Simon Rasmussen

Research output

Research output per year 2009 2014 2017 2018 2021 2022 2023 2024 2024

• 20056 Citations
• 104 Journal article
• 5 Letter
• 3 Preprint
• 2 Review
• 1 More
  • 1 Comment/debate

Research output per year

Research output per year

Search results

• 2024

  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

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  14 Citations (Scopus)

  86 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

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  3 Downloads (Pure)

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

  Koutrouli, M., Nastou, K., Piera Líndez, P., Bouwmeester, R., Rasmussen, S., Martens, L. & Jensen, L. J., 2024, In: Bioinformatics. 40, 2, 11 p., btae010.

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  20 Downloads (Pure)

• Gut heavy metal and antibiotic resistome of humans living in the high Arctic

  Hauptmann, A. L., Johansen, J., Stæger, F. F., Nielsen, D. S., Mulvad, G., Hanghøj, K., Rasmussen, S., Hansen, T. & Albrechtsen, A., 2024, In: Frontiers in Microbiology. 15, 15 p., 1493803.

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

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• Imputation of label-free quantitative mass spectrometry-based proteomics data using self-supervised deep learning

  Webel, H., Niu, L., Nielsen, A. B., Locard-Paulet, M., Mann, M., Jensen, L. J. & Rasmussen, S., 2024, In: Nature Communications. 15, 15 p., 5405.

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

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  2 Citations (Scopus)

  7 Downloads (Pure)

• Mass spectrometry-based proteomics data from thousands of HeLa control samples

  Webel, H., Perez-Riverol, Y., Nielsen, A. B. & Rasmussen, S., 2024, In: Scientific Data. 11, 7 p., 112.

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

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  1 Citation (Scopus)

  10 Downloads (Pure)

• 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, H., Margaryan, A., Ilardo, M., Vaughn, A., Mortensen, M. F., Nielsen, A. B., Hede, M. U., Johannsen, N. N., Rasmussen, P., Vinner, L., Renaud, G., Stern, A., Jensen, T. Z. T., Scorrano, G., Schroeder, H., Lysdahl, P., Ramsøe, A. D., Skorobogatov, A., Schork, A. J., Rosengren, A., Ruter, A., Outram, A., Timoshenko, A. A., Buzhilova, A., Coppa, A., Zubova, A., Silva, A. M., Hansen, A. J., Gromov, A., Logvin, A., Gotfredsen, A. B., Nielsen, B. H., González-Rabanal, B., Lalueza-Fox, C., McKenzie, C. J., Gaunitz, C., 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, E., Petersen, E. B., Kannegaard, E., Radina, F., Yediay, F. E., Duday, H., Gutiérrez-Zugasti, I., Merts, I., Potekhina, I., Shevnina, I., Altinkaya, I., Guilaine, J., Hansen, J., Tortosa, J. E. A., Zilhão, J., Vega, J., Pedersen, K. B., Tunia, K., Zhao, L., 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, M., 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, P., de Barros Damgaard, P., Vang Petersen, P., Martinez, P. P., Włodarczak, P., Smolyaninov, R. V., Maring, R., Menduiña, R., Badalyan, R., Iversen, R., 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, K. H., Lynnerup, N., Lawson, D. J., Sudmant, P. H., Rasmussen, S., Korneliussen, T. S., Durbin, R., Nielsen, R., Delaneau, O., Werge, T., Racimo, F., Kristiansen, K. & Willerslev, E., 2024, In: Nature. 625, 7994, p. 301-311

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

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  27 Citations (Scopus)

  60 Downloads (Pure)

• Taxometer: Improving taxonomic classification of metagenomics contigs

  Kutuzova, S., Nielsen, M., Piera, P., Nissen, J. N. & Rasmussen, S., 2024, In: Nature Communications. 15, 1, 9 p., 8357.

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

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• The evolutionary impact of childhood cancer on the human gene pool

  Stoltze, U. K., Foss-Skiftesvik, J., Hansen, T. V. O., Rasmussen, S., Karczewski, K. J., Wadt, K. A. W. & Schmiegelow, K., 2024, In: Nature Communications. 15, 15 p., 1881.

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

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  2 Citations (Scopus)

  9 Downloads (Pure)
• 2023

  Acknowledging Lack of Inclusion in Genetic Analyses-Reply

  Benros, M. E., Allesøe, R. L. & Rasmussen, S., 2023, In: JAMA Psychiatry. 80, 6, p. 647-648

  Research output: Contribution to journal › Comment/debate › Research
  1 Citation (Scopus)

• Adversarial and variational autoencoders improve metagenomic binning

  Líndez, P. P., Johansen, J., Kutuzova, S., Sigurdsson, A. I., Nissen, J. N. & Rasmussen, S., 2023, In: Communications Biology . 6, 10 p., 1073.

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

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  4 Citations (Scopus)

  18 Downloads (Pure)

• An immunogenetic investigation of 30 autoimmune and autoinflammatory diseases and their links to psychiatric disorders in a nationwide sample

  Nudel, R., Allesøe, R. L., Werge, T., Thompson, W. K., Rasmussen, S. & Benros, M. E., 2023, In: Immunology. 168, 4, p. 622-639

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

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  6 Citations (Scopus)

  40 Downloads (Pure)

• Centenarians have a diverse gut virome with the potential to modulate metabolism and promote healthy lifespan

  Johansen, J., Atarashi, K., Arai, Y., Hirose, N., Sørensen, S. J., Vatanen, T., Knip, M., Honda, K., Xavier, R. J., Rasmussen, S. & Plichta, D. R., 2023, In: Nature Microbiology. 8, p. 1064-1078 18 p.

  Research output: Contribution to journal › Journal article › Research › peer-review
  31 Citations (Scopus)

• Combinatorial batching of DNA for ultralow-cost detection of pathogenic variants

  Stoltze, U. K., Hagen, C. M., van Overeem Hansen, T., Byrjalsen, A., Gerdes, A. M., Yakimov, V., Rasmussen, S., Bækvad-Hansen, M., Hougaard, D. M., Schmiegelow, K., Hjalgrim, H., Wadt, K. & Bybjerg-Grauholm, J., 2023, In: Genome Medicine. 15, 12 p., 17.

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

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• Deep integrative models for large-scale human genomics

  Sigurdsson, A. I., Louloudis, I., Banasik, K., Westergaard, D., Winther, O., Lund, O., Ostrowski, S. R., Erikstrup, C., Pedersen, O. B., Nyegaard, M., Brunak, S., Vilhjálmsson, BJ. & Rasmussen, S., 2023, In: Nucleic Acids Symposium Series. 51, 12, 16 p.

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

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• 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, M., Werge, T., Rasmussen, S. & Benros, M. E., 2023, In: JAMA Psychiatry. 80, 2, p. 146-155 10 p.

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

  Open Access

• 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-G., 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, H., Hansen, E., Hansen, T. H., Vestergaard, H., Muilwijk, M., Blom, M. T., 't Hart, L. M., Pattou, F., Raverdy, V., Brage, S., Ridderstråle, M., Pedersen, O., Hansen, T., Banasik, K., Rasmussen, S., Brunak, S. & IMI-DIRECT consortium, 2023, In: Nature Biotechnology. 41, 3, p. 399–408 18 p.

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  37 Citations (Scopus)

  89 Downloads (Pure)

• 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, K. D., Vangipurapu, J., Vestergaard, H., Brunak, S., Franks, P. W., Frost, G., Grallert, H., Jablonka, B., McCarthy, M. I., Pavo, I., Pedersen, O., Ruetten, H., Walker, M., Adragni, K., Allesøe, R. L. L., Artati, A. A., Arumugam, M., Atabaki-Pasdar, N., Baltauss, T., Banasik, K., 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., Engelbrechtsen, L., Eriksen, R., Fan, Y., 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, U. P., Jennison, C., Johansen, J., Jonsson, A., Karaderi, T., Kaye, J., Kennedy, G., Klintenberg, M., Kuulasmaa, T., Lehr, T., Loftus, H., Lundgaard, A. T. T., 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, S., 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, C. E. E., 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.

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  6 Citations (Scopus)

  36 Downloads (Pure)

• 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., van Overeem Hansen, T., Byrjalsen, A., Sehested, A., Scheie, D., Mikkelsen, T. S., Rasmussen, S., Bak, M., Okkels, H., Callesen, M. T., Skjøth-Rasmussen, J., Gerdes, A-M., Schmiegelow, K., Mathiasen, R. & Wadt, K., 2023, In: Neuro-Oncology. 25, 4, p. 761-773

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

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  12 Citations (Scopus)

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

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

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  3 Citations (Scopus)

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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, S. & Malaspinas, A-S., 2023, In: Bioinformatics (Online). 39, 2, 3 p.

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  5 Citations (Scopus)

  11 Downloads (Pure)

• Markers of inflammation predict survival in newly diagnosed cirrhosis: a prospective registry study

  Mynster Kronborg, T., Webel, H., O’Connell, M. B., Danielsen, K. V., Hobolth, L., Møller, S., Jensen, R. T., Bendtsen, F., Hansen, T., Rasmussen, S., Juel, H. B. & Kimer, N., 2023, In: Scientific Reports. 13, 11 p., 20039.

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  3 Citations (Scopus)

  10 Downloads (Pure)
• 2022

  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, L. H., 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, J., Nurk, S., Oliker, L., Paoli, L., Peterlongo, P., Piro, V. C., Porter, J. S., Rasmussen, S., 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, S. J., 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

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  134 Citations (Scopus)

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• Cross-generational bacterial strain transfer to an infant after fecal microbiota transplantation to a pregnant patient: a case report

  Wei, S., Jespersen, M. L., Baunwall, S. M. D., Myers, P. N., Smith, E. M., Dahlerup, J. F., Rasmussen, S., Nielsen, H. B., Licht, T. R., Bahl, M. I. & Hvas, C. L., 2022, In: Microbiome. 10, 1, 14 p., 193.

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  5 Citations (Scopus)

  14 Downloads (Pure)

• 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, M., Børglum, A. D., Hougaard, D. M., Werge, T., Rasmussen, S. & Benros, M. E., 2022, In: Science Advances. 8, 26, eabi7293.

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

• Genome binning of viral entities from bulk metagenomics data

  Johansen, J., Plichta, D. R., Nissen, J. N., Jespersen, M. L., Shah, S. A., Deng, L., Stokholm, J., Bisgaard, H., Nielsen, D. S., Sørensen, S. J. & Rasmussen, S., 2022, In: Nature Communications. 13, 12 p., 965.

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  48 Citations (Scopus)

  56 Downloads (Pure)

• Machine learning and deep learning applications in microbiome research

  Hernandez Medina, R., Kutuzova, S., Nielsen, K. N., Johansen, J., Hansen, L. H., Nielsen, M. & Rasmussen, S., 2022, In: ISME Communications. 2, 7 p., 98.

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• Noninvasive proteomic biomarkers for alcohol-related liver disease

  Niu, L., Thiele, M., Geyer, P. E., Rasmussen, D. N., Webel, H. E., Santos, A., Gupta, R., Meier, F., Strauss, M., Kjaergaard, M., Lindvig, K., Jacobsen, S., Rasmussen, S., Hansen, T., Krag, A. & Mann, M., 2022, In: Nature Medicine. 28, 6, p. 1277-1287 11 p.

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  114 Citations (Scopus)

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• 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, T., McColl, H., Margaryan, A., Ilardo, M., Vaughn, A., Mortensen, M. F., Nielsen, A. B., Hede, M. U., Rasmussen, P., Vinner, L., Renaud, G., Stern, A., Trolle Jensen, T. Z., Johannsen, N. N., Scorrano, G., Schroeder, H., Lysdahl, P., Ramsøe, A. D., Skorobogatov, A., Schork, A. J., Rosengren, A., Ruter, A., Outram, A., Timoshenko, A. A., Buzhilova, A., Coppa, A., Zubova, A., Silva, A. M., Hansen, A. J., Gromov, A., Logvin, A., Gotfredsen, A. B., Nielsen, B. H., González-Rabanal, B., Lalueza-Fox, C., McKenzie, C. J., Gaunitz, C., 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, E., Petersen, E. B., Kannegaard, E., Radina, F., Yediay, F. E., Duday, H., Gutiérrez-Zugasti, I., Potekhina, I., Shevnina, I., Altinkaya, I., Guilaine, J., Hansen, J., Tortosa, J. E. A., Zilhão, J., Vega, J., Pedersen, K. B., Tunia, K., Zhao, L., 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, M., 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, P., Damgaard, P. D. B., Petersen, P. V., Martinez, P. P., Włodarczak, P., Smolyaninov, R. V., Maring, R., Menduiña, R., Badalyan, R., Iversen, R., 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, K. H., Lynnerup, N., Lawson, D. J., Sudmant, P. H., Rasmussen, S., Korneliussen, T., Durbin, R., Nielsen, R., Delaneau, O., Werge, T., Racimo, F., Kristiansen, K. & Willerslev, E., 2022, p. 1-71, (bioRxiv).

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• SCAI promotes error-free repair of DNA interstrand crosslinks via the Fanconi anemia pathway

  Schubert, L., Hendriks, I. A., Hertz, E. P. T., Wu, W., Sellés-Baiget, S., Hoffmann, S., Viswalingam, K. S., Gallina, I., Pentakota, S., Benedict, B., Johansen, J., Apelt, K., Luijsterburg, M. S., Rasmussen, S., Lisby, M., Liu, Y., Nielsen, M. L., Mailand, N. & Duxin, J. P., 2022, In: EMBO Reports. 23, 4, 20 p., e53639.

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• 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., Fotakis, A. K., Iraeta-Orbegozo, M., Vågene, Å. J., Denham, S. D., Christophersen, A., Stenøien, H. K., Vieira, F. G., Liu, S., Günther, T., Kivisild, T., Moseng, O. G., Skar, B., Cheung, C., Sandoval-Velasco, M., Wales, N., Schroeder, H., Campos, P. F., Guðmundsdóttir, V. B., Sicheritz-Ponten, T., Petersen, B., Halgunset, J., Gilbert, E., Cavalleri, G. L., Hovig, E., Kockum, I., Olsson, T., Alfredsson, L., Hansen, T. F., Werge, T., Willerslev, E., Balloux, F., Marques-Bonet, T., Lalueza-Fox, C., Nielsen, R., Stefánsson, K., Helgason, A. & Gilbert, M. T. P., 2022, In: Current Biology. 32, 21, p. 4743-4751.e6

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• Whole-Exome Sequencing Implicates Neuronal Calcium Channel with Familial Atrial Fibrillation

  Vad, O. B., Yan, Y., Denti, F., Ahlberg, G., Refsgaard, L., Bomholtz, S. H., Santos, J. L., Rasmussen, S., Haunsø, S., Svendsen, J. H., Christophersen, I. E., Schmitt, N., Olesen, M. S. & Bentzen, B. H., 2022, In: Frontiers in Genetics. 13, 8 p., 806429.

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• 2021

  A large-scale investigation into the role of classical HLA loci in multiple types of severe infections, with a focus on overlaps with autoimmune and mental disorders

  Nudel, R., Allesøe, R. L., Thompson, W. K., Werge, T., Rasmussen, S. & Benros, M. E., 2021, In: Journal of Translational Medicine. 19, 230.

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  4 Citations (Scopus)

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• Defining NASH from a multi-omics systems biology perspective

  Niu, L., Sulek, K., Vasilopoulou, C. G., Santos, A., Wewer Albrechtsen, N. J., Rasmussen, S., Meier, F. & Mann, M., 2021, In: Journal of Clinical Medicine. 10, 20, 22 p., 4673.

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• Extension of Plant Phenotypes by the Foliar Microbiome

  Hawkes, C. V., Kjøller, R., Raaijmakers, J. M., Riber, L., Christensen, S., Rasmussen, S., Christensen, J. H., Dahl, A. B., Westergaard, J. C., Nielsen, M., Brown-Guedira, G. & Hestbjerg Hansen, L., 2021, In: Annual Review of Plant Biology. 72, p. 823-846 24 p.

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  31 Citations (Scopus)

• 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, S., Allesøe, R. L., Werge, T., Mors, O., Børglum, A. D., Hougaard, D. M., Mortensen, P. B., Nordentoft, M. & Benros, M. E., 2021, In: Brain, Behavior, and Immunity. 91, p. 10-23 14 p.

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• Gut microbial changes of patients with psychotic and affective disorders: A systematic review

  Vindegaard, N., Speyer, H., Nordentoft, M., Rasmussen, S. & Benros, M. E., 2021, In: Schizophrenia Research. 234, p. 41-50 10 p.

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  37 Citations (Scopus)

• Improved metagenome binning and assembly using deep variational autoencoders

  Nissen, J. N., Johansen, J., Allesoe, R. L., Sonderby, C. K., Armenteros, J. J. A., Gronbech, C. H., Jensen, L. J., Nielsen, H. B., Petersen, T. N., Winther, O. & Rasmussen, S., 2021, In: Nature Biotechnology. 39, p. 555-560

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• Streptococcus pseudopneumoniae: Use of whole-genome sequences to validate species identification methods

  Jensen, C. S., Iversen, K. H., Dargis, R., Shewmaker, P., Rasmussen, S., Christensen, J. J. & Nielsen, X. C., 2021, In: Journal of Clinical Microbiology. 59, 2, 11 p., e02503-20.

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• The ubiquitin ligase RFWD3 is required for translesion DNA synthesis

  Gallina, I., Hendriks, I. A., Hoffmann, S., Larsen, N. B., Johansen, J., Colding-Christensen, C. S., Schubert, L., Sellés-Baiget, S., Fábián, Z., Kühbacher, U., Gao, A. O., Räschle, M., Rasmussen, S., Nielsen, M. L., Mailand, N. & Duxin, J. P., 2021, In: Molecular Cell. 81, 3, p. 442-458.e9 27 p.

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• 2020

  A draft genome sequence of the elusive giant squid, Architeuthis dux

  da Fonseca, R. R., Couto, A., Machado, A. M., Brejova, B., Albertin, C. B., Silva, F., Gardner, P., Baril, T., Hayward, A., Campos, A., Ribeiro, Â. M., Barrio-Hernandez, I., Hoving, H-J., Tafur-Jimenez, R., Chu, C., Frazão, B., Petersen, B., Peñaloza, F., Musacchia, F., Alexander, G. C. & 24 others, Osório, H., Winkelmann, I., Simakov, O., Rasmussen, S., Rahman, M. Z., Pisani, D., Vinther, J., Jarvis, E., Zhang, G., Strugnell, J. M., Castro, L. F. C., Fedrigo, O., Patricio, M., Li, Q., Rocha, S., Antunes, A., Wu, Y., Ma, B., Sanges, R., Vinar, T., Blagoev, B., Sicheritz-Pontén, T., Nielsen, R. & Gilbert, M. T. P., 2020, In: GigaScience. 9, 1, 12 p., giz152.

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• 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.

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• 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, E., Scorrano, G., McColl, H., Buzhilova, A., Fox, A., Albrechtsen, A., Schütz, B., Skar, B., Arcini, C., Lundstrøm, I., Cheng, J., Stenderup, J., Iversen, K. H., Arge, S. V., Ellingvåg, S., Orlando, L., Pentz, P., Jessen, M. D., Pedersen, A., Jørkov, M. L., Lynnerup, N., Gilbert, M. T. P., Allentoft, M. E., Sindbæk, S. M., Kristiansen, K., Nielsen, R., Werge, T. & Willerslev, E., 2020, In: Nature. 585, 7825, p. 390-396 7 p.

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  123 Citations (Scopus)

• 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, S., 17 Feb 2020, In: Scientific Reports. 10, 1, 11 p., 2728.

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• 2019

  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, S. & Schroeder, H., 2019, In: Nature Communications. 10, 10 p., 5520.

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• 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

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  183 Citations (Scopus)

• 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, S., De Masi, F., Pedersen, H., Banasik, K., Thomas, C., Lundgaard, A., Nielsen, A., Mazzoni, G., Karaderi, T., Rasmussen, S., Johansen, J., Allesøe, R., Arumugam, M., Allin, K., Hansen, T., Hansen, T., Jonsson, A., Pedersen, O., Dutta, A., Vogt, J., Vestergaard, H. & IMI-DIRECT consortium, 2019, In: Journal of Hepatology. 71, 3, p. 594-602 9 p.

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• 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-Ponten, T., 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.

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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, M. E., Krebs, M. D., Allesøe, R. L., Lemvigh, C. K., Bybjerg-Grauholm, J., Børglum, A. D., Daly, M. J., Nordentoft, M., Mors, O., Hougaard, D. M., Mortensen, P. B., Buil, A., Werge, T., Rasmussen, S. & Thompson, W. K., 2019, In: European Journal of Human Genetics. 27, p. 1445-1455

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• The population history of northeastern Siberia since the Pleistocene

  Sikora, M., Pitulko, V. V., Sousa, V. C., Allentoft, M. E., Vinner, L., Rasmussen, S., Margaryan, A., Damgaard, P. D. B., de la Fuente Castro, C., Renaud, G., Yang, M. A., Fu, Q., Dupanloup, I., Giampoudakis, K., Nogues, D. B., Rahbek, C., Kroonen, G., Peyrot, M., McColl, H., Vasilyev, S. V. & 27 others, Veselovskaya, E., Gerasimova, M., Pavlova, E. Y., Chasnyk, V. G., Nikolskiy, P. A., Gromov, A. V., Khartanovich, V. I., Moiseyev, V., Grebenyuk, P. S., Fedorchenko, A. Y., Lebedintsev, A. I., Slobodin, S. B., Malyarchuk, B. A., Martiniano, R., Meldgaard, M., Arppe, L., Palo, J. U., Sundell, T., Mannermaa, K., Putkonen, M., Alexandersen, V., Primeau, C., Baimukhanov, N., Malhi, R. S., Sjögren, K. G., Nielsen, R. & Willerslev, E., 2019, In: Nature. 570, p. 182–188

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