Computational and RNA Biology

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  1. 2019
  2. Published

    Global network of computational biology communities: ISCB's Regional Student Groups breaking barriers [version 1; peer review: not peer reviewed]

    Shome, S., Parra, R. G., Fatima, N., Monzon, A. M., Cuypers, B., Moosa, Y., Coimbra, N. D. R., Assis, J., Giner-Delgado, C., Dönertaş, H. M., Cuesta-Astroz, Y., Saarunya, G., Allali, I., Gupta, S., Srivastava, A., Kalsan, M., Valdivia, C., Olguin-Orellana, G. J., Papadimitriou, S., Parisi, D. & 22 others, Kristensen, N. P., Rib, Leonor, Guebila, M. B., Bauer, E., Zaffaroni, G., Bekkar, A., Ashano, E., Paladin, L., Necci, M., Moreyra, N. N., Rydén, M., Villalobos-Solís, J., Papadopoulos, N., Rafael, C., Karakulak, T., Kaya, Y., Gladbach, Y., Dhanda, S. K., Šoštarić, N., Alex, A., DeBlasio, D. & Rahman, F., 1 Jan 2019, In: F1000Research. 8, 9 p., 1574.

    Research output: Contribution to journal › Editorial › Research

  3. Published

    The transmembrane autophagy cargo receptors ATI1 and ATI2 interact with ATG8 through intrinsically disordered regions with distinct biophysical properties

    Sjøgaard, Ida Marie Zobbe, Bressendorff, Simon, Prestel, Andreas, Kausika, S., Oksbjerg, Emilie Duus, Kragelund, Birthe Brandt & Brodersen, Peter, 2019, In: Biochemical Journal. 476, 3, p. 449-465 17 p.

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

  4. Published

    Ancestry-specific association mapping in admixed populations

    Skotte, L., Jørsboe, E., Korneliussen, Thorfinn Sand, Moltke, Ida & Albrechtsen, Anders, 2019, In: Genetic Epidemiology. 43, 5, p. 506-521

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

  5. Published

    More grist for the mill? Species delimitation in the genomic era and its implications for conservation

    Stanton, D. W. G., Frandsen, P., Waples, R. K., Heller, Rasmus, Russo, I. M., Orozco-terWengel, P. A., Pedersen, C. T., Siegismund, Hans Redlef & Bruford, M. W., 2019, In: Conservation Genetics. 20, 1, p. 101-113

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

  6. Published

    ERG Controls B Cell Development by Promoting Igh V-to-DJ Recombination

    Søndergaard, E., Rauch, A., Michaut, Magali, Rapin, N., Rehn, M., Wilhelmson, Anna, Camponeschi, A., Hasemann, M. S., Bagger, F. O., Jendholm, J., Knudsen, K. J., Mandrup, S., Mårtensson, I. L. & Porse, Bo Torben, 26 Nov 2019, In: Cell Reports. 29, 9, p. 2756-2769.e6 21 p.

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

  7. Published

    Bioinformatic Analysis of Breast Tumor Interstitial Fluids: Insights into a Pan-molecular Secretome

    Terkelsen, Thilde Bagger, 2019, Department of Biology, Faculty of Science, University of Copenhagen.

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

  8. Published

    A step-by-step guide to analyzing CAGE data using R/Bioconductor

    Thodberg, Malte & Sandelin, Albin Gustav, 18 Jun 2019, In: F1000Research. 8, 49 p., 886.

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

  9. Published

    CAGEfightR: analysis of 5'-end data using R/Bioconductor

    Thodberg, Malte, Thieffry, A., Vitting-Seerup, K., Andersson, Robin & Sandelin, Albin Gustav, 2019, In: BMC Bioinformatics. 20, 13 p., 487.

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

  10. Published

    Comprehensive profiling of the fission yeast transcription start site activity during stress and media response

    Thodberg, Malte, Thieffry, A., Lange, Jette Bornholdt, Boyd, M., Holmberg, Christian, Azad, A., Workman, C. T., Chen, Y., Ekwall, K., Nielsen, Olaf & Sandelin, Albin Gustav, 28 Feb 2019, In: Nucleic Acids Research. 47, 4, p. 1671-1691 21 p.

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

  11. Published

    IsoformSwitchAnalyzeR: analysis of changes in genome-wide patterns of alternative splicing and its functional consequences

    Vitting-Seerup, K. & Sandelin, Albin Gustav, 2019, In: Bioinformatics. 35, 21, p. 4469-4471

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

  12. Published

    Genetic basis of ruminant headgear and rapid antler regeneration

    Wang, Y., Zhang, C., Wang, N., Li, Z., Heller, R., Liu, R., Zhao, Y., Han, J., Pan, X., Zheng, Z., Dai, X., Chen, C., Dou, M., Peng, S., Chen, X., Liu, J., Li, M., Wang, K., Liu, C., Lin, Z. & 18 others, Chen, L., Hao, F., Zhu, W., Song, C., Zhao, C., Zheng, C., Wang, J., Hu, S., Li, C., Yang, H., Jiang, L., Li, G., Liu, M., Sonstegard, T. S., KU, thw266, Jiang, Y., Wang, W. & Qiu, Q., 2019, In: Science. 364, 6446, p. 1153-+ eaav6335.

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

  13. Published

    Relatedness, admixture and the genetic history of Greenland-European contact

    Waples, R., 2019, Department of Biology, Faculty of Science, University of Copenhagen.

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

  14. Published

    Allele frequency-free inference of close familial relationships from genotypes or low-depth sequencing data

    Waples, R. K., Albrechtsen, Anders & Moltke, Ida, 2019, In: Molecular Ecology. 28, 1, p. 35-48 14 p.

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

  15. Published

    Consequences of breed formation on patterns of genomic diversity and differentiation: the case of highly diverse peripheral Iberian cattle

    Rodrigues da Fonseca, Rute Andreia, Urena, I., Afonso, S., Pires, A. E., Jørsboe, E., Chikhi, L. & Ginja, C., 2019, In: BMC Genomics. 20, p. 1-13 334.

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

  16. 2018
  17. Published

    Genomic insights into the origin and diversification of late maritime hunter-gatherers from the Chilean Patagonia

    De la Fuente, C., Avila-Arcos, M. C., Galimany, J., Carpenter, M. L., Homburger, J. R., Blanco, A., Contreras, P., Davalos, D. C., Reyes, O., Roman, M. S., Moreno-Estrada, A., Campos, P., Eng, C., Huntsman, S., Burchard, E. G., Malaspinas, A-S., Bustamante, C. D., Willerslev, E., Llop, E., Verdugo, R. A. & 1 others, Moraga, M., 2018, In: Proceedings of the National Academy of Sciences of the United States of America. 115, 17, p. E4006-E4012 7 p.

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

  18. Published

    Probabilistic Programming for Voucher Information Extraction: Preliminary Practical Experiences

    Al-Sibahi, A. S., Hamelryck, Thomas Wim & Henglein, Fritz, 2018.

    Research output: Contribution to conference › Poster › Research

  19. Published

    Genetic architecture of obesity and related metabolic traits - recent insights from isolated populations

    Lepola, Mette Andersen, Grarup, Niels, Moltke, Ida, Albrechtsen, Anders & Hansen, Torben, 2018, In: Current Opinion in Genetics and Development. 50, p. 74-78 5 p.

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

  20. Published

    Genetic determinants of glycated hemoglobin levels in the Greenlandic Inuit population

    Appel, V. R., Moltke, Ida, Jørgensen, M. E., Bjerregaard, P., Linneberg, Allan René, Pedersen, Oluf Borbye, Albrechtsen, Anders, Hansen, Torben & Grarup, Niels, 2018, In: European Journal of Human Genetics. 26, 6, p. 868-875 8 p.

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

  21. Published

    An m6A-YTH Module Controls Developmental Timing and Morphogenesis in Arabidopsis

    Arribas Hernandez, Laura, Bressendorff, Simon, Hansen, M. H., Poulsen, C., Erdmann, S. & Brodersen, Peter, 2018, In: Plant Cell. 30, 5, p. 952-967 16 p.

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

  22. Published

    Shared activity patterns arising at genetic susceptibility loci reveal underlying genomic and cellular architecture of human disease

    Baillie, J. K., Bretherick, A., Haley, C. S., Clohisey, S., Gray, A., Neyton, L. P. A., Barrett, J., Stahl, E. A., Tenesa, A., Andersson, R., Brown, J. B., Faulkner, G. J., Lizio, M., Schaefer, U., Daub, C., Itoh, M., Kondo, N., Lassmann, T., Kawai, J., Mole, D. & 14 others, Bajic, V. B., Heutink, P., Rehli, M., Kawaji, H., Sandelin, Albin Gustav, Suzuki, H., Satsangi, J., Wells, C. A., Hacohen, N., Freeman, T. C., Hayashizaki, Y., Carninci, P., Forrest, A. R. R. & Hume, D. A., 2018, In: PLoS Computational Biology. 14, 3, 24 p., e1005934.

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

  23. Published

    Genome sequence and effectorome of Moniliophthora perniciosa and Moniliophthora roreri subpopulations

    Barbosa, C. S., Rodrigues da Fonseca, Rute Andreia, Batista, T. M., Barreto, M. A., Argolo, C. S., de Carvalho, M. R., Jordao do Amaral, D. O., de Andrade Silva, E. M., Arevalo-Gardini, E., Hidalgo, K. S., Franco, G. R., Pirovani, C. P., Micheli, F. & Gramacho, K. P., 3 Jul 2018, In: BMC Genomics. 19, 12 p., 509.

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

  24. Published

    Characterization of the enhancer and promoter landscape of inflammatory bowel disease from human colon biopsies

    Boyd, M., Thodberg, M., Vitezic, M., Lange, J. B., Vitting-Seerup, K., Chen, Y., Coskun, M., Li, Y., Lo, B. Z. S., Klausen, P., Schweiger, P., Pedersen, A. G., Rapin, N. P. J-P., Skovgaard, K., Dahlgaard, K., Andersson, R., Terkelsen, T. B., Lilje, B., Troelsen, J. T., Petersen, A. M. & 7 others, Jensen, Kim Bak, Gögenur, Ismail, Thielsen, P., Seidelin, Jakob Benedict, Nielsen, Ole Haagen, Bjerrum, Jakob Tveiten & Sandelin, Albin Gustav, 2018, In: Nature Communications. 9, 19 p., 1661.

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

  25. Published

    High definition urban fashion: Proteins reveal preferred resources for medieval leather shoes

    Brandt, Luise Ørsted, 2018, Urban Network Evolutions: Towards a high-definition archaeology. Aarhus: Aarhus University Press, p. 241-247 7 p.

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

  26. Published

    Jagten på antikkens bindemidler

    Brandt, Luise Ørsted, 2018, In: Sfinx. 41, 1, p. 26-29 4 p.

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

  27. Published

    Skind og Ben - Forskning med fokus på dyr fra middelalderens Odense

    Brandt, Luise Ørsted, Amsgaard Ebsen, J. & Haase, K., 2018

    Research output: Non-textual form › Interactive production › Communication

  28. Published

    Vejledning i forskning

    Brandt, Luise Ørsted, 2018

    Research output: Other contribution › Net publication - Internet publication › Education

  29. Published

    Regulation and Maintenance of Transcriptional Specificity

    Dalby, M., 2018, Department of Biology, Faculty of Science, University of Copenhagen.

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

  30. Published

    Toroidal Diffusions and Protein Structure Evolution

    Garcia Portugues, E., Golden, M., Sørensen, Michael, Mardia, K. V., Hamelryck, Thomas Wim & Hein, J., 2018, Applied Directional Statistics: Modern Methods and Case Studies. Ley, C. & Verdebout, H. (eds.). CRC Press, 34 p.

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

  31. Published

    YeastFab: High-Throughput Genetic Parts Construction, Measurement, and Pathway Engineering in Yeast

    Garcia-Ruiz, E., Auxillos, Jamie Yam, Li, T., Dai, J. & Cai, Y., 1 Jan 2018, Methods in Enzymology. Scrutton, N. (ed.). Academic Press, p. 277-306 30 p. (Methods in Enzymology, Vol. 608).

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

  32. Published

    Ancient genomes revisit the ancestry of domestic and Przewalski's horses

    Gaunitz, C., Fages, A. A., Hanghøj, K. E., Albrechtsen, A., Khan, N., Schubert, M., Seguin-Orlando, A., Owens, I. J., Felkel, S., Bignon-Lau, O., Damgaard, P. D. B., Mittnik, A., Mohaseb, A. F., Davoudi, H., Alquraishi, S., Alfarhan, A. H., Al-Rasheid, K. A. S., Crubézy, E., Benecke, N., Olsen, S. & 27 others, Brown, D., Anthony, D., Massy, K., Pitulko, V., Kasparov, A., Brem, G., Hofreiter, M., Mukhtarova, G., Baimukhanov, N., Lõugas, L., Onar, V., Stockhammer, P. W., Krause, J., Boldgiv, B., Undrakhbold, S., Erdenebaatar, D., Lepetz, S., Mashkour, M., Ludwig, A., Wallner, B., Merz, V., Merz, I., Zaibert, V., Willerslev, Eske, Sanz, P. L., Outram, A. K. & Orlando, L. A. A., 2018, In: Science. 360, 6384, p. 111-114 4 p.

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

  33. Published

    Cohort-wide deep whole genome sequencing and the allelic architecture of complex traits

    Gilly, A., Suyeges, D., Kuchenbaecker, K., Pollard, M., Southam, L., Hatzikotoulas, K., Farmaki, A-E., Bjornland, T., Waples, R., Appel, E. V. R., Casalone, E., Melloni, G., Kilian, B., Rayner, N. W., Ntalla, I., Kundu, K., Walter, K., Danesh, J., Butterworth, A., Barroso, I. & 5 others, Tsafantakis, E., Dedoussis, G., Zeggini, E., Moltke, Ida & Zeggini, E., 1 Dec 2018, In: Nature Communications. 9, p. 1-9 4674.

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

  34. Published

    Identification of novel high-impact recessively inherited type 2 diabetes risk variants in the Greenlandic population

    Grarup, Niels, Moltke, Ida, Lepola, Mette Andersen, Bjerregaard, P., Larsen, C. V. L., Dahl-Petersen, I. K., Jørsboe, E., Tiwari, H. K., Hopkins, S. E., Wiener, H. W., Boyer, B. B., Linneberg, Allan René, Pedersen, Oluf Borbye, Jørgensen, M. E., Albrechtsen, Anders & Hansen, Torben, 1 Sep 2018, In: Diabetologia. 61, 9, p. 2005–2015

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

  35. Published

    Loss-of-function variants in ADCY3 increase risk of obesity and type 2 diabetes

    Grarup, Niels, Moltke, Ida, Lepola, Mette Andersen, Dalby, M., Vitting-Seerup, K., Kern, T. S., Mahendran, Y., Jørsboe, E., Larsen, C. V. L., Dahl-Petersen, I. K., Gilly, A., Suveges, D., Dedoussis, G., Zeggini, E., Pedersen, Oluf Borbye, Andersson, Robin, Bjerregaard, P., Jørgensen, M. E., Albrechtsen, Anders & Hansen, Torben, 2018, In: Nature Genetics. 50, 2, p. 172-174 3 p.

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

  36. Published

    CTCF-KDM4A complex correlates with histone modifications that negatively regulate CHD5 gene expression in cancer cell lines

    Guerra-Calderas, L., González-Barrios, R., Patiño, C. C., Alcaraz, N., Salgado-Albarrán, M., de León, D. C., Hernández, C. C., Sánchez-Pérez, Y., Maldonado-Martínez, H. A., De la Rosa-Velazquez, I. A., Vargas-Romero, F., Herrera, L. A., García-Carrancá, A. & Soto-Reyes, E., 2018, In: OncoTarget. 9, 24, p. 17028-17042 15 p.

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

  37. Published

    FoxA1 in synergy with IFNβ controls PDL1 expression in anti-inflammatory T cells via binding to a 60-nucleotide region in the Pdl1 promoter

    Hadi, M., Rasmussen, L. M., Kosicki, M., Carlsson, R. & Issazadeh-Navikas, Shohreh, Oct 2018, p. 596-597.

    Research output: Contribution to conference › Conference abstract for conference › Research

  38. Published

    Genomic investigations of horse domestication using ancient DNA and a novel statistical method for epigenomic inference from ancient DNA sequencing data

    Hanghøj, Kristian Ebbesen, 2018, Department of Biology, Faculty of Science, University of Copenhagen.

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

  39. Published

    The Muskox Lost a Substantial Part of Its Genetic Diversity on Its Long Road to Greenland

    Hansen, C. C. R., Hvilsom, C., Schmidt, N. M., Aastrup, P., de Groot, P. J. V. C., Siegismund, Hans Redlef & Heller, Rasmus, 2018, In: Current Biology. 28, 24, p. 4022-4028, e1-e5

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

  40. Published

    Physiological and Genetic Adaptations to Diving in Sea Nomads

    Ilardo, M. A., Moltke, Ida, Korneliussen, Thorfinn Sand, Cheng, J., Stern, A. J., Racimo, Fernando, Damgaard, P. D. B., Sikora, Martin, Seguin-Orlando, A., Rasmussen, Simon, van den Munckhof, I. C. L., ter Horst, R., Joosten, L. A. B., Netea, M. G., Salingkat, S., Nielsen, Rasmus & Willerslev, Eske, 2018, In: Cell. 173, 3, p. 569-580 12 p., e15.

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

  41. Published

    The GBAF chromatin remodeling complex binds H3K27ac and mediates enhancer transcription

    Jefimov, K., Alcaraz, N., Kloet, S. L., Värv, S., Sakya, S. A., Vaagenso, C., Vermeulen, M., Aasland, R. & Andersson, Robin, 2018, 31 p.

    Research output: Working paper › Preprint › Research

  42. Published

    JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework

    Khan, A., Fornes, O., Stigliani, A., Gheorghe, M., Castro-Mondragon, J. A., van der Lee, R., Bessy, A., Chèneby, J., Kulkarni, S. R., Tan, G., Baranasic, D., Arenillas, D. J., Sandelin, Albin Gustav, Vandepoele, K., Lenhard, B., Ballester, B., Wasserman, W. W., Parcy, F. & Mathelier, A., 2018, In: Nucleic Acids Research. 46, D1, p. D260-D266 7 p., gkx1126.

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

  43. Published

    Exploring the central dogma from both ends. Omics integration of Hi-C sequencing and Raman spectroscopic data

    Kumar, V., 2018, Department of Biology, Faculty of Science, University of Copenhagen.

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

  44. Published

    Genomic Analyses from Non-invasive Prenatal Testing Reveal Genetic Associations, Patterns of Viral Infections, and Chinese Population History

    Liu, S., Huang, S., Chen, F., Zhao, L., Yuan, Y., Francis, S. S., Fang, L., Li, Z., Lin, L., Liu, R., Zhang, Y., Xu, H., Li, S., Zhou, Y., Davies, R. W., Liu, Q., Walters, R. G., Lin, K., Ju, J., Komeliussen, T. & 18 others, Yang, M. A., Fu, Q., Wang, J., Zhou, L., Krogh, Anders, Zhang, H., Wang, W., Chen, Z., Cai, Z., Yin, Y., Yang, H., Mao, M., Shendure, J., Wang, J., Albrechtsen, Anders, Jin, X., Nielsen, Rasmus & Xu, X., 2018, In: Cell. 175, 2, p. 347-359, e1-e7

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

  45. Published

    The RNA exosome contributes to gene expression regulation during stem cell differentiation

    Llinares, M. L., Karadoulama, Evdoxia, Chen, Y., Wojenski, L. A., Villafano, G. J., Lange, Jette Bornholdt, Andersson, Robin, Core, L., Sandelin, Albin Gustav & Jensen, T. H., 2018, In: Nucleic Acids Research. 46, 21, p. 11502-11513

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

  46. Published

    "Out of the Can": A Draft Genome Assembly, Liver Transcriptome, and Nutrigenomics of the European Sardine, Sardina pilchardus

    Machado, A. M., Tørresen, O. K., Kabeya, N., Couto, A., Petersen, Bent, Felicio, M., Campos, P. F., Fonseca, E., Bandarra, N., Lopes-Marques, M., Ferraz, R., Ruivo, R., Fonseca, M. M., Jentoft, S., Monroig, Ó., Rodrigues da Fonseca, Rute Andreia & Castro, L. F. C., 2018, In: Genes. 9, 10, p. 1-13 485.

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

  47. Published

    A resource for sustainable management: De novo assembly and annotation of the liver transcriptome of the Atlantic chub mackerel, Scomber colias

    Machado, A. M., Felício, M., Fonseca, E., Rodrigues da Fonseca, Rute Andreia & Castro, L. F. C., 2018, In: Data in Brief. 18, p. 276-284 9 p.

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

  48. Published

    Orthologous proteins of experimental de- and remyelination are differentially regulated in the CSF proteome of multiple sclerosis subtypes

    Martin, N. A., Nawrocki, A., Molnar, V., Elkjaer, M. L., Thygesen, E. K., Palkovits, M., Acs, P., Sejbaek, T., Nielsen, H. H., Hegedus, Z., Sellebjerg, Finn Thorup, Molnar, T., Barbosa, E. G. V., Alcaraz, N., Gallyas, F. J., Svenningsen, A. F., Baumbach, J., Lassmann, H., Larsen, M. R. & Illes, Z., 2018, In: PLOS ONE. 13, 8, p. 1-26 e0202530.

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

  49. Published

    Benchmarking the HLA typing performance of Polysolver and Optitype in 50 Danish parental trios

    Matey-Hernandez, M. L., Danish Pan Genome Consortium, D. P. G. C., Brunak, Søren, Izarzugaza, J. M. G., Sørensen, L. M., Petersen, Bent, Sibbesen, Jonas Andreas, Liu, S., Belling, K. G., Have, C. T., Bork-Jensen, J., Sun, J., Hansen, Torben, Krogh, Anders, Sørensen, Thorkild I.A., Pedersen, Oluf Borbye, Wang, J., Eiberg, Hans Rudolf Lytchoff & Kristiansen, Karsten, 2018, In: BMC Bioinformatics. 19, p. 1-12 239.

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

  50. Published

    Estimating the timing of multiple admixture pulses during local ancestry inference

    Medina, P., Thornlow, B., Nielsen, Rasmus & Corbett-Detig, R., 2018, In: Genetics. 210, 3, p. 1089-1107 19 p.

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

  51. Published

    Inferring Population Structure and Admixture Proportions in Low-Depth NGS Data

    Meisner, Jonas & Albrechtsen, Anders, 2018, In: Genetics. 210, 2, p. 719-731

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

  52. Published

    Terminal Pleistocene Alaskan genome reveals first founding population of Native Americans

    Moreno Mayar, J. Víctor, Potter, B. A., Vinner, Lasse, Steinrucken, M., Rasmussen, Simon, Terhorst, J., Kamm, J. A., Albrechtsen, Anders, Malaspinas, A., Sikora, Martin, Reuther, J. D., Irish, J. D., Malhi, R. S., Orlando, L. A. A., Song, Y. S., Nielsen, Rasmus, Meltzer, D. J. & Willerslev, Eske, 2018, In: Nature Genetics. 553, 7687, p. 203-207 5 p.

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

  53. Published

    Circular DNA elements of chromosomal origin are common in healthy human somatic tissue

    Møller, H. D., Mohiyuddin, M., Prada Luengo, Inigo, Sailani, M. R., Halling, Jens Frey, Plomgaard, Peter Stendahl, Maretty, L., Hansen, Anders Johannes, Snyder, M. P., Pilegaard, Henriette, Lam, H. Y. K. & Regenberg, Birgitte, 1 Dec 2018, In: Nature Communications. 9, 12 p., 1069.

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

  54. Published

    Binning microbial genomes using deep learning

    Nissen, J. N., Sønderby, C. K., Armenteros, J. J. A., Grønbech, Christopher Heje, Nielsen, H. B., Petersen, T. N., Winther, Ole & Rasmussen, Simon, 2018, (bioRxiv).

    Research output: Working paper › Preprint › Research

  55. Published

    The Neuronal Gene Arc Encodes a Repurposed Retrotransposon Gag Protein that Mediates Intercellular RNA Transfer

    Pastuzyn, E. D., Day, C. E., Kearns, R. B., Kyrke-Smith, M., Taibi, A. V., McCormick, J., Yoder, N., Belnap, D. M., qrc243, qrc243, Morado, D. R., Briggs, J. A. G., Feschotte, C. & Shepherd, J. D., 2018, In: Cell. 172, 1-2, p. 275-288, E18 33 p.

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

  56. Published

    A southern African origin and cryptic structure in the highly mobile plains zebra

    Pedersen, C. T., Albrechtsen, Anders, Etter, P. D., Johnson, E. A., Orlando, L., Chikhi, L., Siegismund, Hans Redlef & Heller, Rasmus, 2018, In: Nature Ecology & Evolution. 2, 3, p. 491-498 8 p.

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

  57. Published

    MCM2 promotes symmetric inheritance of modified histones during DNA replication

    Petryk, N., Dalby, M., Wenger, Alice, Stromme, C. B., Strandsby, A., Andersson, Robin & Groth, Anja, 2018, In: Science. 361, 6409, p. 1389-1392 3 p.

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

  58. Published

    MyPMFs: a simple tool for creating statistical potentials to assess protein structural models

    Postic, G., Hamelryck, Thomas Wim, Chomilier, J. & Stratmann, D., 2018, In: Biochimie. 151, p. 37-41 5 p.

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

  59. Published

    RNA-Seq for Bacterial Gene Expression

    Poulsen, L. D. & Vinther, Jeppe, 2018, In: Current Protocols in Nucleic Acid Chemistry. 73, 1, p. 1-12 e55.

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

  60. Published

    Enhancer and Transcription Factor Dynamics during Myeloid Differentiation Reveal an Early Differentiation Block in Cebpa null Progenitors

    Pundhir, Sachin, Bratt Lauridsen, F. K., Schuster, Mikkel Bruhn, Jakobsen, J. S., Ge, Y., Schoof, E. M., Rapin, N. P. J., Waage, J., Hasemann, M. S. & Porse, Bo Torben, 2018, In: Cell Reports. 23, 9, p. 2744-2757 14 p.

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

  61. Published

    Human adult HSCs can be discriminated from lineage-committed HPCs by the expression of endomucin

    Reckzeh, K., Kizilkaya, Hüsün Sheyma, Helbo, A. S., Estruch Alrich, Montserrat, Deslauriers, A. G., Grover, A., Rapin, N., Asmar, F., Grønbæk, Kirsten, Porse, Bo Torben, Borregaard, N., Vestweber, D., Nerlov, C. & Theilgaard-Mønch, Kim, 2018, In: Blood advances. 2, 13, p. 1628-1632 5 p.

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

  62. Published

    Transcription start site analysis reveals widespread divergent transcription in D. melanogaster and core promoter-encoded enhancer activities

    Rennie, Sarah, Dalby, M., Lloret-Llinares, M., Bakoulis, Stylianos, Dalager Vaagensø, C., Jensen, T. H. & Andersson, Robin, 2018, In: Nucleic Acids Research. 46, 11, p. 5455-5469 15 p.

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

  63. Published

    Transcriptional decomposition reveals active chromatin architectures and cell specific regulatory interactions

    Rennie, Sarah, Dalby, M., van Duin, Lucas & Andersson, Robin, 2018, In: Nature Communications. 9, 16 p., 487.

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

  64. Published

    The genetic history of whaling in the Cantabrian Sea during the 13th-18th centuries: Were North Atlantic right whales (Eubalaena glacialis) the main target species?

    Rey-Iglesia, A., Martinez-Cedeira, J., Lopez, A., Fernandez, R. & Campos, P., 2018, In: Journal of Archaeological Science: Reports. 18, p. 393-398 6 p.

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

  65. Published

    Accurate genotyping across variant classes and lengths using variant graphs

    Sibbesen, Jonas Andreas, Maretty, L., Krogh, Anders, Petersen, Bent, Sibbesen, Jonas Andreas, Liu, S., Have, C. T., Bork-Jensen, J., Guo, X., Hansen, Torben, Krogh, Anders, Sørensen, Thorkild I.A., Pedersen, Oluf Borbye, Wang, J. & Brunak, Søren, 2018, In: Nature Genetics. 50, p. 1054-1059 6 p.

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

  66. Published

    SinaPlot: an enhanced chart for simple and truthful representation of single observations over multiple classes

    Sidiropoulos, N., Sohi, S. H., Pedersen, T. L., Porse, Bo Torben, Winther, Ole, Rapin, N. & Bagger, F. O., 2018, In: Journal of Computational and Graphical Statistics. 27, 3, p. 673-676 4 p.

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

  67. Published

    Farnesylated heat shock protein 40 is a component of membrane-bound RISC in Arabidopsis

    Sjögren, L., Floris, M., Barghetti, A., Völlmy, F., Linding, R. & Brodersen, Peter, 2018, In: Journal of Biological Chemistry. 293, 43, p. 16608-16622

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

  68. Published

    Powerful Inference With the D-Statistic on Low-Coverage Whole-Genome Data

    Soraggi, S., Wiuf, Carsten & Albrechtsen, Anders, 2018, In: G3: Genes, Genomes, Genetics (Bethesda). 8, 2, p. 551-566

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

  69. Published

    Characterization of the human RFX transcription factor family by regulatory and target gene analysis

    Sugiaman-Trapman, D., Vitezic, M., Jouhilahti, E., Mathelier, A., Lauter, G., Misra, S., Daub, C. O., Kere, J. & Swoboda, P., 2018, In: BMC Genomics. 19, 15 p., 181.

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

  70. Published

    Inference and Learning in Deep Generative Models

    Sønderby, C. K., 2018, Department of Biology, Faculty of Science, University of Copenhagen.

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

  71. Published

    Transfer RNA instability as a stress response in Escherichia coli: rapid dynamics of the tRNA pool as a function of demand

    Sørensen, Michael Askvad, Fehler, A. O. & Svenningsen, Sine Lo, 2018, In: RNA Biology. 15, 4/5, p. 586-593 8 p.

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

  72. Published

    CAGEfightR: Cap Analysis of Gene Expression (CAGE) in R/Bioconductor

    Thodberg, Malte, Thieffry, A., Vitting-Seerup, K., Andersson, Robin & Sandelin, Albin Gustav, Apr 2018

    Research output: Other contribution › Research

  73. Published

    Organism- and disease-specific atlases of transcription start sites using Cap Analysis of Gene Expression (CAGE)

    Thodberg, Malte, 2018, Department of Biology, Faculty of Science, University of Copenhagen.

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

  74. Published

    Oral health status in historic population: Macroscopic and metagenomic evidence

    Willmann, C., Mata, X., Hanghøj, Kristian Ebbesen, Tonasso, L., Tisseyre, L., Jeziorski, C., Cabot, E., Chevet, P., Crubézy, E., Orlando, L., Esclassan, R., Thèves, C. & Caramelli, D., 2018, In: PLOS ONE. 13, 5, 18 p., e0196482.

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

  75. Published

    Discovering novel hydrolases from hot environments

    Wohlgemuth, R., Littlechild, J., Monti, D., Schnorr, K., van Rossum, T., Siebers, B., Menzel, P., Kublanov, I. V., Rike, A. G., Skretas, G., Szabo, Z., Peng, Xu & Young, M. J., 2018, In: Biotechnology Advances. 36, 8, p. 2077-2100

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

  76. Published

    Genomic insights into early maritime adaptations in Western Patagonia

    jxb425, jxb425, Moreno Mayar, J. Víctor, Alfonso-Durruty, M., Morello, F., Vilar, M., Wells, S., Campos, P. & Willerslev, Eske, 2018, p. 64. 1 p.

    Research output: Contribution to conference › Conference abstract for conference › Research

  77. Published

    A new class of genic nuclear RNA species in Arabidopsis

    van Wonterghem, M., Thieffry, A., Boyd, M., Lange, Jette Bornholdt & Brodersen, Peter, 2018, In: FEBS Letters. 592, 4, p. 631-643 13 p.

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

  78. 2017
  79. Published

    De novo pathway-based biomarker identification

    Alcaraz, N., List, M., Batra, R., Vandin, F., Ditzel, H. J. & Baumbach, J., 19 Sep 2017, In: Nucleic Acids Research. 45, 16, 11 p., e151.

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

  80. Published

    DeepLoc: prediction of protein subcellular localization using deep learning

    Almagro Armenteros, J. J., Sønderby, C. K., Sønderby, S. K., Nielsen, H. & Winther, Ole, 1 Nov 2017, In: Bioinformatics. 33, 21, p. 3387-3395 9 p.

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

  81. Published

    Heat-shock protein 40 is the key farnesylation target in meristem size control, abscisic acid signaling, and drought resistance

    Barghetti, A., Sjögren, L. L. E., Floris, M. H. J., Botterweg Paredes, E., Wenkel, Stephan & Brodersen, Peter, 15 Nov 2017, In: Genes & Development. 31, 22, p. 2282-2295 14 p.

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

  82. Published

    Investigating membrane-bound Argonaute functions in Arabidopsis

    Barghetti, A., 2017, Department of Biology, Faculty of Science, University of Copenhagen.

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

  83. Published

    Toxin inhibition in C. crescentus VapBC1 is mediated by a flexible pseudo-palindromic protein motif and modulated by DNA binding

    Bendtsen, K. L., Xu, K., Luckmann, M., Winther, K. S., Shah, S. A., Pedersen, C. N. S. & Brodersen, D. E., 2017, In: Nucleic Acids Research. 45, 5, p. 2875-2886 12 p.

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

  84. Published

    Discrete structural dynamics of pseudo-palindromic motifs control DNA binding of bacterial toxin-antitoxin complexes

    Brodersen, D. E., Bendtsen, K. L., Xu, K., Luckmann, M., Winther, K. S., Shah, S. A. & Pedersen, C. N. S., 2017, In: F A S E B Journal. 31, S1, 1 p., 777.2.

    Research output: Contribution to journal › Conference abstract in journal › Research › peer-review

  85. Published

    Relation between NOD2 genotype and changes in innate signaling in Crohn's disease on mRNA and miRNA levels

    Chen, Y., Salem, M., Boyd, M., Lange, Jette Bornholdt, Li, Yuan, Coskun, M., Seidelin, Jakob Benedict, Sandelin, Albin Gustav & Nielsen, Ole Haagen, 2017, In: npj Genomic Medicine. 2, 11 p., 3.

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

  86. Published

    Novel targeted therapies for inflammatory bowel disease

    Coskun, M., Vermeire, S. & Nielsen, Ole Haagen, Feb 2017, In: Trends in Pharmacological Sciences. 38, 2, p. 127-142 16 p.

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

  87. Published

    Regulation of laminin γ2 expression by CDX2 in colonic epithelial cells is impaired during active inflammation

    Coskun, M., Soendergaard, C., Joergensen, S., Dahlgaard, K., Riis, Lene Buhl, Nielsen, Ole Haagen, Sandelin, Albin Gustav & Troelsen, J. T., 2017, In: Journal of Cellular Biochemistry. 118, 2, p. 298-307 10 p.

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

  88. Published

    Genome-wide analysis of differential transcriptional and epigenetic variability across human immune cell types

    Ecker, S., Chen, L., Pancaldi, V., Bagger, F. O., Fernández, J. M., Carrillo de Santa Pau, E., Juan, D., Mann, A. L., Watt, S., Casale, F. P., Sidiropoulos, N., Rapin, N. P. J-P., Merkel, A., Stunnenberg, H. G., Stegle, O., Frontini, M., Downes, K., Pastinen, T., Kuijpers, T. W., Rico, D. & 50 others, Valencia, A., Beck, S., Soranzo, N., Paul, D. S., Albers, C. A., Amstislavskiy, V., Ashford, S., Bomba, L., Bujold, D., Burden, F., Busche, S., Caron, M., Chen, S., Cheung, W. A., Clarke, L., Colgiu, I., Datta, A., Delaneau, O., Elding, H., Farrow, S., Garrido-Martín, D., Ge, B., Guigo, R., Iotchkova, V., Kundu, K., Kwan, T., Lambourne, J. J., Lowy, E., Mead, D., Pourfarzad, F., Redensek, A., Rehnstrom, K., Rendon, A., Richardson, D. M., Risch, T., Rowlston, S., Shao, X., Simon, M. M., Sultan, M., Walter, K., Wilder, S. P., Yan, Y., Antonarakis, S. E., Bourque, G., Dermitzakis, E. T., Flicek, P., Lehrach, H., Martens, J. H. A., Yaspo, M. & Ouwehand, W. H., 26 Jan 2017, In: Genome Biology. 18, 1, 17 p., 18.

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

  89. Published

    Transcriptional dynamics during human adipogenesis and its link to adipose morphology and distribution

    Ehrlund, A., Mejhert, N., Björk, C., Andersson, Robin, Kulyté, A., Åström, G., Itoh, M., Kawaji, H., Lassmann, T., Daub, C. O., Carninci, P., Forrest, A. R. R., Hayashizaki, Y., Sandelin, Albin Gustav, Ingelsson, E., FANTOM Consortium, Rydén, M., Laurencikiene, J., Arner, P. & Arner, E., 2017, In: Diabetes. 66, 1, p. 218-230 13 p.

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

  90. Published

    Sugar metabolism of the first thermophilic Planctomycete Thermogutta terrifontis: comparative genomic and transcriptomic approaches

    Elcheninov, A. G., Menzel, P., Gudbergsdottir, S. R., Slesarev, A. I., Kadnikov, V. V., Krogh, Anders, Bonch-Osmolovskaya, E. A., Peng, Xu & Kublanov, I. V., 2 Nov 2017, In: Frontiers in Microbiology. 8, 11 p., 2140.

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

  91. Published

    A Generative Angular Model of Protein Structure Evolution

    Golden, M., Garcia-Portugues, E., Sørensen, Michael, Mardia, K. V., Hamelryck, Thomas Wim & Hein, J., Aug 2017, In: Molecular Biology and Evolution. 34, 8, p. 2085-2100

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

  92. Published

    Targeted next-generation sequencing analysis identifies novel mutations in families with severe familial exudative vitreoretinopathy

    Huang, X., Zhuang, H., Wu, J., Li, J., Hu, F., Zheng, Y., Tellier, L. C. A. M., Zhang, S., Gao, F., Zhang, J. & Xu, G., 23 Aug 2017, In: Molecular Vision. 23, p. 605-613 9 p.

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

  93. Published

    Chirality in microbial biofilms is mediated by close interactions between the cell surface and the substratum

    Jauffred, Liselotte, Vejborg, R. M., Korolev, K. S., Brown, Stanley & Oddershede, L. B., 14 Apr 2017, In: I S M E Journal. 11, 7, p. 1688-1701

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

  94. Published

    Assembly and analysis of 100 full MHC haplotypes from the Danish population

    Jensen, J. M., Villesen, P., Friborg, R. M., Mailund, T., Besenbacher, S., Sørensen, L. M., Petersen, B., Sibbesen, J. A., Liu, S., Skov, L., Belling, K. G., Have, C. T., Izarzugaza, J. M. G., Grosjean, M., Bork-Jensen, J., Grove, J., Als, T. D., Huang, S., Chang, Y., Xu, R. & 39 others, Ye, W., Rao, J., Guo, X., Sun, J., Cao, H., Ye, C., Beusekom, J. V., Espeseth, T., Flindt, E., Halager, A. E., Hellard, S. L., Hultman, C. M., Lescai, F., Li, S., Lund, O., Løngren, P., Matey-Hernandez, M. L., Mors, O., Pedersen, C. N. S., Sicheritz-Pontén, T., Sullivan, P., Syed, A., Westergaard, D., Yadav, R., Li, N., Xu, X., Hansen, Torben, Bolund, L., Krogh, Anders, Sørensen, Thorkild I.A., Pedersen, Oluf Borbye, Gupta, R., Rasmussen, Simon, Børglum, A. D., Wang, J., Eiberg, Hans Rudolf Lytchoff, Kristiansen, Karsten, Brunak, Søren & Schierup, M. H., Sep 2017, In: Genome Research. 27, 9, p. 1597-1607 11 p.

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

  95. Published

    Deep Recurrent Conditional Random Field Network for Protein Secondary Prediction

    Johansen, A. R., Sønderby, C. K., Sønderby, S. K. & Winther, O., 2017, ACM-BCB '17: Proceedings of the 8th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics. p. 73-78 6 p.

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

  96. Published

    An introduction to deep learning on biological sequence data: examples and solutions

    Jurtz, V. I., Johansen, A. R., Nielsen, M., Almagro Armenteros, J. J., Nielsen, H., Sønderby, C. K., Winther, Ole & Sønderby, S. K., 15 Nov 2017, In: Bioinformatics. 33, 22, p. 3685-3690 6 p.

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

  97. Published

    fastNGSadmix: admixture proportions and principal component analysis of a single NGS sample

    Jørsboe, E., Hanghøj, Kristian Ebbesen & Albrechtsen, Anders, 1 Oct 2017, In: Bioinformatics. 33, 19, p. 3148-3150 3 p.

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

  98. Published

    The Bipolar Illness Onset study: research protocol for the BIO cohort study

    Kessing, Lars Vedel, Munkholm, K., Faurholt-Jepsen, M., Miskowiak, Kamilla, Nielsen, L. B., Frikke-Schmidt, Ruth, Ekstrøm, Claus Thorn, Winther, Ole, Pedersen, Bente Klarlund, Poulsen, Henrik Enghusen, McIntyre, R. S., Kapczinski, F., Gattaz, W. F., Bardram, J., Frost, M., Mayora, O., Knudsen, Gitte Moos, Phillips, M. & Vinberg, Maj, 2017, In: BMJ Open. 7, 6, 12 p., e015462.

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

  99. Published

    RNase H sequence preferences influence antisense oligonucleotide efficiency

    Kiełpiński, Ł. J., Hagedorn, P. H., Lindow, M. & Vinther, Jeppe, 15 Dec 2017, In: Nucleic Acids Research. 45, 22, p. 12932-12944 13 p.

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

  100. Published

    Identification of gene transcription start sites and enhancers responding to pulmonary carbon nanotube exposure in Vivo

    Lange, Jette Bornholdt, Saber, A. T., Lilje, B., Boyd, M., Jørgensen, M., Chen, Y., Vitezic, M., Jacobsen, N. R., Poulsen, S. S., Berthing, T., Bressendorff, Simon, Vitting-Seerup, K., Andersson, Robin, Hougaard, K. S., Yauk, C. L., Halappanavar, S., Wallin, E. H. R., Vogel, U. & Sandelin, Albin Gustav, 2017, In: A C S Nano. 11, 4, p. 3597-3613 17 p.

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

  101. Published

    Analysing human genomes at different scales

    Liu, S., 2017, Department of Biology, Faculty of Science, University of Copenhagen.

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

  102. Published

    Update of the FANTOM web resource: high resolution transcriptome of diverse cell types in mammals

    Lizio, M., Harshbarger, J., Abugessaisa, I., Noguchi, S., Kondo, A., Severin, J., Mungall, C., Arenillas, D., Mathelier, A., Medvedeva, Y. A., Lennartsson, A., Drabløs, F., Ramilowski, J. A., Rackham, O., Gough, J., Andersson, R., Sandelin, A. G., Ienasescu, H-I., Ono, H., Bono, H. & 5 others, Hayashizaki, Y., Carninci, P., Forrest, A. R. R., Kasukawa, T. & Kawaji, H., 2017, In: Nucleic Acids Research. 45, D1, p. D737-D743 7 p.

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

  103. Published

    Eight millennia of matrilineal genetic continuity in the South Caucasus

    Margaryan, Ashot, Derenko, M., Hovhannisyan, H., Malyarchuk, B., Heller, Rasmus, Khachatryan, Z., Avetisyan, P., Badalyan, R., Bobokhyan, A., Melikyan, V., Sargsyan, G., Piliposyan, A., Simonyan, H., Mkrtchyan, R., Denisova, G., Yepiskoposyan, L., Willerslev, Eske & Allentoft, Morten Erik, 10 Jul 2017, In: Current Biology. 27, 13, p. 2023-2028 6 p.

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

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