Simon Rasmussen

Simon Rasmussen

Professor

ORCID: 0000-0001-6323-9041

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  1. Published

    A draft genome sequence of the elusive giant squid, Architeuthis dux

    da Fonseca, R. R., Couto, A., Machado, A. M., Brejova, B., Albertin, C. B., Silva, F., Gardner, P., Baril, T., Hayward, A., Campos, A., Ribeiro, Â. M., Barrio-Hernandez, I., Hoving, H-J., Tafur-Jimenez, R., Chu, C., Frazão, B., Petersen, B., Peñaloza, F., Musacchia, F., Alexander, G. C. & 24 others, Osório, H., Winkelmann, I., Simakov, O., Rasmussen, Simon, Rahman, M. Z., Pisani, D., Vinther, J., Jarvis, E., KU, thw266, Strugnell, J. M., Castro, L. F. C., Fedrigo, O., Patricio, M., Li, Q., Rocha, S., Antunes, A., Wu, Y., Ma, B., Sanges, R., Vinar, T., Blagoev, B., Sicheritz-Pontén, Thomas, Nielsen, Rasmus & Gilbert, M Thomas P, 2020, In: GigaScience. 9, 1, 12 p., giz152.

    Research output: Contribution to journal › Journal article › Research › peer-review

  2. Identification of acquired antimicrobial resistance genes

    Zankari, E., Hasman, H., Cosentino, S., Vestergaard, M., Rasmussen, Simon, Lund, O., Aarestrup, F. M. & Larsen, M. V., 2012, In: Journal of Antimicrobial Chemotherapy. 67, 11, p. 2640-4 5 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  3. Published

    Ancient nuclear genomes enable repatriation of Indigenous human remains

    Wright, J. L., Wasef, S., Heupink, T. H., Westaway, M. C., Rasmussen, S., Pardoe, C., Fourmile, G. G., Young, M., Johnson, T., Slade, J., Kennedy, R., Winch, P., Pappin, M., Wales, T., Bates, W. ., Hamilton, S., Whyman, N., Van Holst Pellekaan, S., Mcallister, P. J., Taçon, P. S. C. & 8 others, Curnoe, D., Li, R., Millar, C., Subramanian, S., Willerslev, Eske, Malaspinas, A., Sikora, Martin & Lambert, D. M., 1 Dec 2018, In: Science Advances. 4, 12, 13 p., eaau5064.

    Research output: Contribution to journal › Journal article › Research › peer-review

  4. Published

    Genetic studies of abdominal MRI data identify genes regulating hepcidin as major determinants of liver iron concentration

    Wilman, H. R., Parisinos, C. A., Atabaki-Pasdar, N., Kelly, M., Thomas, E. L., Neubauer, S., Jennison, C., Ehrhardt, B., Baum, P., Schoelsch, C., Freijer, J., Grempler, R., Graefe-Mody, U., Hennige, A., Dings, C., Lehr, T., Scherer, N., Sihinecich, I., Pattou, F., Raverdi, V. & 31 others, Caiazzo, R., Torres, F., Verkindt, H., Mari, A., Tura, A., Giorgino, T., Bizzotto, Froguel, P., Brorsson, C., Brunak, Søren, De Masi, F., Pedersen, H., Banasik, Karina, Thomas, Cecilia Engel, Lundgaard, Agnete Troen, Nielsen, A., Mazzoni, G., Karaderi, Tugce, Rasmussen, Simon, Johansen, Joachim, Allesøe, R., Arumugam, Mani, Allin, K., Hansen, Torben, Hansen, T., Jonsson, Anna Elisabet, Pedersen, Oluf Borbye, Dutta, A., Vogt, J., drb459, drb459 & IMI-DIRECT consortium, I. C., 2019, In: Journal of Hepatology. 71, 3, p. 594-602 9 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  5. Published

    Lactobacillus acidophilus induces virus immune defence genes in murine dendritic cells by a Toll-like receptor-2-dependent mechanism

    Weiss, G. M., Rasmussen, Simon, Zeuthen, L., Nielsen, B. M. N., Jarmer, H. Ø., Jespersen, Lene & Frøkiær, Hanne, 2010, In: Immunology. 131, 2, p. 268-281 14 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  6. Published

    Bifidobacterium bifidum actively changes the gene expression profile induced by Lactobacillus acidophilus in murine dendritic cells

    Weiss, G. M., Rasmussen, Simon, Fink, L. N., Jarmer, H. Ø., Nielsen, B. M. N. & Frøkiær, Hanne, 2010, In: PLoS ONE. 5, 6, 10 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  7. Published

    Cross-generational bacterial strain transfer to an infant after fecal microbiota transplantation to a pregnant patient: a case report

    Wei, S., Jespersen, Marie Louise, Baunwall, S. M. D., Myers, P. N., Smith, E. M., Dahlerup, J. F., Rasmussen, Simon, Nielsen, H. B., Licht, T. R., Bahl, M. I. & Hvas, C. L., 2022, In: Microbiome. 10, 1, 14 p., 193.

    Research output: Contribution to journal › Journal article › Research › peer-review

  8. Published

    Mass spectrometry-based proteomics data from thousands of HeLa control samples

    Webel, Henry, Perez-Riverol, Y., Nielsen, A. B. & Rasmussen, Simon, 2024, In: Scientific Data. 11, 7 p., 112.

    Research output: Contribution to journal › Journal article › Research › peer-review

  9. Published

    Gut microbial changes of patients with psychotic and affective disorders: A systematic review

    Vindegaard, N., Speyer, H., Nordentoft, Merete, Rasmussen, Simon & Benros, Michael Eriksen, 2021, In: Schizophrenia Research. 234, p. 41-50 10 p.

    Research output: Contribution to journal › Review › Research › peer-review

  10. Published

    Whole-Exome Sequencing Implicates Neuronal Calcium Channel with Familial Atrial Fibrillation

    Vad, Oliver Tim Bundgaard, Yan, Y., Denti, F., Ahlberg, Gustav, Refsgaard, L., Bomholtz, Sofia Hammami, Santos, J. L., Rasmussen, Simon, Haunsø, Stig, Svendsen, Jesper Hastrup, Christophersen, I. E., Schmitt, Nicole, Olesen, Morten Steen Salling & Bentzen, Bo Hjorth, 2022, In: Frontiers in Genetics. 13, 8 p., 806429.

    Research output: Contribution to journal › Journal article › Research › peer-review

  11. Targeted metabolic engineering guided by computational analysis of single-nucleotide polymorphisms (SNPs)

    Udatha, D. B. R. K. G., Rasmussen, Simon, Sicheritz-Pontén, T. & Panagiotou, G., 2013, In: Methods in molecular biology (Clifton, N.J.). 985, p. 409-28 20 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  12. Published

    Hybridization capture using short PCR products enriches small genomes by Capturing Flanking Sequences (CapFlank)

    Tsangaras, K., Wales, N., Sicheritz-Pontén, T., Rasmussen, Simon, Michaux, J., Ishida, Y., Morand, S., Kampmann, Marie-Louise, Gilbert, M Thomas P & Greenwood, A. D., 2014, In: PLoS ONE. 9, 10, 10 p., e109101.

    Research output: Contribution to journal › Journal article › Research › peer-review

  13. Genome sequence of Talaromyces atroroseus, which produces red colorants for the food industry

    Thrane, U., Rasmussen, K. B., Petersen, Bent, Rasmussen, Simon, Sicheritz-Pontén, Thomas & Mortensen, U. H., 2017, In: Genome Announcements. 5, 9, 2 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  14. Published

    Sequencing and de novo assembly of 150 genomes from Denmark as a population reference

    Sørensen, L. M., Jensen, J. M., Petersen, B., Sibbesen, J. A., Liu, S., Villesen, P., Skov, L., Belling, K. G., Have, C. T., Izarzugaza, J. M. G., Grosjean, M., Bork-Jensen, J., Grove, J., Als, T. D., Huang, S., Chang, Y., Xu, R., Ye, W., Rao, J., Guo, X. & 39 others, Sun, J., Cao, H., Ye, C., van Beusekom, J., Espeseth, T., Flindt, E., Friborg, R. M., Halager, A. E., Le Hellard, S., Hultman, C. M., Lescai, F., Li, S., Lund, O., Løngren, P., Mailund, T., Matey-Hernandez, M. L., Mors, O., Pedersen, C. N. S., Sicheritz-Pontén, T., Sullivan, P., Syed, A., Westergaard, David, Yadav, R., Li, N., Xu, X., Hansen, Torben, Krogh, Anders, Bolund, L., Sørensen, Thorkild I.A., Pedersen, Oluf Borbye, Gupta, R., Rasmussen, Simon, Besenbacher, S., Børglum, A. D., Wang, J., Eiberg, Hans Rudolf Lytchoff, Kristiansen, Karsten, Brunak, Søren & Schierup, M. H., 2017, In: Nature. 548, 7665, p. 87-91 5 p.

    Research output: Contribution to journal › Letter › Research › peer-review

  15. Published

    Metagenomic species profiling using universal phylogenetic marker genes

    Sunagawa, S., Mende, D. R., Zeller, G., Izquierdo-Carrasco, F., Berger, S. A., Kultima, J. R., Coelho, L. P., Arumugam, M., Tap, J., Nielsen, H. B., Rasmussen, S., Brunak, S., Pedersen, O. B., Guarner, F., de Vos, W. M., Wang, J., Li, J., Doré, J., Ehrlich, S. D., Stamatakis, A. & 1 others, Bork, P., 2013, In: Nature Methods. 10, 12, p. 1196-1199 4 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  16. Published

    Genetic predisposition & evolutionary traces of pediatric cancer risk: a prospective 5-year population-based genome sequencing study of children with CNS tumors

    Stoltze, U. K., Foss-Skiftesvik, J., Hansen, Thomas van Overeem, Byrjalsen, A., Sehested, A., Scheie, David, Mikkelsen, T. S., Rasmussen, Simon, Bak, M., Okkels, H., Callesen, M. T., Skjøth-Rasmussen, J., Gerdes, Anne-Marie Axø, Schmiegelow, Kjeld, Mathiasen, R. & Wadt, Karin Anna Wallentin, 2023, In: Neuro-Oncology. 25, 4, p. 761-773

    Research output: Contribution to journal › Journal article › Research › peer-review

  17. Published

    The evolutionary impact of childhood cancer on the human gene pool

    Stoltze, U. K., Foss-Skiftesvik, J., Hansen, Thomas van Overeem, Rasmussen, Simon, Karczewski, K. J., Wadt, Karin Anna Wallentin & Schmiegelow, Kjeld, 2024, In: Nature Communications. 15, 15 p., 1881.

    Research output: Contribution to journal › Journal article › Research › peer-review

  18. Published

    Combinatorial batching of DNA for ultralow-cost detection of pathogenic variants

    Stoltze, U. K., Hagen, C. M., Hansen, Thomas van Overeem, Byrjalsen, A., Gerdes, Anne-Marie Axø, Yakimov, V., Rasmussen, Simon, Bækvad-Hansen, M., Hougaard, D. M., Schmiegelow, Kjeld, Hjalgrim, Henrik, Wadt, Karin Anna Wallentin & Bybjerg-Grauholm, J., 2023, In: Genome Medicine. 15, 12 p., 17.

    Research output: Contribution to journal › Journal article › Research › peer-review

  19. Complete genes may pass from food to human blood

    Spisák, S., Solymosi, N., Ittzés, P., Bodor, A., Kondor, D., Vattay, G., Barták, B. K., Sipos, F., Galamb, O., Tulassay, Z., Szállási, Z., Rasmussen, Simon, Sicheritz-Ponten, T., Brunak, Søren, Molnár, B. & Csabai, I., 2013, In: PloS one. 8, 7, p. e69805

    Research output: Contribution to journal › Journal article › Research › peer-review

  20. Published

    Analysis of 62 hybrid assembled human Y chromosomes exposes rapid structural changes and high rates of gene conversion

    Skov, L., Schierup, M. H., Danish Pan Genome Consortium, D. P. G. C., Sørensen, L. M., Petersen, Bent, Sibbesen, Jonas Andreas, Liu, S., Belling, K. G., Have, C. T., Bork-Jensen, J., Hansen, Torben, Krogh, Anders, Sørensen, Thorkild I.A., Pedersen, Oluf Borbye, Rasmussen, Simon, Kristiansen, Karsten & Brunak, Søren, 2017, In: PLOS Genetics. 13, 8, p. e1006834

    Research output: Contribution to journal › Journal article › Research › peer-review

  21. Published

    The population history of northeastern Siberia since the Pleistocene

    Sikora, M., Pitulko, V. V., Sousa, V. C., Allentoft, M. E., Vinner, L., Rasmussen, S., Margaryan, A., Damgaard, P. D. B., de la Fuente Castro, C., Renaud, G., Yang, M. A., Fu, Q., Dupanloup, I., Giampoudakis, K., Nogues, D. B., Rahbek, C., Kroonen, G., Peyrot, M., McColl, H., Vasilyev, S. V. & 27 others, Veselovskaya, E., Gerasimova, M., Pavlova, E. Y., Chasnyk, V. G., Nikolskiy, P. A., Gromov, A. V., Khartanovich, V. I., Moiseyev, V., Grebenyuk, P. S., Fedorchenko, A. Y., Lebedintsev, A. I., Slobodin, S. B., Malyarchuk, B. A., Martiniano, R., Meldgaard, Morten, Arppe, L., Palo, J. U., Sundell, T., Mannermaa, K., Putkonen, M., Alexandersen, V., Primeau, C., Baimukhanov, N., Malhi, R. S., Sjögren, K. G., Nielsen, Rasmus & Willerslev, Eske, 2019, In: Nature. 570, p. 182–188

    Research output: Contribution to journal › Journal article › Research › peer-review

  22. Published

    Ancient genomes show social and reproductive behavior of early Upper Paleolithic foragers

    Sikora, M., Seguin-Orlando, A., Sousa, V. C., Albrechtsen, A., Korneliussen, T. S., Ko, A., Rasmussen, S., Dupanloup, I., Nigst, P. R., Bosch, M. D., Renaud, G., Allentoft, M. E., Margaryan, A., Vasilyev, S. V., Veselovskaya, E. V., Borutskaya, S. B., Deviese, T., Comeskey, D., Higham, T., Manica, A. & 7 others, Foley, R., Meltzer, D. J., Nielsen, Rasmus, Excoffler, L., Lahr, M. M., Orlando, L. A. A. & Willerslev, Eske, 3 Nov 2017, In: Science. 358, 6363, p. 659-662 4 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  23. Published

    Deep integrative models for large-scale human genomics

    Sigurdsson, Arnór Ingi, Louloudis, Ioannis, Banasik, Karina, Westergaard, David, Winther, Ole, Lund, O., Ostrowski, Sisse Rye, Erikstrup, C., Pedersen, Ole Birger Vesterager, Nyegaard, Mette, Brunak, Søren, Vilhjálmsson, B. & Rasmussen, Simon, 2023, In: Nucleic Acids Symposium Series. 51, 12, 16 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  24. Transcriptome analysis of root-knot nematode (Meloidogyne incognita)-infected tomato (Solanum lycopersicum) roots reveals complex gene expression profiles and metabolic networks of both host and nematode during susceptible and resistance responses

    Shukla, N., Yadav, R., Kaur, P., Rasmussen, Simon, Goel, S., Agarwal, M., Jagannath, A., Gupta, R. & Kumar, A., 2018, In: Molecular Plant Pathology. 19, 3, p. 615-633 19 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  25. Published

    SCAI promotes error-free repair of DNA interstrand crosslinks via the Fanconi anemia pathway

    Schubert, Lisa, Hendriks, Ivo Alexander, Hertz, Emil Peter Thrane, Wu, Wei, Sellés Baiget, Selene, Hoffmann, Saskia, Bagge, Keerthana Stine Viswalingam, Gallina, I., Pentakota, S., Benedict, Bente, Johansen, Joachim, Apelt, K., Luijsterburg, M. S., Rasmussen, Simon, Lisby, Michael, Liu, Ying, Nielsen, Michael Lund, Mailand, Niels & Duxin, Julien, 2022, In: EMBO Reports. 23, 4, 20 p., e53639.

    Research output: Contribution to journal › Journal article › Research › peer-review

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ID: 204201681