Computational and RNA Biology

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  1. 2023
  2. Published

    Systematic Analysis of Long Non-Coding RNAs in Inflammasome Activation in Monocytes/Macrophages

    Qian, N., Distefano, R., Ilieva, M., Madsen, J. H., Rennie, Sarah & Uchida, S., 2023, In: Non-coding RNA. 9, 5, 16 p., 50.

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

  3. Published

    T2DB: A Web Database for Long Non-Coding RNA Genes in Type II Diabetes

    Distefano, R., Ilieva, M., Madsen, J. H., Ishii, H., Aikawa, M., Rennie, Sarah & Uchida, S., 2023, In: Non-coding RNA. 9, 3, 20 p., 30.

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

  4. Published

    The N-coil and the globular N-terminal domain of plant ARGONAUTE1 are interaction hubs for regulatory factors

    Bressendorff, Simon, Kausika, S., Sjøgaard, Ida Marie Zobbe, Oksbjerg, Emilie Duus, Michels, A., Poulsen, C. & Brodersen, Peter, 2023, In: Biochemical Journal. 480, 13, p. 957-974 18 p.

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

  5. Published

    The extinct Sicilian wolf shows a complex history of isolation and admixture with ancient dogs

    Ciucani, M. M., Ramos-Madrigal, J., Hernández-Alonso, G., Carmagnini, A., Aninta, S. G., Sun, X., Scharff-Olsen, C. H., Lanigan, L. T., Fracasso, I., Clausen, C. G., Aspi, J., Kojola, I., Baltrūnaitė, L., Balčiauskas, L., Moore, J., Åkesson, M., Saarma, U., Hindrikson, M., Hulva, P., Bolfíková, B. Č. & 19 others, Nowak, C., Godinho, R., Smith, S., Paule, L., Nowak, S., Mysłajek, R. W., Lo Brutto, S., Ciucci, P., Boitani, L., Vernesi, C., Stenøien, H. K., Smith, O., Frantz, L., Rossi, L., Angelici, F. M., Cilli, E., Sinding, Mikkel Holger Strander, Gilbert, M Thomas P & Gopalakrishnan, Shyam, 2023, In: iScience. 26, 8, 22 p., 107307.

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

  6. Published

    The histone demethylase KDM5C functions as a tumor suppressor in AML by repression of bivalently marked immature genes

    Trempenau, M. L., Schuster, Mikkel Bruhn, Pundhir, Sachin, Araújo Pereira, Mafalda, Kalvisa, A., Tapia, Marta Cecylia, Su, Jinyu, Ge, Y., de Boer, Bauke, Balhuizen, Alexander, Bagger, F. O., Shliaha, P., Sroczynska, P., Walfridsson, J., Grønbæk, Kirsten, Theilgaard-Mønch, Kim, Jensen, O. N., Helin, K. & Porse, Bo Torben, 2023, In: Leukemia. 37, 13 p.

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

  7. Published

    The history of Coast Salish “woolly dogs” revealed by ancient genomics and Indigenous Knowledge

    Lin, A. T., Hammond-Kaarremaa, L., Liu, H-L., Stantis, C., McKechnie, I., Pavel, M., Pavel, S. S. M., Wyss, S. S., Sparrow, D. Q., Carr, K., Aninta, S. G., Perri, A., Hartt, J., Bergström, A., Carmagnini, A., Charlton, S., Dalén, L., Feuerborn, T. R., France, C. A. M., Gopalakrishnan, S. & 13 others, Grimes, V., Harris, A., Kavich, G., Sacks, B. N., Sinding, Mikkel Holger Strander, Skoglund, P., Stanton, D. W. G., Ostrander, E. A., Larson, G., Armstrong, C. G., Frantz, L. A. F., Hawkins, M. T. R. & Kistler, L., 2023, In: Science. 382, 6676, p. 1303-1309 7 p.

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

  8. Published

    Towards in silico CLIP-seq: predicting protein-RNA interaction via sequence-to-signal learning

    Horlacher, M., Wagner, N., Moyon, L., Kuret, K., Goedert, N., Salvatore, Marco, Ule, J., Gagneur, J., Winther, Ole & Marsico, A., 2023, In: Genome Biology. 24, 1, 37 p., 180.

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

  9. Published

    Towards routine chromosome-scale haplotype-resolved reconstruction in cancer genomics

    Garg, S., 2023, In: Nature Communications. 14, 1, 11 p., 1358.

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

  10. Published

    Transcription factor expression is the main determinant of variability in gene co-activity

    van Duin, Lucas, Krautz, Robert, Rennie, Sarah & Andersson, Robin, 2023, In: Molecular Systems Biology. 19, 7, 17 p., e11392.

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

  11. Published

    Transcriptional and epigenomic profiling identifies YAP signaling as a key regulator of intestinal epithelium maturation

    Pikkupeura, Laura Maarit, Bardini Bressan, Raul, Guiu, J., Chen, Y., Maimets, Martti, Mayer, Daniela, Schweiger, P. J., Hansen, Stine Lind, Maciag, Grzegorz Jerzy, Larsen, Hjalte List, Lõhmussaar, Kadi, Pedersen, M. T., Teves, Joji Marie Yap, Lange, Jette Bornholdt, Benes, V., Sandelin, Albin Gustav & Jensen, Kim Bak, 2023, In: Science Advances. 9, 28, 16 p., eadf9460.

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

  12. Published

    Transfer learning identifies sequence determinants of cell-type specific regulatory element accessibility

    Salvatore, Marco, Horlacher, M., Marsico, A., Winther, Ole & Andersson, Robin, 2023, In: NAR Genomics and Bioinformatics. 5, 2, 10 p., 026.

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

  13. Published

    Two Novel α-Thalassemia Mutations CD 39 -C [Thr > Pro] and CD 109 ACC > CCC [Thr > Pro] Identified in Two Chinese Families: A Case Report

    Zhang, W., Han, X., Deng, J., Zhou, R., Du, X., Wu, C. & Li, M., 2023, In: Hemoglobin. 47, 4, 8 p.

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

  14. Published

    Uncertainty-aware and explainable machine learning for early prediction of battery degradation trajectory

    Rieger, L. H., Flores, E., Nielsen, K. F., Norby, P., Ayerbe, E., Winther, Ole, Vegge, T. & Bhowmik, A., 2023, In: Digital Discovery. 2, 1, p. 112-122 11 p.

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

  15. Published

    Unraveling the genetic basis of neurological diseases and thalassemia: the clinical utility of high throughput sequencing

    ZHANG, W., 2023, Department of Biology, Faculty of Science, University of Copenhagen. 117 p.

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

  16. Published

    Variational Open-Domain Question Answering

    Liévin, V., Motzfeldt, A. G., Jensen, I. R. & Winther, Ole, 2023, In: Proceedings of Machine Learning Research. 202, p. 20950-20977 28 p.

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

  17. 2022
  18. Published

    In vivo, genome-wide profiling of endogenously tagged chromatin-binding proteins with spatial and temporal resolution using NanoDam in Drosophila

    Tang, J. L. Y., Krautz, Robert, Llorà-Batlle, O., Hakes, A. E., Fox, P. M. & Brand, A. H., 2022, In: STAR Protocols. 3, 4, 30 p., 101788.

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

  19. Published

    A polygenic architecture with habitat-dependent effects underlies ecological differentiation in Silene

    Gramlich, S., Liu, Xiaodong, Favre, A., Buerkle, C. A. & Karrenberg, S., 2022, In: New Phytologist. 235, 4, p. 1641-1652 12 p.

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

  20. Published

    A review on ethnobotany, phytochemistry, and pharmacology of the genus Didymocarpus wall. (Gesneriaceae)

    Nanjala, C., Odago, W. O., Rono, P. C., Waswa, E. N., Mutinda, E. S., Oulo, M. A., Muema, F. W., Wanga, V. O., Mkala, E. M., Kuja, J., Njire, M. M. & Hu, G. W., 2022, In: Journal of Ethnopharmacology. 295, 25 p., 115404.

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

  21. Published

    A structural biology community assessment of AlphaFold2 applications

    Akdel, M., Pires, D. E., Porta Pardo, E., Jänes, J., Zalevsky, A. O., Meszaros, B., Bryant, P., Good, L. L., Laskowski, R. A., Pozzati, G., Shenoy, A., Zhu, W., Kundrotas, P., Serra, V. R., Rodrigues, C. H. M., Dunham, A. S., Burke, D., Borkakoti, N., Velankar, S., Frost, A. & 14 others, Basquin, J., Lindorff-Larsen, Kresten, Bateman, A., Kajava, A., Valencia, A., Ovchinnikov, S., Durairaj, J., Ascher, D. B., Thornton, J. M., Davey, N. E., Stein, Amelie, Elofsson, A., Croll, T. & Beltrao, P., 2022, In: Nature Structural & Molecular Biology. 29, 11, 16 p.

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

  22. Published

    African climate and geomorphology drive evolution and ghost introgression in sable antelope

    Rocha, J. L., Vaz Pinto, P., Siegismund, Hans Redlef, Meyer, M., Jansen van Vuuren, B., Veríssimo, L., Ferrand, N. & Godinho, R., 2022, In: Molecular Ecology. 31, 10, p. 2968-2984 17 p.

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

  23. Published

    An LDLR missense variant poses high risk of familial hypercholesterolemia in 30% of Greenlanders and offers potential of early cardiovascular disease intervention

    Jørsboe, E., Andersen, M. K., Skotte, L., Stæger, F. F., Færgeman, N. J., Hanghøj, K., Santander, C. G., Senftleber, N. K., Diaz, L. J., Overvad, M., Waples, R. K., Geller, F., Bjerregaard, P., Melbye, M., Larsen, C. V. L., Feenstra, B., Anders Koch, K., Jørgensen, M. E., Grarup, N., Moltke, I. & 2 others, Albrechtsen, Anders & Hansen, Torben, 2022, In: Human Genetics and Genomics Advances. 3, 4, 10 p., 100118.

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

  24. Published

    An update on principles of m6A targeting

    Bai, B., 2022, In: Trends in Plant Science. 27, 3, p. 224-226 3 p.

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

  25. Published

    Ancient and historical DNA in conservation policy

    Jensen, E. L., Díez-del-Molino, D., Gilbert, M Thomas P, Bertola, Laura, Borges, F., Cubric-Curik, V., de Navascués, M., Frandsen, P., Heuertz, M., Hvilsom, C., Jiménez-Mena, B., Miettinen, A., Moest, M., Chrzanová Pecnerová, Patrícia, Barnes, I. & Vernesi, C., 2022, In: Trends in Ecology and Evolution. 37, 5, p. 420-429 10 p.

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

  26. Published

    Bioinformatics of transcription factor binding prediction

    Navarro-Delgado, E. I., Salgado-Albarrán, M., Torres-Arciga, K., Alcaraz, N., Soto-Reyes, E., Herrera, L. A. & González-Barrios, R., 2022, Bioinformatics and Human Genomics Research. CRC Press, p. 203-221 19 p.

    Research output: Chapter in Book/Report/Conference proceeding › Book chapter › Research › peer-review

  27. Published

    CRISPR/Cas9 gRNA activity depends on free energy changes and on the target PAM context

    Corsi, G. I., Qu, Kunli, Alkan, F., Pan, Xiaoguang, Luo, Y. & Gorodkin, Jan, 2022, In: Nature Communications. 13, 14 p., 3006.

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

  28. Published

    Calibrated uncertainty for molecular property prediction using ensembles of message passing neural networks

    Busk, J., Jørgensen, P. B., Bhowmik, A., Schmidt, M. N., Winther, Ole & Vegge, T., 2022, In: Machine Learning: Science and Technology. 3, 1, 12 p., 015012.

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

  29. Published

    Cardiovascular Autonomic Neuropathy in Type 1 Diabetes Is Associated With Disturbances in TCA, Lipid, and Glucose Metabolism

    Hansen, C. S., Suvitaival, T., Theilade, Karen Simone, Mattila, I., Lajer, M., Trošt, K., Ahonen, L., Hansen, T. W., Legido-Quigley, C., Rossing, Peter & Ahluwalia, Tarun Veer Singh, 2022, In: Frontiers in Endocrinology. 13, 831793.

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

  30. Published

    Chromatin modifier HUSH co-operates with RNA decay factor NEXT to restrict transposable element expression

    Garland, W., Müller, I., Wu, M., Schmid, M., Imamura, K., Rib, Leonor, Sandelin, Albin Gustav, Helin, K. & Jensen, T. H., 2022, In: Molecular Cell. 82, 9, p. 1691-1707.e8

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

  31. Published

    Chromosome evolution and the genetic basis of agronomically important traits in greater yam

    Bredeson, J. V., Lyons, J. B., Oniyinde, I. O., Okereke, N. R., Kolade, O., Nnabue, I., Nwadili, C. O., Hřibová, E., Parker, M., Nwogha, J., Shu, S., Carlson, J., Kariba, R., Muthemba, S., Knop, K., Barton, G. J., Sherwood, A. V., Lopez-Montes, A., Asiedu, R., Jamnadass, R. & 13 others, Muchugi, A., Goodstein, D., Egesi, C. N., Featherston, J., Asfaw, A., Simpson, G. G., Doležel, J., Hendre, P. S., Van Deynze, A., Kumar, P. L., Obidiegwu, J. E., Bhattacharjee, R. & Rokhsar, D. S., 2022, In: Nature Communications. 13, 16 p., 2001.

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

  32. Published

    Chromosome-scale haplotype-resolved pangenomics

    Garg, S., Balboa, Renzo Fidel Ferdinando & Kuja, J., 2022, In: Trends in Genetics. 38, 11, p. 1103-1107 5 p.

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

  33. Published

    Circle-Seq reveals genomic and disease-specific hallmarks in urinary cell-free extrachromosomal circular DNAs

    Lv, W., Pan, X., Han, P., Wang, Z., Feng, W., Xing, X., Wang, Q., Qu, K., Zeng, Y., Zhang, C., Xu, Z., Li, Y., Zheng, T., Lin, L., Liu, C., Liu, X., Li, H., Henriksen, R. A., Bolund, L., Lin, L. & 7 others, Jin, X., Yang, H., Zhang, X., Yin, T., Regenberg, Birgitte, He, F. & Luo, Y., 2022, In: Clinical and Translational Medicine. 12, 4, 16 p., e817.

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

  34. 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

  35. 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

  36. Published

    Conflicts between large carnivores and local pastoralists around Niokolo Koba National Park, Senegal

    Gueye, M., Van Cauteren, D., Mengual, L., Pellaton, R., Leirs, H., Bertola, Laura & de Iongh, H., 2022, In: European Journal of Wildlife Research. 68, 1, 11 p., 9.

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

  37. Published

    Context dependency of nucleotide probabilities and variants in human DNA

    Liang, Yuhu, Grønbæk, Christian, Fariselli, P. & Krogh, Anders, 2022, In: BMC Genomics. 23, 1, 15 p., 87.

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

  38. Published

    Context dependent prediction in DNA sequence using neural networks

    Grønbæk, Christian, Liang, Yuhu, Elliott, Desmond & Krogh, Anders, 2022, In: PeerJ. 10, 22 p., e13666.

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

  39. 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

  40. 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

  41. Published

    De Novo Assembly of 20 Chicken Genomes Reveals the Undetectable Phenomenon for Thousands of Core Genes on Microchromosomes and Subtelomeric Regions

    Li, M., Sun, C., Xu, N., Bian, P., Tian, X., Wang, X., Wang, Y., Jia, X., Heller, R., Wang, M., Wang, F., Dai, X., Luo, R., Guo, Y., Wang, X., Yang, P., Hu, D., Liu, Z., Fu, W., Zhang, S. & 10 others, Li, X., Wen, C., Lan, F., Siddiki, A. Z., Suwannapoom, C., Zhao, X., Nie, Q., Hu, X., Jiang, Y. & Yang, N., 2022, In: Molecular Biology and Evolution. 39, 4, 16 p., msac066.

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

  42. 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

  43. Published

    Development and Optimization of a Silica Column-Based Extraction Protocol for Ancient DNA

    Dehasque, M., Chrzanová Pecnerová, Patrícia, Kempe Lagerholm, V., Ersmark, E., Danilov, G. K., Mortensen, P., Vartanyan, S. & Dalén, L., 2022, In: Genes. 13, 4, 16 p., 687.

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

  44. Published

    Disease-linked mutations cause exposure of a protein quality control degron

    Kampmeyer, Caroline, Larsen-Ledet, Sven, Wagnkilde, M. R., Michelsen, M., Iversen, Henriette Kring Mangor, Nielsen, S. V., Lindemose, Søren, Caregnato, A., Ravid, T., Stein, Amelie, Teilum, Kaare, Lindorff-Larsen, Kresten & Hartmann-Petersen, Rasmus, 2022, In: Structure. 30, 9, p. 1245-1253.e5

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

  45. Published

    Efficient approaches for large-scale GWAS with genotype uncertainty

    Jørsboe, E. & Albrechtsen, Anders, 2022, In: G3: Genes, Genomes, Genetics (Bethesda). 12, 1, 9 p., jkab385.

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

  46. Published

    Endogenous retroviruses co-opted as divergently transcribed regulatory elements shape the regulatory landscape of embryonic stem cells

    Bakoulis, Stylianos, Krautz, Robert, Alcaraz, N., Salvatore, Marco & Andersson, Robin, 2022, In: Nucleic acids symposium series. 50, 4, p. 2111-2127 17 p., 088.

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

  47. Published

    Estimation of site frequency spectra from low-coverage sequencing data using stochastic EM reduces overfitting, runtime, and memory usage

    Rasmussen, Malthe Sebro, Garcia Erill, Genís, Korneliussen, Thorfinn Sand, Wiuf, Carsten & Albrechtsen, Anders, 2022, In: Genetics. 222, 4, 15 p., iyac148.

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

  48. 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

  49. Published

    Evolutionary consequences of genomic deletions and insertions in the woolly mammoth genome

    van der Valk, T., Dehasque, M., Chacón-Duque, J. C., Oskolkov, N., Vartanyan, S., Heintzman, P. D., Chrzanová Pecnerová, Patrícia, Díez-del-Molino, D. & Dalén, L., 2022, In: iScience. 25, 8, 11 p., 104826.

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

  50. Published

    Flagella disruption in Bacillus subtilis increases amylase production yield

    Fehler, A. O., Kallehauge, T. B., Geissler, Adrian Sven, González-Tortuero, E., Seemann, Ernst Stefan, Gorodkin, Jan & Vinther, Jeppe, 2022, In: Microbial Cell Factories. 21, 11 p., 131.

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

  51. Published

    Genetic guidelines for translocations: Maintaining intraspecific diversity in the lion (Panthera leo)

    Bertola, Laura, Miller, S. M., Williams, V. L., Naude, V. N., Coals, P., Dures, S. G., Henschel, P., Chege, M., Sogbohossou, E. A., Ndiaye, A., Kiki, M., Gaylard, A., Ikanda, D. K., Becker, M. S. & Lindsey, P., 2022, In: Evolutionary Applications. 15, 1, p. 22-39 18 p.

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

  52. Published

    Genetic loci and prioritization of genes for kidney function decline derived from a meta-analysis of 62 longitudinal genome-wide association studies

    Gorski, M., Rasheed, H., Teumer, A., Thomas, L. F., Graham, S. E., Sveinbjornsson, G., Winkler, T. W., Günther, F., Stark, K. J., Chai, J-F., Tayo, B. O., Wuttke, M., Li, Y., Tin, A., Ahluwalia, T. S., Ärnlöv, J., Åsvold, B. O., Bakker, S. J. L., Banas, B., Bansal, N. & 29 others, Biggs, M. L., Biino, G., Böhnke, M., Boerwinkle, E., Bottinger, E. P., Brenner, H., Brumpton, B., Carroll, R. J., Chaker, L., Chalmers, J., Chee, M., Chee, M., Cheng, C., Chu, A. Y., Ciullo, M., Cocca, M., Cook, J. P., Coresh, J., Cusi, D., de Borst, M. H., Degenhardt, F., Eckardt, K., Endlich, K., Evans, M. K., Feitosa, M. F., Franke, A., Freitag-Wolf, S., Rossing, Peter & LifeLines Cohort Study, L. C. S., 2022, In: Kidney International. 102, 3, p. 624-639 16 p.

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

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