Department of Biology

 

 
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  1. 2022
  2. Published

    The Behaviour of Short Linear Motifs in the DREB2A Transcription Factor and the Effect of Molecular Context

    Theisen, Frederik Friis, 2022, Department of Biology, Faculty of Science, University of Copenhagen. 160 p.

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

  3. Published

    αα-hub coregulator structure and flexibility determine transcription factor binding and selection in regulatory interactomes

    Theisen, Frederik Friis, Salladini, Edoardo, Davidsen, R., Rasmussen, C. J., Staby, L., Kragelund, Birthe Brandt & Skriver, Karen, 2022, In: Journal of Biological Chemistry. 298, 6, 16 p., 101963.

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

  4. Published

    PAMP-triggered genetic reprogramming involves widespread alternative transcription initiation and an immediate transcription factor wave

    Thieffry, A., López Márquez, Diego, Lange, Jette Bornholdt, Gholami Malekroudi, M., Bressendorff, Simon, Barghetti, A., Sandelin, Albin Gustav & Brodersen, Peter, 2022, In: The Plant Cell. 34, 7, 23 p.

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

  5. Published

    Conformational ensembles of intrinsically disordered proteins and flexible multidomain proteins

    Thomasen, Emil & Lindorff-Larsen, Kresten, 2022, In: Biochemical Society Transactions. 50, 1, p. 541-554 14 p.

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

  6. Published

    Improving Martini 3 for Disordered and Multidomain Proteins

    Thomasen, Emil, Pesce, Francesco, Roesgaard, M. A., Tesei, Giulio & Lindorff-Larsen, Kresten, 2022, In: Journal of Chemical Theory and Computation. 18, 4, p. 2033-2041 9 p.

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

  7. Published

    Effects of Lifetime Exposures to Environmental Contaminants on the Adult Gut Microbiome

    Thompson, K. N., Oulhote, Y., Weihe, P., Wilkinson, J. E., Ma, S., Zhong, H., Li, J., Kristiansen, Karsten, Huttenhower, C. & Grandjean, P., 2022, In: Environmental Science & Technology. 56, 23, p. 16985-16995 11 p.

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

  8. Published

    Asthma and Wheeze Severity and the Oropharyngeal Microbiota in Children and Adolescents

    Thorsen, J., Stokholm, J., Rasmussen, M. A., Roggenbuck-Wedemeyer, M., Vissing, N. H., Mortensen, M. S., Brejnrod, A. D., Fleming, L., Bush, A., Roberts, G., Singer, F., Frey, U., Hedlin, G., Nordlund, B., Murray, C. S., Abdel-Aziz, M. I., Hashimoto, S., van Aalderen, W., Maitland-van der Zee, A. H., Shaw, D. & 13 others, Fowler, S. J., Sousa, A., Sterk, P. J., Chung, K. F., Adcock, I. M., Djukanovic, R., Auffray, C., Bansal, A. T., Wagers, S., Chawes, Bo Lund Krogsgaard, Bønnelykke, Klaus, Sørensen, Søren Johannes & Bisgaard, H., 2022, In: Annals of the American Thoracic Society. 19, 12, p. 2031-2043 13 p.

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

  9. Published

    Benchmarking freely available HLA typing algorithms across varying genes, coverages and typing resolutions

    Thuesen, N. H., Klausen, M. S., Gopalakrishnan, Shyam, Trolle, T. & Renaud, Gabriel, 2022, In: Frontiers in Immunology. 13, 15 p., 987655.

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

  10. Published

    DeepLoc 2.0: multi-label subcellular localization prediction using protein language models

    Thumuluri, V., Almagro Armenteros, J. J., Johansen, A. R., Nielsen, H. & Winther, Ole, 2022, In: Nucleic Acids Research. 50, W1, p. W228-W234

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

  11. Published

    Whole-genome sequence of the planarian Dugesia japonica combining Illumina and PacBio data

    Tian, Q., Guo, Q., Guo, Y., Luo, L., Kristiansen, Karsten, Han, Z., Fang, H. & Zhang, S., 2022, In: Genomics. 114, 2, 10 p., 110293.

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

  12. Published

    Phylogenomics resolves ambiguous relationships within Aciculata (Errantia, Annelida)

    Tilic, E., Stiller, Josefin, Campos, E., Pleijel, F. & Rouse, G. W., 2022, In: Molecular Phylogenetics and Evolution. 166, 10 p., 107339.

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

  13. Published

    Characterization of Divalent Cation Interactions with AASTY Nanodiscs

    Timcenko, Milena, Autzen, A. A. A. & Autzen, Henriette Elisabeth, 2022, In: ACS Applied Polymer Materials. 4, 2, p. 1071-1083

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

  14. Published

    Successful treatment of psoriasis with adalimumab induced no changes in the gut microbiota

    Todberg, T., Egeberg, Alexander, Zachariae, Claus, Sørensen, N., Pedersen, Oluf Borbye & Skov, Lone, 2022, In: Journal of the European Academy of Dermatology and Venereology. 36, 6, p. e464-e467 4 p.

    Research output: Contribution to journal › Comment/debate › Research

  15. Published

    A haplotype-resolved genome assembly of the Nile rat facilitates exploration of the genetic basis of diabetes

    Toh, H., Yang, C., Formenti, G., Raja, K., Yan, L., Tracey, A., Chow, W., Howe, K., Bergeron, L. A., Zhang, G., Haase, B., Mountcastle, J., Fedrigo, O., Fogg, J., Kirilenko, B., Munegowda, C., Hiller, M., Jain, A., Kihara, D., Rhie, A. & 9 others, Phillippy, A. M., Swanson, S. A., Jiang, P., Clegg, D. O., Jarvis, E. D., Thomson, J. A., Stewart, R., Chaisson, M. J. P. & Bukhman, Y. V., 2022, In: BMC Biology. 20, 21 p., 245.

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

  16. 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

  17. Published

    Conserved conformational dynamics determine enzyme activity

    Torgeson, K. R., Clarkson, M. W., Granata, D., Lindorff-Larsen, Kresten, Page, R. & Peti, W., 2022, In: Science Advances. 8, 31, 10 p., eabo5546.

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

  18. Published

    On Single-Cell Enzyme Assays in Marine Microbial Ecology and Biogeochemistry

    Traving, Sachia Jo, Balmonte, J. P., Seale, D., Arnosti, C., Glud, R. N., Hallam, S. J. & Middelboe, Mathias, 2022, In: Frontiers in Marine Science. 9, 9 p., 846656.

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

  19. Published

    Diet and food selection by fish larvae in turbid and clear water shallow temperate lakes

    Trochine, C., Risholt, C., Schou, M. O., Lauridsen, T. L., Jacobsen, L., Skov, C., Søndergaard, M., Berg, S., Christoffersen, Kirsten Seestern & Jeppesen, E., 2022, In: Science of the Total Environment. 804, 12 p., 150050.

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

  20. Published

    The role of water coordination in the pH-dependent gating of hAQP10

    Truelsen, S. F., Missel, Julie Winkel, Gotfryd, K., Pedersen, Per Amstrup, Gourdon, Pontus Emanuel, Lindorff-Larsen, Kresten & Hélix-Nielsen, C., 2022, In: B B A - Biomembranes. 1864, 1, 13 p., 183809.

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

  21. Published

    Heat waves affect prey and predators differently via developmental plasticity: who may benefit most from global warming?

    Tscholl, T., Nachman, Gøsta Støger, Spangl, B. & Walzer, A., 2022, In: Pest Management Science. 78, 3, p. 1099-1108 10 p.

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

  22. Published

    The use of paracetamol during pregnancy: A qualitative study and possible strategies for a clinical trial

    Vedel, C., Jørgensen, D. S., Kristensen, D. M., Petersen, Olav Bennike Bjørn & Greisen, Gorm, 2022, In: PLoS ONE. 17, e0271537.

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

  23. Published

    Nuclear and cytoplasmic RNA exosomes and PELOTA1 prevent miRNA-induced secondary siRNA production in Arabidopsis

    Vigh, Maria Louisa, Bressendorff, Simon, Thieffry, A., Arribas Hernandez, Laura & Brodersen, Peter, 2022, In: Nucleic Acids Research. 50, 3, p. 1396-1415 20 p.

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

  24. Published

    Mechanisms Underlying siRNA Amplification in Arabidopsis thaliana

    Vigh, Maria Louisa, 2022, Department of Biology, Faculty of Science, University of Copenhagen. 201 p.

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

  25. Published

    The drivers of avian-haemosporidian prevalence in tropical lowland forests of New Guinea in three dimensions

    Vinagre-Izquierdo, C., Bodawatta, Kasun Harshana, Chmel, K., Renelies-Hamilton, J., Paul, L., Munclinger, P., Poulsen, Michael & Jønsson, Knud Andreas, 2022, In: Ecology and Evolution. 12, 2, 14 p., e8497.

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

  26. Published

    Production of an Active, Human Membrane Protein in Saccharomyces cerevisiae: Full-Length FICD

    Virolainen, M. S., Søltoft, C. L., Pedersen, Per Amstrup & Ellgaard, Lars, 2022, In: International Journal of Molecular Sciences. 23, 5, 17 p., 2458.

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

  27. Published

    Appraisal of a novel fishery of whelks (Buccinum undatum) in Danish waters

    Vismann, Bent, Nielsen, J. W. & Ronfeldt, J. L., 2022, In: Regional Studies in Marine Science. 56, 11 p., 102710.

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

  28. Published

    Genetics of early-life head circumference and genetic correlations with neurological, psychiatric and cognitive outcomes

    Vogelezang, S., Bradfield, J. P., Early Growth Genetics Consortium, Ahluwalia, T. V. S., Liu, X., Schnurr, T. M., Frithioff-Bøjsøe, C., Bønnelykke, K., Lind, M. V., Lauritzen, L., Michaelsen, K. F., Lund, M. A. V., Melbye, M., Morgen, C. S., Pedersen, O. B., Holm, J-C., Grarup, N., Hansen, T., Nohr, E. A., Bisgaard, H. & 3 others, Grant, S. F. A., Felix, J. F. & Jaddoe, V. W. V., 2022, In: BMC Medical Genomics. 15, 16 p., 124.

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

  29. Published

    Trans- and Within-Generational Developmental Plasticity May Benefit the Prey but Not Its Predator during Heat Waves

    Walzer, A., Nachman, Gøsta Støger, Spangl, B., Stijak, M. & Tscholl, T., Aug 2022, In: Biology. 11, 8, 20 p., 1123.

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

  30. Published

    CReSIL: accurate identification of extrachromosomal circular DNA from long-read sequences

    Wanchai, V., Jenjaroenpun, P., Leangapichart, T., Arrey Tané, Gerard, Burnham, C. M., Tümmler, M. C., Delgado-Calle, J., Regenberg, Birgitte & Nookaew, I., 2022, In: Briefings in Bioinformatics. 23, 6, 11 p., bbac422.

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

  31. Published

    In vitro digestion mimicking conditions in young and elderly reveals marked differences between profiles and potential bioactivity of peptides from meat and soy proteins

    Wang, Chong, Zhao, Fan, Bai, Y., Li, C., Xu, X., Kristiansen, Karsten & Zhou, G., 2022, In: Food Research International. 157, 11 p., 111215.

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

  32. Published

    Effect of gastrointestinal alterations mimicking elderly conditions on in vitro digestion of meat and soy proteins

    Wang, Chong, Zhao, Fan, Bai, Y., Li, C., Xu, X., Kristiansen, Karsten & Zhou, G., 2022, In: Food Chemistry. 383, 9 p., 132465.

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

  33. Published

    Proteomic Analysis of the Protective Effect of Eriodictyol on Benzo(a)pyrene-Induced Caco-2 Cytotoxicity

    Wang, Chong, Zhao, Fan, Bai, Y., Li, C., Xu, X., Kristiansen, Karsten & Zhou, G., 2022, In: Frontiers in Nutrition. 9, 14 p., 839364.

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

  34. Published

    Endothelial cell heterogeneity and microglia regulons revealed by a pig cell landscape at single-cell level

    Wang, F., Ding, P., Liang, X., Ding, X., Brandt, C. B., Sjöstedt, E., Zhu, J., Bolund, S., Zhang, L., de Rooij, L. P. M. H., Luo, L., Wei, Y., Zhao, W., Lv, Z., Haskó, J., Li, R., Qin, Q., Jia, Y., Wu, W., Yuan, Y. & 25 others, Pu, M., Wang, H., Wu, A., Xie, L., Liu, P., Chen, F., Herold, J., Kalucka, J., Karlsson, M., Zhang, X., Helmig, R. B., Fagerberg, L., Lindskog, C., Pontén, F., Uhlen, M., Bolund, L., Jessen, N., Jiang, H., Xu, X., Yang, H., Carmeliet, P., Mulder, J., Chen, D., Lin, L. & Luo, Y., 2022, In: Nature Communications. 13, 18 p., 3620.

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

  35. Published

    A draft genome of the medicinal plant Cremastra appendiculata (D. Don) provides insights into the colchicine biosynthetic pathway

    Wang, J., Xie, J., Chen, H., Qiu, X., Cui, H., Liu, Y., Sahu, S. K., Fang, D., Li, T., Wang, M., Chen, Y., Liu, Huan, Zhang, J. & Wang, B., 2022, In: Communications Biology . 5, 12 p., 1294.

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

  36. Published

    An easily modifiable conjugative plasmid for studying horizontal gene transfer

    Wang, Q., Olesen, Asmus Kalckar, Maccario, Lorrie & Madsen, Jonas Stenløkke, 2022, In: Plasmid. 123-124, 10 p., 102649.

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

  37. Published

    The maintenance and spread of cooperative antibiotic resistance

    Wang, Q., 2022, Department of Biology, Faculty of Science, University of Copenhagen. 280 p.

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

  38. Published

    Combined berberine and probiotic treatment as an effective regimen for improving postprandial hyperlipidemia in type 2 diabetes patients: a double blinded placebo controlled randomized study

    Wang, S., Ren, H., Zhong, H., Zhao, X., Li, C., Ma, J., Gu, X., Xue, Y., Huang, S., Yang, J., Chen, L., Chen, G., Qu, S., Liang, J., Qin, L., Huang, Q., Peng, Y., Li, Q., Wang, X., Zou, Y. & 10 others, Shi, Z., Li, X., Li, T., Yang, H., Lai, S., Xu, G., Li, J., Zhang, Y., Gu, Y. & Wang, W., 2022, In: Gut Microbes. 14, 1, 18 p., 2003176.

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

  39. Published

    The chromosome-scale genomes of Dipterocarpus turbinatus and Hopea hainanensis (Dipterocarpaceae) provide insights into fragrant oleoresin biosynthesis and hardwood formation

    Wang, S., Liang, H., Wang, H., Li, L., Xu, Y., Liu, Y., Liu, M., Wei, J., Ma, T., Le, C., Yang, J., He, C., Liu, J., Zhao, J., Zhao, Y., Lisby, Michael, Sahu, S. K. & Liu, H., 2022, In: Plant Biotechnology Journal. 20, 3, p. 538-553 16 p.

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

  40. Published

    Too much of a good thing? Inorganic nitrogen (N) inhibits moss-associated N2 fixation but organic N can promote it

    Wang, Y., Lett, Signe & Rousk, Kathrin, 2022, In: Biogeochemistry. 159, 2, p. 179-191 13 p.

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

  41. Published

    Understanding Yeast Phenotypes via the Evolution of Synthetic Genome

    Wang, Y., 2022, Department of Biology, Faculty of Science, University of Copenhagen. 222 p.

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

  42. Published

    Transcriptomic signatures responding to PKM2 activator TEPP-46 in the hyperglycemic human renal proximal epithelial tubular cells

    Wang, Z., Yu, J., Hao, Dan, Liu, X. & Wang, X., 2022, In: Frontiers in Endocrinology. 13, 16 p., 965379.

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

  43. Published

    Phylogeny and sex chromosome evolution of palaeognathae

    Wang, Z., Zhang, J., Xu, X., Witt, C., Deng, Y., Chen, G., Meng, G., Feng, S., Xu, L., Szekely, T., KU, thw266 & Zhou, Q., 2022, In: Journal of Genetics and Genomics. 49, 2, p. 109-119 11 p.

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

  44. Published

    Pseudoreplication in genomics-scale data sets

    Waples, R. S., Waples, R. K. & Ward, E. J., 2022, In: Molecular Ecology Resources. 22, 2, p. 503-518 16 p.

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

  45. Published

    Impact of intensive lifestyle intervention on gut microbiota composition in type 2 diabetes: a post-hoc analysis of a randomized clinical trial

    Wei, S., Brejnrod, A. D., Trivedi, Urvish, Mortensen, M. S., Johansen, M. Y., Karstoft, Kristian, Vaag, A. A., Ried-Larsen, M. & Sørensen, Søren Johannes, 2022, In: Gut Microbes. 14, 1, 15 p., 2005407.

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

  46. Published

    Single-cell Stereo-seq reveals induced progenitor cells involved in axolotl brain regeneration

    Wei, X., Fu, S., Li, H., Liu, Y., Wang, S., Feng, W., Yang, Y., Liu, X., Zeng, Y-Y., Cheng, M., Lai, Y., Qiu, X., Wu, L., Zhang, N., Jiang, Y., Xu, J., Su, X., Peng, C., Han, L., Lou, W. P-K. & 16 others, Liu, C., Yuan, Y., Ma, K., Yang, T., Pan, X., Gao, S., CHEN, Ao, Esteban, M. A., Yang, H., Wang, J., Fan, G., Liu, L., Chen, L., Xu, X., Fei, J. & Gu, Y., 2022, In: Science. 377, 6610, 10 p., eabp9444.

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

  47. Published

    Identification of Potential Peptide Marker(s) for Evaluating Pork Meat Freshness via Mass Spectrometry-Based Peptidomics during Storage under Different Temperatures

    Wei, Z., Dai, C., Bassey, A. P., Tang, C., Han, Y., Wang, Chong & Zhou, G., 2022, In: Foods. 11, 8, 14 p., 1144.

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

  48. Published

    Key Knowledge Gaps to Fill at the Cell-To-Ecosystem Level in Marine B-Vitamin Cycling

    Wienhausen, G., Bittner, Meriel Jennifer & Paerl, R. W., 2022, In: Frontiers in Marine Science. 9, 9 p., 876726.

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

  49. Published

    Physiological responses of narwhals to anthropogenic noise: A case study with seismic airguns and vessel traffic in the Arctic

    Williams, T. M., Blackwell, S. B., Tervo, O., Garde, E., Sinding, Mikkel Holger Strander, Richter, B. & Heide-Jørgensen, M. P., 2022, In: Functional Ecology. 36, 9, p. 2251-2266 16 p.

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

  50. Published

    Does childhood exposure to biodiverse greenspace reduce the risk of developing asthma?

    Winnicki, M. H., Dunn, R. R., Winther-Jensen, M., Jess, T., Allin, K. H. & Bruun, Hans Henrik, 2022, In: Science of the Total Environment. 850, 11 p., 157853.

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

  51. Published

    (180-183) Proposals to amend Article 40.1 and Article 44.1 and to add a new Article 44.3 and a Note to facilitate the valid publication of names of "dinoflagellates"

    Woelkerling, W. J. & Moestrup, Øjvind, 2022, In: Taxon. 71, 6, p. 1337-1338 2 p.

    Research output: Contribution to journal › Comment/debate › Research

  52. Published

    Biosolids for safe land application: does wastewater treatment plant size matters when considering antibiotics, pollutants, microbiome, mobile genetic elements and associated resistance genes?

    Wolters, B., Hauschild, K., Blau, K., Mulder, I., Heyde, B. J., Sørensen, Søren Johannes, Siemens, J., Jechalke, S., Smalla, K. & Nesme, Joseph, 2022, In: Environmental Microbiology. 24, 3, p. 1573-1589 17 p.

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

  53. Published

    Initiation of the Primate Genome Project

    Wu, D., Qi, X., Yu, L., Li, M., Liu, Z., Yoder, A. D., Roos, C., Hayakawa, T., Rogers, J., Marques-Bonet, T., Su, B., Yao, Y., Zhang, Y. & KU, thw266, 2022, In: Zoological research. 43, 2, p. 147-149 3 p.

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

  54. Published

    Computational identification of signals predictive for nuclear RNA exosome degradation pathway targeting

    Wu, M., Schmid, M., Jensen, T. H. & Sandelin, Albin Gustav, 2022, In: NAR Genomics and Bioinformatics. 4, 3, 18 p., lqac071.

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

  55. Published

    The sensitivity of ginkgo leaf unfolding to the temperature and photoperiod decreases with increasing elevation

    Wu, Z., Lin, C., Wang, S., Gong, Y., Fu, Y. H., Tang, Jing, De Boeck, H. J., Vitasse, Y. & Zhao, Y., 2022, In: Agricultural and Forest Meteorology. 315, 8 p., 108840.

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

  56. Published

    Nanopore-based long-read metagenomics uncover the resistome intrusion by antibiotic resistant bacteria from treated wastewater in receiving water body

    Wu, Bruce, Che, Y., Dang, C., Zhang, M., Zhang, X., Sun, Y., Li, X., Zhang, T. & Xia, Y., 2022, In: Water Research. 226, 10 p., 119282.

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

  57. Published

    Novel Sequencing Approaches for the High-Throughput Identification of Full-length Poly(A) RNA Transcripts at the Single-cell Level

    XIE, Z., 2022, Department of Biology, Faculty of Science, University of Copenhagen. 88 p.

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

  58. Published

    Hypoxia in tomato fruit during ripening caused by contrasting tissue-specific diffusion resistance and respiration

    Xiao, H., Tong, Shuai, Salagovic, J., Pedersen, Ole, Verboven, P. & Nicolaï, B. M., 2022, p. 48.

    Research output: Contribution to conference › Conference abstract for conference › Research › peer-review

  59. Published

    Chord: an ensemble machine learning algorithm to identify doublets in single-cell RNA sequencing data

    Xiong, K., Zhou, H., Lin, C., Yin, J., Kristiansen, Karsten, Yang, H. & Li, G., 2022, In: Communications Biology . 5, 11 p., 510.

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

  60. Published

    Survival and Genome Diversity of Vibrio parahaemolyticus Isolated from Edible Aquatic Animals

    Xu, D., Peng, Xu, Xie, L. & Chen, L., 2022, In: Diversity. 14, 5, 23 p., 350.

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

  61. Published

    Transcriptomic Profile of the Mouse Postnatal Liver Development by Single-Nucleus RNA Sequencing

    Xu, J., Hao, S., Shi, Q., Deng, Q., Jiang, Y., Guo, P., Yuan, Y., Shi, X., Shangguan, S., Zheng, H., Lai, G., Huang, Y., Wang, Y., Song, Y., Liu, Y., Wu, L., Wang, Z., Cheng, J., Wei, X., Cheng, M. & 6 others, Lai, Y., Volpe, G., Esteban, M. A., Hou, Y., Liu, C. & Liu, L., 2022, In: Frontiers in Cell and Developmental Biology. 10, 11 p., 833392.

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

  62. Published

    Genomic and microbial factors affect the prognosis of anti-pd-1 immunotherapy in nasopharyngeal carcinoma

    Xu, L., Ma, Y., Fang, Chao, Peng, Z., Gao, F., Moll, J. M., Qin, S., Yu, Q., Hou, Y., Kristiansen, Karsten, Fang, W., Brix, S. & Zhang, L., 2022, In: Frontiers in Oncology. 12, 11 p., 953884.

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

  63. Published

    Two novel truncating variants of the ASPM gene identified in a nonconsanguineous Chinese family associated with primary microcephaly

    Xu, S., Zhang, W., Zhou, R., Huang, H., Chen, W., Xiang, W., Liu, L. & Song, J., 2022, In: Clinical Dysmorphology. 31, 1, p. 1-5 5 p.

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

  64. Published

    Molecular mechanisms that underlie the root cortex expansion in response to low oxygen

    Yamauchi, T., Sumi, K., Morishita, H., Pedersen, Ole, Inukai, Y. & Nakazono, M., 2022, p. 22.

    Research output: Contribution to conference › Conference abstract for conference › Research › peer-review

  65. Published

    Diverse Aquatic Animal Matrices Play a Key Role in Survival and Potential Virulence of Non-O1/O139 Vibrio cholerae Isolates

    Yan, L., Jin, Y., Zhang, B., Xu, Y., Peng, Xu, Qin, S. & Chen, L., 2022, In: Frontiers in Microbiology. 13, 21 p., 896767.

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

  66. Published

    Contrastive learning enables rapid mapping to multimodal single-cell atlas of multimillion scale

    YANG, Meng, Yang, Y., Xie, C., Ni, M., Liu, J., Yang, H., Mu, F. & Wang, J., 2022, In: Nature Machine Intelligence. 4, 8, p. 696-709 14 p.

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

  67. Published

    Integrating convolution and self-attention improves language model of human genome for interpreting non-coding regions at base-resolution

    YANG, Meng, Huang, L., Huang, H., Tang, H., Zhang, N., Yang, H., Wu, J. & Mu, F., 2022, In: Nucleic Acids Research. 50, 14, 19 p., e81.

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

  68. Published

    TrustGWAS: A full-process workflow for encrypted GWAS using multi-key homomorphic encryption and pseudorandom number perturbation

    YANG, Meng, Zhang, C., Wang, X., Liu, X., Li, S., Huang, J., Feng, Z., Sun, X., Chen, F., Yang, S., Ni, M., Li, L., Cao, Y. & Mu, F., 2022, In: Cell Systems. 13, 9, p. 752-767.e6 23 p.

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

  69. Published

    Comparative Analyses of 3,654 Plastid Genomes Unravel Insights Into Evolutionary Dynamics and Phylogenetic Discordance of Green Plants

    Yang, T., Sahu, S. K., Yang, L., Liu, Y., Mu, W., Liu, X., Strube, M. L., Liu, Huan & Zhong, B., 2022, In: Frontiers in Plant Science. 13, 13 p., 808156.

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

  70. Published

    Living on fire: Deactivating fire coral polyps for larval settlement and symbiosis in the fire coral-associated barnacle Wanella milleporae (Thoracicalcarea: Wanellinae)

    Yap, F. C., Høeg, Jens Thorvald & Chan, B. K. K., 2022, In: Ecology and Evolution. 12, 7, 17 p., e9057.

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

  71. Published

    Soil texture is a stronger driver of the maize rhizosphere microbiome and extracellular enzyme activities than soil depth or the presence of root hairs

    Yim, B., Ibrahim, Z., Rüger, L., Ganther, M., Maccario, Lorrie, Sørensen, Søren Johannes, Heintz-Buschart, A., Tarkka, M. T., Vetterlein, D., Bonkowski, M., Blagodatskaya, E. & Smalla, K., 2022, In: Plant and Soil. 478, 1-2, p. 229-251 23 p.

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

  72. Published

    Comparative phylogeography study reveals introgression and incomplete lineage sorting during rapid diversification of Rhodiola

    You, J., Lougheed, S. C., Zhao, Y., KU, thw266, Liu, W., Lu, F., Wang, Y., Zhang, W., Yang, J., Qiong, L. & Song, Z., 2022, In: Annals of Botany. 129, 2, p. 185-200 16 p.

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

  73. Published

    The Wastewater Plasmidome and its Derived Resistome: Insight Into Their Dynamics in the Urban Water Systems

    Yu, Z., 2022, Department of Biology, Faculty of Science, University of Copenhagen. 196 p.

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

  74. Published

    Single-cell transcriptomic landscape of the sheep rumen provides insights into physiological programming development and adaptation of digestive strategies

    Yuan, Y., Sun, D., Qin, T., Mao, S., Zhu, W., Yin, Y., Huang, J., Heller, Rasmus, Li, Z., Liu, J. & Qiu, Q., 2022, In: Zoological research. 43, 4, p. 634-647 14 p.

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

  75. Published

    Clinical application of high-throughput sequencing technology in prenatal screening and diagnosis of birth defects

    ZENG, F., 2022, Department of Biology, Faculty of Science, University of Copenhagen. 118 p.

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

  76. Published

    Exudates from Miscanthus x giganteus change the response of a root-associated Pseudomonas putida strain towards heavy metals

    Zadel, U., Cruzeiro, C., Raj Durai, A. C., Nesme, Joseph, May, R., Balázs, H., Michalke, B., Płaza, G., Schröder, P., Schloter, M. & Radl, V., 2022, In: Environmental Pollution. 313, 13 p., 119989.

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

  77. Published

    Morphometrics, Distribution, and DNA Barcoding: An Integrative Identification Approach to the Genus Odontotermes (Termitidae: Blattodea) of Khyber Pakhtunkhwa, Pakistan

    Zaman, M., Khan, I. A., Schmidt, Suzanne, Murphy, Rob & Poulsen, Michael, 2022, In: Forests. 13, 5, 17 p., 674.

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

  78. Published

    Current challenges in understanding the role of enhancers in disease

    Zaugg, J. B., Sahlén, P., Andersson, Robin, Alberich-Jorda, M., de Laat, W., Deplancke, B., Ferrer, J., Mandrup, S., Natoli, G., Plewczynski, D., Rada-Iglesias, A. & Spicuglia, S., 2022, In: Nature Structural and Molecular Biology. 29, 12, p. 1148-1158 11 p.

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

  79. Published

    Oxygen-sensitive nanoparticles reveal the spatiotemporal dynamics of oxygen reduction during magnesium implant biodegradation

    Zeller-Plumhoff, B., Akkineni, A. R., Helmholz, H., Orlov, D., Moßhammer, Maria, Kühl, Michael, Willumeit-Roemer, R. & Gelinsky, M., 2022, In: npj Materials Degradation. 6, 8 p., 95.

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

  80. Published

    A short prokaryotic Argonaute activates membrane effector to confer antiviral defense

    Zeng, Z., Chen, Y., Pinilla Redondo, Rafael, Shah, S. A., Zhao, F., Wang, C., Hu, Z., Wu, C., Zhang, C., Whitaker, R. J., She, Q. & Han, W., 2022, In: Cell Host and Microbe. 30, 7, p. 930-943.e6 21 p.

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

  81. Published

    A novel approach for the non-invasive diagnosis of pulmonary nodules using low-depth whole-genome sequencing of cell-free DNA

    Zhang, B., Liang, H., Liu, W., Zhou, X., Qiao, S., Li, F., Tian, P., Li, C., Ma, Y., Zhang, H., Zhang, Z., Nanjo, S., Russo, A., Puig-Butillé, J. A., Wu, K., Wang, C., Zhao, X. & Yue, D., 2022, In: Translational Lung Cancer Research. 11, 10, p. 2094-2110 17 p.

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

  82. Published

    Isolation and Crystallization of the D156C Form of Optogenetic ChR2

    Zhang, L., Wang, Kaituo, Ning, S., Pedersen, Per Amstrup, Duelli, A. S. & Gourdon, Pontus Emanuel, 2022, In: Cells. 11, 5, 11 p., 895.

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

  83. Published

    Effects of Epiphytic Biofilm Activity on the Photosynthetic Activity, pH and Inorganic Carbon Microenvironment of Seagrass Leaves (Zostera marina L.)

    Zhang, Q., Kühl, Michael & Brodersen, Kasper Elgetti, 2022, In: Frontiers in Marine Science. 9, 11 p., 835381.

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

  84. Published

    Iron oxide coated sand (IOS): Scale-up analysis and full-scale application for phosphorus removal from goat farm wastewater

    Zhang, R., Wang, L., Lakho, F. H., Yang, X., Depuydt, V., Igodt, W., Le, H. Q., Rousseau, D. P. L. & Van Hulle, S., 2022, In: Separation and Purification Technology. 284, 10 p., 120213.

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

  85. Published

    Metagenomic analysis reveals crosstalk between gut microbiota and glucose-lowering drugs targeting the gastrointestinal tract in Chinese patients with type 2 diabetes: a 6 month, two-arm randomised trial

    Zhang, X., Ren, H., Zhao, C., Shi, Z., Qiu, L., Yang, F., Zhou, X., Han, X., Wu, K., Zhong, H., Li, Y., Li, J. & Ji, L., 2022, In: Diabetologia. 65, 11, p. 1613-1626 14 p.

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

  86. Published

    Inactivation of Target RNA Cleavage of a III-B CRISPR-Cas System Induces Robust Autoimmunity in Saccharolobus islandicus

    Zhang, Y., Lin, Jinzhong, Tian, X., Wang, Y., Zhao, R., Wu, C., Wang, X., Zhao, P., Bi, X., Yu, Z., Han, W., Peng, N., Liang, Y. X. & She, Q., 2022, In: International Journal of Molecular Sciences . 23, 15, 16 p., 8515.

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

  87. Published

    Casein and red meat proteins differentially affect the composition of the gut microbiota in weaning rats

    Zhao, Fan, Wang, Chong, Song, S., Fang, C., Zhou, G., Li, C. & Kristiansen, Karsten, 2022, In: Food Chemistry. 397, 11 p., 133769.

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

  88. Published

    Effects of Different Storage Temperatures on Bacterial Communities and Functional Potential in Pork Meat

    Zhao, Fan, Wei, Z., Zhou, G., Kristiansen, Karsten & Wang, Chong, 2022, In: Foods. 11, 15, 12 p., 2307.

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

  89. Published

    Intake of a Chicken Protein-Based or Soy Protein-Based Diet Differentially Affects Growth Performance, Absorptive Capacity, and Gut Microbiota in Young Rats

    Zhao, Fan, Wang, Chong, Song, S., Fang, C., Kristiansen, Karsten & Li, C., 2022, In: Molecular Nutrition and Food Research. 66, 13, 14 p., 2101124.

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

  90. Published

    Proteomics and Metabolomics Profiling of Pork Exudate Reveals Meat Spoilage during Storage

    Zhao, Fan, Wei, Z., Bai, Y., Li, C., Zhou, G., Kristiansen, Karsten & Wang, Chong, 2022, In: Metabolites. 12, 7, 15 p., 570.

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

  91. Published

    Exploration of Intratumor Heterogeneity and Tumoral Microenvironment in Non-small Cell Lung Cancer

    Zhao, X., 2022, Department of Biology, Faculty of Science, University of Copenhagen. 137 p.

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

  92. Published

    Three novel structural variations at the major histocompatibility complex and IL12B predispose to psoriasis

    Zhen, Q., Zhang, Y., Yu, Y., Yang, H., Zhang, T., Li, X., Mo, X., Li, B., Wu, J., Liang, Y., Ge, H., Xu, Q., Chen, W., Qian, W., Xu, H., Chen, G., Bai, B., Zhang, J., Lu, Y., Chen, S. & 31 others, Zhang, H., Zhang, Y., Chen, X., Li, X., Jin, X., Lin, X., Yong, L., Fang, M., Zhao, J., Lu, Y., Wu, S., Jiang, D., Shi, J., Cao, H., Qiu, Y., Li, S., Kang, X., Shen, J., Ma, H., Sun, S., Fan, Y., Chen, W., Bai, M., Jiang, Q., Li, W., Lv, C., Li, S., Chen, M., Li, F., Li, Y. & Sun, L., 2022, In: British Journal of Dermatology. 186, 2, p. 307-317 11 p.

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

  93. Published

    Performance characterization of PCR-free whole genome sequencing for clinical diagnosis

    Zhou, G., Zhou, M., Zeng, F., Zhang, N., Sun, Y., Qiao, Z., Guo, X., Zhou, S., Yun, G., Xie, J., Wang, X., Liu, F., Fan, C., Wang, Y., Fang, Z., Tian, Z., Dai, W., Sun, J., Peng, Z. & Song, L., 2022, In: Medicine. 101, 10, 8 p., e28972.

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

  94. Published

    Over 50,000 Metagenomically Assembled Draft Genomes for the Human Oral Microbiome Reveal New Taxa

    Zhu, J., Tian, L., Chen, P., Han, M., Song, L., Tong, X., Sun, X., Yang, F., Lin, Z., Liu, X., Liu, C., Wang, X., Lin, Y., Cai, K., Hou, Y., Xu, X., Yang, H., Wang, J., Kristiansen, K., Xiao, L. & 3 others, Zhang, T., Jia, H. & Jie, Zhuye, 2022, In: Genomics, Proteomics and Bioinformatics. 20, 2, p. 246-259

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

  95. Published

    Unparalleled details of soft tissues in a Cretaceous ant

    Zhuang, Y., Xu, W., KU, thw266, Mai, H., Li, X., He, H., Ran, H. & Liu, Y., 2022, In: BMC Ecology and Evolution. 22, 1, 10 p., 146.

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

  96. Published

    Phylogenomic analysis and metabolic role reconstruction of mutualistic Rhizobiales hindgut symbionts of Acromyrmex leaf-cutting ants

    Zhukova, M., Sapountzis, P., Schiott, M. & Boomsma, Jacobus J., 2022, In: FEMS Microbiology Ecology. 98, 9, 13 p., fiac084.

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

  97. Published

    mRNA Decapping Factors LSM1 and PAT Paralogs Are Involved in Turnip Mosaic Virus Viral Infection

    Zuo, Zhangli Thomsen, Roux, M., Rodriguez, Eleazar & Petersen, Morten, 2022, In: Molecular plant-microbe interactions : MPMI. 35, 2, p. 125-130 6 p.

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

  98. Published

    The rice wax synthesis-related gene Leaf Gas Film-1 (LGF1) is involved in the formation of the radial oxygen loss barrier

    de la Cruz Jiménez, J., Noorrohmah, S., Zeisler, V., Schreiber, L., Peralta Ogorek, Lucas León, Pellegrini, Elisa, Pedersen, Ole, Nagai, K., Ashikari, M., Takahashi, H. & Nakazono, M., 2022, p. 67.

    Research output: Contribution to conference › Conference abstract for conference › Research › peer-review

  99. Published

    Estimation of the covariance structure from SNP allele frequencies

    van Waaij, J., Li, Z. & Wiuf, Carsten, 2022, In: Statistical Applications in Genetics and Molecular Biology. 21, 1, 20 p., 20220005.

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

  100. Published

    Four new genera and six new species of lyophylloid agarics (Agaricales, Basidiomycota) from three different continents

    van de Peppel, L. J. J., Aime, M. C., Læssøe, Thomas, Pedersen, O. S., Coimbra, V. R. M., Kuyper, T. W., Stubbe, D., Aanen, D. K. & Baroni, T. J., 2022, In: Mycological Progress. 21, 10, 14 p., 85.

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

  101. Published

    Reduced chromatin accessibility correlates with resistance to Notch activation

    van den Ameele, J., Krautz, Robert, Cheetham, S. W., Donovan, A. P. A., Llorà-Batlle, O., Yakob, R. & Brand, A. H., 2022, In: Nature Communications. 13, 1, 10 p., 2210.

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

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