Research output per year
Research output per year
- 32 results
Search results
-
2024
ARGprofiler—a pipeline for large-scale analysis of antimicrobial resistance genes and their flanking regions in metagenomic datasets
Martiny, H.-M., Pyrounakis, N., Petersen, T. N., Lukjančenko, O., Aarestrup, F. M., Clausen, P. T. L. C. & Munk, P., 2024, In: Bioinformatics. 40, 3, 8 p., btae086.Research output: Contribution to journal › Journal article › Research › peer-review
Open AccessFile68 Downloads (Orbit) -
Metagenomic analysis of sewage for surveillance of bacterial pathogens: A release experiment to determine sensitivity
Kohle, S., Petersen, T. N., Vigre, H., Johansson, M. H. K. & Aarestrup, F. M., 2024, In: PLOS ONE. 19, 5, 12 p., e0300733.Research output: Contribution to journal › Journal article › Research › peer-review
Open AccessFile65 Downloads (Orbit) -
The European livestock resistome
Munk, P., Yang, D., Röder, T., Maier, L., Petersen, T. N., Duarte, A. S. R., Clausen, P. T. L. C., Brinch, C., Van Gompel, L., Luiken, R., Wagenaar, J. A., Schmitt, H., Heederik, D. J. J., Mevius, D. J., Smit, L. A. M., EFFORT consortium, Bosser, A. & Aarestrup, F. M., 2024, In: mSystems. 9, 4, 20 p., e0132823.Research output: Contribution to journal › Journal article › Research › peer-review
Open AccessFile242 Downloads (Orbit) -
Utilizing co-abundances of antimicrobial resistance genes to identify potential co-selection in the resistome
Martiny, H.-M., Munk, P., Brinch, C., Aarestrup, F. M., Calle, M. L. & Petersen, T. N., 2024, In: Microbiology Spectrum. 12, 7, e0410823.Research output: Contribution to journal › Journal article › Research › peer-review
Open AccessFile34 Downloads (Orbit) -
2023
Antimicrobial resistance monitoring in the Danish swine production by phenotypic methods and metagenomics from 1999 to 2018
Duarte, A. S. R., Marques, A. R., Andersen, V. D., Korsgaard, H. B., Mordhorst, H., Møller, F. D., Petersen, T. N., Vigre, H., Hald, T. & Aarestrup, F. M., 2023, In: Eurosurveillance. 28, 20, 11 p.Research output: Contribution to journal › Journal article › Research › peer-review
Open AccessFile71 Downloads (Orbit) -
Importance of mobile genetic elements for dissemination of antimicrobial resistance in metagenomic sewage samples across the world
Johansson, M. H. K., Aarestrup, F. M. & Petersen, T. N., 2023, In: P L o S One. 18, 10, 17 p., e0293169.Research output: Contribution to journal › Journal article › Research › peer-review
Open AccessFile83 Downloads (Orbit) -
2022
A curated data resource of 214K metagenomes for characterization of the global antimicrobial resistome
Martiny, H.-M., Munk, P., Brinch, C., Aarestrup, F. M. & Petersen, T. N., 2022, In: PLOS Biology. 20, 9, 11 p., e3001792.Research output: Contribution to journal › Journal article › Research › peer-review
Open AccessFile114 Downloads (Orbit) -
Genomic analysis of sewage from 101 countries reveals global landscape of antimicrobial resistance
Munk, P., Brinch, C., Møller, F. D., Petersen, T. N., Hendriksen, R. S., Seyfarth, A. M., Kjeldgaard, J. S., Svendsen, C. A., van Bunnik, B., Berglund, F., Global Sewage Surveillance Consortium, Larsson, D. G. J., Koopmans, M., Woolhouse, M. & Aarestrup, F. M., 2022, In: Nature Communications. 13, 1, 16 p., 7251.Research output: Contribution to journal › Journal article › Research › peer-review
Open AccessFile93 Downloads (Orbit) -
Global Distribution of mcr Gene Variants in 214K Metagenomic Samples
Martiny, H.-M., Munk, P., Brinch, C., Szarvas, J., Aarestrup, F. M. & Petersen, T. N., 2022, In: mSystems. 7, 2, 15 p., e0010522.Research output: Contribution to journal › Journal article › Research › peer-review
Open AccessFile131 Downloads (Orbit) -
2021
Detection of mobile genetic elements associated with antibiotic resistance in Salmonella enterica using a newly developed web tool: MobileElementFinder
Johansson, M. H. K., Bortolaia, V., Tansirichaiya, S., Aarestrup, F. M., Roberts, A. P. & Petersen, T. N., 2021, In: Journal of Antimicrobial Chemotherapy. 76, 1, p. 101–109Research output: Contribution to journal › Journal article › Research › peer-review
Open AccessFile339 Downloads (Orbit) -
Metagenomics-Based Approach to Source-Attribution of Antimicrobial Resistance Determinants - Identification of Reservoir Resistome Signatures
Duarte, A. S. R., Röder, T., Van Gompel, L., Petersen, T. N., Hansen, R. B., Hansen, I. M., Bossers, A., Aarestrup, F. M., Wagenaar, J. A. & Hald, T., 2021, In: Frontiers in Microbiology. 11, 17 p., 601407.Research output: Contribution to journal › Journal article › Research › peer-review
Open AccessFile141 Downloads (Orbit) -
2020
Data integration for prediction of weight loss in randomized controlled dietary trials
Nielsen, R. L., Helenius, M., Garcia, S. L., Roager, H. M., Aytan-Aktug, D., Hansen, L. B. S., Lind, M. V., Vogt, J. K., Dalgaard, M. D., Bahl, M. I., Jensen, C. B., Muktupavela, R., Warinner, C., Aaskov, V., Gøbel, R., Kristensen, M., Frøkiær, H., Sparholt, M. H., Christensen, A. F. & Vestergaard, H. & 8 others, , 2020, In: Scientific Reports. 10, 1, 15 p., 20103.Research output: Contribution to journal › Journal article › Research › peer-review
Open AccessFile173 Downloads (Orbit) -
Metagenomics-Based Proficiency Test of Smoked Salmon Spiked with a Mock Community
Sala, C., Mordhorst, H., Grützke, J., Brinkmann, A., Petersen, T. N., Poulsen, C. S., Cotter, P. D., Crispie, F., Ellis, R. J., Castellani, G., Amid, C., Hakhverdyan, M., Guyader, S. L., Manfreda, G., Mossong, J., Nitsche, A., Ragimbeau, C., Schaeffer, J., Schlundt, J. & Tay, M. Y. F. & 4 others, , 2020, In: Microorganisms. 8, 12, 16 p., 1861.Research output: Contribution to journal › Journal article › Research › peer-review
Open AccessFile56 Downloads (Orbit) -
Proficiency Testing of Metagenomics-Based Detection of Food-Borne Pathogens Using a Complex Artificial Sequencing Dataset
Höper, D., Grützke, J., Brinkmann, A., Mossong, J., Matamoros, S., Ellis, R. J., Deneke, C., Tausch, S. H., Cuesta, I., Monzón, S., Juliá, M., Petersen, T. N., Hendriksen, R. S., Pamp, S. J., Leijon, M., Hakhverdyan, M., Walsh, A. M., Cotter, P. D., Chandrasekaran, L. & Tay, M. Y. F. & 6 others, , 2020, In: Frontiers in Microbiology. 11, 11 p., 575377.Research output: Contribution to journal › Journal article › Research › peer-review
Open AccessFile86 Downloads (Orbit) -
The gut microbiome but not the resistome is associated with urogenital schistosomiasis in preschool-aged children
Osakunor, D. N. M., Munk, P., Mduluza, T., Petersen, T. N., Brinch, C., Ivens, A., Chimponda, T., Amanfo, S. A., Murray, J., Woolhouse, M. E. J., Aarestrup, F. M. & Mutapi, F., 2020, In: Communications Biology. 3, 1, 11 p., 155.Research output: Contribution to journal › Journal article › Research › peer-review
Open AccessFile112 Downloads (Orbit) -
2019
Global monitoring of antimicrobial resistance based on metagenomics analyses of urban sewage
Hendriksen, R. S., Munk, P., Njage, P. M. K., van Bunnik, B., McNally, L., Lukjancenko, O., Röder, T., Nieuwenhuijse, D., Karlsmose Pedersen, S., Kjeldgaard, J. S., 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. & Global, S. S. P. C. & 14 others, , 2019, In: Nature Communications. 10, 12 p., 1124.Research output: Contribution to journal › Journal article › Research › peer-review
Open AccessFile665 Downloads (Orbit) -
Proficiency testing of virus diagnostics based on bioinformatics analysis of simulated in silico high-throughput sequencing datasets
Brinkmann, A., Andrusch, A., Belka, A., Wylezich, C., Höper, D., Pohlmann, A., Petersen, T. N., Lucas, P., Blanchard, Y., Papa, A., Melidou, A., Oude Munnink, B. B., Matthijnssens, J., Deboutte, W., Ellis, R. J., Hansmann, F., Baumgärtner, W., van der Vries, E., Osterhaus, A. & Camma, C. & 16 others, , 2019, In: Journal of Clinical Microbiology. 57, 8, 12 p., e00466-19.Research output: Contribution to journal › Journal article › Research › peer-review
Open AccessFile477 Downloads (Orbit) -
SignalP 5.0 improves signal peptide predictions using deep neural networks
Almagro Armenteros, J. J., Tsirigos, K. D., Sønderby, C. K., Petersen, T. N., Winther, O., Brunak, S., von Heijne, G. & Nielsen, H., 2019, In: Nature Biotechnology. 37, p. 420-423Research output: Contribution to journal › Journal article › Research › peer-review
Open AccessFile3029 Downloads (Orbit) -
2018
Abundance and diversity of the faecal resistome in slaughter pigs and broilers in nine European countries
Munk, P., Knudsen, B. E., Lukjacenko, O., Duarte, A. S. R., Van Gompel, L., Luiken, R. E. C., Smit, L. A. M., Schmitt, H., Garcia, A. D., Hansen, R. B., Petersen, T. N., Bossers, A., Ruppé, E., Graveland, H., van Essen, A., Gonzalez-Zorn, B., Moyano, G., Sanders, P., Chauvin, C. & David, J. & 21 others, , 1 Aug 2018, In: Nature Microbiology. 3, 8, p. 898-908Research output: Contribution to journal › Journal article › Research › peer-review
Open AccessFile1242 Downloads (Orbit) -
2017
MGmapper: Reference based mapping and taxonomy annotation of metagenomics sequence reads
Petersen, T. N., Lukjancenko, O., Thomsen, M. C. F., Sperotto, M. M., Lund, O., Aarestrup, F. M. & Sicheritz-Pontén, T., 2017, In: P L o S One. 12, 5, 13 p., e0176469.Research output: Contribution to journal › Journal article › Research › peer-review
Open AccessFile807 Downloads (Orbit) -
Norgal: Extraction and de novo assembly of mitochondrial DNA from whole-genome sequencing data
Al-Nakeeb, K. A. A., Petersen, T. N. & Sicheritz-Pontén, T., 2017, In: B M C Bioinformatics. 18, 1, 7 p., 510.Research output: Contribution to journal › Journal article › Research › peer-review
Open AccessFile739 Downloads (Orbit) -
Protein features as determinants of wild-type glycoside hydrolase thermostability
Geertz-Hansen, H. M., Kiemer, L., Nielsen, M., Stanchev, K., Blom, N., Brunak, S. & Petersen, T. N., 2017, In: Proteins: Structure, Function, and Bioinformatics. 85, 11, p. 2036-2044Research output: Contribution to journal › Journal article › Research › peer-review
Open AccessFile489 Downloads (Orbit) -
2015
Meta-genomic analysis of toilet waste from long distance flights; a step towards global surveillance of infectious diseases and antimicrobial resistance
Petersen, T. N., Rasmussen, S., Hasman, H., Carøe, C., Bælum, J., Schultz, A. C., Bergmark, L., Svendsen, C. A., Lund, O., Sicheritz-Pontén, T. & Aarestrup, F. M., 2015, In: Scientific Reports. 5, 9 p., 11444.Research output: Contribution to journal › Journal article › Research › peer-review
Open AccessFile610 Downloads (Orbit) -
2014
Cofactory: Sequence-based prediction of cofactor specificity of Rossmann folds
Geertz-Hansen, H. M., Blom, N., Feist, A., Brunak, S. & Petersen, T. N., 2014, In: Proteins: Structure, Function, and Bioinformatics. 82, 9, p. 1819-1828Research output: Contribution to journal › Journal article › Research › peer-review
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Compass: A hybrid method for clinical and biobank data mining
Krysiak-Baltyn, K., Petersen, T. N., Audouze, K. M. L., Jørgensen, N., Ängquist, L. & Brunak, S., 2014, In: Journal of Biomedical Informatics. 47, p. 160-170Research output: Contribution to journal › Journal article › Research › peer-review
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2013
Prediction of Disease Causing Non-Synonymous SNPs by the Artificial Neural Network Predictor NetDiseaseSNP.
Johansen, M. B., Gonzalez-Izarzugaza, J. M., Brunak, S., Petersen, T. N. & Gupta, R., 2013, In: PloS one.. 8, 7, e68370.Research output: Contribution to journal › Journal article › Research › peer-review
Open AccessFile546 Downloads (Orbit) -
2011
A Systematic Study of Site-specific GalNAc-type O-Glycosylation Modulating Proprotein Convertase Processing
Schjoldager, K.T.-B. G., Vester-Christensen, M. B., Goth, C. K., Petersen, T. N., Brunak, S., Bennett, E. P., Levery, S. B. & Clausen, H., 2011, In: Journal of Biological Chemistry. 286, 46, p. 40122-40132Research output: Contribution to journal › Journal article › Research › peer-review
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2010
CPHmodels-3.0--remote homology modeling using structure-guided sequence profiles
Nielsen, M., Lundegaard, C., Lund, O. & Petersen, T. N., 2010, In: Nucleic Acids Research. 38, p. W576-W581Research output: Contribution to journal › Journal article › Research › peer-review
Open AccessFile581 Downloads (Orbit) -
NetTurnP – Neural Network Prediction of Beta-turns by Use of Evolutionary Information and Predicted Protein Sequence Features
Petersen, B., Lundegaard, C. & Petersen, T. N., 2010, In: P L o S One. 5, 11Research output: Contribution to journal › Journal article › Research › peer-review
Open AccessFile552 Downloads (Orbit) -
2009
A generic method for assignment of reliability scores applied to solvent accessibility predictions
Petersen, B., Petersen, T. N., Andersen, P., Nielsen, M. & Lundegaard, C., 2009, In: BMC Structural Biology. 9, p. 51Research output: Contribution to journal › Journal article › Research › peer-review
Open AccessFile387 Downloads (Orbit) -
2007
Midbrain expression of Delta-like 1 homologue is regulated by GDNF and is associated with dopaminergic differentiation
Christophersen, N. S., Gronborg, M., Petersen, T. N., Fjord-Larsen, L., Jorgensen, J. R., Juliusson, B., Blom, N., Rosenblad, C. & Brundin, P., 2007, In: Experimental Neurology. 2, p. 791-801Research output: Contribution to journal › Journal article › Research › peer-review
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2006
Identification of novel genes regulated in the developing human ventral mesencephalon
Jørgensen, J., Juliusson, B., Henriksen, K., Hansen, C., Knudsen, S., Petersen, T. N., Blom, N., Seiger, A. & Wahlberg, L., 2006, In: Experimental Neurology. 198, 2, p. 427-437Research output: Contribution to journal › Journal article › Research › peer-review