Simon Rasmussen

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• CV
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The scientific drive of Simon Rasmussen is his curiosity and interest in transforming large and complex datasets from biological experiments into knowledge and biological understanding. He is established as a strong initiator of analysis efforts within large scale genomics data including areas such human genomics, metagenomics, bacterial genomics and evolution. This is emphasized by the publication of more than 20 papers in the most prestigious journals (Nature, Science and Cell) such as analyses of thousands of human genomes as well as the discovery of plague epidemics during the Bronze Age. The achievement of the latter was emphasized by it being selected as a scientific breakthrough by the European Research Council. Currently, he is building an infrastructure around human proteome variation as genome graph representations which will be used to store and analyse 100,000s of genomes. Here an important challenge is to translate individual genome variation to functional proteome variation. He aims to study this through differential prediction of protein features such as secondary structure, cleavage events and post-translational modifications. Furthermore, he develops methods for unsupervised deep learning of massive omics data and has shown the ability of this approach to integrate data from different fields. Here, he is developing methods for integration of genomics and proteomics data with metabolomics and clinical data in human disease systems and applies this to datasets of schizophrenia and depression.

RESEARCH INTERESTS

• Protein sequence variation
• Variation affecting protein complexes and functional sites
• Variation in disease
• Data integration and deep learning

Selected publications

1. Published

   Emergence and Spread of Basal Lineages of Yersinia pestis during the Neolithic Decline

   Rascovan, N., Sjogren, K., Kristiansen, K., Nielsen, Rasmus, Willerslev, Eske, Desnues, C. & Rasmussen, Simon, 2019, In: Cell. 176, 1-2, p. 295-305.e10

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

2. 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

3. Published

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

   Sørensen, L. M., Jensen, J. M., Petersen, Bent, Sibbesen, Jonas Andreas, 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., 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 › peer-review

4. Published

   Early divergent strains of Yersinia pestis in Eurasia 5,000 years ago

   Rasmussen, Simon, Allentoft, Morten Erik, Nielsen, K., Orlando, L. A. A., Sikora, Martin, Sjögren, K., Pedersen, A. G., Schubert, M., Van Dam, A., Kapel, Christian, Nielsen, H. B., Brunak, Søren, Avetisyan, P., Epimakhov, A., Khalyapin, M. V., Gnuni, A., Kriiska, A., Lasak, I., Metspalu, M., Moiseyev, V., Gromov, A., Pokutta, D., Saag, L., Varul, L., Yepiskoposyan, L., Sicheritz-Ponten, T., Foley, R. A., Lahr, M. M., Nielsen, R., Kristiansen, K. & Willerslev, Eske, 2015, In: Cell. 163, 3, p. 571-582 12 p.

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

5. Published

   Genomic evidence for the Pleistocene and recent population history of Native Americans

   Raghavan, M., Steinrücken, M., Harris, K., Schiffels, S., Rasmussen, Simon, DeGiorgio, M., Albrechtsen, Anders, Valdiosera Morales, C. E., Avila Arcos, M. D. C., Malaspinas, A. S., Eriksson, A., Moltke, Ida, Metspalu, M., Homburger, J. R., Wall, J., Cornejo, O. E., Moreno Mayar, J. Víctor, Korneliussen, Thorfinn Sand, Pierre, T. L., Rasmussen, M., Campos, P., Damgaard, P. D. B., Allentoft, Morten Erik, Lindo, J., Metspalu, E., Rodríguez-Varela, R., Mansilla, J., Henrickson, C., Seguin-Orlando, A., Malmström, H., Stafford jr., T., Shringarpure, S. S., Moreno-Estrada, A., Karmin, M., Tambets, K., Bergström, A., Xue, Y., Warmuth, V., Friend, A. D., Singarayer, J., Valdes, P., Balloux, F., Leboreiro, I., Vera, J. L., Rangel-Villalobos, H., Pettener, D., Luiselli, D., Davis, L. G., Heyer, E., Zollikofer, C. P. E., Ponce de León, M. S., Smith, C. I., Grimes, V., Pike, K., Deal, M., Fuller, B. T., Arriaza, B., Standen, V., Luz, M. F., Ricaut, F., Guidon, N., Osipova, L., Voevoda, M. I., Posukh, O. L., Balanovsky, O., Lavryashina, M., Bogunov, Y., Khusnutdinova, E., Gubina, M., Balanovska, E., Fedorova, S., Litvinov, S., Malyarchuk, B., Derenko, M., Mosher, M. J., Archer, D., Cybulski, J., Petzelt, B., Mitchell, J., Worl, R., Norman, P. J., Parham, P., Kemp, B. M., Kivisild, T., Tyler-Smith, C., Sandhu, M. S., Crawford, M., Villems, R., Smith, D. G., Waters, M. R., Goebel, T., Johnson, J. R., Malhi, R. S., Jakobsson, M., Meltzer, D. J., Manica, A., Durbin, R., Bustamante, C. D., Song, Y. S., Nielsen, Rasmus & Willerslev, Eske, 2015, In: Science (New York, N.Y.). 349, 6250, 6250.

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

6. 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., 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 journal › Journal article › peer-review