Department of Biology

 

 
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  1. 2023
  2. Published

    DeepPeptide predicts cleaved peptides in proteins using conditional random fields

    Teufel, Felix Georg, Refsgaard, J. C., Madsen, C. T., Stahlhut, C., Grønborg, M., Winther, Ole & Madsen, D., 2023, In: Bioinformatics (Oxford, England). 39, 10, 6 p., btad616.

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

  3. Published

    Deepened snow in combination with summer warming increases growing season nitrous oxide emissions in dry tundra, but not in wet tundra

    Xu, W., Frendrup, L. L., Michelsen, Anders, Elberling, Bo & Ambus, Per Lennart, 2023, In: Soil Biology and Biochemistry. 180, 12 p., 109013.

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

  4. Published

    Delayed benefits for fallow bucks: more fights decrease same day mating success, but increase matings the next day

    Bateman-Neubert, A., Briefer, Elodie & McElligott, A. G., 2023, In: Animal Behaviour. 200, p. 37-48 12 p.

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

  5. Published

    Deorphanizing Peptides Using Structure Prediction

    Teufel, Felix Georg, Refsgaard, J. C., Kasimova, M. A., Deibler, K., Madsen, C. T., Stahlhut, C., Grønborg, M., Winther, Ole & Madsen, D., 2023, In: Journal of Chemical Information and Modeling. 63, 9, 5 p.

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

  6. Published

    DermX: An end-to-end framework for explainable automated dermatological diagnosis

    Jalaboi, R., Faye, F., Orbes-Arteaga, M., Jørgensen, D., Winther, Ole & Galimzianova, A., 2023, In: Medical Image Analysis. 83, 12 p., 102647.

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

  7. Published

    Detecting host responses to microbial stimulation using primary epithelial organoids

    Lange, Jette Bornholdt, Müller, C. V., Nielsen, M. J., Strickertsson, J., Rago, D., Chen, Y., Maciag, Grzegorz Jerzy, Skov, Jonathan, Wellejus, A., Schweiger, P. J., Hansen, Stine Lind, Broholm, C., Gögenur, Ismail, Maimets, Martti, Sloth, S., Hendel, J., Baker, A., Sandelin, Albin Gustav & Jensen, Kim Bak, 2023, In: Gut Microbes. 15, 2, 16 p., 2281012.

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

  8. Published

    Determination of heavy metals (Pb, Cr, As, Hg, and Cd) into the body organs of selected fish, water, sediment, and soil samples from Head Punjnad and Head Taunsa, Punjab, Pakistan

    Iqbal, K. J., Khan, N., Fatima, M., Lashari, M. H., Asad, M., Ashraf, A., Fatima, H., Majeed, H., Baboo, I., Iqbal, K. J., Asghar, M., Saeed, Usama, Ali, W., Nazir, S., Bano, S. & Tanveer, A., 2023, In: PLoS ONE. 18, 9, 10 p., e0288163.

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

  9. Published

    Development and validation of a minimally invasive and image-guided tape stripping method to sample atopic skin in children

    Yélamos, O., Andersen, D., Pont, M., Iglesias, P., Potrony, M., Domínguez, M., Herrero, A., Alejo, B., Mateu, J., Røpke, Mads Almose, Danneskiold-Samsøe, Niels Banhos, Malvehy, J., Guy, R. H., Brix, S. & Puig, S., 2023, In: Clinical and Experimental Dermatology. 48, 2, p. 80-88 9 p.

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

  10. Published

    Development of a novel SRAP-SCAR marker for rapid identification of lager and ale types in brewer's yeast

    Liu, J., Cai, G., Li, X. & Lu, J., 2023, In: Molecular Biology Reports. 50, 6 p.

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

  11. Published

    Did circular DNA shape the evolution of mammalian genomes?

    Holt, Sylvester, Arrey Tané, Gerard & Regenberg, Birgitte, 2023, In: Trends in Biochemical Sciences. 48, 4, 4 p.

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

  12. Published

    Dietary diversity, sociality, and the evolution of ant gustation

    Smith, E. J., Vizueta Moraga, Joel, Younger, M. A. A., Mullen, S. P. P. & Traniello, J. F. A., 2023, In: Frontiers in Ecology and Evolution. 11, 9 p., 1175719.

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

  13. Published

    Differential responses of the gut microbiome and resistome to antibiotic exposures in infants and adults

    Li, Xuan Ji, Brejnrod, A., Thorsen, J., Zachariasen, Trine, Trivedi, Urvish, Russel, J., Vestergaard, G. A., Stokholm, Jakob, Rasmussen, Morten Arendt & Sørensen, Søren Johannes, 2023, In: Nature Communications. 14, 1, 16 p., 8526.

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

  14. Published

    Discovering functionally important sites in proteins

    Cagiada, Matteo, Bottaro, S., Lindemose, Søren, Schenstrøm, S. M., Stein, Amelie, Hartmann-Petersen, Rasmus & Lindorff-Larsen, Kresten, 2023, In: Nature Communications. 14, 1, 13 p., 4175.

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

  15. Published

    Dissecting aneuploidy phenotypes by constructing Sc2.0 chromosome VII and SCRaMbLEing synthetic disomic yeast

    Shen, Y., Gao, F., Wang, Y., Wang, Y., Zheng, J., Gong, J., Zhang, J., Luo, Z., Schindler, D., Deng, Y., Ding, W., Lin, T., Swidah, R., Zhao, H., Jiang, S., Zeng, C., Chen, S., Chen, T., Wang, Y., Luo, Y. & 11 others, Mitchell, L., Bader, J. S., KU, thw266, Shen, X., Wang, J., Fu, X., Dai, J., Boeke, J. D., Yang, H., Xu, X. & Cai, Y., 2023, In: Cell Genomics. 3, 11, 19 p., 100364.

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

  16. Published

    Distribution patterns of selenium and its fractions in penguin and seal colony soil profiles in response to their population dynamics in maritime Antarctica

    Shui, Y., Ye, W., Zhang, W., Yuan, L., Jiao, Yi, Sun, B., Zang, H., Yin, X. & Zhu, R., 2023, In: Polar Biology. 46, 17 p.

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

  17. Published

    Do Nitrogen and Phosphorus Additions Affect Nitrogen Fixation Associated with Tropical Mosses?

    Avila Clasen, Lina, Permin, Aya Tora Foged, Horwath, A. B., Metcalfe, D. B. & Rousk, Kathrin, 2023, In: Plants. 12, 7, 13 p., 1443.

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

  18. Published

    DoxoDB: A Database for the Expression Analysis of Doxorubicin-Induced lncRNA Genes

    Distefano, R., Ilieva, M., Madsen, J. H., Rennie, Sarah & Uchida, S., 2023, In: Non-coding RNA. 9, 4, 24 p., 39.

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

  19. Published

    Draft genomes of seven isolates from Danish wastewater facilities belonging to Pseudomonas, Bacillus, Pseudochrobactrum, Brevundimonas, and Pandoraea

    Maccario, Lorrie, Silva, A. F., Nesme, Joseph, Amador Hierro, Cristina Isabel, Sørensen, Søren Johannes, Cooper, V. S. & Røder, Henriette Lyng, 2023, In: Microbiology resource announcements. 12, 12, 4 p.

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

  20. Published

    Drivers and ecology of Ceratium furcoides invasion of a Brazilian subtropical reservoir and its interaction with the phytoplankton community

    Rojas-Castillo, O. A., Pereira, L., Buffon, P. & de Souza Cardoso, L., 2023, In: Limnologica. 101, 13 p., 126080.

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

  21. Published

    Drying of Springs in the Himalayan Region of Nepal: Perspectives of Local Government Leaders on Causes, Consequences, and Conservation Efforts

    Thapa, B., Bhattarai, C., Dahal, N., Tiwari, S. & Jacobsen, Dean, 2023, In: Mountain Research and Development. 43, 4, p. R9-R15 7 p.

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

  22. Published

    Dynamic localization of the Na+-HCO3- co-transporter NBCn1 to the plasma membrane, centrosomes, spindle and primary cilia

    Severin, M., Pedersen, E. L., Borre, M. T., Axholm, I., Christiansen, F. B., Ponniah, M., Czaplinska, D., Larsen, T., Pardo, L. A. & Pedersen, Stine Helene Falsig, 2023, In: Journal of Cell Science. 136, 7, 20 p., jcs260687.

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

  23. Published

    Dynamic social interactions and keystone species shape the diversity and stability of mixed-species biofilms – an example from dairy isolates

    Sadiq, F. A., De Reu, K., Steenackers, H., Van De Walle, A., Burmølle, Mette & Heyndrickx, M., 2023, In: ISME communications. 3, 1, 12 p., 118.

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

  24. Published

    ERK and USP5 govern PD-1 homeostasis via deubiquitination to modulate tumor immunotherapy

    Xiao, X., Shi, J., He, C., Bu, X., Sun, Y., Gao, M., Xiang, B., Xiong, W., Dai, P., Mao, Q., Xing, X., Yao, Y., Yu, H., Xu, G., Li, S., Ren, Y., Chen, B., Jiang, C., Meng, G., Lee, Y. R. & 4 others, Wei, W., Freeman, G. J., Xie, C. & Zhang, J., 2023, In: Nature Communications. 14, 1, 19 p., 2859.

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

  25. Published

    Ecological Indicator Values for Europe (EIVE) 1.0

    Dengler, J., Jansen, F., Chusova, O., Hüllbusch, E., Nobis, M. P., Van Meerbeek, K., Axmanová, I., Bruun, H. H., Chytrý, M., Guarino, R., Karrer, G., Moeys, K., Raus, T., Steinbauer, M. J., Tichý, L., Tyler, T., Batsatsashvili, K., Bita-Nicolae, C., Didukh, Y., Diekmann, M. & 14 others, Englisch, T., Fernández-Pascual, E., Frank, D., Graf, U., Hájek, M., Jelaska, S. D., Jiménez-Alfaro, B., Julve, P., Nakhutsrishvili, G., Ozinga, W. A., Ruprecht, E. K., Šilc, U., Theurillat, J. P. & Gillet, F., 2023, In: Vegetation Classification and Survey. 4, p. 7-29 23 p.

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

  26. Published

    Ecological strategies of (pl)ants: Towards a world-wide worker economic spectrum for ants

    Gibb, H., Bishop, T. R., Leahy, L., Parr, C. L., Lessard, J., Sanders, N. J., Shik, Jonathan Z., Ibarra-Isassi, J., Narendra, A., Dunn, R. R. & Wright, I. J., 2023, In: Functional Ecology. 37, 1, 13 p.

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

  27. Published

    Ecomorphological correlates of inner ear shape in Australian limb-reduced skinks (Scincidae: Sphenomorphini)

    Camaiti, M., Wiles, J., Aguilar, R., Hutchinson, M. N., Hipsley, Christy Anna, Chapple, D. G. & Evans, A. R., 2023, In: Zoological Journal of the Linnean Society. 199, 4, p. 994-1012 19 p.

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

  28. Published

    Editorial: Signaling by primary cilia in development and disease

    Kim, S. E., Nechipurenko, I. & Christensen, Søren Tvorup, 2023, In: Frontiers in Cell and Developmental Biology. 11, 3 p., 1186367.

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

  29. Published

    Editorial: Long-read sequencing—Pitfalls, benefits and success stories

    Wohlers, I., Garg, S. & Hehir-Kwa, J. Y., 2023, In: Frontiers in Genetics. 13, 3 p., 1114542.

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

  30. Published

    Editorial: Drivers of host-microbiome interactions in the rhizosphere

    Topalovic, Olivera, Koorem, K. & Wilschut, R. A., 2023, In: Frontiers in Plant Science. 14, 3 p., 1294388.

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

  31. Published

    Effects of Glacial Flour on Marine Micro-plankton: Evidences from Natural Communities of Greenlandic Fjords and Experimental Studies

    Maselli, Maira, Meire, L., Meire, P. & Hansen, Per Juel, 2023, In: Protist. 174, 1, 17 p., 125928.

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

  32. Published

    Eighty million years of rapid evolution of the primate Y chromosome

    Zhou, Y., Zhan, X., Jin, J., Zhou, L., Bergman, J., Li, X., Rousselle, M. M. C., Belles, M. R., Zhao, L., Fang, M., Chen, J., Fang, Q., Kuderna, L., Marques-Bonet, T., Kitayama, H., Hayakawa, T., Yao, Y. G., Yang, H., Cooper, D. N., Qi, X. & 3 others, Wu, D. D., Schierup, M. H. & KU, thw266, 2023, In: Nature Ecology and Evolution. 7, 20 p.

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

  33. Published

    Emerging roles of the CIP2A–TopBP1 complex in genome integrity

    Ummethum, Henning Ole, Li, Jiayi, Lisby, Michael & Østergaard, Vibe Hallundbæk, 2023, In: NAR Cancer. 5, 4, 6 p.

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

  34. Published

    Enhanced foliar 15N enrichment with increasing nitrogen addition rates: Role of plant species and nitrogen compounds

    Wang, Y., Niu, G., Wang, R., Rousk, Kathrin, Li, A., Hasi, M., Wang, C., Xue, J., Yang, G., Lü, X., Jiang, Y., Han, X. & Huang, J., 2023, In: Global Change Biology. 29, 6, 15 p.

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

  35. Published

    Environmental predictors of lake fish diversity across gradients in lake age and spatial scale

    Martinsen, K. T., Kristensen, E., Båstrup-Spohr, Lars, Søndergaard, M., Carl, Henrik, Jeppesen, E., Sand-Jensen, Kaj & Kragh, T., 2023, In: Freshwater Biology. 68, 7, 14 p.

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

  36. Published

    Epigenetic Regulation of Driver Genes in Testicular Tumorigenesis

    von Eyben, F. E., Kristiansen, Karsten, Kapp, D. S., Hu, R., Preda, O. & Nogales, F. F., 2023, In: International Journal of Molecular Sciences. 24, 4, 28 p., 4148.

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

  37. Published

    Epithelium dynamics differ in time and space when exposed to the permeation enhancers penetramax and EGTA. A head-to-head mechanistic comparison

    Panou, D. A., Pedersen, Stine Helene Falsig, Kristensen, Mie & Nielsen, Hanne Mørck, 2023, In: Frontiers in Drug Delivery. 3, 16 p., 1221628.

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

  38. Published

    Erstnachweis von Jaapiella chelidonii in Deutschland und von Mayetiola hellwigi in Schleswig-Holstein (Diptera: Cecidomyiidae)

    Bruun, Hans Henrik, 2023, In: Virgo - Mitteilungsblatt des Entomologischen Vereins Mecklenburg. 26, p. 91-92 2 p.

    Research output: Contribution to journal › Journal article › Research

  39. Published

    Estimating admixture pedigrees of recent hybrids without a contiguous reference genome

    Garcia Erill, Genís, Hanghøj, Kristian Ebbesen, Heller, Rasmus, Wiuf, Carsten & Albrechtsen, Anders, 2023, In: Molecular Ecology Resources. 23, 7, p. 1604-1619 16 p.

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

  40. Published

    Evaluation of population structure inferred by principal component analysis or the admixture model

    Van Waaij, J., Li, Song, Garcia Erill, Genís, Albrechtsen, Anders & Wiuf, Carsten, 2023, In: Genetics. 225, 2, 14 p., iyad157.

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

  41. Published

    Evaluation of the Impact of BaP Exposure on the Gut Microbiota and Allergic Responses in an OVA-Sensitized Mouse Model

    Du, B., Xiao, X., Wang, H., Li, W., Xia, Z., Yang, P., Huang, S. K., Yuan, R., Liu, J., Han, M., Zou, Y., Zhu, J., He, D., Lyu, J., Jin, X., Xu, X., Wang, J., Yang, H., Xiao, L., Liu, X. & 1 others, Kristiansen, Karsten, 2023, In: Environmental Health Perspectives. 131, 6, 15 p.

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

  42. Published

    Every refuge has its price: Ostreobium as a model for understanding how algae can live in rock and stay in business

    Tandon, K., Pasella, M. M., Iha, C., Ricci, F., Hu, J., O'Kelly, C. J., Medina, M., Kühl, Michael & Verbruggen, H., 2023, In: Seminars in Cell and Developmental Biology. 134, p. 27-36 10 p.

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

  43. Published

    Evidence for early domestic yak, taurine cattle, and their hybrids on the Tibetan Plateau

    Chen, N., Zhang, Z., Hou, J., Chen, J., Gao, X., Tang, L., Wangdue, S., Zhang, X., Sinding, Mikkel Holger Strander, Liu, X., Han, J., Lü, H., Lei, C., Marshall, F. & Liu, X., 2023, In: Science Advances. 9, 50, 13 p., eadi6857.

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

  44. Published

    Evidence that the domesticated fungus Leucoagaricus gongylophorus recycles its cytoplasmic contents as nutritional rewards to feed its leafcutter ant farmers

    A. Leal-Dutra, Caio, Yuen, L. M., Guedes, B. A. M., Contreras Serrano, Marta, Marques, P. E. & Shik, Jonathan Z., 2023, In: IMA Fungus. 14, 1, 13 p., 19.

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

  45. Published

    Evolution of the germline mutation rate across vertebrates

    Bergeron, Lucie Adrienne, Besenbacher, S., Zheng, J., Li, P., Bertelsen, Mads Frost, Quintard, B., Hoffman, J. I., Li, Z., Leger, J. S., Shao, C., Stiller, Josefin, Gilbert, M Thomas P, Schierup, M. H. & KU, thw266, 2023, In: Nature. 615, p. 285-291

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

  46. Published

    Evolutionary fine-tuning of residual helix structure in disordered proteins manifests in complex structure and lifetime

    Elkjær, Steffie Martina H, Due, Amanda Duncan, Christensen, L. F., Theisen, Frederik Friis, Staby, L., Kragelund, Birthe Brandt & Skriver, Karen, 2023, In: Communications Biology . 6, 11 p., 63.

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

  47. Published

    Expanding known viral diversity in the healthy infant gut

    Shah, S. A., Deng, L., Thorsen, J., Pedersen, A. G., Dion, M. B., Castro-Mejía, J. L., Silins, R., Romme, F. O., Sausset, R., Jessen, L. E., Ndela, E. O., Hjelmsø, M., Rasmussen, M. A., Redgwell, T. A., Rodríguez, C. L., Vestergaard, G., Zhang, Y., Chawes, B., Bønnelykke, K., Sørensen, S. J. & 6 others, Bisgaard, H., Enault, F., Stokholm, Jakob, Moineau, S., Petit, M. A. & Nielsen, Dennis Sandris, 2023, In: Nature Microbiology. 8, p. 986–998

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

  48. Published

    Expanding the Echinoderes coulli group (Kinorhyncha Cyclorhagida) with a new species from the Chuuk Islands, Micronesia

    Herranz, Maria, Moreleon, A. D., Rho, H. S. & Sørensen, Martin Vinther, 2023, In: Zoologischer Anzeiger. 302, p. 67-74 8 p.

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

  49. Published

    Explainable Image Quality Assessments in Teledermatological Photography

    Jalaboi, R., Winther, Ole & Galimzianova, A., 2023, In: Telemedicine and e-Health. 29, 9, p. 1342-1348 7 p.

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

  50. Published

    Expression of genes and enzymes involved in ovarian steroidogenesis in relation to human follicular development

    Zheng, M., tcg964, tcg964, Rasmussen, F. R., Cadenas, J., Christensen, Søren Tvorup & Mamsen, L. S., 2023, In: Frontiers in Endocrinology. 14, 17 p., 1268248.

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

  51. Published

    Extracting DNA from soil or directly from isolated nematodes indicate dissimilar community structure for Europe-wide forest soils

    Donhauser, J., Briones, M. J. I., Mikola, J., Jones, D. L., Eder, R., Filser, J., Frossard, A., Krogh, P. H., Sousa, J. P., Cortet, J., Desie, E., Domene, X., Djuric, S., Hackenberger, D., Jimenez, J. J., Iamandei, M., Rissmann, C., Schmidt, O., Shanskiy, M., Silfver, T. & 4 others, Vancampenhout, K., Vasutova, M., Velizarova, E. & Frey, B., 2023, In: Soil Biology and Biochemistry. 185, 16 p., 109154.

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

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