Microbiology

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  1. Published

    Comparative genomic analysis reveals ecological differentiation in the genus Carnobacterium

    Iskandar, C. F., Borges, F., Taminiau, B., Daube, G., Zagorec, M., Remenant, B., Leisner, Jørgen, Hansen, M. A., Sørensen, Søren Johannes, Mangavel, C., Cailliez-Grimal, C. & Revol-Junelles, A., 2017, In: Frontiers in Microbiology. 8, 14 p., 357.

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

  2. Published

    Comparison of aerobic and anaerobic [3H]leucine incorporation assays for determining pollution-induced bacterial community tolerance in copper-polluted, irrigated soils

    Aaen, K. N., Holm, Peter Engelund, Priemé, Anders, Hung, N. N. & Brandt, Kristian Koefoed, 2011, In: Environmental Toxicology and Chemistry. 30, 3, p. 588-595 8 p.

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

  3. Published

    Comparison of antibiotic-resistant bacteria and antibiotic resistance genes abundance in hospital and community wastewater: A systematic review

    Hassoun-Kheir, N., Stabholz, Y., Kreft, J., de la Cruz, R., Romalde, J. L., Nesme, Joseph, Sørensen, Søren Johannes, Smets, B. F., Graham, D. & Paul, M., 2020, In: Science of the Total Environment. 743, 11 p., 140804.

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

  4. Published

    Comparison of the occurrence of the saprophytic soil fungi in two differently cultivated field soils

    Elmholt, S. & Kjøller, Annelise Helene, 1 Jan 1989, In: Biological Agriculture and Horticulture. 6, 3, p. 229-239 11 p.

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

  5. Published

    Compatibility of X-ray computed tomography with plant gene expression, rhizosphere bacterial communities and enzyme activities

    Ganther, M., Yim, B., Ibrahim, Z., Bienert, M. D., Lippold, E., Maccario, Lorrie, Sørensen, Søren Johannes, Bienert, G. P., Vetterlein, D., Heintz-Buschart, A., Blagodatskaya, E., Smalla, K. & Tarkka, M. T., 2020, In: Journal of Experimental Botany. 71, 18, p. 5603-5614 12 p.

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

  6. Published

    Complete genome sequence of Staphylococcus aureus strain M1, a unique t024-ST8-IVa Danish methicillin-resistant S. aureus clone

    Larner-Svensson, H., Worning, P., Bartels, Mette Damkjær, Hansen, Lars Hestbjerg, Boye, K. & Westh, H., 2013, In: Genome Announcements. 1, 3, 2 p., e00336-13.

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

  7. Published

    Complete genome sequence of the cystic fibrosis pathogen Achromobacter xylosoxidans NH44784-1996 complies with important pathogenic phenotypes

    Jakobsen, T. H., Hansen, M. A., Jensen, P. Ø., Hansen, L., Riber, L., Cockburn, A. P. I., Kolpen, M., Hansen, C. R., Ridderberg, W., Eickhardt-Sørensen, S. R., Hansen, M., Kerpedjiev, P., Alhede, M., Qvortrup, K., Burmølle, M., Moser, C. E., Kühl, M., Ciofu, O., Givskov, M., Sørensen, S. J. & 2 others, Høiby, Niels & Bjarnsholt, Thomas, 2013, In: P L o S One. 8, 7, 17 p., e68484.

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

  8. Published

    Complete genome sequences of four novel Lactococcus lactis phages distantly related to the Rare 1706 Phage Species

    Kot, Witold, Neve, H., Vogensen, Finn Kvist, Heller, K. J., Sørensen, Søren Johannes & Hansen, L. H., 2014, In: Genome Announcements. 2, 4, 2 p., e00265-14.

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

  9. Published

    Complete nucleotide sequence of the self-transmissible TOL plasmid pD2RT provides new insight into arrangement of toluene catabolic plasmids

    Jutkina, J., Hansen, Lars Hestbjerg, Li, L., Heinaru, E., Vedler, E., Joesaar, M. & Heinaru, A., Jan 2013, In: Plasmid. 70, 3, p. 393-405 13 p.

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

  10. Published

    Composted sewage sludge influences the microbiome and persistence of human pathogens in soil

    Major, N., Schierstaedt, J., Jechalke, S., Nesme, Joseph, Ban, S. G., Černe, M., Sørensen, Søren Johannes, Ban, D. & Schikora, A., 2020, In: Microorganisms. 8, 7, 14 p., 1020.

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

  11. Published

    Conjugative Plasmid Conferring Resistance to Olaquindox

    Sørensen, A. H., Hansen, Lars Hestbjerg, Johannesen, E. & Sørensen, Søren Johannes, 2003, In: Antimicrobial agents and Chemotheraphy. 47, 2, p. 798-799 2 p.

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

  12. Published

    Conjugative plasmids inhibit extracellular electron transfer in Geobacter sulfurreducens

    Fessler, M., Madsen, Jonas Stenløkke & Zhang, Y., 2023, In: Frontiers in Microbiology. 14, 12 p., 1150091.

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

  13. Published

    Conjugative plasmids: Vessels of the communal gene pool

    Norman, A., Hansen, Lars Hestbjerg & Sørensen, Søren Johannes, 2009, In: Philosophical Transactions of the Royal Society of London. Biological Sciences. 364, 1527, p. 2275-2289 15 p.

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

  14. Published

    Construction and Use of Flow Cytometry Optimized Plasmid-Sensor Strains: Genomes in Flux

    Bahl, M. I., Oregaard, G., Sørensen, Søren Johannes & Hansen, Lars Hestbjerg, 2009, Horizontal Gene Transfer. Gogarten, M. B., Gogarten, J. P. & Olendzenski, L. C. (eds.). Humana Press, Vol. 532. p. 257-268 (Methods in Molecular Biology).

    Research output: Chapter in Book/Report/Conference proceeding › Book chapter › Research

  15. Published

    Construction of Simplified Microbial Consortia to Degrade Recalcitrant Materials Based on Enrichment and Dilution-to-Extinction Cultures

    Kang, D., Jacquiod, S., Herschend, J., Wei, S., Nesme, Joseph & Sørensen, Søren Johannes, 2020, In: Frontiers in Microbiology. 10, 10 p., 3010.

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

  16. Published

    Construction of a ColD cda Promoter-Based SOS-Green Fluorescent Protein Whole-Cell Biosensor with Higher Sensitivity toward Genotoxic Compounds than Constructs Based on recA, umuDC, or sulA Promoters

    Norman, A., Hansen, Lars Hestbjerg & Sørensen, Søren Johannes, 2005, In: Applied and Environmental Microbiology. 71, 5, p. 2338-2346

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

  17. Published

    Construction of biosensors to investigate physiological diversity in fermentation processes

    Han, S., Lundin, L. & Sørensen, Søren Johannes, 2011.

    Research output: Contribution to conference › Poster › Research

  18. Published

    Contamination in the draft of the human genome masquerades as lateral gene transfer

    Willerslev, Eske, Mourier, T., Hansen, Anders Johannes, Christensen, Professor Emeritus, B., Barnes, I. & Salzberg, S. L., 2002, In: DNA sequence: the journal of DNA sequencing and mapping. 13, 2, p. 75-6

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

  19. Published

    Context dependency and saturating effects of loss of rare soil microbes on plant productivity

    Hol, W. H. G., de Boer, W., de Hollander, M., Kuramae, E. E., Meisner, A. & van der Putten, W. H., 2015, In: Frontiers in Plant Science. 6, 10 p., 485.

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

  20. Published

    Continuous measurements of nitrous oxide isotopomers during incubation experiments

    Winther, M. N., Balslev-Harder, D., Christensen, Søren, Priemé, Anders, Elberling, Bo, Crosson, E. & Blunier, Thomas, 2016, In: Biogeosciences. 15, p. 767-780 19 p.

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

  21. Published

    Continuous measurements of nitrous oxide isotopomers during incubation experiments

    Winther, M., Balslev-Harder, D., Christensen, S., Priemé, Anders, Elberling, Bo, Crosson, E. & Blunier, Thomas, 16 May 2017, 24 p. Copernicus/EGU.

    Research output: Other contribution › Research

  22. Published

    Contribution to habitat types visited

    Rasmussen, Finn N., 1973, The Danish-Ethiopian Botanical expedtion 1972-1973. Friis, I. (ed.). Copenhagen: Institut for Systematisk Botanik

    Research output: Chapter in Book/Report/Conference proceeding › Report chapter › Research

  23. Published

    Contributions of rpb2 and tef1 to the phylogeny of mushrooms and allies (Basidiomycota, Fungi)

    Brandon Matheny, P., Wang, Z., Binder, M., Curtis, J. M., Lim, Y. W., Nilsson, R. H., Hughes, K. W., Hofstetter, V., Ammirati, J. F., Schoch, C. L., Langer, E., Langer, G., McLaughlin, D. J., Wilson, A. W., Frøslev, T., Ge, Z. W., Kerrigan, R. W., Slot, J. C., Yang, Z. L., Baroni, T. J. & 6 others, Fischer, M., Hosaka, K., Matsuura, K., Seidl, M. T., Vauras, J. & Hibbett, D. S., 2007, In: Molecular Phylogenetics and Evolution. 43, 2, p. 430-451 22 p.

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

  24. Published

    Control region sequences indicate that multiple externae represent multiple infections by Sacculina carcini (Cirripedia: Rhizocephala)

    Rees, D. & Glenner, Henrik, 2014, In: Ecology and Evolution. 4, 16, p. 3290-3297 8 p.

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

  25. Published

    Conversion of cropland to forest increases soil CH4 oxidation and abundance of CH4 oxidizing bacteria with stand age

    Bárcena, T. G., D'Imperio, Ludovica, Gundersen, Per, Vesterdal, Lars, Priemé, Anders & Christiansen, Jesper Riis, 2014, In: Applied Soil Ecology. 79, p. 49-58 10 p.

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

  26. Published

    Cooperative antibiotic resistance facilitates horizontal gene transfer

    Wang, Q., Wei, S., Silva, A. F. & Madsen, Jonas Stenløkke, 2023, In: ISME Journal. 17, 9 p.

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

  27. Published

    Cooperative microbial interactions drive spatial segregation in porous environments

    Wu, Y., Fu, C., Peacock, C. L., Sørensen, Søren Johannes, Redmile-Gordon, M. A., Xiao, K. Q., Gao, C., Liu, J., Huang, Q., Li, Z., Song, P., Zhu, Y., Zhou, J. & Cai, P., 2023, In: Nature Communications. 14, 1, 14 p., 4226.

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

  28. Published

    Coping with Stress: Exploring the Use of RNA-Based Approaches for the Study of Soil Microbial Communities

    Nunes, I. M., 2015, Department of Biology, Faculty of Science, University of Copenhagen. 206 p.

    Research output: Book/Report › Ph.D. thesis › Research

  29. Published

    Coping with copper: legacy effect of copper on potential activity of soil bacteria following a century of exposure

    Nunes, I. M., Jacquiod, S. J. A., Brejnrod, A. D., Holm, Peter Engelund, Johansen, A., Brandt, Kristian Koefoed, Priemé, Anders & Sørensen, Søren Johannes, 2016, In: F E M S Microbiology Ecology. 92, 11, 12 p., fiw175.

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

  30. Published

    Crispr-Cas Repurposed: Defense and Counter-defense on Mobile Genetic Elements

    Camara, Sarah, 2024, Department of Biology, Faculty of Science, University of Copenhagen. 186 p.

    Research output: Book/Report › Ph.D. thesis › Research

  31. Published

    Critical Assessment of Metagenome Interpretation: a benchmark of metagenomics software

    Sczyrba, A., Hofmann, P., Belmann, P., Koslicki, D., Janssen, S., Dröge, J., Gregor, I., Majda, S., Fiedler, J., Dahms, E., Bremges, A., Fritz, A., Garrido-Oter, R., Jørgensen, T. S., Shapiro, N., Blood, P. D., Gurevich, A., Bai, Y., Turaev, D., DeMaere, M. Z. & 47 others, Chikhi, R., Nagarajan, N., Quince, C., Meyer, F., Balvociute, M., Hansen, L. H., Sørensen, Søren Johannes, Chia, B. K. H., Denis, B., Froula, J. L., Wang, Z., Egan, R., Kang, D. D., Cook, J. J., Deltel, C., Beckstette, M., Lemaitre, C., Peterlongo, P., Rizk, G., Lavenier, D., Wu, Y., Singer, S. W., Jain, C., Strous, M., Klingenberg, H., Meinicke, P., Barton, M. D., Lingner, T., Lin, H., Liao, Y., Silva, G. G. Z., Cuevas, D. A., Edwards, R. A., Saha, S., Piro, V. C., Renard, B. Y., Pop, M., Klenk, H., Göker, M., Kyrpides, N. C., Woyke, T., Vorholt, J. A., Schulze-Lefert, P., Rubin, E. M., Darling, A. E., Rattei, T. & McHardy, A. C., 2017, In: Nature Methods. 14, 11, p. 1063-1071 9 p.

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

  32. 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

  33. Published

    Cross-feeding während der Ausbreitung auf Oberflächen

    Kovács, Á. T. & Kiesewalter, Heiko T., 2024, In: BioSpektrum. 30, 1, p. 71 1 p.

    Research output: Contribution to journal › Comment/debate › Research › peer-review

  34. Published

    Crystal structure of ATVORF273, a new fold for a thermo- and acido-stable protein from the Acidianus two-tailed virus

    Felisberto-Rodrigues, C., Blangy, S., Goulet, A., Vestergaard, G. A., Cambillau, C., Garrett, Roger Antony & Ortiz-Lombardía, M., 2012, In: P L o S One. 7, 10, 10 p.

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

  35. Published

    Cultivation of hard-to-culture subsurface mercury-resistant bacteria and discovery of new merA gene sequences

    Rasmussen, L. D., Zawadsky, C., Binnerup, S. J., Øregaard, G., Sørensen, Søren Johannes & Kroer, Niels, 2008, In: Applied and Environmental Microbiology. 74, 12, p. 3795-803 8 p.

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

  36. Published

    Cultivation-independent examination of horizontal transfer and host range of an IncP-1 plasmid among gram-positive and gram-negative bacteria indigenous to the barley rhizosphere

    Musovic, S., Oregaard, G., Kroer, Niels & Sørensen, Søren Johannes, 2006, In: Applied and Environmental Microbiology. 72, 10, p. 6687-6692 6 p.

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

  37. Published

    Culture-dependent and -independent investigations of microbial diversity on urinary catheters

    Xu, Y., Moser, Claus Ernst, Abu Al-Soud, W., Sørensen, Søren Johannes, Høiby, Niels, Nielsen, P. H. & Thomsen, T. R., 2012, In: Journal of Clinical Microbiology. 50, 12, p. 3901-3908 8 p.

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

  38. Published

    Current strategies for mobilome research

    Jørgensen, T. S., Kiil, A. S., Hansen, M. A., Sørensen, Søren Johannes & Hansen, Lars Hestbjerg, 2015, In: Frontiers in Microbiology. 5, 6 p., 750.

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

  39. Published

    Cypris metamorphosis, injection and earliest internal development of theRrizocephalan Loxothylacus panopaei (Gissler). Crustacea: Cirripedia: Rhizocephala: Sacculinidae

    Glenner, Henrik, 2001, In: Journal of Morphology. 249, 1, p. 43-75 32 p.

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

  40. Published

    DGGE and Pyrosequencing characterization of microbial community and methane-metabolizing microorganisms in livestock slurry surface crusts

    Duan, Y. (., Abu Al-Soud, W., Sørensen, Søren Johannes, Elsgaard, L., Petersen, S. O. & Boon, N., 2012.

    Research output: Contribution to conference › Poster › Research

  41. Published

    DNA extraction from dry museum beetles without conferring external morphological damage.

    Gilbert, M Thomas P, Moore, W., Melchior, L. & Worobey, M., 2007, In: PLoS ONE. 2, 3, p. e272

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

  42. Published

    DNA from Pre-Clovis Human Coprolites in Oregon, North America.

    Gilbert, M Thomas P, Jenkins, D. L., Götherstrom, A., Naveran, N., Sanchez, J. J., Hofreiter, M., Thomsen, P. F., Binladen, J., Higham, T. F. G., Yohe, R. M., Parr, R., Cummings, L. S. & Willerslev, Eske, 2008, In: Science. 320, 5877, p. 786 - 789

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

  43. Published

    DNA-and RNA-SIP Reveal Nitrospira spp. as Key Drivers of Nitrification in Groundwater-Fed Biofilters

    Gülay, A., Fowler, S. J., Tatari, K., Thamdrup, B., Albrechtsen, H., Abu Al-Soud, W., Sørensen, Søren Johannes & Smets, B. F., 2019, In: mBio. 10, 6, 14 p., e01870-19.

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

  44. Published

    DPS - a rapid method for genome sequencing of DNA-containing bacteriophages directly from a single plaque

    Kot, Witold, Vogensen, Finn Kvist, Sørensen, Søren Johannes & Hansen, Lars Hestbjerg, 2014, In: Journal of Virological Methods. 196, p. 152-156 5 p.

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

  45. Published

    Damage and repair of ancient DNA

    Mitchell, D., Willerslev, Eske & Hansen, Anders Johannes, 2005, In: Mutation Research - Fundamental and Molecular Mechanisms of Mutagenesis. 571, 1-2, p. 265-76 11 p.

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

  46. Published

    Dansk flora

    Frederiksen, S. E. (ed.), Rasmussen, Finn N. (ed.) & Seberg, Ole (ed.), 2006, København: Gyldendal. 701 p.

    Research output: Book/Report › Book › Research

  47. Published

    Darwinian and demographic forces affecting human protein coding genes.

    Nielsen, Rasmus, Hubisz, M. J., Hellmann, I., Torgerson, D., Andres, A. M., Albrechtsen, Anders, Gutenkunst, R., Adams, M. D., Cargill, M., Boyko, A., Indap, A., Bustamante, C. D. & Clark, A. G., 2009, In: Genome Research. 19, 5, p. 838-49 12 p.

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

  48. Published

    Deciphering bacteria associated with a pre-parasitic stage of the root-knot nematode Meloidogyne hapla in nemato-suppressive and nemato-conducive soils

    Topalović, O., Santos, S. S., Heuer, H., Nesme, Joseph, Kanfra, X., Hallmann, J., Sørensen, Søren Johannes & Vestergård, M., 2022, In: Applied Soil Ecology. 172, 9 p., 104344.

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

  49. Published

    Deciphering conjugative plasmid permissiveness in wastewater microbiomes

    Jacquiod, S. J. A., Brejnrod, A. D., Milani, S. M., Abu Al-Soud, W., Sørensen, Søren Johannes & Riber, Leise, Jul 2017, In: Molecular Ecology. 26, 13, p. 3556-3571 16 p.

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

  50. Published

    Deciphering horizontal transfer of plasmids and β-lactamase protection in microbial communities

    Olesen, Asmus Kalckar, 2022, Department of Biology, Faculty of Science, University of Copenhagen. 180 p.

    Research output: Book/Report › Ph.D. thesis › Research

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