., Vogel, S., Simmel, F. C., Hatzakis, Nikos & Kjems, J., 2019, In : Nature Communications. 10, 1

    Research output: Contribution to journalJournal articleResearchpeer-review

  15. Published

    A large-cohort, longitudinal study determines pre-cancer disease routes across different cancer types

    Hjaltelin, Jessica Xin, Helleberg, M., Jensen, A. B., Brunak, Søren & Lundgren, Jens, 2019, In : Cancer Research. 79, 4, p. 864-872

    Research output: Contribution to journalJournal articleResearchpeer-review

  16. Published

    A quantitative Streptococcus pyogenes - human protein - protein interaction map reveals localization of opsonizing antibodies

    Happonen, L., Hauri, S., Svensson Birkedal, G., Karlsson, C., de Neergaard, T., Khakzad, H., Nordenfelt, P., Wikström, M., Wisniewska, M., Björck, L., Malmström, L. & Malmström, J., 2019, In : Nature Communications. 10, 15 p., 2727.

    Research output: Contribution to journalJournal articleResearchpeer-review

  17. Published

    A spatially resolved proteomic atlas of human skin and its associated immune system

    Dyring-Andersen, Beatrice, Coscia, Fabian, Santos, A., Løvendorf, M. B., Sørensen, L. B. P., Niu, Lili, Andersen, J. L., Clark, R., Skov, L., Teunissen, M. B. & Mann, Matthias, 2019, In : Journal of Investigative Dermatology. 139, 9, suppl., p. S259 1 p.

    Research output: Contribution to journalConference abstract in journalResearch

  18. Published

    A spatially resolved proteomic atlas of psoriatic skin

    Dyring-Andersen, Beatrice, Lovendorf, M. B., Santos, A., Coscia, Fabian, Sørensen, L. B. P., Niu, Lili, Andersen, J. L., Teunissen, M. B., Skov, L. & Mann, Matthias, 2019, In : Journal of Investigative Dermatology. 139, 9, suppl., p. S260 1 p.

    Research output: Contribution to journalConference abstract in journalResearch

  19. Published

    Acetyltransferases Gcn5 and PCAF regulate B cell development

    Beck, C., Daniel, J. & Oksenych, V., 2019, In : Scandinavian Journal of Immunology. 90, 6

    Research output: Contribution to journalConference abstract in journalResearch

  20. 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

  21. Published

    Alternative Translation Initiation Generates a Functionally Distinct Isoform of the Stress-Activated Protein Kinase MK2

    Trulley, P., Snieckute, Goda, Bekker-Jensen, D., Menon, M. B., Freund, R., Kotlyarov, A., Olsen, Jesper Velgaard, Diaz-Muñoz, M. D., Turner, M., Bekker-Jensen, Simon Holst, Gaestel, M. & Tiedje, C., 2019, In : Cell Reports. 27, 10, p. 2859-2870.e6 19 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  22. Published

    An advanced strategy for comprehensive profiling of ADP-ribosylation sites using mass spectrometry-based proteomics

    Hendriks, Ivo Alexander, Buch-Larsen, Sara Charlotte & Nielsen, Michael Lund, 2019, In : Molecular and Cellular Proteomics. 18, 5, p. 1010-1026

    Research output: Contribution to journalJournal articleResearchpeer-review

  23. Published

    An unorthodox partnership in DNA repair pathway choice

    Typas, Dimitris & Mailand, Niels, 2019, In : EMBO Reports. 20, 11, e49105.

    Research output: Contribution to journalEditorialResearchpeer-review

  24. Published

    Analysis and Interpretation of Protein Post-Translational Modification Site Stoichiometry

    Prus, Gabriela Zofia, Hoegl, A., Weinert, B. T. & Choudhary, Chuna Ram, 2019, In : Trends in Biochemical Sciences. 44, 11, p. 943-960

    Research output: Contribution to journalReviewResearchpeer-review

  25. Published

    Analysis of Predicted Host-Parasite Interactomes Reveals Commonalities and Specificities Related to Parasitic Lifestyle and Tissues Tropism

    Cuesta-Astroz, Y., Santos Delgado, Alberto, Oliveira, G. & Jensen, Lars Juhl, 2019, In : Frontiers in Immunology. 10, 17 p., 212.

    Research output: Contribution to journalJournal articleResearchpeer-review

  26. Published

    Analysis of human acetylation stoichiometry defines mechanistic constraints on protein regulation

    Hansen, B. K., Gupta, R., Baldus, L., Lyon, D., Narita, Takeo, Lammers, M., Choudhary, Chuna Ram & Weinert, B. T., 2019, In : Nature Communications. 10, 11 p., 1055.

    Research output: Contribution to journalJournal articleResearchpeer-review

  27. Published

    Anti-HER2 single domain antibody-conjugated dendrimers for targeted delivery of truncated-Bid transgene to breast cancer cells

    Sofla, F. J. I., Rahbarizadeh, F., Ahmadvand, D., Nomani, A. & Vernet, E., 2019, In : Journal of Bioactive and Compatible Polymers. 34, 1, p. 39-57

    Research output: Contribution to journalJournal articleResearchpeer-review

  28. Published

    Bile acids drive colonic secretion of glucagon-like-peptide 1 and peptide-YY in rodents

    Christiansen, Charlotte Bayer, Trammell, Sam, Albrechtsen, Nicolai Jacob Wewer, Schoonjans, K., Albrechtsen, Reidar, Gillum, Matthew Paul, Kuhre, Rune Ehrenreich & Holst, Jens Juul, 2019, In : American Journal of Physiology: Gastrointestinal and Liver Physiology. 316, 5, p. G574-G584 11 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  29. Published

    BioReader: a text mining tool for performing classification of biomedical literature

    Simon, C., Davidsen, K., Hansen, C., Seymour, E., Barnkob, M. B. & Olsen, L. R., 2019, In : BMC Bioinformatics. 19, Suppl. 13, 6 p., 57.

    Research output: Contribution to journalConference articleResearchpeer-review

  30. Published

    Bone Status in Obese, Non-diabetic, Antipsychotic-Treated Patients, and Effects of the Glucagon-Like Peptide-1 Receptor Agonist Exenatide on Bone Turnover Markers and Bone Mineral Density

    Eriksson, Robert, Broberg, B. V., Ishoy, P. L., Bak, N., Andersen, U. B., Jorgensen, N. R., Knop, Filip Krag & Ebdrup, Bjørn, 2019, In : Frontiers in Psychiatry. 9, 7 p., 781.

    Research output: Contribution to journalJournal articleResearchpeer-review

  31. Published

    Breast milk alkylglycerols sustain beige adipocytes through adipose tissue macrophages

    Yu, H., Dilbaz, S., Coßmann, J., Hoang, A. C., Diedrich, V., Herwig, A., Harauma, A., Hoshi, Y., Moriguchi, T., Landgraf, K., Körner, A., Lucas, C., Brodesser, S., Balogh, L., Thuróczy, J., Karemore, Gopal, Kuefner, M. S., Park, E. A., Rapp, C., Travers, J. B. & Röszer, T., 2019, In : The Journal of Clinical Investigation. 129, 6, p. 2485-2499

    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

    Characterization of Familial and Sporadic Migraine

    Ravn, J., Chalmer, M. A., Oehrstroem, E. L., Kogelman, L. J. A. & Hansen, Thomas Folkmann, 2019, In : Headache. 59, 10, p. 1802-1807 6 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  34. Published

    Citrullination of HP1γ chromodomain affects association with chromatin

    Wiese, M., Bannister, A. J., Basu, S., Boucher, W., Wohlfahrt, K., Christophorou, M. A., Nielsen, Michael Lund, Klenerman, D., Laue, E. D. & Kouzarides, T., 2019, In : Epigenetics & Chromatin. 12, 17 p., 21.

    Research output: Contribution to journalJournal articleResearchpeer-review

  35. Published

    Clinical association to FKBP5 rs1360780 in patients with depression

    Dam, Henrik, Buch, J. O. D., Nielsen, Annelaura Bach, Weikop, P., Werge, Thomas & Jørgensen, M. B., 2019, In : Psychiatric Genetics. 29, 6, p. 220-225 6 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  36. Published

    CoCoScore: Context-aware co-occurrence scoring for text mining applications using distant supervision

    Junge, A. & Jensen, Lars Juhl, 2019, In : Bioinformatics. 8 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  37. Published

    Combined Ensemble Docking and Machine Learning in Identification of Therapeutic Agents with Potential Inhibitory Effect on Human CES1

    Briand, E., Thomsen, Ragnar, Linnet, Kristian, Rasmussen, H. B., Brunak, Søren & Taboureau, Olivier Thierry, 2019, In : Molecules. 24, 15, 17 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  38. Published

    Combined GLP-1, Oxyntomodulin, and Peptide YY Improves Body Weight and Glycemia in Obesity and Prediabetes/Type 2 Diabetes: A Randomized Single-Blinded Placebo Controlled Study

    Behary, P., Tharakan, G., Alexiadou, K., Johnson, N., Albrechtsen, Nicolai Jacob Wewer, Kenkre, J., Cuenco, J., Hope, D., Anyiam, O., Choudhury, S., Alessimii, H., Poddar, A., Minnion, J., Doyle, C., Frost, G., Le Roux, C., Purkayastha, S., Moorthy, K., Dhillo, W., Holst, Jens Juul, Ahmed, A. R., Prevost, A. T., Bloom, S. R. & Tan, T. M., 2019, In : Diabetes Care. 42, 7, 8 p., dc190449.

    Research output: Contribution to journalJournal articleResearchpeer-review

  39. Published

    Combing the Hairball: Improving Visualization of miRNA-Target Interaction Networks

    Russo, Francesco, Hjaltelin, Jessica Xin, Romero Herrera, Jose Alejandro & Brunak, Søren, 2019, MicroRNA Target Identification: Methods and Protocols. Laganà, A. (ed.). Humana Press, p. 279-289 11 p. (Methods in Molecular Biology, Vol. 1970).

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

  40. Published

    Comorbidity landscape of the Danish patient population affected by chromosome abnormalities

    Jørgensen, Isabella Friis, Russo, Francesco, Jensen, A. B., Westergaard, David, zmw894, zmw894, Hjaltelin, Jessica Xin, Brunak, Søren & Belling, Kirstine G, 2019, In : Genetics In Medicine. 21, 11 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  41. 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

  42. Published

    Comparison of quantitative trait loci methods: Total expression and allelic imbalance method in brain RNA-seq

    Gådin, J. R., Buil, A., Colantuoni, C., Jaffe, A. E., Nielsen, J., Shin, J., Hyde, T. M., Kleinman, J. E., Plath, N., Eriksson, P., Brunak, Søren, Didriksen, M., Weinberger, D. R., Folkersen, L. & BrainSeq Consortium, B. C., 2019, In : PLoS ONE. 14, 6, 16 p., e0217765.

    Research output: Contribution to journalJournal articleResearchpeer-review

  43. Published

    Contaminating viral sequences in high-throughput sequencing viromics: a linkage study of 700 sequencing libraries

    Asplund, M., Kjartansdóttir, K. R., Mollerup, S., Vinner, Lasse, Fridholm, H., Romero Herrera, Jose Alejandro, Friis-Nielsen, J., Hansen, T. A., Jensen, R. H., Nielsen, Ida Broman, Richter, S. R., Rey de la Iglesia, Alba, Matey-Hernandez, M. L., Alquezar-Planas, D. E., Olsen, Pernille Vibeke Selmer, Sicheritz-Pontén, Thomas, Willerslev, Eske, Lund, O., Brunak, Søren, Mourier, T., Nielsen, L. P., Izarzugaza, J. M. G. & Hansen, Anders Johannes, 2019, In : Clinical Microbiology and Infection. 25, 10, p. 1277-1285

    Research output: Contribution to journalJournal articleResearchpeer-review

  44. Published

    Cyprus Women's Health Research (COHERE) initiative: determining the relative burden of women's health conditions and related co-morbidities in an Eastern Mediterranean population

    Hocaoglu, M. B., Gurkas, S., Karaderi, Tugce, Taneri, B., Erguler, K., Barin, B., Bilgin, E. M., Eralp, G., Allison, M., Findikli, N., Boynukalin, K., Bahceci, M., Naci, H., Vincent, K., Missmer, S. A., Becker, C. M., Zondervan, K. T. & Rahmioglu, N., 2019, In : BMC Women's Health. 19, 7 p., 50.

    Research output: Contribution to journalJournal articleResearchpeer-review

  45. Published

    Cytoscape stringApp: Network analysis and visualization of proteomics data

    Doncheva, Nadezhda Tsankova, Morris, J., Gorodkin, Jan & Jensen, Lars Juhl, 2019, In : Journal of Proteome Research. 18, 2, p. 623-632

    Research output: Contribution to journalJournal articleResearchpeer-review

  46. Published

    Design, implementation, and operation of a rapid, robust named entity recognition web service

    Pletscher-Frankild, S. & Jensen, Lars Juhl, 2019, In : Journal of Cheminformatics. 11, 6 p., 19.

    Research output: Contribution to journalJournal articleResearchpeer-review

  47. Published

    Development, use, application of novel TIMS-Tof system

    Mann, Matthias, 2019, In : Molecular & Cellular Proteomics. 18, 8, p. S20 1 p.

    Research output: Contribution to journalConference abstract in journalResearch

  48. Published

    Direct observation of Thermomyces lanuginosus lipase diffusional states by Single Particle Tracking and their remodeling by mutations and inhibition

    Bohr, Søren Schmidt-Rasmussen, Lund, P. M., Kallenbach, A. S., Pinholt, H., Thomsen, J., Iversen, L., Svendsen, A., Christensen, S. M. & Hatzakis, Nikos, 2019, In : Scientific Reports. 9, 11 p., 16169.

    Research output: Contribution to journalJournal articleResearchpeer-review

  49. 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

  50. 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

  51. 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

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