Department of Biology

 

 
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  1. Published

    SOAPdenovo-Trans: de novo transcriptome assembly with short RNA-Seq reads

    Xie, Y., Wu, G., Tang, J., Luo, R., Patterson, J., Liu, S., Huang, W., He, G., Gu, S., Li, S., Zhou, X., Lam, T., Li, Y., Xu, X., Wong, G. K. & Wang, J., 2014, In: Bioinformatics. 30, 12, p. 1660-1666 7 p.

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

  2. Published

    Noninvasive prenatal paternity testing by maternal plasma DNA sequencing in twin pregnancies

    Xie, Y., Qu, N., Lin, S., Jiang, H., Zhang, Y., Zhang, X., Liang, H., Chen, F. & Ou, X., 2020, In: Electrophoresis. 41, 12, p. 1095-1102

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

  3. Published

    Spatial chromatin accessibility sequencing resolves high-order spatial interactions of epigenomic markers

    Xie, Y., Ruan, F., Li, Y., Luo, M., Zhang, C., Chen, Z., Xie, Z., Weng, Z., Chen, W., Chen, W., Fang, Y., Sun, Y., Guo, M., Wang, J., Xu, S., Wang, H. & Tang, C., 2024, In: eLife. 12, 20 p., RP87868.

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

  4. Published

    Shotgun metagenomics of 250 adult twins reveals genetic and environmental impacts on the gut microbiome

    Xie, H., Guo, R., Zhong, H., Feng, Q., Lan, Z., Qin, B., Ward, K. J., Jackson, M. A., Xia, Y., Chen, X., Chen, B., Xia, H., Xu, C., Li, F., Xu, X., Al-Aama, J. Y., Yang, H., Wang, J., Kristiansen, K., Wang, J. & 5 others, Steves, C. J., Bell, J. T., Li, J., Spector, T. D. & Jia, H., 2016, In: Cell Systems. 3, 6, p. 572-584.e3 13 p.

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

  5. Published

    An integrated gene catalog and over 10,000 metagenome-assembled genomes from the gastrointestinal microbiome of ruminants

    Xie, F., Jin, W., Si, H., Yuan, Y., Tao, Y., Liu, J., Wang, X., Yang, C., Li, Q., Yan, X., Lin, L., Jiang, Q., Zhang, L., Guo, C., Greening, C., Heller, R., Guan, L. L., Pope, P. B., Tan, Z., Zhu, W. & 4 others, Wang, M., Qiu, Q., Li, Z. & Mao, S., 2021, In: Microbiome. 9, 20 p., 137.

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

  6. 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

  7. Published

    High-fat feeding rather than obesity drives taxonomical and functional changes in the gut microbiota in mice

    Xiao, L., Sonne, S. B., Feng, Q., Chen, N., Xia, Z., Li, X., Fang, Z., Zhang, D., Fjære, E., Midtbø, L. K., Derrien, M., Hugenholtz, F., Tang, L., Li, J., Zhang, J., Liu, C., Hao, Q., Vogel, U. B., Mortensen, A., Kleerebezem, M. & 8 others, Licht, T. R., Yang, H., Wang, J., Li, Y., Arumugam, Mani, Wang, J., Madsen, L. & Kristiansen, Karsten, 8 Apr 2017, In: Microbiome. 5, 12 p., 43.

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

  8. Published

    A catalog of the mouse gut metagenome: [incl. Author Correction]

    Xiao, L., Feng, Q., Liang, S., Sonne, S. B., Xia, Z., Qiu, X., Li, X., Long, H., Zhang, J., Zhang, D., Liu, C., Fang, Z., Chou, J., Glanville, J., Hao, Q., Kotowska, D. E., Colding, C. S., Licht, T. R., Wu, D., Yu, J. & 17 others, Sung, J. J. Y., Liang, Q., Li, J., Jia, H., Lan, Z., Tremaroli, V., Dworzynski, P., Nielsen, H. B., Bäckhed, G. F., Dore, J., Le Chatelier, E., Ehrlich, S. D., Lin, J. C., Arumugam, Mani, Wang, J., Madsen, L. & Kristiansen, Karsten, 2015, In: Nature Biotechnology. 33, 10, p. 1103-1108 6 p.

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

  9. Published

    A reference gene catalogue of the pig gut microbiome

    Xiao, L., Estellé, J., Kiilerich, P., Ramayo-Caldas, Y., Xia, Z., Feng, Q., Liang, S., Pedersen, A. Ø., Kjeldsen, N. J., Liu, C., Maguin, E., Doré, J., Pons, N., Le Chatelier, E., Prifti, E., Li, J., Jia, H., Liu, X., Xu, X., Ehrlich, S. D. & 4 others, Madsen, L., Kristiansen, Karsten, Rogel-Gaillard, C. & Wang, J., 2016, In: Nature Microbiology. 1, 6 p., 16161.

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

  10. Published

    Identification of a disease-causing mutation in a Chinese patient with retinitis pigmentosa by targeted next-generation sequencing

    Xiao, J., Guo, X., Wang, Y., Shao, M., Wei, X., Du, L., Li, L., Sun, Y. & Yang, Y., 8 Nov 2017, In: European Journal of Ophthalmology. 27, 6, p. 791-796 6 p.

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

  11. E-pub ahead of print

    Hypoxia in tomato (Solanum lycopersicum) fruit during ripening: Biophysical elucidation by a 3D reaction–diffusion model

    Xiao, H., Verboven, P., Tong, Shuai, Pedersen, Ole & Nicolaï, B., 2024, (E-pub ahead of print) In: Plant Physiology.

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

  12. 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

  13. Published

    Integrative analysis of genomic sequencing data reveals higher prevalence of LRP1B mutations in lung adenocarcinoma patients with COPD

    Xiao, D., Li, F., Pan, H., Liang, H., Wu, K. & He, J., 18 May 2017, In: Scientific Reports. 7, 8 p., 2121.

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

  14. Published

    Enhancing CRISPR-Cas9 gRNA efficiency prediction by data integration and deep learning

    Xiang, X., Corsi, G. I., Anthon, C., Qu, K., Pan, X., Liang, X., Han, P., Dong, Z., Liu, L., Zhong, J., Ma, T., Wang, J., Zhang, X., Jiang, H., Xu, F., Liu, X., Xu, X., Wang, J., Yang, H., Bolund, L. & 4 others, Church, G. M., Lin, L., Gorodkin, Jan & Luo, Y., 2021, In: Nature Communications. 12, 1, 9 p., 3238.

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

  15. Published

    Identification and functional analysis of circulating extrachromosomal circular DNA in schizophrenia implicate its negative effect on the disorder

    Xiang, X., Pan, Xiaoguang, Lv, W., Chen, S., Li, J., Zhang, H., Liao, Y., Yu, J., Li, J., Dang, Y., You, Z., Wang, L., Chen, W., Han, Peng & Tang, J., 2023, In: Clinical and Translational Medicine. 13, 11, 7 p.

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

  16. Published

    Single base-resolution methylome of the silkworm reveals a sparse epigenomic map

    Xiang, H., Zhu, J., Chen, Q., Dai, F., Li, X., Li, M., Zhang, H., Zhang, G., Li, D., Dong, Y., Zhao, L., Lin, Y., Cheng, D., Yu, J., Sun, J., Zhou, X., Ma, K., He, Y., Zhao, Y., Guo, S. & 13 others, Ye, M., Guo, G., Li, Y., Li, R., Zhang, X., Ma, L., Kristiansen, Karsten, Guo, Q., Jiang, J., Beck, S., Xia, Q., Wang, W. & Wang, J., 2010, In: Nature Biotechnology. 28, 5, p. 516-20 4 p.

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

  17. Published

    Global dispersal and adaptive evolution of domestic cattle: a genomic perspective

    Xia, X., Qu, K., Wang, Y., Sinding, Mikkel Holger Strander, Wang, F., Hanif, Q., Ahmed, Z., Lenstra, J. A., Han, J., Lei, C. & Chen, N., 2023, In: Stress Biology. 3, 1, 13 p., 8.

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

  18. Published

    Complete resequencing of 40 genomes reveals domestication events and genes in silkworm (Bombyx)

    Xia, Q., Guo, Y., Zhang, Z., Li, D., Xuan, Z., Li, Z., Dai, F., Li, Y., Cheng, D., Li, R., Cheng, T., Jiang, T., Becquet, C., Xu, X., Liu, C., Zha, X., Fan, W., Lin, Y., Shen, Y., Jiang, L. & 38 others, Jensen, J., Hellmann, I., Tang, S., Zhao, P., Xu, H., Yu, C., Zhang, G., Li, J., Cao, J., Liu, S., He, N., Zhou, Y., Liu, H., Zhao, J., Ye, C., Du, Z., Pan, G., Zhao, A., Shao, H., Zeng, W., Wu, P., Li, C., Pan, M., Li, J., Yin, X., Li, D., Wang, J., Zheng, H., Wang, W., Zhang, X., Li, S., Yang, H., Lu, C., Nielsen, Rasmus, Zhou, Z., Wang, J., Xiang, Z. & Wang, J., 2009, In: Science. 326, 5951, p. 433-6 3 p.

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

  19. Published

    Ursolic acid induces cell death and modulates autophagy through JNK pathway in apoptosis-resistant colorectal cancer cells

    Xavier, C. P. R., Lima, C. F., Pedro, D. F. N., Wilson, J. M., Kristiansen, Karsten & Pereira-Wilson, C., 2013, In: Journal of Nutritional Biochemistry. 24, 4, p. 706-712 7 p.

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

  20. 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

  21. Published

    The needle mycobiome of Picea glauca – A dynamic system reflecting surrounding environment and tree phenological traits

    Würth, D. G., Dahl, M. B., Trouillier, M., Wilmking, M., Unterseher, M., Scholler, M., Sørensen, Søren Johannes, Mortensen, M. & Schnittler, M., 2019, In: Fungal Ecology. 41, p. 177-186 10 p.

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

  22. Published

    Genetic structure of fragmented November moth (Lepidoptera: Geometridae) populations in farmland

    Wynne, I. R., Loxdale, H. D., Brookes, C. P. & Woiwod, I. P., 2003, In: Biological Journal of the Linnean Society. Vol. 78, Issue 4, p. 467-477

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

  23. Published

    When less is more: shortening the Lpp protein leads to increased vancomycin resistance in Escherichia coli

    Wykes, H., Le, Van Hung Vuong, Olivera, Catrina Diane Peralta & Rakonjac, J., 2023, In: Journal of Antibiotics. 76, p. 746-750 5 p.

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

  24. Published

    Purification and sequence determination of a yellow protein from sexually mature males of the desert locust, Schistocerca gregaria

    Wybrandt, G. B. & Andersen, S. O., 2001, In: Insect Biochemistry and Molecular Biology. 31, p. 1183-1189

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

  25. Published

    Cuticle-catalyzed coupling between polyamino acids and N-acetyldopamine

    Wybrandt, G. B. & Andersen, S. O., 1994, In: BBA General Subjects. 1201, p. 15-18

    Research output: Contribution to journal › Journal article › Research

  26. Published

    Historical mammal extinction on Christmas Island (Indian Ocean) correlates with introduced infectious disease

    Wyatt, K. B., Campos, P. F., Gilbert, M Thomas P, Kolokotronis, S., Hynes, W. H., DeSalle, R., Daszak, P., MacPhee, R. D. E. & Greenwood, A. D., 2008, In: PLoS ONE. 3, 11, p. e3602

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

  27. Published

    Histone H3 lysine 56 acetylation and the response to DNA replication fork damage

    Wurtele, H., Kaiser, G. S., Bacal, J., St-Hilaire, E., Lee, E., Tsao, S., Dorn, J., Maddox, P., Lisby, Michael, Pasero, P. & Verreault, A., 2012, In: Molecular and Cellular Biology. 32, 1, p. 154-172 19 p.

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

  28. Published

    The genome of the fire ant Solenopsis invicta

    Wurm, Y., Wang, J., Riba-Grognuz, O., Corona, M., Nygaard, S., Hunt, B. G., Ingram, K. K., Falquet, L., Nipitwattanaphon, M., Gotzek, D., Dijkstra, M. B., Oettler, J., Comtesse, F., Shih, C-J., Wu, W-J., Yang, C-C., Thomas, J., Beaudoing, E., Pradervand, S., Flegel, V. & 18 others, Cook, E. D., Fabbretti, R., Stockinger, H., Long, L., Farmerie, W. G., Oakey, J., Boomsma, Jacobus J., Pamilo, P., Yi, S. V., Heinze, J., Goodisman, M. A. D., Farinelli, L., Harshman, K., Hulo, N., Cerutti, L., Xenarios, I., Shoemaker, D. & Keller, L., 2011, In: Proceedings of the National Academy of Sciences of the United States of America. 108, 14, p. 5679-84 6 p.

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

  29. Published

    Co-expression of mCysLT1 receptors and IK channels in Xenopus laevis oocytes elicits LTD4-stimulated IK current, independent of an increase in [Ca2+]i.

    Wulff, T., Hougaard, C., Klærke, Dan Arne & Hoffmann, E. K., 2004, In: BBA General Subjects. 1660, 1-2, p. 75-9 4 p.

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

  30. Published

    mCysLT1 receptor mediated activation of various K+ channels by co-expression in Xenopus laevis oocytes

    Wulff, T., Hougaard, C., Klærke, D. A. & Hoffmann, E. K., 2004, In: Acta Physiologica (Print Edition). A45-A163, p. A139

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

  31. Published

    Investigation of two different anoxia models by 2-dimensional gel electrophoresis

    Wulff, T., Jessen, F. & Hoffmann, E. K., 2006, In: The FASEB Journal. 5, p. A1433

    Research output: Contribution to journal › Conference abstract in journal › Research

  32. Published

    A comparison of two anoxia models by 2-DE and MS/MS

    Wulff, T., 2008, Department of Biology: Museum Tusculanum. 198 p.

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

  33. Published

    Comparison of two anoxia models in rainbow trout cells by a 2-DE and MS/MS-based proteome approach.

    Wulff, T., Hoffmann, E. K., Roepstorff, P. & Jessen, F., 2008, In: Proteomics. 8, 10, p. 2035-44 9 p.

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

  34. Published

    Activation of certain K+ channels by the eicosanoid leukotrine D4 (LTD4)

    Wulff, T., Hougaard, C., Klaerke, D. A. & Hoffmann, E. K., 2003, In: Molecular Biology of the Cell. p. 222a

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

  35. Published

    Long term anoxia in rainbow trout investigated by 2-DE and MS/MS.

    Wulff, T., Jessen, F., Roepstorff, P. & Hoffmann, E. K., 2008, In: Proteomics. p. 1009 - 1018

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

  36. Published

    Ocean acidification and desalination: climate-driven change in a Baltic Sea summer microplanktonic community

    Wulff, A., Karlberg, M., Olofsson, M., Torstensson, A., Riemann, Lasse, Steinhoff, F. S., Mohlin, M., Ekstrand, N. & Chierici, M., 1 Apr 2018, In: Marine Biology. 165, 4, 15 p., 63.

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

  37. Published

    Next Generation Sequencing Library Preparation Technologies and Applications

    Wu, Zongze, 2023, Department of Biology, Faculty of Science, University of Copenhagen. 143 p.

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

  38. 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

  39. Published

    Atmospheric brightening counteracts warming-induced delays in autumn phenology of temperate trees in Europe

    Wu, Z., Chen, S., De Boeck, H. J., Stenseth, N. C., Tang, Jing, Vitasse, Y., Wang, S., Zohner, C. & Fu, Y. H., 2021, In: Global Ecology and Biogeography. 30, 12, p. 2477-2487 11 p.

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

  40. 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

  41. 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

  42. Published

    Tumor suppressor ASXL1 is essential for the activation of INK4B expression in response to oncogene activity and anti-proliferative signals

    Wu, X., Bekker-Jensen, I. H., Christensen, J., Rasmussen, K. D., Sidoli, S., Qi, Y., Kong, Y., Wang, X., Cui, Y., Xiao, Z., Xu, G., Williams, K., Rappsilber, J., Sønderby, C. K., Winther, Ole, Jensen, O. N. & Helin, K., 2015, In: Cell Research. 25, p. 1205-1218 14 p.

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

  43. Published

    Fbxl10/Kdm2b recruits polycomb repressive complex 1 to CpG islands and regulates H2A ubiquitylation

    Wu, X., Johansen, Jens Vilstrup & Helin, K., 28 Mar 2013, In: Molecular Cell. 49, 6, p. 1134-46 13 p.

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

  44. Published

    Conformational heterogeneity of Savinase from NMR, HDX-MS and X-ray diffraction analysis

    Wu, S., Nguyen, T. T. T. N., Moroz, O. V., Turkenburg, J. P., Nielsen, J. E., Wilson, K. S., Rand, Kasper Dyrberg & Teilum, Kaare, 2020, In: PeerJ. 8, 17 p., e9408.

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

  45. Published

    Dynamic Properties of Savinase by Integrative Structural Biology — Indications to Structural Stability

    Wu, S., 2017, Department of Biology, Faculty of Science, University of Copenhagen. 253 p.

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

  46. Published

    Integrated genome sequence and linkage map of physic nut (Jatropha curcas L.), a biodiesel plant

    Wu, P., Zhou, C., Cheng, S., Wu, Z., Lu, W., Han, J., Chen, Y., Chen, Y., Ni, P., Wang, Y., Xu, X., Huang, Y., Song, C., Wang, Z., Shi, N., Zhang, X., Fang, X., Yang, Q., Jiang, H., Chen, Y. & 5 others, Li, M., Wang, Y., Chen, F., Wang, J. & Wu, G., 2015, In: Plant Journal. 81, 5, p. 810-821 12 p.

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

  47. Published

    The RNA exosome shapes the expression of key protein-coding genes

    Wu, M., Karadoulama, Evdoxia, Lloret-llinares, M., Rouviere, J. O., Vaagensø, C. S., Moravec, M., Li, B., Wang, J., Wu, G., Gockert, M. A. M., Pelechano, V., Jensen, T. H. & Sandelin, Albin Gustav, 2020, In: Nucleic Acids Research. 48, 15, p. 8509-8528

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

  48. Published

    Investigation of the Impact of the RNA Exosome on Cellular Transcriptome and Function

    Wu, M., 2021, Department of Biology, Faculty of Science, University of Copenhagen. 154 p.

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

  49. 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

  50. Published

    Interaction of extremophilic archaeal viruses with human and mouse complement system and viral biodistribution in mice

    Wu, L., Uldahl, K. B., Chen, F., Benasutti, H., Logvinski, D., Vu, V., Banda, N. K., Peng, Xu, Simberg, D. & Moghimi, S. M., Oct 2017, In: Molecular Immunology. 90, p. 273-279 7 p.

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

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