Simon Rasmussen

Simon Rasmussen

Professor

ORCID: 0000-0001-6323-9041

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  1. 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

  2. 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

  3. 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 journal › Journal article › Research › peer-review

  4. Published

    Critical Assessment of Metagenome Interpretation: the second round of challenges

    Meyer, F., Fritz, A., Deng, Z. L., Koslicki, D., Lesker, T. R., Gurevich, A., Robertson, G., Alser, M., Antipov, D., Beghini, F., Bertrand, D., Brito, J. J., Brown, C. T., Buchmann, J., Buluç, A., Chen, B., Chikhi, R., Clausen, P. T. L. C., Cristian, A., Dabrowski, P. W. & 83 others, Darling, A. E., Egan, R., Eskin, E., Georganas, E., Goltsman, E., Gray, M. A., Hansen, Lars Hestbjerg, Hofmeyr, S., Huang, P., Irber, L., Jia, H., Jørgensen, T. S., Kieser, S. D., Klemetsen, T., Kola, A., Kolmogorov, M., Korobeynikov, A., Kwan, J., LaPierre, N., Lemaitre, C., Li, C., Limasset, A., Malcher-Miranda, F., Mangul, S., Marcelino, V. R., Marchet, C., Marijon, P., Meleshko, D., Mende, D. R., Milanese, A., Nagarajan, N., Nissen, Jakob Nybo, Nurk, S., Oliker, L., Paoli, L., Peterlongo, P., Piro, V. C., Porter, J. S., Rasmussen, Simon, Rees, E. R., Reinert, K., Renard, B., Robertsen, E. M., Rosen, G. L., Ruscheweyh, H. J., Sarwal, V., Segata, N., Seiler, E., Shi, L., Sun, F., Sunagawa, S., Sørensen, Søren Johannes, Thomas, A., Tong, C., Trajkovski, M., Tremblay, J., Uritskiy, G., Vicedomini, R., Wang, Z., Wang, Z., Wang, Z., Warren, A., Willassen, N. P., Yelick, K., You, R., Zeller, G., Zhao, Z., Zhu, S., Zhu, J., Garrido-Oter, R., Gastmeier, P., Hacquard, S., Häußler, S., Khaledi, A., Maechler, F., Mesny, F., Radutoiu, S., Schulze-Lefert, P., Smit, N., Strowig, T., Bremges, A., Sczyrba, A. & McHardy, A. C., 2022, In: Nature Methods. 19, 4, p. 429-440

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

  5. 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

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

  7. 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

  8. 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 journal › Journal article › Research › peer-review

  9. Published

    Defining NASH from a multi-omics systems biology perspective

    Niu, Lili, Sulek, K., Vasilopoulou, C. G., Santos, A., Albrechtsen, Nicolai Jacob Wewer, Rasmussen, Simon, Meier, F. & Mann, Matthias, 2021, In: Journal of Clinical Medicine. 10, 20, 22 p., 4673.

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

  10. Published

    Derived immune and ancestral pigmentation alleles in a 7,000-year-old Mesolithic European

    Olalde, I., Allentoft, M. E., Sánchez-Quinto, F., Santpere, G., Chiang, C. W. K., DiGeorgio, M., Prado-Martínez, J., Rodríguez Pérez, J. A., Rasmussen, S., Quilez, J., Ramírez, O., Marigorta, U. M., Fernández-Callejo, M., Prada, M. E., Encinas, J. M. V., Nielsen, R., Netea, M. G., Novembre, J., Sturm, R. A., Sabeti, P. & 4 others, Marquès-Bonet, T., Navarro, A., Willerslev, Eske & Lalueza-Fox, C., 2014, In: Nature. 507, 7491, p. 225-228 4 p.

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

  11. Published

    Dhurrin metabolism in the developing grain of Sorghum bicolor (L.) Moench investigated by metabolite profiling and novel clustering analyses of time-resolved transcriptomic data

    Nielsen, L. J., Stuart, P., Picmanova, M., Rasmussen, Simon, Olsen, C. E., Harholt, J., Møller, Birger Lindberg & Bjarnholt, Nanna, 2016, In: BMC Genomics. 17, 24 p., 1021.

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

  12. 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 journal › Journal article › Research › peer-review

  13. 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 journal › Journal article › Research › peer-review

  14. Published

    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, Eske, 2015, In: Cell. 163, 3, p. 571-582 12 p.

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

  15. Published

    Early human dispersals within the Americas

    Moreno-Mayar, J. V., Vinner, L., de Barros Damgaard, P., de la Fuente, C., Allentoft, M. E., Vimala, T., Racimo, F., Rasmussen, S., Margaryan, A., Iraeta Orbegozo, M., Mylopotamitaki, D., Alexandersen, V., Primeau, C., Gregersen, K., Hansen, K. L., Lynnerup, N., Kjær, K., Schroeder, H., Malaspinas, A. S., Sikora, M. & 2 others, Nielsen, Rasmus & Willerslev, Eske, 7 Dec 2018, In: Science (New York, N.Y.). 362, 6419, p. 1, 1-11 12 p., eaav2621.

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

  16. 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 › Research › peer-review

  17. 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 journal › Journal article › Research › peer-review

  18. 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 journal › Journal article › Research › peer-review

  19. 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 journal › Journal article › Research › peer-review

  20. 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 journal › Journal article › Research › peer-review

  21. 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 journal › Journal article › Research › peer-review

  22. 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

  23. 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

  24. 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 journal › Journal article › Research › peer-review

  25. 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

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ID: 204201681