Department of Biology

 

 
  1. 2021
  2. Published

    Carbon cycling in freshwater ecosystems — from pond to stream network

    Martinsen, K. T., 2021, Department of Biology, Faculty of Science, University of Copenhagen. 120 p.

    Research output: Book/ReportPh.D. thesisResearch

  3. Published

    Cardiovascular autonomic neuropathy and the impact on progression of diabetic kidney disease in type 1 diabetes

    Bjerre-Christensen, T., Winther, S. A., Tofte, N., Theilade, S., Ahluwalia, Tarun Veer Singh, Lajer, M., Hansen, T. W., Rossing, Peter & Hansen, C. S., 2021, In: B M J Open Diabetes Research & Care. 9, 1, 9 p., e002289.

    Research output: Contribution to journalJournal articleResearchpeer-review

  4. Published

    Caste-specific recognition patterns in a fungus-growing termite

    Bos, N. & van Zweden, J. S., 2021, In: Animal Behaviour. 182, p. 125-133 9 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  5. Published

    Catalogue of lichens (and some related fungi) of Navarino Island, Cape Horn Biosphere Reserve, Chile

    Etayo, J., Sancho, L. G., Gómez-Bolea, A., Søchting, Ulrik, Aguirre, F. & Rozzi, R., 2021, In: Anales del Instituto de la Patagonia. 49, p. 1-110

    Research output: Contribution to journalJournal articleResearchpeer-review

  6. Published

    Century-long records reveal shifting challenges to seagrass recovery

    Krause-Jensen, D., Duarte, C. M., Sand-Jensen, Kaj & Carstensen, J., 2021, In: Global Change Biology. 27, 3, p. 563-575 13 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  7. Published

    Cervicovaginal microbiome dynamics after taking oral probiotics

    Chen, Chen, Hao, L., Zhang, Z., Tian, L., Zhang, X., Zhu, J., Jie, Zhuye, Tong, X., Xiao, L., Zhang, T., Jin, X., Xu, X., Yang, H., Wang, J., Kristiansen, Karsten & Jia, H., 2021, In: Journal of Genetics and Genomics. 48, 8, p. 716-726 11 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  8. Published

    Characterization and description of Faecalibacterium butyricigenerans sp. nov. and F. longum sp. nov., isolated from human faeces

    Zou, Y., Lin, X., Xue, W., Tuo, L., Chen, M., Chen, X., Sun, C., Li, F., Liu, S., Dai, Y., Kristiansen, Karsten & Xiao, L., 2021, In: Scientific Reports. 11, 13 p., 11340.

    Research output: Contribution to journalJournal articleResearchpeer-review

  9. Published

    Characterization of an archaeal virus replication initiator protein and first insights into virus assembly of spindle-shaped virus SMV1

    Zhang, W., 2021, Department of Biology, Faculty of Science, University of Copenhagen. 140 p.

    Research output: Book/ReportPh.D. thesisResearch

  10. Published

    Characterization of genomic clones by targeted deep sequencing of ctDNA to monitor liver cancer

    Sun, Y., Kong, X., Yu, J., Zheng, X., Lin, M., Cheng, Z., Wang, H., An, N., Xie, Y., Zeng, S., Xue, S., Xia, M., Wei, X., Song, L., Liu, F., Fan, C., Fang, Z., Gao, L., Yang, Y., Zhu, S. & 1 others, Shi, T., 2021, In: Translational Cancer Research. 10, 10, p. 4387-4402 24 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  11. Published

    Characterization of respiratory microbial dysbiosis in hospitalized COVID-19 patients

    Zhong, H., Wang, Y., Shi, Z., Zhang, L., Ren, H., He, W., Zhang, Z., Zhu, A., Zhao, J., Xiao, F., Yang, F., Liang, T., Ye, F., Zhong, B., Ruan, S., Gan, M., Zhu, J., Li, F., Li, F., Wang, D. & 13 others, Li, J., Ren, P., Zhu, S., Yang, H., Wang, J., Kristiansen, Karsten, Tun, H. M., Chen, W., Zhong, N., Xu, X., Li, Y., Li, J. & Zhao, J., 2021, In: Cell Discovery. 7, 14 p., 23.

    Research output: Contribution to journalJournal articleResearchpeer-review

  12. Published

    Characterization of the human skin resistome and identification of two microbiota cutotypes

    Li, Z., Xia, J., Jiang, L., Tan, Y., An, Y., Zhu, X., Ruan, J., Chen, Z., Zhen, H., Ma, Y., Jie, Z., Xiao, L., Yang, H., Wang, J., Kristiansen, K., Xu, X., Jin, L., Nie, C., Krutmann, J., Liu, X. & 1 others, Wang, J., 2021, In: Microbiome. 9, 18 p., 47.

    Research output: Contribution to journalJournal articleResearchpeer-review

  13. Published

    Characterizing Conformational Changes of ASIC1a During Gating and Peptide Modulation

    Heusser, Stephanie, Sheikh, Zeshan Pervez, Borg, C. B., Galleano, I. & Pless, Stephan, 2021, p. 337A-337A.

    Research output: Contribution to conferenceConference abstract for conferenceResearchpeer-review

  14. Published

    Charge Engineering Reveals the Roles of Ionizable Side Chains in Electrospray Ionization Mass Spectrometry

    Abramsson, M. L., Sahin, C., Hopper, J. T. S., Branca, R. M. M., Danielsson, J., Xu, M., Chandler, S. A., Österlund, N., Ilag, L. L., Leppert, A., Costeira-Paulo, J., Lang, L., Teilum, K., Laganowsky, A., Benesch, J. L. P., Oliveberg, M., Robinson, C. V., Marklund, E. G., Allison, T. M., Winther, J. R. & 1 others, Landreh, M., 2021, In: JACS Au. 1, 12, p. 2385-2393 9 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  15. Published

    Charge Interactions in a Highly Charge-Depleted Protein

    Hervø-Hansen, S., Højgaard, C., Johansson, Kristoffer Enøe, Wang, Y., Wahni, K., Young, D., Messens, J., Teilum, Kaare, Lindorff-Larsen, Kresten & Winther, Jakob R., 2021, In: Journal of the American Chemical Society. 143, 6, p. 2500-2508 9 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  16. Published

    Chlorophyll-a concentrations in 82 large alpine lakes on the Tibetan Plateau during 2003–2017: temporal–spatial variations and influencing factors

    Pi, X., Feng, L., Li, W., Liu, J., Kuang, X., Shi, K., Qi, W., Chen, D. & Tang, Jing, 2021, In: International Journal of Digital Earth. 14, 6, p. 714-735 22 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  17. Published

    Chromosome-scale genomes provide new insights into subspecies divergence and evolutionary characteristics of the giant panda

    Guang, X., Lan, T., Wan, Q. H., Huang, Y., Li, H., Zhang, M., Li, R., Zhang, Z., Lei, Y., Zhang, L., Zhang, H., Li, D., Li, X., Li, H., Xu, Y., Qiao, M., Wu, D., Tang, K., Zhao, P., Lin, J-Q. & 11 others, Sahu, S. K., Liang, Q., Jiang, W., Zhang, D., Xu, X., Liu, X., Lisby, Michael, Yang, H., Kristiansen, Karsten, Liu, Huan & Fang, S., 2021, In: Science Bulletin. 66, 19, p. 2002-2013 12 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  18. Published

    Circulating Free Fatty Acid and Phospholipid Signature Predicts Early Rapid Kidney Function Decline in Patients With Type 1 Diabetes

    Afshinnia, F., Rajendiran, T. M., He, C., Byun, J., Montemayor, D., Darshi, M., Tumova, J., Kim, J., Limonte, C. P., Miller, R. G., Costacou, T., Orchard, T. J., Ahluwalia, Tarun Veer Singh, Rossing, Peter, Snell-Bergeon, J. K., de Boer, I. H., Natarajan, L., Michailidis, G., Sharma, K. & Pennathur, S., 2021, In: Diabetes Care. 44, 9, p. 2098-2106 9 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  19. Published

    Co-occurrence of contaminants in marine fish from the North East Atlantic Ocean: Implications for human risk assessment

    Ho, Q. T., Bank, M. S., Azad, A. M., Nilsen, B. M., Frantzen, S., Boitsov, S., Maage, A., Kögel, T., Sanden, M., Frøyland, L., Hannisdal, R., Hove, H., Lundebye, A. K., Nøstbakken, O. J. & Madsen, L., 2021, In: Environment International. 157, 13 p., 106858.

    Research output: Contribution to journalJournal articleResearchpeer-review

  20. Published

    Co-option of immune effectors by the hormonal signalling system triggering metamorphosis in Drosophila melanogaster

    Nunes, C., Koyama, Takashi & Sucena, É., 2021, In: PLOS Genetics. 17, 11, 24 p., e1009916.

    Research output: Contribution to journalJournal articleResearchpeer-review

  21. Published

    Co-selection of antibiotic resistance genes, and mobile genetic elements in the presence of heavy metals in poultry farm environments

    Mazhar, S. H., Li, Xuan Ji, Rashid, A., Su, J., Xu, J., Brejnrod, A. D., Su, J., Wu, Y., Zhu, Y., Zhou, S. G., Feng, R. & Rensing, C., 2021, In: Science of the Total Environment. 755, Part 2, 10 p., 142702.

    Research output: Contribution to journalJournal articleResearchpeer-review

  22. Published

    Combining Bayesian age models and genetics to investigate population dynamics and extinction of the last mammoths in northern Siberia

    Dehasque, M., Chrzanová Pecnerová, Patrícia, Muller, H., Tikhonov, A., Nikolskiy, P., Tsigankova, V. I., Danilov, G. K., Díez-del-Molino, D., Vartanyan, S., Dalén, L. & Lister, A. M., 2021, In: Quaternary Science Reviews. 259, 10 p., 106913.

    Research output: Contribution to journalJournal articleResearchpeer-review

  23. Published

    Commercially available kelp and seaweed products – valuable iodine source or risk of excess intake?

    Aakre, I., Solli, D. D., Markhus, M. W., Mæhre, H. K., Dahl, L., Henjum, S., Alexander, J., Korneliussen, P., Madsen, L. & Kjellevold, M., 2021, In: Food & Nutrition Research. 65, 17 p., 7584.

    Research output: Contribution to journalJournal articleResearchpeer-review

  24. Published

    Community-wide changes reflecting bacterial interspecific interactions in multispecies biofilms

    Sadiq, F. A., Burmølle, Mette, Heyndrickx, M., Flint, S., Lu, W., Chen, W., Zhao, J. & Zhang, H., 2021, In: Critical Reviews in Microbiology. 47, 3, p. 338-358 21 p.

    Research output: Contribution to journalReviewResearchpeer-review

  25. Published

    Comparative Genomic Analyses of Flavobacterium psychrophilum Isolates Reveals New Putative Genetic Determinants of Virulence Traits

    Castillo, D., Donati, V. L., Jørgensen, J., Sundell, K., Dalsgaard, I., Madsen, L., Wiklund, T. & Middelboe, Mathias, 2021, In: Microorganisms. 9, 8, 15 p., 1658.

    Research output: Contribution to journalJournal articleResearchpeer-review

  26. Published

    Comparative Genomic and Metabolic Analysis of Streptomyces sp. RB110 Morphotypes Illuminates Genomic Rearrangements and Formation of a New 46-Membered Antimicrobial Macrolide

    Um, S., Guo, H., Thiengmag, S., Benndorf, R., Murphy, Rob, Rischer, M., Braga, D., Poulsen, Michael, de Beer, Z. W., Lackner, G. & Beemelmanns, C., 2021, In: ACS chemical biology. 16, 8, p. 1482-1492

    Research output: Contribution to journalJournal articleResearchpeer-review

  27. Published

    Comparative Genomics Analysis of Keratin-Degrading Chryseobacterium Species Reveals Their Keratinolytic Potential for Secondary Metabolite Production

    Kang, D., Shoaie, S., Jacquiod, S., Sørensen, Søren Johannes & Ledesma-Amaro, R., 2021, In: Microorganisms. 9, 5, 15 p., 1042.

    Research output: Contribution to journalJournal articleResearchpeer-review

  28. Published

    Comparative Genomics of Novel Agrobacterium G3 Strains Isolated From the International Space Station and Description of Agrobacterium tomkonis sp. nov.

    Singh, N. K., Lavire, C., Nesme, Joseph, Vial, L., Nesme, X., Mason, C. E., Lassalle, F. & Venkateswaran, K., 2021, In: Frontiers in Microbiology. 12, 15 p., 765943.

    Research output: Contribution to journalJournal articleResearchpeer-review

  29. Published

    Comparative analysis of the alveolar microbiome in COPD, ECOPD, Sarcoidosis, and ILD patients to identify respiratory illnesses specific microbial signatures

    Gupta, S., Shariff, M., Chaturvedi, G., Sharma, A., Goel, N., Yadav, M., Mortensen, M. S., Sørensen, Søren Johannes, Mukerji, M. & Chauhan, N. S., 2021, In: Scientific Reports. 11, 11 p., 3963.

    Research output: Contribution to journalJournal articleResearchpeer-review

  30. Published

    Comparative bioacoustics: a roadmap for quantifying and comparing animal sounds across diverse taxa

    Odom, K. J., Araya-Salas, M., Morano, J. L., Ligon, R. A., Leighton, G. M., Taff, C. C., Dalziell, A. H., Billings, A. C., Germain, Ryan Ross, Pardo, M., de Andrade, L. G., Hedwig, D., Keen, S. C., Shiu, Y., Charif, R. A., Webster, M. S. & Rice, A. N., 2021, In: Biological Reviews. 96, 4, p. 1135-1159 25 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  31. Published

    Comparative transcriptome analysis reveals key epigenetic targets in SARS-CoV-2 infection

    Salgado-Albarrán, M., Navarro-Delgado, E. I., Del Moral-Morales, A., Alcaraz, N., Baumbach, J., González-Barrios, R. & Soto-Reyes, E., 2021, In: n p j Systems Biology and Applications. 7, 14 p., 21.

    Research output: Contribution to journalJournal articleResearchpeer-review

  32. Published

    Comparison of Delivery Methods in Phage Therapy against Flavobacterium columnare Infections in Rainbow Trout

    Kunttu, H. M. T., Runtuvuori-Salmela, A., Middelboe, Mathias, Clark, J. & Sundberg, L. R., 2021, In: Antibiotics. 10, 8, 19 p., 914.

    Research output: Contribution to journalJournal articleResearchpeer-review

  33. Published

    Competition-based screening helps to secure the evolutionary stability of a defensive microbiome

    Worsley, S. F., Innocent, T. M., Holmes, N. A., Al-Bassam, M. M., Schiøtt, M., Wilkinson, B., Murrell, J. C., Boomsma, Jacobus J., Yu, D. W. & Hutchings, M. I., 2021, In: BMC Biology. 19, 20 p., 205.

    Research output: Contribution to journalJournal articleResearchpeer-review

  34. Published

    Comprehensive analysis of genetic and clinical characteristics of 30 patients with X-linked juvenile retinoschisis in China

    Gao, F., Dong, J., Wang, D., Chen, F., Hu, F., Chang, Q., Xu, P., Liu, W., Li, J., Huang, Y., Wu, J. & Xu, G., 2021, In: Acta Ophthalmologica. 99, 4, p. e470-e479 10 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  35. Published

    Computational and Experimental Assessment of Backbone Templates for Computational Redesign of the Thioredoxin Fold

    Marin, Frederikke Isa, Johansson, Kristoffer Enøe, O'Shea, Charlotte, Lindorff-Larsen, Kresten & Winther, Jakob R., 2021, In: The Journal of Physical Chemistry B. 125, 40, p. 11141-11149

    Research output: Contribution to journalJournal articleResearchpeer-review

  36. Published
  37. Published

    Computational methods for chromosome-scale haplotype reconstruction

    Garg, S., 2021, In: Genome Biology. 22, 24 p., 101.

    Research output: Contribution to journalReviewResearchpeer-review

  38. Published

    Conformational Ensembles of Noncoding Elements in the SARS-CoV-2 Genome from Molecular Dynamics Simulations

    Bottaro, S., Bussi, G. & Lindorff-Larsen, Kresten, 2021, In: Journal of the American Chemical Society. 143, 22, p. 8333-8343

    Research output: Contribution to journalJournal articleResearchpeer-review

  39. Published

    Connecting the αα-hubs: same fold, disordered ligands, new functions

    Staby, L., Bugge, K., Falbe-Hansen, R. G., Salladini, Edoardo, Skriver, Karen & Kragelund, Birthe Brandt, 2021, In: Cell Communication and Signaling. 19, 5 p., 2.

    Research output: Contribution to journalLetterResearchpeer-review

  40. Published

    Conservation of Long-tailed Macaques: Implications of the Updated IUCN Status and the CoVID-19 Pandemic

    Hansen, Malene Friis, Gill, M., Nawangsari, V. A., Sanchez, K. L., Cheyne, S. M., Nijman, V. & Fuentes, A., 2021, In: Primate Conservation. 35, 11 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  41. Published

    Conservative route to genome compaction in a miniature annelid

    Martín-Durán, J. M., Vellutini, B. C., Marlétaz, F., Cetrangolo, V., Cvetesic, N., Thiel, D., Henriet, S., Grau-Bové, X., Carrillo-Baltodano, A. M., Gu, W., Kerbl, A., Marquez, Y., Bekkouche, N., Chourrout, D., Gómez-Skarmeta, J. L., Irimia, M., Lenhard, B., Worsaae, Katrine & Hejnol, A., 2021, In: Nature Ecology and Evolution. 5, 2, p. 231-242

    Research output: Contribution to journalJournal articleResearchpeer-review

  42. Published

    Contingency and determinism in the evolution of bird song sound frequency

    Friis, J. I., Dabelsteen, Torben & Cardoso, G. C., 2021, In: Scientific Reports. 11, 9 p., 11600.

    Research output: Contribution to journalJournal articleResearchpeer-review

  43. Published

    Contrasting responses of major and minor volatile compounds to warming and gall-infestation in the Arctic willow Salix myrsinites

    Swanson, L., Li, Tao & Rinnan, Riikka, 2021, In: Science of the Total Environment. 793, 10 p., 148516.

    Research output: Contribution to journalJournal articleResearchpeer-review

  44. Published

    Contrasting use of space by two migratory Afro-Palearctic warblers on their African non-breeding grounds

    Mostafa, D. A. A., Willemoes, M., Salewski, V., Ortvad, T. E., Dabelsteen, Torben & Thorup, Kasper, 2021, In: Journal of Ornithology. 162, 3, p. 813-821 9 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  45. Published

    Contributions to OH reactivity from unexplored volatile organic compounds measured by PTR-ToF-MS – a case study in a suburban forest of the Seoul metropolitan area during the Korea–United States Air Quality Study (KORUS-AQ) 2016

    Sanchez, D., Seco, Roger, Gu, D., Guenther, A., Mak, J., Lee, Y., Kim, D., Ahn, J., Blake, D., Herndon, S., Jeong, D., Sullivan, J. T., Mcgee, T., Park, R. & Kim, S., 2021, In: Atmospheric Chemistry and Physics. 21, 8, p. 6331-6345 15 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  46. Published

    Correlated transcriptional responses provide insights into the synergy mechanisms of the furazolidone, vancomycin, and sodium deoxycholate triple combination in escherichia coli

    Olivera, Catrina Diane Peralta, Cox, M. P., Rowlands, G. J. & Rakonjac, J., 2021, In: mSphere. 6, 5, 14 p., e00627-21.

    Research output: Contribution to journalJournal articleResearchpeer-review

  47. Published

    Cruise Report EUROFLEETS2 ESAW-2 ‘Evolution and spreading of the Southern Adriatic Waters'(ESAW) ESAW-2

    Kovacevic, V., Bensi, M., Giani, M., Dellisanti, Walter, Urbini, L., Pacciaroni, M., Muslim, S., Mihanovic, H., Pavlovic, M. & Karthauser, C., 2021, Relazione Interna OGS 2021/50 OCE 21.

    Research output: Chapter in Book/Report/Conference proceedingBook chapterCommunication

  48. Published

    Crustacean Fauna of the Aral Sea and its Relation to Ichthyofauna During the Modern Regression Crisis and Efforts at Restoration

    Plotnikov, I. S., Aladin, N. V., Mossin, J. & Høeg, Jens Thorvald, 2021, In: Zoological Studies. 60, 24 p., 25.

    Research output: Contribution to journalJournal articleResearchpeer-review

  49. Published

    Cryo-EM reveals the architecture of placental malaria VAR2CSA and provides molecular insight into chondroitin sulfate binding

    Wang, Kaituo, Dagil, Robert, Lavstsen, Thomas, Misra, S. K., Spliid, C. B., Wang, Y., Gustavsson, Tobias, Sandoval, D. R., Vidal-Calvo, E. E., Choudhary, Swati, Agerbæk, Mette Ørskov, Lindorff-Larsen, Kresten, Nielsen, Morten Agertoug, Theander, Thor Grundtvig, Sharp, J. S., Clausen, Thomas Mandel, Gourdon, Pontus Emanuel & Salanti, Ali, 2021, In: Nature Communications. 12, 1, 10 p., 2956.

    Research output: Contribution to journalJournal articleResearchpeer-review

  50. Published

    DEER-PREdict: Software for efficient calculation of spin-labeling EPR and NMR data from conformational ensembles

    Tesei, Giulio, Martins, J. M., Kunze, M. B. A., Wang, Y., Crehuet, R. & Lindorff-Larsen, Kresten, 2021, In: PLOS Computational Biology. 17, 1, 18 p., e1008551.

    Research output: Contribution to journalJournal articleResearchpeer-review

  51. Published

    DNA Double-Strand Break-Induced Gene Amplification in Yeast

    Strucko, T., Lisby, Michael & Mortensen, U. H., 2021, Homologous Recombination: Methods and Protocols. Aguilera, A. & Carreira, A. (eds.). Humana Press, p. 239-252 14 p. (Methods in Molecular Biology, Vol. 2153).

    Research output: Chapter in Book/Report/Conference proceedingBook chapterResearchpeer-review