Simon Rasmussen

Simon Rasmussen

Associate professor, group leader, Professor


  1. Published

    Rare truncating variants in the sarcomeric protein titin associate with familial and early-onset atrial fibrillation

    Ahlberg, G., Refsgaard, L., Lundegaard, Pia Rengtved, Andreasen, Laura Korsholm, Ranthe, M. F., Linscheid, N., Nielsen, J. B., Melbye, M., Haunsø, Stig, Sajadieh, Ahmad, Camp, L., Olesen, Søren-Peter, Rasmussen, Simon, Lundby, Alicia, Ellinor, P. T., Holst, A. G., Svendsen, Jesper Hastrup & Olesen, Morten Steen Salling, 2018, In: Nature Communications. 9, 1, 11 p., 4316.

    Research output: Contribution to journalJournal articleResearchpeer-review

  2. Published

    Population Genomics of Stone Age Eurasia

    Allentoft, M. E., Sikora, M., Refoyo-Martínez, A., Irving-Pease, E. K., Fischer, A., Barrie, W., Ingason, A., Stenderup, J., Sjögren, K-G., Pearson, A., Mota, B., Paulsson, B. S., Halgren, A., Macleod, R., Schjellerup Jørkov, M. L., Demeter, F., Novosolov, M., Sørensen, L., Nielsen, P-O., Henriksen, R. H. A. & 143 others, Vimala, Tharsika, McColl, Hugh, Margaryan, Ashot, Ilardo, M., Vaughn, A., Mortensen, M. F., Nielsen, A. B., Hede, M. U., Rasmussen, P., Vinner, Lasse, Renaud, Gabriel, Stern, A., Jensen, Theis Zetner Trolle, Johannsen, N. N., Scorrano, Gabriele, Schroeder, Hannes, Lysdahl, P., Ramsøe, Abigail Daisy, Skorobogatov, A., Schork, A. J., Rosengren, A., Ruter, Anthony Henry, Outram, A., Timoshenko, A. A., Buzhilova, A., Coppa, A., Zubova, A., Silva, A. M., Hansen, Anders Johannes, Gromov, A., Logvin, A., Gotfredsen, Anne Birgitte, Nielsen, B. H., González-Rabanal, B., Lalueza-Fox, C., McKenzie, C. J., Gaunitz, Charleen, Blasco, C., Liesau, C., Martinez-Labarga, C., Pozdnyakov, D. V., Cuenca-Solana, D., Lordkipanidze, D. O., En’shin, D., Salazar-García, D. C., Price, T. D., Borić, D., Kostyleva, E., Veselovskaya, E. V., Usmanova, E. R., Cappellini, Enrico, Petersen, Erik Brinch, Kannegaard, E., Radina, F., Yediay, Fulya Eylem, Duday, H., Gutiérrez-Zugasti, I., Potekhina, I., Shevnina, I., Altinkaya, Isin, Guilaine, J., Hansen, J., Tortosa, J. E. A., Zilhão, J., Vega, J., Pedersen, K. B., Tunia, K., Zhao, Lei, Mylnikova, L. N., Larsson, L., Metz, L., Yeppiskoposyan, L., Pedersen, L., Sarti, L., Orlando, L., Slimak, L., Klassen, L., Blank, M., González-Morales, M., Silvestrini, M., Vretemark, M., Nesterova, M. S., Rykun, M., Rolfo, M. F., Szmyt, M., Przybyła, M., Calattini, M., Sablin, M., Dobisíková, M., Meldgaard, Morten, Johansen, M., Berezina, N., Card, N., Saveliev, N. A., Poshekhonova, O., Rickards, O., Lozovskaya, O. V., Uldum, O. C., Aurino, P., Kosintsev, P., Courtaud, P., Ríos, P., Mortensen, P., Lotz, P., Persson, P. Å., Bangsgaard, Pernille, Damgaard, P. D. B., Petersen, P. V., Martinez, P. P., Włodarczak, P., Smolyaninov, R. V., Maring, R., Menduiña, R., Badalyan, R., Iversen, Rune, Turin, R., Vasilyiev, S., Wåhlin, S., Borutskaya, S., Skochina, S., Sørensen, S. A., Andersen, S. H., Jørgensen, T., Serikov, Y. B., Molodin, V. I., Smrcka, V., Merz, V., Appadurai, V., Moiseyev, V., Magnusson, Y., Kjær, Kurt H., Lynnerup, Niels, Lawson, D. J., Sudmant, P. H., Rasmussen, Simon, Korneliussen, Thorfinn Sand, Durbin, R., Nielsen, R., Delaneau, O., Werge, Thomas, Racimo, Fernando, Kristiansen, K. & Willerslev, Eske, 2022, p. 1-71, (bioRxiv).

    Research output: Working paperPreprintResearch

  3. 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 journalJournal articleResearchpeer-review

  4. Published

    Population genomics of post-glacial western Eurasia

    Allentoft, M. E., Sikora, M., Refoyo-Martínez, A., Irving-Pease, E. K., Fischer, A., Barrie, W., Ingason, A., Stenderup, J., Sjögren, K-G., Pearson, A., da Mota, B. S., Paulsson, B. S., Halgren, A., Macleod, R., Jørkov, M. L. S., Demeter, F., Sørensen, L., Nielsen, P. O., Henriksen, R. A., Vimala, T. & 144 others, McColl, Hugh, Margaryan, Ashot, Ilardo, M., Vaughn, Andrew Howland, Mortensen, M. F., Nielsen, A. B., Hede, M. U., Johannsen, N. N., Rasmussen, P., Vinner, Lasse, Renaud, Gabriel, Stern, A., Jensen, Theis Zetner Trolle, Scorrano, Gabriele, Schroeder, Hannes, Lysdahl, P., Ramsøe, Abigail Daisy, Skorobogatov, A., Schork, A. J., Rosengren, A., Ruter, Anthony Henry, Outram, A., Timoshenko, A. A., Buzhilova, A., Coppa, A., Zubova, A., Silva, A. M., Hansen, Anders Johannes, Gromov, A., Logvin, A., Gotfredsen, Anne Birgitte, Nielsen, B. H., González-Rabanal, B., Lalueza-Fox, C., McKenzie, C. J., Gaunitz, Charleen, Blasco, C., Liesau, C., Martinez-Labarga, C., Pozdnyakov, D. V., Cuenca-Solana, D., Lordkipanidze, D. O., En’shin, D., Salazar-García, D. C., Price, T. D., Borić, D., Kostyleva, E., Veselovskaya, E. V., Usmanova, E. R., Cappellini, Enrico, Petersen, Erik Brinch, Kannegaard, E., Radina, F., Yediay, Fulya Eylem, Duday, H., Gutiérrez-Zugasti, I., Merts, I., Potekhina, I., Shevnina, I., Altinkaya, Isin, Guilaine, J., Hansen, J., Tortosa, J. E. A., Zilhão, J., Vega, J., Pedersen, K. B., Tunia, K., Zhao, Lei, Mylnikova, L. N., Larsson, L., Metz, L., Yepiskoposyan, L., Pedersen, L., Sarti, L., Orlando, L., Slimak, L., Klassen, L., Blank, M., González-Morales, M., Silvestrini, M., Vretemark, M., Nesterova, M. S., Rykun, M., Rolfo, M. F., Szmyt, M., Przybyła, M., Calattini, M., Sablin, M., Dobisíková, M., Meldgaard, Morten, Johansen, M., Berezina, N., Card, N., Saveliev, N. A., Poshekhonova, O., Rickards, O., Lozovskaya, O. V., Gábor, O., Uldum, O. C., Aurino, P., Kosintsev, P., Courtaud, P., Ríos, P., Mortensen, P., Lotz, P., Persson, P., Bangsgaard, Pernille, de Barros Damgaard, P., Vang Petersen, P., Martinez, P. P., Włodarczak, P., Smolyaninov, R. V., Maring, R., Menduiña, R., Badalyan, R., Iversen, Rune, Turin, R., Vasilyev, S., Wåhlin, S., Borutskaya, S., Skochina, S., Sørensen, S. A., Andersen, S. H., Jørgensen, T., Serikov, Y. B., Molodin, V. I., Smrcka, V., Merts, V., Appadurai, V., Moiseyev, V., Magnusson, Y., Kjær, Kurt H., Lynnerup, Niels, Lawson, D. J., Sudmant, P. H., Rasmussen, Simon, Korneliussen, Thorfinn Sand, Durbin, R., Nielsen, Rasmus, Delaneau, O., Werge, Thomas, Racimo, Fernando, Kristiansen, Kristian & Willerslev, Eske, 2024, In: Nature. 625, 7994, p. 301-311

    Research output: Contribution to journalJournal articleResearchpeer-review

  5. Published

    Deep Learning for Cross-Diagnostic Prediction of Mental Disorder Diagnosis and Prognosis Using Danish Nationwide Register and Genetic Data

    Allesøe, R. L., Thompson, W. K., Bybjerg-Grauholm, J., Hougaard, D. M., Nordentoft, Merete, Werge, Thomas, Rasmussen, Simon & Benros, Michael Eriksen, 2023, In: JAMA Psychiatry. 80, 2, p. 146-155 10 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  6. Published

    Discovery of drug-omics associations in type 2 diabetes with generative deep-learning models: [with Author Correction]

    Allesøe, R. L., Lundgaard, A. T., Hernández Medina, R., Aguayo-Orozco, A., Johansen, J., Nissen, J. N., Brorsson, C., Mazzoni, G., Niu, L., Biel, J. H., Brasas, V., Webel, H., Benros, M. E., Pedersen, A. G., Chmura, P. J., Jacobsen, U. P., Mari, A., Koivula, R., Mahajan, A., Vinuela, A. & 31 others, Tajes, J. F., Sharma, S., Haid, M., Hong, M., Musholt, P. B., De Masi, F., Vogt, J., Pedersen, H. K., Gudmundsdottir, V., Jones, A., Kennedy, G., Bell, J., Thomas, E. L., Frost, G., Thomsen, Henrik S., Hansen, E., Hansen, T. H., drb459, drb459, Muilwijk, M., Blom, M. T., 't Hart, L. M., Pattou, F., Raverdy, V., Brage, S., Ridderstråle, M., Pedersen, Oluf Borbye, Hansen, Torben, Banasik, Karina, Rasmussen, Simon, Brunak, Søren & IMI-DIRECT consortium, I. C., 2023, In: Nature Biotechnology. 41, 3, p. 399–408 18 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  7. Published

    Deep learning-based integration of genetics with registry data for stratification of schizophrenia and depression

    Allesøe, R. L., Nudel, R., Thompson, W. K., Wang, Y., Nordentoft, Merete, Børglum, A. D., Hougaard, D. M., Werge, Thomas, Rasmussen, Simon & Benros, Michael Eriksen, 2022, In: Science Advances. 8, 26, eabi7293.

    Research output: Contribution to journalJournal articleResearchpeer-review

  8. Construction of a dairy microbial genome catalog opens new perspectives for the metagenomic analysis of dairy fermented products

    Almeida, M., Hébert, A., Abraham, A., Rasmussen, Simon, Monnet, C., Pons, N., Delbès, C., Loux, V., Batto, J., Leonard, P., Kennedy, S., Ehrlich, S. D., Pop, M., Montel, M., Irlinger, F. & Renault, P., 13 Dec 2014, In: BMC Genomics. 15, p. 1101

    Research output: Contribution to journalJournal articleResearchpeer-review

  9. Impaired uptake and/or utilization of leucine by Saccharomyces cerevisiae is suppressed by the SPT15-300 allele of the TATA-binding protein gene

    Baerends, R. J. S., Qiu, J., Rasmussen, Simon, Nielsen, H. B. & Brandt, A., 2009, In: Applied and Environmental Microbiology. 75, 19, p. 6055-6061 7 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  10. Published

    Genome-scale cold stress response regulatory networks in ten Arabidopsis thaliana ecotypes

    Barah, P., Jayavelu, N. D., Rasmussen, Simon, Nielsen, H. B., Mundy, J. & Bones, A. M., 2013, In: B M C Genomics. 14, 16 p., 722 .

    Research output: Contribution to journalJournal articleResearchpeer-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 journalComment/debateResearch

  12. Published

    Novel variation and de novo mutation rates in population-wide de novo assembled Danish trios

    Besenbacher, S., Liu, S., Gonzalez-Izarzugaza, J. M., Grove, J., Belling, K. G., Bork-Jensen, J., Huang, S., Als, T. D., Li, S., Yadav, R., Rubio García, A., Lescai, F., Demontis, D., Rao, J., Ye, W., Mailund, T., Møllegaard Friborg, R., Pedersen, C. N. S., Xu, R., Sun, J. & 27 others, Liu, H., Wang, O., Cheng, X., Flores, D., Rydza, E. K., Rapacki, K., Sørensen, J. D., Chmura, P. J., Westergaard, David, Dworzynski, P., Sørensen, Thorkild I.A., Lund, O., Hansen, Torben, Xu, X., Li, N., Bolund, L., Pedersen, Oluf Borbye, Eiberg, Hans Rudolf Lytchoff, Krogh, Anders, Børglum, A. D., Brunak, Søren, Kristiansen, Karsten, Schierup, M. H., Wang, J., Gupta, R., Villesen, P. & Rasmussen, Simon, 2015, In: Nature Communications. 6, 9 p., 5969.

    Research output: Contribution to journalJournal articleResearchpeer-review

  13. Microbial community structure of Arctic multiyear sea ice and surface seawater by 454 sequencing of the 16S RNA gene

    Bowman, J. S., Rasmussen, Simon, Blom, N., Deming, J. W., Rysgaard, S. & Sicheritz-Ponten, T., Jan 2012, In: I S M E Journal. 6, 1, p. 11-20 10 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  14. Published

    Paleogenomic insights into the red complex bacteria Tannerella forsythia in Pre-Hispanic and Colonial individuals from Mexico

    Bravo-Lopez, M., Villa-Islas, V., Rocha Arriaga, C., Villasenor-Altamirano, A. B., Guzman-Solis, A., Sandoval-Velasco, M., Wesp, J. K., Alcantara, K., Lopez-Corral, A., Gomez-Valdes, J., Mejia, E., Herrera, A., Meraz-Moreno, A., Moreno-Cabrera, M. D. L. L., Moreno-Estrada, A., Nieves-Colon, M. A., Olvera, J., Perez-Perez, J., Iversen, K. H., Rasmussen, S. & 3 others, Sandoval, K., Zepeda, G. & Avila-Arcos, M. C., 2020, In: Philosophical Transactions of the Royal Society B: Biological Sciences. 375, 1812, 13 p., 20190580.

    Research output: Contribution to journalJournal articleResearchpeer-review

  15. Published

    Genetic analysis of blood molecular phenotypes reveals common properties in the regulatory networks affecting complex traits

    Brown, A. A., Fernandez-Tajes, J. J., Hong, M. G., Brorsson, C. A., Koivula, R. W., Davtian, D., Dupuis, T., Sartori, A., Michalettou, T. D., Forgie, I. M., Adam, J., Allin, K. H., Caiazzo, R., Cederberg, H., De Masi, F., Elders, P. J. M., Giordano, G. N., Haid, M., Hansen, T., Hansen, T. H. & 134 others, Hattersley, A. T., Heggie, A. J., Howald, C., Jones, A. G., Kokkola, T., Laakso, M., Mahajan, A., Mari, A., McDonald, T. J., McEvoy, D., Mourby, M., Musholt, P. B., Nilsson, B., Pattou, F., Penet, D., Raverdy, V., Ridderstråle, M., Romano, L., Rutters, F., Sharma, S., Teare, H., ‘t Hart, L., Tsirigos, Konstantinos, Vangipurapu, J., drb459, drb459, Brunak, Søren, Franks, P. W., Frost, G., Grallert, H., Jablonka, B., McCarthy, M. I., Pavo, I., Pedersen, Oluf Borbye, Ruetten, H., Walker, M., Adragni, K., Allesøe, R. L. L., Artati, A. A., Arumugam, Mani, Atabaki-Pasdar, N., Baltauss, T., Banasik, Karina, Barnett, A. L., Baum, P., Bell, J. D., Beulens, J. W., Bianzano, S. B., Bizzotto, R., Bonnefond, A., Cabrelli, L., Dale, M., Dawed, A. Y., de Preville, N., Dekkers, K. F., Deshmukh, H. A., Dings, C., Donnelly, L., Dutta, A., Ehrhardt, B., pjx571, pjx571, Eriksen, R., Fan, Yong, Ferrer, J., Fitipaldi, H., Forman, A., Fritsche, A., Froguel, P., Gassenhuber, J., Gough, S., Graefe-Mody, U., Grempler, R., Groeneveld, L., Groop, L., Gudmundsdóttir, V., Gupta, R., Hennige, A. M. H., Hill, A. V., Holl, R. W., Hudson, M., Jacobsen, Ulrik Plesner, Jennison, C., Johansen, Joachim, Jonsson, Anna Elisabet, Karaderi, Tugce, Kaye, J., Kennedy, G., Klintenberg, M., Kuulasmaa, T., Lehr, T., Loftus, H., Lundgaard, Agnete Troen, Mazzoni, G., McRobert, N., McVittie, I., Nice, R., Nicolay, C., Nijpels, G., Palmer, C. N., Pedersen, H. K., Perry, M. H., Pomares-Millan, H., Prehn, C. P., Ramisch, A., Rasmussen, Simon, Robertson, N., Rodriquez, M., Sackett, P., Scherer, N., Shah, N., Sihinevich, I., Slieker, R. C., Sondertoft, N. B., Steckel-Hamann, B., Thomas, M. K., Thomas, Cecilia Engel, Thomas, E. L. L., Thorand, B., Thorne, C. E., Tillner, J., Tura, A., Uhlen, M., van Leeuwen, N., van Oort, S., Verkindt, H., Vogt, J., Wad Sackett, P. W., Wesolowska-Andersen, A., Whitcher, B., White, M. W., Adamski, J., Schwenk, J. M., Pearson, E. R., Dermitzakis, E. T. & Viñuela, A., 2023, In: Nature Communications. 14, 17 p., 5062.

    Research output: Contribution to journalJournal articleResearchpeer-review

  16. Published

    Global network reorganization during dynamic adaptations of Bacillus subtilis metabolism

    Buescher, J. M., Liebermeister, W., Jules, M., Uhr, M., Muntel, J., Botella, E., Hessling, B., Kleijn, R. J., Le Chat, L., Lecointe, F., Mäder, U., Nicolas, P., Piersma, S., Rügheimer, F., Becher, D., Bessieres, P., Bidnenko, E., Denham, E. L., Dervyn, E., Devine, K. M. & 30 others, Doherty, G., Drulhe, S., Felicori, L., Fogg, M. J., Goelzer, A., Hansen, A., Harwood, C. R., Hecker, M., Hubner, S., Hultschig, C., Jarmer, H., Klipp, E., Leduc, A., Lewis, P., Molina, F., Noirot, P., Peres, S., Pigeonneau, N., Pohl, S., Rasmussen, Simon, Rinn, B., Schaffer, M., Schnidder, J., Schwikowski, B., Van Dijl, J. M., Veiga, P., Walsh, S., Wilkinson, A. J., Stelling, J. & Aymerich, S., 2 Mar 2012, In: Science (New York, N.Y.). 335, 6072, p. 1099-103 5 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  17. Published

    Genomic characterization, phylogenetic analysis, and identification of virulence factors in Aerococcus sanguinicola and Aerococcus urinae strains isolated from infection episodes

    Carkaci, D., Højholt, K., Nielsen, X. C., Dargis, R., Rasmussen, Simon, Skovgaard, O., Fuursted, K., Andersen, P. S., Stegger, M. & Christensen, J. J., Nov 2017, In: Microbial Pathogenesis. 112, p. 327-340 14 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  18. Gene expression plasticity across hosts of an invasive scale insect species

    Christodoulides, N., Van Dam, A. R., Peterson, D. A., Frandsen, R. J. N., Mortensen, U. H., Petersen, Bent, Rasmussen, Simon, Normark, B. B. & Hardy, N. B., 2017, In: PLoS ONE. 12, 5

    Research output: Contribution to journalJournal articleResearchpeer-review

  19. 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 journalJournal articleResearchpeer-review

  20. Published

    The first horse herders and the impact of early Bronze Age steppe expansions into Asia

    Damgaard, P. D. B., Martiniano, R., Kamm, J., Moreno Mayar, J. V., Kroonen, G., Peyrot, M., Barjamovic, G., Rasmussen, S., Zacho, C. G., Baimukhanov, N., Zaibert, V., Merz, V., Biddanda, A., Merz, I., Loman, V., Evdokimov, V., Usmanova, E., Hemphill, B., Seguin-Orlando, A., Yediay, F. E. & 31 others, Ullah, I., Sjögren, K., Iversen, K. H., Choin, J., jxb425, jxb425, Ilardo, M., Schroeder, Hannes, Moiseyev, V., Gromov, A., Polyakov, A., Omura, S., Senyurt, S. Y., Orlando, L. A. A., Ahmad, H., McKenzie, C., Margaryan, Ashot, Hameed, A., Samad, A., Gul, N., Khokhar, M. H., Goriunova, O. I., Bazaliiskii, V. I., Novembre, J., Weber, A. W., Allentoft, Morten Erik, Nielsen, R., Kristiansen, K., Sikora, Martin, Outram, A. K., Durbin, R. & Willerslev, Eske, 2018, In: Science. 360, 6396, 11 p., 1422.

    Research output: Contribution to journalJournal articleResearchpeer-review

  21. 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 journalJournal articleResearchpeer-review

  22. 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 journalJournal articleResearchpeer-review

  23. Published

    The ubiquitin ligase RFWD3 is required for translesion DNA synthesis

    Gallina, I., Hendriks, Ivo Alexander, Hoffmann, Saskia, Larsen, N. B., Johansen, Joachim, S.Colding-Christensen, Camilla, Schubert, Lisa, Sellés Baiget, Selene, Fábián, Z., Kühbacher, U., Gao, A. O., Räschle, M., Rasmussen, Simon, Nielsen, Michael Lund, Mailand, Niels & Duxin, Julien, 2021, In: Molecular Cell. 81, 3, p. 442-458.e9 27 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  24. Published

    The population genomic legacy of the second plague pandemic

    Gopalakrishnan, S., Ebenesersdóttir, S. S., Lundstrøm, I. K. C., Turner-Walker, G., Moore, K. H. S., Luisi, P., Margaryan, A., Martin, M. D., Ellegaard, M. R., Magnússon, Ó., Sigurðsson, Á., Snorradóttir, S., Magnúsdóttir, D. N., Laffoon, J. E., van Dorp, L., Liu, X., Moltke, I., Ávila-Arcos, M. C., Schraiber, J. G., Rasmussen, S. & 40 others, Juan, D., Gelabert, P., de-Dios, T., Fotaki, Anna Katerina, Iraeta Orbegozo, Miren, Vågene, Åshild Joanne, Denham, S. D., Christophersen, A., Stenøien, H. K., Vieira, Filipe Garrett, Liu, Shanlin, Günther, T., Kivisild, T., Moseng, O. G., Skar, B., Cheung, C., Sandoval-Velasco, Marcela, Wales, N., Schroeder, Hannes, Campos, P. F., Guðmundsdóttir, V. B., Sicheritz-Pontén, Thomas, Petersen, Bent, Halgunset, J., Gilbert, E., Cavalleri, G. L., Hovig, E., Kockum, I., Olsson, T., Alfredsson, L., Hansen, Thomas Folkmann, Werge, Thomas, Willerslev, Eske, Balloux, F., Marques-Bonet, T., Lalueza-Fox, C., Nielsen, Rasmus, Stefánsson, K., Helgason, A. & Gilbert, M Thomas P, 2022, In: Current Biology. 32, 21, p. 4743-4751.e6

    Research output: Contribution to journalJournal articleResearchpeer-review

  25. Published

    Transcriptome profiling of brown adipose tissue during cold exposure reveals extensive regulation of glucose metabolism

    Hao, Q., Yadav, R., Basse, A. L., Petersen, S., Sonne, Si Brask, Rasmussen, Simon, Zhu, Q., Lu, Z., Wang, J., Audouze, K., Gupta, R., Madsen, L., Kristiansen, Karsten & Hansen, Jacob B., 2015, In: American Journal of Physiology: Endocrinology and Metabolism. 308, 5, p. E380-E392 13 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  26. Published

    Extension of Plant Phenotypes by the Foliar Microbiome

    Hawkes, C. V., Kjøller, Rasmus, Raaijmakers, J. M., Riber, Leise, Christensen, Svend, Rasmussen, Simon, Christensen, Jan H., Dahl, A. B., Westergaard, Jesper Cairo, Nielsen, Mads, Brown-Guedira, G. & Hansen, Lars Hestbjerg, 2021, In: Annual Review of Plant Biology. 72, p. 823-846 24 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  27. Global monitoring of antimicrobial resistance based on metagenomics analyses of urban sewage

    Hendriksen, R. S., Munk, P., Njage, P., van Bunnik, B., McNally, L., Lukjancenko, O., Röder, T., Nieuwenhuijse, D., Pedersen, S. K., Kjeldgaard, J., Kaas, R. S., Clausen, P. T. L. C., Vogt, J. K., Leekitcharoenphon, P., van de Schans, M. G. M., Zuidema, T., de Roda Husman, A. M., Rasmussen, S., Petersen, B., Bego, A. & 108 others, Rees, C., Cassar, S., Coventry, K., Collignon, P., Allerberger, F., Rahube, T. O., Oliveira, G., Ivanov, I., Vuthy, Y., Sopheak, T., Yost, C. K., Ke, C., Zheng, H., Baisheng, L., Jiao, X., Donado-Godoy, P., Coulibaly, K. J., Jergović, M., Hrenovic, J., Karpíšková, R., Villacis, J. E., Legesse, M., Eguale, T., Heikinheimo, A., Malania, L., Nitsche, A., Brinkmann, A., Saba, C. K. S., Kocsis, B., Solymosi, N., Thorsteinsdottir, T. R., Hatha, A. M., Alebouyeh, M., Morris, D., Cormican, M., O’Connor, L., Moran-Gilad, J., Alba, P., Battisti, A., Shakenova, Z., Kiiyukia, C., Ng’eno, E., Raka, L., Avsejenko, J., Bērziņš, A., Bartkevics, V., Penny, C., Rajandas, H., Parimannan, S., Haber, M. V., Pal, P., Jeunen, G. J., Gemmell, N., Fashae, K., Holmstad, R., Hasan, R., Shakoor, S., Rojas, M. L. Z., Wasyl, D., Bosevska, G., Kochubovski, M., Radu, C., Gassama, A., Radosavljevic, V., Wuertz, S., Zuniga-Montanez, R., Tay, M. Y. F., Gavačová, D., Pastuchova, K., Truska, P., Trkov, M., Esterhuyse, K., Keddy, K., Cerdà-Cuéllar, M., Pathirage, S., Norrgren, L., Örn, S., Larsson, D. G. J., Heijden, T. V. D., Kumburu, H. H., Sanneh, B., Bidjada, P., Njanpop-Lafourcade, B. M., Nikiema-Pessinaba, S. C., Levent, B., Meschke, J. S., Beck, N. K., Van, C. D., Phuc, N. D., Tran, D. M. N., Kwenda, G., Tabo, D. A., Wester, A. L., Cuadros-Orellana, S., Amid, C., Cochrane, G., Sicheritz-Pontén, Thomas, Schmitt, H., Alvarez, J. R. M., Aidara-Kane, A., Pamp, S. J., Lund, O., Hald, T., Woolhouse, M., Koopmans, M. P., Vigre, H., Petersen, T. N. & Aarestrup, F. M., 2019, In: Nature Communications. 10, 1, 12 p., 1124.

    Research output: Contribution to journalJournal articleResearchpeer-review

  28. Published

    Machine learning and deep learning applications in microbiome research

    Hernandez Medina, Ricardo, Kutuzova, Svetlana, Nielsen, Knud Nor, Johansen, Joachim, Hansen, Lars Hestbjerg, Nielsen, Mads & Rasmussen, Simon, 2022, In: ISME Communications. 2, 7 p., 98.

    Research output: Contribution to journalJournal articleResearchpeer-review

  29. 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 journalJournal articleResearchpeer-review

  30. Published

    Physiological and Genetic Adaptations to Diving in Sea Nomads

    Ilardo, M. A., Moltke, Ida, Korneliussen, Thorfinn Sand, Cheng, J., Stern, A. J., Racimo, Fernando, Damgaard, P. D. B., Sikora, Martin, Seguin-Orlando, A., Rasmussen, Simon, van den Munckhof, I. C. L., ter Horst, R., Joosten, L. A. B., Netea, M. G., Salingkat, S., Nielsen, Rasmus & Willerslev, Eske, 2018, In: Cell. 173, 3, p. 569-580 12 p., e15.

    Research output: Contribution to journalJournal articleResearchpeer-review

  31. Published

    Similar genomic patterns of clinical infective endocarditis and oral isolates of Streptococcus sanguinis and Streptococcus gordonii

    Iversen, K. H., Rasmussen, L. H., Al-Nakeeb, K., Armenteros, J. J. A., Jensen, C. S., Dargis, R., Lukjancenko, O., Justesen, U. S., Moser, C., Rosenvinge, F. S., Nielsen, X. C., Christensen, J. J. & Rasmussen, Simon, 17 Feb 2020, In: Scientific Reports. 10, 1, 11 p., 2728.

    Research output: Contribution to journalJournal articleResearchpeer-review

  32. 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 journalJournal articleResearchpeer-review

  33. 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 journalJournal articleResearchpeer-review

  34. Published
  35. 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 journalJournal articleResearchpeer-review

  36. Published

    Global within-species phylogenetics of sewage microbes suggest that local adaptation shapes geographical bacterial clustering

    Jespersen, Marie Louise, Munk, P., Johansen, Joachim, Kaas, R. S., Webel, Henry, Vigre, H., Nielsen, H. B., Rasmussen, Simon & Aarestrup, F. M., 2023, In: Communications Biology . 6, 9 p., 700.

    Research output: Contribution to journalJournal articleResearchpeer-review

  37. 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 journalJournal articleResearchpeer-review

  38. Published

    Genome binning of viral entities from bulk metagenomics data

    Johansen, Joachim, Plichta, D. R., Nissen, J. N., Jespersen, Marie Louise, Shah, S. A., Deng, Ling, Stokholm, Jakob, Bisgaard, H., Nielsen, Dennis Sandris, Sørensen, Søren Johannes & Rasmussen, Simon, 2022, In: Nature Communications. 13, 12 p., 965.

    Research output: Contribution to journalJournal articleResearchpeer-review

  39. Published

    FAVA: High-quality functional association networks inferred from scRNA-seq and proteomics data

    Koutrouli, Mikaela, Nastou, Katerina, Piera Líndez, Pau, Bouwmeester, R., Rasmussen, Simon, Martens, L. & Jensen, Lars Juhl, 2024, In: Bioinformatics. 40, 2, 11 p., btae010.

    Research output: Contribution to journalJournal articleResearchpeer-review

  40. Published

    Re-theorising mobility and the formation of culture and language among the Corded Ware Culture in Europe: [incl. Corrigendum]

    Kristiansen, K., Allentoft, Morten Erik, Frei, K. M., Iversen, Rune, Johannsen, N. N., Kroonen, Guus, Pospieszny, L., Price, T. D., Rasmussen, Simon, Sjögren, K., Sikora, Martin & Willerslev, Eske, Apr 2017, In: Antiquity. 91, 356, p. 334-347

    Research output: Contribution to journalJournal articleResearchpeer-review

  41. 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 journalJournal articleResearchpeer-review

  42. Published

    Multilocus sequence typing of total-genome-sequenced bacteria

    Larsen, Mette Vang, Cosentino, S., Rasmussen, Simon, Friis, Carsten, Hasman, H., Marvig, R. L., Jelsbak, L., Sicheritz-Pontén, T., Ussery, D. W., Aarestrup, F. M. & Lund, O., Apr 2012, In: Journal of Clinical Microbiology. 50, 4, p. 1355-61 7 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  43. Published

    Richness of human gut microbiome correlates with metabolic markers

    Le Chatelier, E., Nielsen, T., Qin, J., Prifti, E., Hildebrand, F., Falony, G., Almeida, M., Arumugam, M., Batto, J-M., Kennedy, S., Leonard, P., Li, J., Burgdorf, K. S., Grarup, N., Jørgensen, T., Brandslund, I., Nielsen, H. B., Juncker, A., dos Santos, M. B. Q., Levenez, F. & 62 others, Pons, N., Rasmussen, Simon, Sunagawa, S., Tap, J., Tims, S., Zoetendal, E. G., Brunak, S., Clément, K., Doré, J., Kleerebezem, M., Kristiansen, Karsten, Renault, P., Sicheritz-Ponten, T., de Vos, W. M., Zucker, J., Raes, J., Hansen, Torben, Bork, P., Wang, J., Ehrlich, S. D., Pedersen, Oluf Borbye, Guedon, E., Delorme, C., Layec, S., Khaci, G., van de Guchte, M., Vandemeulebrouck, G., Jamet, A., Dervyn, R., Sanchez, N., Maguin, E., Haimet, F., Winogradski, Y., Cultrone, A., Leclerc, M., Juste, C., Blottière, H., Pelletier, E., LePaslier, D., Artiguenave, F., Bruls, T., Weissenbach, J., Turner, K., Parkhill, J., Antolin, M., Manichanh, C., Casellas, F., Boruel, N., Varela, E., Torrejon, A., Guarner, F., Denariaz, G., Derrien, M., van Hylckama Vlieg, J. E. T., Veiga, P., Oozeer, R., Knol, J., Rescigno, M., Brechot, C., Mérieux, A., M'Rini, C. & Yamada, T., 2013, In: Nature. 500, 7464, p. 541-546 6 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  44. Published

    snpTree--a web-server to identify and construct SNP trees from whole genome sequence data

    Leekitcharoenphon, P., Kaas, R. S., Thomsen, M. C. F., Friis, Carsten, Rasmussen, Simon & Aarestrup, F. M., 2012, In: BMC Genomics. 13 Suppl 7, p. S6

    Research output: Contribution to journalJournal articleResearchpeer-review

  45. Published

    Discovery, genotyping and characterization of structural variation and novel sequence at single nucleotide resolution from de novo genome assemblies on a population scale

    Danish Pan Genome Consortium, D. P. G. C., Belling, K. G. & Rasmussen, Simon, 2015, In: GigaScience. 4, 13 p., 64.

    Research output: Contribution to journalJournal articleResearchpeer-review

  46. Published

    Genetic factors underlying the bidirectional relationship between autoimmune and mental disorders - findings from a Danish population-based study: [Incl. Corrigendum]

    Liu, X., Nudel, R., Thompson, W. K., Appadurai, V., Schork, A. J., Buil, A., Rasmussen, Simon, Allesøe, R. L., Werge, Thomas, Mors, O., Børglum, A. D., Hougaard, D. M., Mortensen, P. B., Nordentoft, Merete & Benros, Michael Eriksen, 2021, In: Brain, Behavior, and Immunity. 91, p. 10-23 14 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  47. 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 journalJournal articleResearchpeer-review

  48. Published

    Two ancient human genomes reveal Polynesian ancestry among the indigenous Botocudos of Brazil

    Malaspinas, A. S., Lao, O., Schroeder, H., Rasmussen, M., Raghavan, M., Moltke, I., Campos, P., Sagredo, F. S., Rasmussen, S., Gonçalves, V. F., Albrechtsen, A., Allentoft, M. E., Johnson, P. L. F., Li, M., Reis, S., Bernardo, D. V., DeGiorgio, M., Duggan, A. T., Bastos, M., Wang, Y. & 20 others, Stenderup, Jesper Tandberg, Moreno Mayar, J. Víctor, Brunak, S., Sicheritz-Ponten, T., Hodges, E., Hannon, G. J., Orlando, L. A. A., Price, T. D., Jensen, J. D., Nielsen, Rasmus, Heinemeier, J., Olsen, J., Rodrigues-Carvalho, C., Lahr, M. M., Neves, W. A., Kayser, M., Higham, T., Stoneking, M., Pena, S. D. J. & Willerslev, Eske, 2014, In: Current biology : CB. 24, 21, p. R1035-R1037 3 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  49. Published

    Population genomics of the Viking world: [incl. correction]

    Margaryan, A., Lawson, D. J., Sikora, M., Racimo, F., Rasmussen, S., Moltke, I., Cassidy, L. M., Jørsboe, E., Ingason, A., Pedersen, M. W., Korneliussen, T., Wilhelmson, H., Buś, M. M., de Barros Damgaard, P., Martiniano, R., Renaud, G., Bhérer, C., Moreno-Mayar, J. V., Fotakis, A. K., Allen, M. & 30 others, Allmäe, R., Molak, M., Cappellini, Enrico, Scorrano, Gabriele, McColl, Hugh, Buzhilova, A., Fox, A., Albrechtsen, Anders, Schütz, B., Skar, B., Arcini, C., Lundstrøm, I., Cheng, J., Stenderup, Jesper Tandberg, Iversen, K. H., Arge, S. V., Ellingvåg, S., Orlando, L., Pentz, P., Jessen, M. D., Pedersen, A., Jørkov, M L S, Lynnerup, Niels, Gilbert, M Thomas P, Allentoft, Morten Erik, Sindbæk, S. M., Kristiansen, K., Nielsen, Rasmus, Werge, Thomas & Willerslev, Eske, 2020, In: Nature. 585, 7825, p. 390-396 7 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  50. 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 journalJournal articleResearchpeer-review

Previous 1 2 3 Next

ID: 204201681