Simon Rasmussen
Professor
Rasmussen Group
- 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 journal › Journal article › Research › peer-review
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Genome-wide Ancestry Patterns in Rapanui Suggest Pre-European Admixture with Native Americans
Moreno Mayar, J. Víctor, Rasmussen, Simon, Seguin-Orlando, A., Rasmussen, M., Liang, M., Flåm, S. T., Lie, B. A., Gilfillan, G. D., Nielsen, Rasmus, Thorsby, E., Willerslev, Eske & Malaspinas, A., 2014, In: Current Biology. 24, 21, p. 2518-2525Research output: Contribution to journal › Journal article › Research › peer-review
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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 journal › Journal article › Research › peer-review
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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, , 2015, In: Science (New York, N.Y.). 349, 6250, 6250.Research output: Contribution to journal › Journal article › Research › peer-review
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, , 2019, In: Nature Communications. 10, 1, 12 p., 1124.Research output: Contribution to journal › Journal article › Research › peer-review
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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, , 2 Mar 2012, In: Science (New York, N.Y.). 335, 6072, p. 1099-103 5 p.Research output: Contribution to journal › Journal article › Research › peer-review
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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 journal › Journal article › Research › peer-review
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Gut microbial changes of patients with psychotic and affective disorders: A systematic review
Vindegaard, N., Speyer, H., Nordentoft, Merete, Rasmussen, Simon & Benros, Michael Eriksen, 2021, In: Schizophrenia Research. 234, p. 41-50 10 p.Research output: Contribution to journal › Review › Research › peer-review
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Hybridization capture using short PCR products enriches small genomes by Capturing Flanking Sequences (CapFlank)
Tsangaras, K., Wales, N., Sicheritz-Pontén, T., Rasmussen, Simon, Michaux, J., Ishida, Y., Morand, S., Kampmann, Marie-Louise, Gilbert, M Thomas P & Greenwood, A. D., 2014, In: PLoS ONE. 9, 10, 10 p., e109101.Research output: Contribution to journal › Journal article › Research › peer-review
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Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes
Nielsen, H. B., Almeida, M., Juncker, A., Rasmussen, S., Li, J., Sunagawa, S., Plichta, D. R., Gautier, L., Pedersen, A. G., Le Chatelier, E., Pelletier, E., Bonde, I., Nielsen, T., Manichanh, C., Arumugam, M., Batto, J-M., dos Santos, M. B. Q., Blom, N., Borruel, N., Burgdorf, K. S. & 31 others, , 2014, In: Nature Biotechnology. 32, 8, p. 822–828 7 p.Research output: Contribution to journal › Journal article › Research › peer-review
Identification of acquired antimicrobial resistance genes
Zankari, E., Hasman, H., Cosentino, S., Vestergaard, M., Rasmussen, Simon, Lund, O., Aarestrup, F. M. & Larsen, M. V., 2012, In: Journal of Antimicrobial Chemotherapy. 67, 11, p. 2640-4 5 p.Research output: Contribution to journal › Journal article › Research › peer-review
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Immunity and mental illness: findings from a Danish population-based immunogenetic study of seven psychiatric and neurodevelopmental disorders
Nudel, R., Benros, Michael Eriksen, Krebs, M. D., Allesøe, R. L., Lemvigh, C. K., Bybjerg-Grauholm, J., Børglum, A. D., Daly, M. J., Nordentoft, Merete, Mors, O., Hougaard, D. M., Mortensen, P. B., Buil, A., Werge, Thomas, Rasmussen, Simon & Thompson, W. K., 2019, In: European Journal of Human Genetics. 27, p. 1445-1455Research output: Contribution to journal › Journal article › Research › peer-review
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 journal › Journal article › Research › peer-review
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Improved metagenome binning and assembly using deep variational autoencoders
Nissen, J. N., Johansen, Joachim, Allesoe, R. L., Sonderby, C. K., Armenteros, J. J. A., Grønbech, Christopher Heje, Jensen, Lars Juhl, Nielsen, H. B., Petersen, T. N., Winther, Ole & Rasmussen, Simon, 2021, In: Nature Biotechnology. 39, p. 555-560Research output: Contribution to journal › Journal article › Research › peer-review
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In silico assessment of virulence factors in strains of streptococcus oralis and Streptococcus mitis isolated from patients with infective endocarditis
Rasmussen, L. H., Højholt, K., Dargis, R., Christensen, J. J., Skovgaard, O., Justesen, U. S., Rosenvinge, F. S., Moser, Claus Ernst, Lukjancenko, O., Rasmussen, Simon & Nielsen, X. C., 1 Sep 2017, In: Journal of Medical Microbiology. 66, p. 1316-1323 8 p.Research output: Contribution to journal › Journal article › Research › peer-review
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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 journal › Journal article › Research › peer-review
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Mapache: a flexible pipeline to map ancient DNA
Neuenschwander, S., Cruz Dávalos, D. I., Anchieri, L., Sousa da Mota, B., Bozzi, D., Rubinacci, S., Delaneau, O., Rasmussen, Simon & Malaspinas, A., 2023, In: Bioinformatics (Online). 39, 2, 3 p.Research output: Contribution to journal › Journal article › Research › peer-review
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Markers of inflammation predict survival in newly diagnosed cirrhosis: a prospective registry study
Mynster Kronborg, T., Webel, Henry, O’Connell, M. B., Danielsen, K. V., Hobolth, L., Møller, Søren, Jensen, Rasmus Tanderup, Bendtsen, Flemming, Hansen, Torben, Rasmussen, Simon, Juel, H. B. & Kimer, N., 2023, In: Scientific Reports. 13, 11 p., 20039.Research output: Contribution to journal › Journal article › Research › peer-review
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Mass spectrometry-based proteomics data from thousands of HeLa control samples
Webel, Henry, Perez-Riverol, Y., Nielsen, A. B. & Rasmussen, Simon, 2024, In: Scientific Data. 11, 7 p., 112.Research output: Contribution to journal › Journal article › Research › peer-review
Meta-genomic analysis of toilet waste from long distance flights; a step towards global surveillance of infectious diseases and antimicrobial resistance
Nordahl Petersen, T., Rasmussen, Simon, Hasman, H., Carøe, C., Bælum, J., Schultz, A. C., Bergmark, L., Svendsen, C. A., Lund, O., Sicheritz-Pontén, T. & Aarestrup, F. M., 10 Jul 2015, In: Scientific Reports. 5, p. 11444Research output: Contribution to journal › Journal article › Research › peer-review
Metagenomic analysis of rapid gravity sand filter microbial communities suggests novel physiology of Nitrospira spp
Palomo, A., Jane Fowler, S., Gülay, A., Rasmussen, Simon, Sicheritz-Ponten, T. & Smets, B. F., Nov 2016, In: I S M E Journal. 10, 11, p. 2569-2581 13 p.Research output: Contribution to journal › Journal article › Research › peer-review
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Metagenomic species profiling using universal phylogenetic marker genes
Sunagawa, S., Mende, D. R., Zeller, G., Izquierdo-Carrasco, F., Berger, S. A., Kultima, J. R., Coelho, L. P., Arumugam, M., Tap, J., Nielsen, H. B., Rasmussen, S., Brunak, S., Pedersen, O. B., Guarner, F., de Vos, W. M., Wang, J., Li, J., Doré, J., Ehrlich, S. D., Stamatakis, A. & 1 others, , 2013, In: Nature Methods. 10, 12, p. 1196-1199 4 p.Research output: Contribution to journal › Journal article › Research › peer-review
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 journal › Journal article › Research › peer-review
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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 journal › Journal article › Research › peer-review
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Noninvasive proteomic biomarkers for alcohol-related liver disease
Niu, Lili, Thiele, M., Geyer, P. E., Rasmussen, D. N., Webel, Henry, Santos, A., Gupta, R., Meier, F., Strauss, Maximilian, Kjaergaard, M., Lindvig, K., Jacobsen, S., Rasmussen, Simon, Hansen, Torben, Krag, A. & Mann, Matthias, 2022, In: Nature Medicine. 28, 6, p. 1277-1287 11 p.Research output: Contribution to journal › Journal article › Research › peer-review
ID: 204201681
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1365
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Genome-scale cold stress response regulatory networks in ten Arabidopsis thaliana ecotypes
Research output: Contribution to journal › Journal article › Research › peer-review
Published -
608
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Bifidobacterium bifidum actively changes the gene expression profile induced by Lactobacillus acidophilus in murine dendritic cells
Research output: Contribution to journal › Journal article › Research › peer-review
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433
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Discovery, genotyping and characterization of structural variation and novel sequence at single nucleotide resolution from de novo genome assemblies on a population scale
Research output: Contribution to journal › Journal article › Research › peer-review
Published