Functional Genomics

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  1. Published

    WAR: webserver for aligning structural RNAs

    Þórarinsson, E. & Lindgreen, S., 2008, In: Nucleic Acids Research. 36, Suppl. 2, p. W79-W84 6 p.

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

  2. Published

    TopBP1 makes the final call for repair on the verge of cell division

    Østergaard, Vibe Hallundbæk & Lisby, Michael, 2016, In: Molecular & Cellular Oncology. 3, 2, 3 p., e1093066.

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

  3. Published

    RNF8 and RNF168 but not HERC2 are required for DNA damage-induced ubiquitylation in chicken DT40 cells

    Østergaard, Vibe Hallundbæk, Pentzold, C., Pedersen, R. T., Iosif, S., Alpi, A., Bekker-Jensen, Simon Holst, Mailand, Niels & Lisby, Michael, 2012, In: D N A Repair. 11, 11, p. 892–905 14 p.

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

  4. Published

    Transcription-replication conflicts at chromosomal fragile sites—consequences in M phase and beyond

    Østergaard, Vibe Hallundbæk & Lisby, Michael, Mar 2017, In: Chromosoma. 126, 2, p. 213-222 10 p.

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

  5. Published

    Two differentially regulated Arabidopsis genes define a new branch of the DFR superfamily.

    Østergaard, L., Lauvergeat, V., Naested, H., Mattsson, O. & Mundy, J., 2001, In: Plant Science. 160, 3, p. 463-472 9 p.

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

  6. Published

    Mediastinalt parathyroideacysteadenom--en sjaelden årsag til primaer hyperparatyroidisme

    Øgard, C. G., Nielsen, S. L., Jakobsen, H., Leth-Espensen, P., drb459, drb459 & drb459, drb459, 28 Aug 2006, In: Ugeskrift for Laeger. 168, 35, p. 2921-2 2 p.

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

  7. Published

    High-throughput screening of Erwinia chrysanthemi pectin methylesterase variants using carbohydrate microarrays

    Øbro, J., Sørensen, I., Derkx, P., Madsen, C. T., Drews, M., Willer, M., Mikkelsen, J. D. & Willats, W. G. T., 2009, In: Proteomics - Practical Proteomics. 9, 7, p. 1861-1868

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

  8. Published

    Morphological classification of plant cell deaths

    van Doorn, W. G., Beers, E. P., Dangl, J. L., Franklin-Tong, V. E., Gallois, P., Hara-Nishimura, I., Jones, A. M., Kawai-Yamada, M., Lam, E., Mundy, J., Mur, L. A. J., Petersen, Morten, Smertenko, A., Taliansky, M., Van Breusegem, F., Wolpert, T., Woltering, E., Zhivotovsky, B. & Bozhkov, P. V., 2011, In: Cell Death and Differentiation. 18, 8, p. 1241-1246 6 p.

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

  9. Published

    Sequence-specific high mobility group box factors recognize 10-12-base pair minor groove motifs

    van Beest, M., Dooijes, D., van De Wetering, M., Kjaerulff, S., Bonvin, A., Nielsen, O., Clevers, H. & Nielsen, Olaf, 1 Sep 2000, In: Journal of Biological Chemistry. 275, 35, p. 27266-73 8 p.

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

  10. Published

    ALG-2 participates in recovery of cells after plasma membrane damage by electroporation and digitonin treatment

    la Cour, J. M., Gojkovic, P. W., Ambjorner, S. E. B., Bagge, J., Jensen, S. M., Panina, S. & Berchtold, Martin Werner, 2018, In: PLOS ONE. 13, 9, p. 1-13 e0204520.

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

  11. Published

    Ciprofloxacin intercalated in fluorohectorite clay: identical pure drug activity and toxicity with higher adsorption and controlled release rate

    dos Santos, E. C., Rozynek, Z., Hansen, E. L., Hartmann-Petersen, Rasmus, Klitgaard, R. N., Løbner-Olesen, Anders, Michels, L., Mikkelsen, A., Plivelic, Nunes Bordallo, Heloisa & Fossum, J. O., 17 May 2017, In: R S C Advances. 7, 43, p. 26537-26545

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

  12. Published

    The rad52-Y66A allele alters the choice of donor template during spontaneous chromosomal recombination

    de Mayolo, A. A., Sunjevaric, I., Reid, R., Mortensen, U. H., Rothstein, R. & Lisby, Michael, 2010, In: DNA Repair. 9, 1, p. 23-32

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

  13. Published

    DISPARE: DIScriminative PAttern REfinement for Position Weight Matrices

    da Piedade, I., Tang, M. E. & Elemento, O., 2009, In: BMC Bioinformatics. 10, 388, 16 p.

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

  14. Published

    The Arabidopsis thaliana mRNA decay factor PAT1 functions in osmotic stress responses and decaps ABA-responsive genes

    Zuo, Zhangli Thomsen, Roux, M. E., Sæmundsson, H. P., Müller, M., Bosch, S. M. & Petersen, Morten, 2021, In: FEBS Letters. 595, 2, p. 253-263 11 p.

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

  15. Published

    PAT mRNA decapping factors are required for proper development in Arabidopsis

    Zuo, Zhangli Thomsen, Roux, M. E., Dagdas, Y. F., Rodriguez, Eleazar & Petersen, Morten, 2024, In: FEBS Letters. 598, 9, p. 1008-1021 14 p.

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

  16. 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

  17. Published

    Functional study of PAT mRNA decapping factors in Arabidopsis

    Zuo, Zhangli Thomsen, 2018, Department of Biology, Faculty of Science, University of Copenhagen.

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

  18. Published

    The mRNA decapping machinery targets LBD3/ASL9 to mediate apical hook and lateral root development

    Zuo, Zhangli Thomsen, Roux, M. E., Chevalier, J. R., Dagdas, Y. F., Yamashino, T., Højgaard, S. D., Knight, E., Østergaard, L., Rodriguez, Eleazar & Petersen, Morten, 2023, In: Life Science Alliance. 6, 9, 11 p.

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

  19. Published

    Comparative Proteomics and Secretomics Revealed Virulence and Antibiotic Resistance-Associated Factors in Vibrio parahaemolyticus Recovered From Commonly Consumed Aquatic Products

    Zhu, Z., Yang, L., Yu, P., Wang, Y., Peng, Xu & Chen, L., 2020, In: Frontiers in Microbiology. 11, 31 p., 1453.

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

  20. Published

    Genome-wide occupancy profile of mediator and the Srb8-11 module reveals interactions with coding regions

    Zhu, X., Wirén, M., Sinha, I., Rasmussen, N. N., Linder, T., Holmberg, Steen, Ekwall, K. & Gustafsson, C. M., 2006, In: Molecular Cell. 22, 2, p. 169-78 9 p.

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

  21. Published

    A putative ABC transporter is involved in negative regulation of biofilm formation by Listeria monocytogenes.

    Zhu, X., Long, F., Chen, Y., Knoechel, Susanne, She, Q. & Shi, X., 2008, In: Applied and Environmental Microbiology. 74, 24, p. 7675-7683

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

  22. Published

    Phenotypic, proteomic, and genomic characterization of a putative ABC-transporter permease involved in Listeria monocytogenes biofilm formation

    Zhu, X., Liu, W., Lametsch, Rene, Aarestrup, F. M., Shi, C., She, Q., Shi, X. & Knoechel, Susanne, 2011, In: Foodborne Pathogens and Disease. 8, 4, p. 495-501 7 p.

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

  23. Published

    Genomic and transcriptomic analyses reveal distinct biological functions for cold shock proteins (VpaCspA and VpaCspD) in Vibrio parahaemolyticus CHN25 during low-temperature survival

    Zhu, C., Sun, B., Liu, T., Zheng, H., Gu, W., He, W., Sun, F., Wang, Y., Yang, M., Bei, W., Peng, Xu, She, Q., Xie, L. & Chen, L., 5 Jun 2017, In: BMC Genomics. 18, 19 p., 436.

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

  24. Published

    Dss1 interaction with Brh2 as a regulatory mechanism for recombinational repair.

    Zhou, Q., Kojic, M., Cao, Z., Lisby, Michael, Mazloum, N. A. & Holloman, W. K., 2007, In: Molecular and Cellular Biology. 27, 7, p. 2512-26 14 p.

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

  25. Published

    Development of a Simvastatin Selection Marker for a Hyperthermophilic Acidophile, Sulfolobus islandicus

    Zheng, T., Huang, Q., Zhang, C., Ni, J., She, Q. & Shen, Y., 2012, In: Applied and Environmental Microbiology. 78, 2, p. 568-574 7 p.

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

  26. Published

    A Membrane-Associated DHH-DHHA1 Nuclease Degrades Type III CRISPR Second Messenger

    Zhao, R., Yang, Y., Zheng, F., Zeng, Z., Feng, W., Jin, X., Wang, J., Yang, K., Liang, Y. X., She, Q. & Han, W., 2020, In: Cell Reports. 32, 11, 16 p., 108133.

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

  27. Published

    (p)ppGpp Regulates a Bacterial Nucleosidase by an Allosteric Two-Domain Switch

    ZHANG, YONG, Bærentsen, R. L., Fuhrer, T., Sauer, U., Gerdes, K. & Brodersen, D. E., 2019, In: Molecular Cell. 74, 6, p. 1239-1249, e1-e4

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

  28. Published

    Novel (p)ppGpp Binding and Metabolizing Proteins of Escherichia coli

    ZHANG, YONG, Zbornikova, E., Rejman, D. & Gerdes, K., 2018, In: mBio. 9, 2, 20 p., e02188-17.

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

  29. Published

    A bacterial ras-like small GTP-binding protein and its cognate GAP establish a dynamic spatial polarity axis to control directed motility

    ZHANG, YONG, Franco, M., Ducret, A. & Mignot, T., Jul 2010, In: PLOS Biology. 8, 7

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

  30. 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

  31. 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/Report › Ph.D. thesis › Research

  32. Published

    Replication Protein Rep Provides Selective Advantage to Viruses in the Presence of CRISPR-Cas Immunity

    Zhang, W., Bhoobalan-Chitty, Y., Zhai, Xichuan, Hui, Y., Hansen, Lars Hestbjerg, Deng, Ling & Peng, Xu, 2023, In: CRISPR Journal. 6, 1, p. 32-42

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

  33. Published

    Molecular cloning and antimicrobial activity of enterolysin A and helveticin J of bacteriolysins from metagenome of Chinese traditional fermented foods

    Zhang, T., Pan, Y., Li, B., Ou, J., Zhang, J., Chen, Y., Peng, Xu & Chen, L., 2013, In: Food Control. 31, 2, p. 499-507 9 p.

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

  34. Published

    Spatial transcriptome unveils a discontinuous inflammatory pattern in proficient mismatch repair colorectal adenocarcinoma

    Zhang, R., Feng, Y., Ma, W., Guo, Y., Luo, M., Li, Y., Zang, Y., Dong, X., Lu, S., Guo, Q., Xu, Q., Chen, H., Li, Y., Liu, L., CHEN, Ao, Chen, G. & Xu, X., 2023, In: Fundamental Research. 3, 4, 7 p.

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

  35. Published

    STAT3 induces transcription of the DNA methyltransferase 1 gene (DNMT1) in malignant T lymphocytes

    Zhang, Q., Wang, H. Y., Woetmann, Anders , Raghunath, P. N., Ødum, Niels & Wasik, M. A., 2006, In: Blood. 108, 3, p. 1058-64 6 p.

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

  36. Published

    New locus important for Myxococcus social motility and development

    Zhang, C. Y., Cai, K., Liu, H., ZHANG, YONG, Pan, H. W., Wang, B., Wu, Z. H., Hu, W. & Li, Y. Z., Nov 2007, In: Journal of Bacteriology. 189, 21, p. 7937-7941 5 p.

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

  37. Published

    Revealing the essentiality of multiple archaeal pcna genes using a mutant propagation assay based on an improved knockout method

    Zhang, C., Guo, L., Deng, L., Wu, Y., Liang, Y., Huang, L. & She, Q., Nov 2010, In: Microbiology. 156, Part 11

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

  38. Published

    Genetic manipulation in Sulfolobus islandicus and functional analysis of DNA repair genes

    Zhang, C., Tian, B., Li, S., Ao, X., Dalgaard, K., Gökce, S., Liang, Y. & She, Q., 2013, In: Biochemical Society Transactions. 41, 1, p. 405-410 6 p.

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

  39. Published

    The apt/6-methylpurine counterselection system and its applications in genetic studies of the hyperthermophilic archaeon Sulfolobus islandicus

    Zhang, C., She, Q., Bi, H. & Whitaker, R. J., 2016, In: Applied and Environmental Microbiology. 82, 10, p. 3070-3081 12 p.

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

  40. Published

    Phosphatidylserine stimulates ceramide 1-phosphate (C1P) intermembrane transfer by C1P transfer proteins

    Zhai, X., Gao, Y., Mishra, S. K., Simanshu, D. K., Boldyrev, I. A., Benson, L. M., Bergen III, H. R., Malinina, L., Mundy, J., Molotkovsky, J. G., Patel, D. J. & Brown, R. E., 10 Feb 2017, In: Journal of Biological Chemistry. 292, 6, p. 2531-2541 11 p.

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

  41. Published

    Discovery and characterization of a thermostable and highly halotolerant GH5 cellulase from an Icelandic hot spring isolate

    Zarafeta, D., Kissas, D., Sayer, C., Islin, S. R., Ladoukakis, E., Isupov, M. N., Chatziioannou, A., Peng, Xu, Littlechild, J. A., Skretas, G. & Kolisis, F. N., 2016, In: P L o S One. 11, 1, 18 p., e0146454.

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

  42. Published

    EstDZ3: a new esterolytic enzyme exhibiting remarkable thermostability

    Zarafeta, D., Szabo, Z., Moschidi, D., Phan, Safir Hien, Chrysina, E. D., Peng, Xu, Ingham, C. J., Kolisis, F. N. & Skretas, G., 2016, In: Frontiers in Microbiology. 7, 14 p., 1779.

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

  43. Published

    Development and application of new bioinformatic tools for large-scale population genomic study

    ZHANG, YONG, 2023, Department of Biology, Faculty of Science, University of Copenhagen. 103 p.

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

  44. Published

    Genomic analysis of Acidianus hospitalis W1 a host for studying crenarchaeal virus and plasmid life cycles

    You, X. Y., Liu, C., Wang, S. Y., Jiang, C. Y., Shah, S. A., Prangishvili, D., She, Q., Liu, S. J. & Garrett, Roger Antony, 2011, In: Extremophiles. 15, p. 487-497 11 p.

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

  45. Published

    The draft genome of mandrill (Mandrillus sphinx): an Old World monkey

    Yin, Y., Yang, T., Liu, Huan, Huang, Z., Zhang, Y., Song, Y., Wang, W., Guang, X., Sahu, S. K. & Kristiansen, Karsten, 2020, In: Scientific Reports. 10, 8 p., 2431.

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

  46. 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

  47. Published

    Emergent bacterial community properties induce enhanced drought tolerance in Arabidopsis

    Yang, Nan, Nesme, Joseph, Røder, Henriette Lyng, Li, Xuan Ji, Zuo, Zhangli Thomsen, Petersen, Morten, Burmølle, Mette & Sørensen, Søren Johannes, 2021, In: npj Biofilms and Microbiomes. 7, 11 p., 82.

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

  48. Published

    Prophage-Related Gene VpaChn25_0724 Contributes to Cell Membrane Integrity and Growth of Vibrio parahaemolyticus CHN25

    Yang, L., Wang, Y., Yu, P., Ren, S., Zhu, Z., Jin, Y., Yan, J., Peng, Xu & Chen, L., 2020, In: Frontiers in Cellular and Infection Microbiology. 10, 18 p., 595709.

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

  49. 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

  50. Published

    Molecular evidence for origin, diversification and ancient gene duplication of plant subtilases (SBTs)

    Xu, Y., Wang, S., Li, L., Sahu, S. K., Petersen, Morten, Liu, X., Melkonian, M., Zhang, G. & Liu, Huan, 2019, In: Scientific Reports. 9, 10 p., 12485.

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

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