Simon Rasmussen

Simon Rasmussen

Associate professor, group leader, Professor

ORCID: 0000-0001-6323-9041

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  1. Published

    100 ancient genomes show repeated population turnovers in Neolithic Denmark

    Allentoft, M. E., Sikora, M., Fischer, A., Sjögren, K-G., Ingason, A., Macleod, R., Rosengren, A., Schulz Paulsson, B., Jørkov, M. L. S., Novosolov, M., Stenderup, J., Price, T. D., Mortensen, M. F., Nielsen, A. B., Hede, M. U., Sørensen, L., Nielsen, P. O., Rasmussen, P., Jensen, T. Z. T., Refoyo-Martínez, A. & 48 others, Irving-Pease, Evan, Barrie, William, Pearson, A., Sousa da Mota, B., Demeter, Fabrice, Henriksen, Rasmus Henrik Amund, Vimala, Tharsika, McColl, Hugh, Vaughn, Andrew Howland, Vinner, Lasse, Renaud, Gabriel, Stern, A., Johannsen, N. N., Ramsøe, Abigail Daisy, Schork, A. J., Ruter, Anthony Henry, Gotfredsen, Anne Birgitte, Nielsen, B. H., Petersen, Erik Brinch, Kannegaard, E., Hansen, J., Pedersen, K. B., Pedersen, L., Klassen, L., Meldgaard, Morten, Johansen, M., Uldum, O. C., Lotz, P., Lysdahl, P., Bangsgaard, Pernille, Petersen, P. V., Maring, R., Iversen, Rune, Wåhlin, S., Sørensen, S. A., Andersen, S. H., Jørgensen, T., Lynnerup, Niels, Lawson, D. J., Rasmussen, Simon, Korneliussen, Thorfinn Sand, Kjær, Kurt H., Durbin, R., Nielsen, Rasmus, Delaneau, O., Werge, Thomas, Kristiansen, Kristian & Willerslev, Eske, 2024, In: Nature. 625, 7994, p. 329-337 9 p.

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

  2. Published

    137 ancient human genomes from across the Eurasian steppes

    Damgaard, P. D. B., Marchi, N., Rasmussen, S., Peyrot, M., Renaud, G., Korneliussen, T. S., Moreno-Mayar, J. V., Pedersen, M. W., Goldberg, A., Usmanova, E., Baimukhanov, N., Loman, V., Hedeager, L., Pedersen, A. G., Nielsen, K., Afanasievl, G., Akmatov, K., Aldashev, A., Alpaslan, A., Baimbetov, G. & 55 others, Bazaliiskii, V. I., Beisenov, A., Boldbaatar, B., Boldgiv, B., Dorzhu, C., Ellingvag, S., Erdenebaatar, D., Dajani, R., Dmitriev, E., Evdokimov, V., Frei, K. M., Gromov, A., Goryachev, A., Hakonarson, H., Hegay, T., Khachatryan, Z., Khaskhanov, R., Kitov', E., Kolbina, A., Kubatbek, T., Kukushkin, A., Kukushkin, I., Lau, N., Margaryan, Ashot, Merkyte, Inga, Mertz, I. V., Mertz, V. K., Mijiddorj, E., Moiyesev, V., Mukhtarova, G., Nurmukhanbetov, B., Orozbekova, Z., Panyushkina, I., Pieta, K., Smrčka, V., Shevnina, I., Logvin, A., Sjögren, K., Štolcová, T., Tashbaeva, K., Tkachev, A., Tulegenov, T., Voyakin, D., Yepiskoposyan, L., Undrakhbold, S., Varfolomeev, V., Weber, A., Kradin, N., Allentoft, Morten Erik, Orlando, L. A. A., Nielsen, Rasmus, Sikora, Martin, Heyer, E., Kristiansen, K. & Willerslev, Eske, 2018, In: Nature. 557, 7705, p. 369-374 6 p.

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

  3. 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

  4. 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

  5. Published

    Streptococcus pseudopneumoniae: Use of whole-genome sequences to validate species identification methods

    Jensen, C. S., Iversen, K. H., Dargis, R., Shewmaker, P., Rasmussen, Simon, Christensen, J. J. & Nielsen, X. C., 2021, In: Journal of Clinical Microbiology. 59, 2, 11 p., e02503-20.

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

  6. Published

    A 5700 year-old human genome and oral microbiome from chewed birch pitch

    Jensen, T. Z. T., Niemann, J., Iversen, K. H., Fotakis, A. K., Gopalakrishnan, S., Vågene, Å. J., Pedersen, M. W., Sinding, M-H. S., Ellegaard, M. R., Allentoft, M. E., Lanigan, L. T., Taurozzi, A. J., Nielsen, S. H., Dee, M. W., Mortensen, M. N., Christensen, M. C., Sørensen, S. A., Collins, M. J., Gilbert, M. T. P., Sikora, M. & 2 others, Rasmussen, Simon & Schroeder, Hannes, 2019, In: Nature Communications. 10, 10 p., 5520.

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

  7. 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

  8. Published

    A genomic history of aboriginal Australia

    Malaspinas, A. S., Westaway, M. C., Muller, C. E., Sousa, V. C., Lao, O., Alves, I., Bergström, A., Athanasiadis, G., Cheng, J. Y., Crawford, J. E., Heupink, T. H., Macholdt, E., Peischl, S., Rasmussen, S., Schiffels, S., Subramanian, S., Wright, J. L., Albrechtsen, A., Barbieri, C., Dupanloup, I. & 55 others, Eriksson, A., Margaryan, Ashot, Moltke, Ida, Pugach, I., Korneliussen, Thorfinn Sand, Levkivskyi, I. P., Moreno Mayar, J. Víctor, Ni, S., Racimo, F., Sikora, Martin, Xue, Y., Aghakhanian, F. A., Brucato, N., Brunak, Søren, Campos, P., Clark, W., Ellingvåg, S., Fourmile, G., Gerbault, P., Injie, D., Koki, G., Leavesley, M., Logan, B., Lynch, A., Matisoo-Smith, E. A., McAllister, P. J., Mentzer, A. J., Metspalu, M., Migliano, A. B., Murgha, L., Phipps, M. E., Pomat, W., Reynolds, D., Ricaut, F., Siba, P., Thomas, M. G., Wales, T., Wall, C. M., Oppenheimer, S. J., Tyler-Smith, C., Durbin, R., Dortch, J., Manica, A., Schierup, M. H., Foley, R. A., Lahr, M. M., Bowern, C., Wall, J. D., Mailund, T., Stoneking, M., Nielsen, Rasmus, Sandhu, M. S., Excoffier, L., Lambert, D. M. & Willerslev, Eske, 2016, In: Nature. 538, 7624, p. 207-214 8 p.

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

  9. Published

    A large-scale investigation into the role of classical HLA loci in multiple types of severe infections, with a focus on overlaps with autoimmune and mental disorders

    Nudel, R., Allesøe, R. L., Thompson, W. K., Werge, Thomas, Rasmussen, Simon & Benros, Michael Eriksen, 2021, In: Journal of Translational Medicine. 19, 230.

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

  10. Published

    A selective sweep on a deleterious mutation in CPT1A in Arctic populations

    Clemente, F. J., Cardona, A., Inchly, C. E., Peters, B. M., Jacobs, G., Pagani, L., Lawson, D. J., Añtao, T., Vicente, M., Mitt, M., DiGiorgio, M., Faltyskova, Z., Xue, Y., Ayub, Q., Szpak, M., Mägi, R., Eriksson, A., Manica, A., Raghavan, M., Rasmussen, M. & 10 others, Rasmussen, Simon, Willerslev, Eske, Vidal-Puig, A., Tyler-Smith, C., Willems, R., Nielsen, R., Metspalu, M., Malyarchuk, B., Derenko, M. & Kivisild, T., 2014, In: American Journal of Human Genetics. 95, 5, p. 584-589 6 p.

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

  11. Published

    Acknowledging Lack of Inclusion in Genetic Analyses-Reply

    Benros, Michael Eriksen, Allesøe, R. L. & Rasmussen, Simon, 2023, In: JAMA Psychiatry. 80, 6, p. 647-648

    Research output: Contribution to journal › Comment/debate › Research

  12. Alpha proteobacterial ancestry of the [Fe-Fe]-hydrogenases in anaerobic eukaryotes

    Degli Esposti, M., Cortez, D., Lozano, L., Rasmussen, Simon, Nielsen, H. B. & Martinez Romero, E., 30 Jul 2016, In: Biology Direct. 11, p. 34

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

  13. Published

    An Aboriginal Australian genome reveals separate human dispersals into Asia

    Rasmussen, M., Guo, X., Wang, Y., Lohmueller, K. E., Rasmussen, S., Albrechtsen, A., Skotte, L., Lindgreen, S., Metspalu, M., Jombart, T., Kivisild, T., Zhai, W., Eriksson, A., Manica, A., Orlando, L., De La Vega, F. M., Tridico, S., Metspalu, E., Nielsen, K., Avila Arcos, M. D. C. & 38 others, Moreno Mayar, J. Víctor, Muller, C., Dortch, J., Gilbert, M Thomas P, Lund, O., Wesolowska, A., Karmin, M., Weinert, L. A., Wang, B., Li, J., Tai, S., Xiao, F., Hanihara, T., van Driem, G., Jha, A. R., Ricaut, F., de Knijff, P., Migliano, A. B., Gallego Romero, I., Kristiansen, Karsten, Lambert, D. M., Brunak, Søren, Forster, P., Brinkmann, B., Nehlich, O., Bunce, M., Richards, M., Gupta, R., Bustamante, C. D., Krogh, Anders, Foley, R. A., Lahr, M. M., Balloux, F., Sicheritz-Pontén, T., Villems, R., Nielsen, Rasmus, Wang, J. & Willerslev, Eske, 2011, In: Science. 334, 6052, p. 94-98 5 p.

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

  14. Published

    An immunogenetic investigation of 30 autoimmune and autoinflammatory diseases and their links to psychiatric disorders in a nationwide sample

    Nudel, R., Allesøe, R. L., Werge, Thomas, Thompson, W. K., Rasmussen, Simon & Benros, Michael Eriksen, 2023, In: Immunology. 168, 4, p. 622-639

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

  15. 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

  16. 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

  17. Published

    Ancient hepatitis B viruses from the Bronze Age to the Medieval period

    Mühlemann, B., Jones, T. C., Damgaard, P. D. B., Allentoft, M. E., Shevnina, I., Logvin, A., Usmanova, E., Panyushkina, I. P., Boldgiv, B., Bazartseren, T., Tashbaeva, K., Merz, V., Lau, N., Smrcka, V., Voyakin, D., Kitov, E., Epimakhov, A., Pokutta, D., Vicze, M., Price, T. D. & 14 others, Moiseyev, V., Hansen, Anders Johannes, Orlando, L. A. A., Rasmussen, Simon, Sikora, Martin, Vinner, Lasse, Osterhaus, A. D. M. E., Smith, D. J., Glebe, D., Fouchier, R. A. M., Drosten, C., Sjögren, K., Kristiansen, K. & Willerslev, Eske, 2018, In: Nature. 557, 7705, p. 418-423 6 p.

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

  18. 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

  19. Published

    Ancient pathogen DNA in human teeth and petrous bones

    Margaryan, Ashot, Hansen, H., Rasmussen, Simon, Sikora, Martin, Moiseyev, V., Khoklov, A., Epimakhov, A., Yepiskoposyan, L., Kriiska, A., Varul, L., Saag, L., Lynnerup, Niels, Willerslev, Eske & Allentoft, Morten Erik, 2018, In: Ecology and Evolution. 8, 6, p. 3534-3542 9 p.

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

  20. Published

    Assembly and analysis of 100 full MHC haplotypes from the Danish population

    Jensen, J. M., Villesen, P., Friborg, R. M., Mailund, T., Besenbacher, S., Sørensen, L. M., Petersen, B., Sibbesen, J. A., Liu, S., 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. & 39 others, Ye, W., Rao, J., Guo, X., Sun, J., Cao, H., Ye, C., Beusekom, J. V., Espeseth, T., Flindt, E., Halager, A. E., Hellard, S. L., Hultman, C. M., Lescai, F., Li, S., Lund, O., Løngren, P., Matey-Hernandez, M. L., Mors, O., Pedersen, C. N. S., Sicheritz-Pontén, T., Sullivan, P., Syed, A., Westergaard, D., Yadav, R., Li, N., Xu, X., Hansen, Torben, Bolund, L., Krogh, Anders, Sørensen, Thorkild I.A., Pedersen, Oluf Borbye, Gupta, R., Rasmussen, Simon, Børglum, A. D., Wang, J., Eiberg, Hans Rudolf Lytchoff, Kristiansen, Karsten, Brunak, Søren & Schierup, M. H., Sep 2017, In: Genome Research. 27, 9, p. 1597-1607 11 p.

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

  21. Published

    Bacterial natural transformation by highly fragmented and damaged DNA

    Overballe-Petersen, S., Harms, K., Orlando, L. A. A., Moreno Mayar, J. Víctor, Rasmussen, Simon, Dahl, Tais Wittchen, Rosing, Minik Thorleif, Poole, A. M., Sicheritz-Ponten, T., Brunak, S., Inselmann, S., de Vries, J., Wackernagel, W., Pybus, O. G., Nielsen, Rasmus, Johnsen, P. J., Nielsen, K. M. & Willerslev, Eske, 3 Dec 2013, In: Proceedings of the National Academy of Sciences of the United States of America. 110, 49, p. 19860–19865 6 p.

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

  22. Benchmarking of methods for genomic taxonomy

    Larsen, M. V., Cosentino, S., Lukjancenko, O., Saputra, D., Rasmussen, Simon, Hasman, H., Sicheritz-Pontén, T., Aarestrup, F. M., Ussery, D. W. & Lund, O., 2014, In: Journal of Clinical Microbiology. 52, 5, p. 1529-39 11 p.

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

  23. Published

    Binning microbial genomes using deep learning

    Nissen, J. N., Sønderby, C. K., Armenteros, J. J. A., Grønbech, Christopher Heje, Nielsen, H. B., Petersen, T. N., Winther, Ole & Rasmussen, Simon, 2018, (bioRxiv).

    Research output: Working paper › Preprint › Research

  24. Published

    Biosynthesis of bioactive diterpenoids in the medicinal plant Vitex agnus-castus

    Heskes, A., Sundram, T. C. M., Boughton, B. A., Bjerg Jensen, N., Hansen, N. L., Crocoll, C., Cozzi, F., Rasmussen, Simon, Hamberger, B., Hamberger, B. R., Stærk, Dan, Møller, Birger Lindberg & Pateraki, Irini, 2018, In: Plant Journal. 93, p. 943-958 16 p.

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

  25. Published

    Centenarians have a diverse gut virome with the potential to modulate metabolism and promote healthy lifespan

    Johansen, Joachim, Atarashi, K., Arai, Y., Hirose, N., Sørensen, Søren Johannes, Vatanen, T., Knip, M., Honda, K., Xavier, R. J., Rasmussen, Simon & Plichta, D. R., 2023, In: Nature Microbiology. 8, p. 1064-1078 18 p.

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

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ID: 204201681