Simon Rasmussen

Phone+4535332159
Emailsrasmusssund.kudk

Blegdamsvej 3B, Mærsk Tårnet, 7. sal
2200 København N.

Research activity per year

Short presentation

The driving force in my research is curiosity and interest in transforming often very large and complex datasets from biological experiments into knowledge and biological understanding. Currently, my group focus on deep learning based data integration of large-scale multi-omics and multi-modal data. Additionally, we focus on applying large scale deep learning to increase understanding of human diseases and use this to pave the way for more precise diagnostics, prevention, and new treatment strategies.

CV

CURRENT POSITION

Professor, Multi Modal Bioinformatics, NNF Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen
Affiliate Researcher, Novo Nordisk Foundation Center for Mechanisms of Disease, Broad Institute of MIT and Harvard, USA

UNIVERSITY STUDIES

(1998-2005) Msc in Engineering (Biotechnology)

Ph. D. STUDIES

(2006-2009) PhD in Systems Biology, Center for Biological Sequence analysis, Technical University of Denmark, Denmark. Advisor: Søren Brunak

POST-DOCORAL STUDIES

(2009-2011) Postdoc at the Center for Biological Sequence analysis, Technical University of Denmark. Advisor: Thomas Sicheritz-Ponten

PREVIOUS ACADEMIC APPOINTMENTS

(2005-2006) Research Scientist

Department of Infectious Disease Immunology, Statens Serum Institut, Denmark

(Aug. 2008-Dec. 2008) Visiting Researcher

Swammerdam Institute for Life Sciences, University of Amsterdam, The Netherlands

(2011-2015) Assistant Professor

Department of Systems Biology, Technical University of Denmark, Denmark

(2015-2018) Associate Professor

Department of Systems Biology, Technical University of Denmark, Denmark

(May 2017-Nov. 2018) Visiting Scholar

Department of Integrative Biology, UC Berkeley, USA

(Mar. 2018-Nov. 2018) Group Leader and Head of Research

Department of Bio and Health Informatics, Technical University of Denmark, Denmark

PRIZES, AWARDS

(2014) Researcher of the Year Department of Systems Biology, Technical University of Denmark, Denmark
(2015) Paper featured as scientific breakthrough in ERC Commission annual report
(2016) Carlsberg Research Stay Grant
(2017) Jorck Foundation Research Prize
(2018) Highly Cited Researcher 2018 (Clarivate Analytics, Web of Science)
(2020) Highly Cited Researcher 2020 (Clarivate Analytics, Web of Science)
(2023) Highly Cited Researcher 2023 (Clarivate Analytics, Web of Science)

BOARD MEMBERSHIPS

(since 2016) Editorial Board, Scientific Data

Short presentation

S.R. is the founder and owner of BioAI

18518 Citations
102 Journal article
5 Letter
3 Preprint
2 Review
More
- 1 Comment/debate

Emergence and Spread of Basal Lineages of Yersinia pestis during the Neolithic Decline
Rascovan, N., Sjogren, K-G., Kristiansen, K., Nielsen, R., Willerslev, E., Desnues, C. & Rasmussen, S., 2019, In: Cell. 176, 1-2, p. 295-305.e10
Research output: Contribution to journal › Journal article › Research › peer-review

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74 Citations (Scopus)
Binning microbial genomes using deep learning
Nissen, J. N., Sønderby, C. K., Armenteros, J. J. A., Grønbech, C. H., Nielsen, H. B., Petersen, T. N., Winther, O. & Rasmussen, S., 2018, (bioRxiv).
Research output: Working paper › Preprint

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236 Downloads (Pure)
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, D., Yadav, R., Li, N., Xu, X., Hansen, T., Krogh, A., Bolund, L., Sørensen, T. I. A., Pedersen, O. B., Gupta, R., Rasmussen, S., Besenbacher, S., Børglum, A. D., Wang, J., Eiberg, H. R. L., Kristiansen, K., Brunak, S. & Schierup, M. H., 2017, In: Nature. 548, 7665, p. 87-91 5 p.
Research output: Contribution to journal › Letter › Research › peer-review

Open Access
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58 Citations (Scopus)

596 Downloads (Pure)
Early divergent strains of Yersinia pestis in Eurasia 5,000 years ago
Rasmussen, S., Allentoft, M. E., Nielsen, K., Orlando, L. A. A., Sikora, M., Sjögren, K-G., Pedersen, A. G., Schubert, M., Van Dam, A., Kapel, C. M. O., Nielsen, H. B., Brunak, S., Avetisyan, P., Epimakhov, A., Khalyapin, M. V., Gnuni, A., Kriiska, A., Lasak, I., Metspalu, M., Moiseyev, V. & 11 others, Gromov, A., Pokutta, D., Saag, L., Varul, L., Yepiskoposyan, L., Sicheritz-Ponten, T., Foley, R. A., Lahr, M. M., Nielsen, R., Kristiansen, K. & Willerslev, E., 2015, In: Cell. 163, 3, p. 571-582 12 p.
Research output: Contribution to journal › Journal article › Research › peer-review

Open Access
File

369 Citations (Scopus)

378 Downloads (Pure)
Genomic evidence for the Pleistocene and recent population history of Native Americans
Raghavan, M., Steinrücken, M., Harris, K., Schiffels, S., Rasmussen, S., DeGiorgio, M., Albrechtsen, A., Valdiosera Morales, C. E., Avila Arcos, M. D. C., Malaspinas, A. S., Eriksson, A., Moltke, I., Metspalu, M., Homburger, J. R., Wall, J., Cornejo, O. E., Moreno Mayar, J. V., Korneliussen, T. S., Pierre, T. L., Rasmussen, M. & 81 others, Campos, P., Damgaard, P. D. B., Allentoft, M. E., 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-A., 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, R. & Willerslev, E., 2015, In: Science (New York, N.Y.). 349, 6250, 6250.
Research output: Contribution to journal › Journal article › Research › peer-review

245 Citations (Scopus)
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, D., Dworzynski, P., Sørensen, T. I. A., Lund, O., Hansen, T., Xu, X., Li, N., Bolund, L., Pedersen, O., Eiberg, H., Krogh, A., Børglum, A. D., Brunak, S., Kristiansen, K., Schierup, M. H., Wang, J., Gupta, R., Villesen, P. & Rasmussen, S., 2015, In: Nature Communications. 6, 9 p., 5969.
Research output: Contribution to journal › Journal article › Research › peer-review

Open Access
File

128 Citations (Scopus)

241 Downloads (Pure)
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, E. K., Barrie, W., Pearson, A., Sousa da Mota, B., Demeter, F., Henriksen, R. A., Vimala, T., McColl, H., Vaughn, A., Vinner, L., Renaud, G., Stern, A., Johannsen, N. N., Ramsøe, A. D., Schork, A. J., Ruter, A., Gotfredsen, A. B., Nielsen, B. H., Petersen, E. B., Kannegaard, E., Hansen, J., Pedersen, K. B., Pedersen, L., Klassen, L., Meldgaard, M., Johansen, M., Uldum, O. C., Lotz, P., Lysdahl, P., Bangsgaard, P., Petersen, P. V., Maring, R., Iversen, R., Wåhlin, S., Sørensen, S. A., Andersen, S. H., Jørgensen, T., Lynnerup, N., Lawson, D. J., Rasmussen, S., Korneliussen, T. S., Kjær, K. H., Durbin, R., Nielsen, R., Delaneau, O., Werge, T., Kristiansen, K. & Willerslev, E., 2024, In: Nature. 625, 7994, p. 329-337 9 p.
Research output: Contribution to journal › Journal article › Research › peer-review

Open Access
File

1 Citation (Scopus)

73 Downloads (Pure)
An assessment of the value of deep neura networks in genetic risk prediction for surgically relevant outcomes
Christensen, M. A., Sigurdsson, A., Bonde, A., Rasmussen, S., Ostrowski, S. R., Nielsen, M. & Sillesen, M., 2024, In: PLoS ONE. 19, 7, e0294368.
Research output: Contribution to journal › Journal article › Research › peer-review

Open Access
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1 Downloads (Pure)

Simon Rasmussen

Personal profile

Short presentation

CV

Short presentation

Collaborations and top research areas from the last five years

Dive into details

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

Binning microbial genomes using deep learning

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

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

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

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

100 ancient genomes show repeated population turnovers in Neolithic Denmark

An assessment of the value of deep neura networks in genetic risk prediction for surgically relevant outcomes

Simon Rasmussen

Personal profile

Short presentation

CV

Short presentation

Collaborations and top research areas from the last five years

Research output