Computational and RNA Biology

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  1. Published

    Niels Bohr – er det ikke noget med nogen antomer? Personer og kanoner i naturvidenskaben.

    Vogel, U. B. & Willemoës, Martin, 2006, In: Biozoom. 1

    Research output: Contribution to journal › Comment/debate › Research

  2. Published

    Genetics of early-life head circumference and genetic correlations with neurological, psychiatric and cognitive outcomes

    Vogelezang, S., Bradfield, J. P., Early Growth Genetics Consortium, Ahluwalia, T. V. S., Liu, X., Schnurr, T. M., Frithioff-Bøjsøe, C., Bønnelykke, K., Lind, M. V., Lauritzen, L., Michaelsen, K. F., Lund, M. A. V., Melbye, M., Morgen, C. S., Pedersen, O. B., Holm, J-C., Grarup, N., Hansen, T., Nohr, E. A., Bisgaard, H. & 3 others, Grant, S. F. A., Felix, J. F. & Jaddoe, V. W. V., 2022, In: BMC Medical Genomics. 15, 16 p., 124.

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

  3. Published

    The Draft Genome of Red Lechwe, Kobus leche leche

    Wang, B., Wang, Z., Zhou, J., Liu, W., Lin, Z., Zhang, C., Liu, G., Zhou, B., Wan, W., Zhao, R., Wang, W., Heller, Rasmus & Chen, L., 2020, In: Frontiers in Genetics. 11, 7 p., 582638.

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

  4. Published

    DeepLocRNA: an interpretable deep learning model for predicting RNA subcellular localization with domain-specific transfer-learning

    Wang, Jun, Horlacher, M., Cheng, L. & Winther, Ole, 2024, In: Bioinformatics. 40, 2, 10 p., btae065.

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

  5. Published

    The diploid genome sequence of an Asian individual

    Wang, J., Wang, W., Li, R., Li, Y., Tian, G., Goodman, L., Fan, W., Zhang, J., Li, J., Zhang, J., Guo, Y., Feng, B., Li, H., Lu, Y., Fang, X., Liang, H., Du, Z., Li, D., Zhao, Y., Hu, Y. & 57 others, Yang, Z., Zheng, H., Hellmann, I., Inouye, M., Pool, J., Yi, X., Zhao, J., Duan, J., Zhou, Y., Qin, J., Ma, L., Li, G., Yang, Z., Zhang, G., Yang, B., Yu, C., Liang, F., Li, W., Li, S., Li, D., Ni, P., Ruan, J., Li, Q., Zhu, H., Liu, D., Lu, Z., Li, N., Guo, G., Zhang, J., Ye, J., Fang, L., Hao, Q., Chen, Q., Liang, Y., Su, Y., San, A., Ping, C., Yang, S., Chen, F., Li, L., Zhou, K., Zheng, H., Ren, Y., Yang, L., Gao, Y., Yang, G., Li, Z., Feng, X., Kristiansen, Karsten, Wong, G. K., Nielsen, Rasmus, Durbin, R., Bolund, L., Zhang, X., Li, S., Yang, H. & Wang, J., 2008, In: Nature. 456, 7218, p. 60-65 5 p.

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

  6. Published

    RNA trafficking and subcellular localization—a review of mechanisms, experimental and predictive methodologies

    Wang, Jun, Horlacher, M., Cheng, L. & Winther, Ole, 2023, In: Briefings in Bioinformatics. 24, 5, 14 p., bbad249.

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

  7. 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

  8. Published

    Pseudoreplication in genomics-scale data sets

    Waples, R. S., Waples, R. K. & Ward, E. J., 2022, In: Molecular Ecology Resources. 22, 2, p. 503-518 16 p.

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

  9. 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

  10. 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

  11. Published

    The genetic history of Greenlandic-European contact

    Waples, R. K., Hauptmann, A. L., Seiding, I. H., Jørsboe, E., Jørgensen, M. E., Grarup, Niels, Andersen, M. K., Larsen, C. V. L., Bjerregaard, P., Hellenthal, G., Hansen, Torben, Albrechtsen, Anders & Moltke, Ida, 2021, In: Current Biology. 31, 10, p. 2214-2219.e4

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

  12. Published

    Limited genetic variations of the Rh5-CyRPA-Ripr invasion complex in Plasmodium falciparum parasite population in selected malaria-endemic regions, Kenya

    Waweru, H., Kanoi, B. N., Kuja, J. O., Maranga, M., Kongere, J., Maina, M., Kinyua, J. & Gitaka, J., 2023, In: Frontiers in Tropical Diseases. 4, 9 p., 1102265.

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

  13. Published

    Genome-wide analysis of noncoding regulatory mutations in cancer

    Weinhold, N., Skanderup, A. M. J., Schultz, N., Sander, C. & Lee, W., 2014, In: Nature Genetics. 46, 11, p. 1160-1165 6 p.

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

  14. Published

    Mammalian tissues defective in nonsense-mediated mRNA decay display highly aberrant splicing patterns

    Weischenfeldt, Joachim Lütken, Waage, J. E., Tian, G., Zhao, J., Damgaard, I., Jakobsen, J. S., Kristiansen, Karsten, Krogh, Anders, Wang, J. & Porse, Bo Torben, 2012, In: Genome Biology (Online Edition). 13, 5, 19 p.

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

  15. Published

    Analysis of recent serotype O foot-and-mouth disease viruses from Livestock in Kenya: evidence of four independently evolving lineages

    Wekesa, S. N., Muwanika, V. B., Siegismund, Hans Redlef, Sangula, A. K., Namatovu, A., Dhikusooka, M. T., Tjørnehøj, K., Balinda, S. N., Wadsworth, J., Knowles, N. J. & Belsham, G. J., 2015, In: Transboundary and Emerging Diseases. 62, 3, p. 305-314 10 p.

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

  16. Published

    Characterisation of recent foot-and-mouth disease viruses from African buffalo ( Syncerus caffer ) and cattle in Kenya is consistent with independent virus populations

    Wekesa, S., Sangula, A., Belsham, G. J., Tjornehoj, K., Muwanika, V. B., Gakuya, F., Mijele, D. & Siegismund, Hans Redlef, 2015, In: B M C Veterinary Research. 11, 17.

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

  17. Published

    Genetic diversity of serotype A foot-and-mouth disease viruses in Kenya from 1964 to 2013; implications for control strategies in eastern Africa

    Wekesa, S. N., Sangula, A. K., Belsham, G., Muwanika, V. B., Heller, Rasmus, Balinda, S. N., Masembe, C. & Siegismund, Hans Redlef, 2014, In: Infection, Genetics and Evolution. 21, p. 408-417 10 p.

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

  18. Published

    Transcriptome dynamics of the microRNA inhibition response

    Wen, J., Leucci, E., Vendramin, R., Kauppinen, S., Lund, Anders H., Krogh, Anders & Parker, B. J., 2015, In: Nucleic Acids Research. 43, 13, p. 6207-6221 15 p.

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

  19. Published

    MicroRNA transfection and AGO-bound CLIP-seq data sets reveal distinct determinants of miRNA action

    Wen, J., Parker, B. J., Jacobsen, A. & Krogh, Anders, 2011, In: R N A. 17, 5, p. 820-34 15 p.

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

  20. Published

    VeTra: a tool for trajectory inference based on RNA velocity

    Weng, Guangzheng, Kim, Junil & Won, K. J., 2021, In: Bioinformatics. 37, 20, p. 3509-3513 btab364.

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

  21. Published

    Symmetric inheritance of parental histones governs epigenome maintenance and embryonic stem cell identity

    Wenger, Alice, Biran, Alva Ada, Alcaraz, N., Redó-Riveiro, A., Sell, Annika Charlotte, Krautz, Robert, Flury, Valentin, Reveron-Gomez, Nazaret, Solis-Mezarino, V., Völker-Albert, M., Imhof, A., Andersson, Robin, Brickman, Joshua Mark & Groth, Anja, 2023, In: Nature Genetics. 55, 9, p. 1567-1578 12 p.

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

  22. Published

    Hyena paleogenomes reveal a complex evolutionary history of cross-continental gene flow between spotted and cave hyena

    Westbury, Michael Vincent, Hartmann, S., Barlow, A., Preick, M., Ridush, B., Nagel, D., Rathgeber, T., Ziegler, R., Baryshnikov, G., Sheng, G., Ludwig, A., Wiesel, I., Dalen, L., Bibi, F., Werdelin, L., Heller, Rasmus & Hofreiter, M., 2020, In: Science Advances. 6, 11, 11 p., eaay0456.

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

  23. Published

    Combined transcriptomic and proteomic analysis of the posterior salivary gland from the southern blue-ringed octopus and the southern sand octopus

    Whitelaw, B. L., Strugnell, J. M., Faou, P., Rodrigues da Fonseca, Rute Andreia, Hall, N. E., Norman, M., Finn, J. & Cooke, I. R., 2016, In: Journal of Proteome Research. 15, 9, p. 3284-3297 14 p.

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

  24. Published

    Steady State Kinetic Model for the Binding of Substrates and Allosteric Effectors to Escherichia coli Phosphoribosyl-diphosphate Synthase.

    Willemoës, Martin, Hove-Jensen, B. & Larsen, Sine, 2000, In: Journal of Biological Chemistry. 45, p. 35408-35412

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

  25. Published

    Om kvalitet i forskningen.

    Willemoës, Martin, 1999, In: Biozoom. 3

    Research output: Contribution to journal › Comment/debate › Research

  26. Published

    Forskningsbaseret undervisning- og hva' så!

    Willemoës, Martin & Vogel, U. B., 2007, In: Biozoom. 3

    Research output: Contribution to journal › Comment/debate › Research

  27. Published

    TGIF1 is a negative regulator of MLL-rearranged acute myeloid leukemia

    Willer, A., Jakobsen, J. S., Ohlsson, E., Rapin, N., Waage, J., Billing, M., Bullinger, L., Karlsson, S. & Porse, Bo Torben, 2015, In: Leukemia. 29, p. 1018-31 14 p.

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

  28. Published

    Physiological responses of narwhals to anthropogenic noise: A case study with seismic airguns and vessel traffic in the Arctic

    Williams, T. M., Blackwell, S. B., Tervo, O., Garde, E., Sinding, Mikkel Holger Strander, Richter, B. & Heide-Jørgensen, M. P., 2022, In: Functional Ecology. 36, 9, p. 2251-2266 16 p.

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

  29. 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

  30. Published

    Teaching computers to fold proteins

    Winther, O. & Krogh, Anders, 2004, In: Physical Review E (Statistical, Nonlinear, and Soft Matter Physics). Vol. 70 (3) pt. 1, p. 030903

    Research output: Contribution to journal › Journal article › Research

  31. Published

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

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

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

  32. 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

  33. Published

    Training HMM structure with genetic algorithm for biological sequence analysis

    Won, K. J. & Krogh, Anders, 2004, In: Bioinformatics. Vol. 20 (18), p. 3613-9

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

  34. Published

    Evolving hidden Markov models for protein secondary structure prediction

    Won, K. J., Hamelryck, Thomas Wim, Prügel-Bennett, A. & Krogh, Anders, 2005, The 2005 IEEE Congress on Evolutionary Computation, IEEE CEC 2005: Proceedings. IEEE, Vol. 3. p. 33-40 8 p.

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

  35. Published

    The Block Hidden Markov Model for Biological Sequence Analysis

    Won, K. J., Prügel-Bennett, A. & Krogh, Anders, 2004, Knowledge-BasedIntelligent Informationand Engineering Systems: 8th International Conference, KES 2004, Proceedings. Negoita, M. G., Howlett, R. J. & Jain, L. (eds.). Springer, Vol. 1. p. 64-70 7 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Vol. 3213).

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

  36. Published

    An evolutionary method for learning HMM structure: prediction of protein secondary structure.

    Won, K., Hamelryck, Thomas Wim, Prügel-Bennett, A. & Krogh, Anders, 2007, In: BMC Bioinformatics. 8, p. 357

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

  37. Published

    Technical Considerations for Transcatheter Aortic Valve Replacement With the Navitor Transcatheter Heart Valve

    Wong, I., Bajoras, V., Wang, X., Bieliauskas, G., De Backer, Ole & Søndergaard, Lars, 2021, In: JACC: Cardiovascular Interventions. 14, 19, p. e259-e261

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

  38. Published

    Identification of physicochemical selective pressure on protein encoding nucleotide sequences

    Wong, W. S. W., Sainudiin, R. & Nielsen, Rasmus, 2006, In: BMC Bioinformatics. 7, 10 p., 148.

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

  39. Published

    A Two-Layered Targeting Mechanism Underlies Nuclear RNA Sorting by the Human Exosome

    Wu, G., Schmid, M., Rib, Leonor, Polak, P., Meola, N., Sandelin, Albin Gustav & Jensen, T. H., 2020, In: Cell Reports. 30, 7, p. 2387-2401, e1-e5

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

  40. 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

  41. 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

  42. 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

  43. 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

  44. 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

  45. 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

  46. 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

  47. 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

  48. 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

  49. Published

    Two novel truncating variants of the ASPM gene identified in a nonconsanguineous Chinese family associated with primary microcephaly

    Xu, S., Zhang, W., Zhou, R., Huang, H., Chen, W., Xiang, W., Liu, L. & Song, J., 2022, In: Clinical Dysmorphology. 31, 1, p. 1-5 5 p.

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

  50. Published

    Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes

    Xu, X., Liu, X., Ge, S., Jensen, J. D., Hu, F., Li, X., Dong, Y., Gutenkunst, R. N., Fang, L., Huang, L., Li, J., He, W., Zhang, G., Zheng, X., Zhang, F., Li, Y., Yu, C., Kristiansen, K., Zhang, X., Wang, J. & 5 others, Wright, M., McCouch, S., Nielsen, Rasmus, Wang, J. & Wang, W., 2012, In: Nature Biotechnology. 30, 1, p. 105-111 7 p.

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

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