Computational and RNA Biology

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  1. 2008
  2. Published

    Roles of multiple surface sites, long substrate binding clefts, and carbohydrate binding modules in the action of amylolytic enzymes on polysaccharide substrates

    Nielsen, M. M., Seo, E. S., Dilokpimol, A., Andersen, J., Hachem, M. A., Naested, H., Willemoës, Martin, Bozonnet, S., Kandra, L., Gymnt, G., Haser, R., Aghajari, N. & Svensson, B., 2008, In: Biocatalysis and Biotransformation. 26, 1 & 2, p. 59-67

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

  3. Published

    Statistical assignment of DNA sequences using Bayesian phylogenetics

    Terkelsen, K. M., Boomsma, Wouter, Huelsenbeck, J. P., Willerslev, Eske & Nielsen, Rasmus, 2008, In: Systematic Biology. 57, 5, p. 750-757 8 p.

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

  4. Published

    Sulfur metabolism in phototrophic sulfur bacteria

    Frigaard, Niels-Ulrik & Dahl, C., 2008, In: Advances in Microbial Physiology. 54, p. 103-200 97 p.

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

  5. Published

    The -250G>A promoter variant in hepatic lipase associates with elevated fasting serum high-density lipoprotein cholesterol modulated by interaction with physical activity in a study of 16,156 Danish subjects

    Grarup, N., Andreasen, C. H., Lepola, Mette Andersen, Albrechtsen, Anders, Sandbaek, A., Lauritzen, T., Borch-Johnsen, K., Jørgensen, T., Schmitz, O., Hansen, T. & Pedersen, Oluf Borbye, 2008, In: Journal of Clinical Endocrinology and Metabolism. 93, 6, p. 2294-9 5 p.

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

  6. 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

  7. Published

    Two-step method for curing Escherichia coli of ColE1-derived plasmids

    Hove-Jensen, B., 2008, In: Journal of Microbiological Methods. 72, 2, p. 208-13 5 p.

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

  8. Published

    What are artificial neural networks?

    Krogh, Anders, 2008, In: Nature Biotechnology. 26, 2, p. 195-7 2 p.

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

  9. Published

    57miRNA regulation during oncogene-induced senescence


    Christoffersen, N. R., Frankel, Lisa, Klausen, M., Jacobsen, A., Krogh, Anders & Lund, Anders H., May 2008.

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

  10. 2009
  11. Published

    A common Greenlandic Inuit BRCA1 RING domain founder mutation

    Hansen, T. V. O., Ejlertsen, Bent Laursen, Albrechtsen, Anders, Bergsten, E., Bjerregaard, P., Hansen, T., Myrhoj, T., Nielsen, P. B., Timmermans-Wielenga, V., Andersen, M. K., Jonson, L. & Nielsen, F. C., 2009, In: Breast Cancer Research and Treatment. 115, 1, p. 69-76 7 p.

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

  12. Published

    A fluorescent substrate for carbon-phosphorus lyase: towards the pathway for organophosphonate metabolism in bacteria

    He, S., Lou, Y., Hove-Jensen, B. & Zechel, D. L., 2009, In: Bioorganic & Medicinal Chemistry Letters. 19, 20, p. 5954-5957

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

  13. Published

    A probabilistic approach to protein structure prediction: PHAISTOS in CASP8

    Borg, M., Boomsma, Wouter, Ferkinghoff-Borg, J., Frellsen, J., Harder, T. P., Mardia, K., Røgen, P., Stovgaard, K. & Hamelryck, Thomas Wim, 2009, LASR 2009 — Statistical Tools for Challenges in Bioinformatics. Proceedings. Gusnanto, A., Mardia, K. V. & Fallaize, C. J. (eds.). University of Leeds, p. 65-70 6 p.

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

  14. Published

    A probabilistic approach to protein structureprediction: PHAISTOS in CASP8

    Borg, M., Boomsma, Wouter, Ferkinghoff-Borg, J., Frellsen, J., Harder, T. P., Mardia, K. V., Røgen, P., Stovgaard, K. & Hamelryck, Thomas Wim, 2009, In: School of Mathematics. p. 65-70

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

  15. Published

    A probabilistic model of RNA conformational space

    Frellsen, J., Moltke, Ida, Thiim, M., Mardia, K. V., Ferkinghoff-Borg, J. & Hamelryck, Thomas Wim, 2009, In: PLoS Computational Biology. 5, 6, p. e1000406

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

  16. Published

    A variant in the G6PC2/ABCB11 locus is associated with increased fasting plasma glucose, increased basal hepatic glucose production and increased insulin release after oral and intravenous glucose loads

    Rose, C. S., Grarup, Niels, Krarup, N. T., Poulsen, P., Wegner, L., Nielsen, T., Banasik, Karina, Faerch, K., Andersen, G., Albrechtsen, Anders, Borch-Johnsen, K., Clausen, J. O., Jørgensen, T., Vaag, Allan, Pedersen, Oluf Borbye & Hansen, Torben, 2009, In: Diabetologia. 52, 10, p. 2122-2129 8 p.

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

  17. Published

    Adaptionism-30 years after Gould and Lewontin

    Nielsen, Rasmus, 2009, In: Evolution. 63, 10, p. 2487-90 3 p.

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

  18. Published

    An investigation of the statistical power of neutrality tests based on comparative and population genetic data

    Zhai, W., Nielsen, Rasmus & Slatkin, M., 2009, In: Molecular Biology and Evolution. 26, 2, p. 273-83 10 p.

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

  19. Published

    Ancient DNA reveals late survival of mammoth and horse in interior Alaska

    Haile, James Seymour, Froese, D. G., Macphee, R. D. E., Roberts, R. G., Arnold, L. J., Reyes, A. V., Rasmussen, M., Nielsen, Rasmus, Brook, B. W., Robinson, S., Demuro, M., Gilbert, M Thomas P, Munch, K., Austin, J. J., Cooper, A., Barnes, I., Möller, P. & Willerslev, Eske, 2009, In: Proceedings of the National Academy of Science of the United States of America. 106, 52, p. 22352-7 5 p.

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

  20. Published

    Applying Undertaker to quality assessment

    Archie, J. G., Paluszewski, M. & Karplus, K., 2009, In: Proteins - Structure Function and Bioinformatics. 77, S9, p. 191-195

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

  21. Published

    Biopython: freely available Python tools for computational molecular biology and bioinformatics

    Cock, P. J. A., Antao, T., Chang, J. T., Chapman, B. A., Cox, C. J., Dalke, A., Friedberg, I., Hamelryck, Thomas Wim, Kauff, F., Wilczynski, B. & de Hoon, M. J. L., 2009, In: Bioinformatics. 25, 11, p. 1422-3 1 p.

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

  22. Published

    CCHMM_PROF: a HMM-based coiled-coil predictor with evolutionary information

    Bartoli, L., Fariselli, P., Krogh, Anders & Casadio, R., 2009, In: Bioinformatics. 25, 21, p. 2757-63 6 p.

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

  23. Published

    CRISPR families of the crenarchaeal genus Sulfolobus: bidirectional transcription and dynamic properties

    Lillestøl, R. K., Shah, S. A., Brügger, K., Redder, P., Phan, Safir Hien, Christiansen, Jan & Garrett, Roger Antony, 2009, In: Molecular Microbiology. 72, 1, p. 259-272

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

  24. Published

    Combined analysis of 19 common validated type 2 diabetes susceptibility gene variants shows moderate discriminative value and no evidence of gene-gene interaction

    Sparsø, T., Grarup, N., Andreasen, C., Albrechtsen, A., Holmkvist, J., Andersen, G., Jørgensen, T., Borch-Johnsen, K., Sandbaek, A., Lauritzen, T., Madsbad, S., Hansen, T., Pedersen, O., Sparsø, T., Grarup, N., Andreasen, C., Albrechtsen, A., Holmkvist, J., Andersen, G., Jørgensen, T. & 6 others, Borch-Johnsen, K., Sandbaek, A., Lauritzen, T., Madsbad, Sten, Hansen, T. & Pedersen, O., 2009, In: Diabetologia. 52, 7, p. 1308-14 6 p.

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

  25. 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

  26. Published

    Correcting estimators of theta and Tajima's D for ascertainment biases caused by the single-nucleotide polymorphism discovery process

    Ramírez-Soriano, A. & Nielsen, Rasmus, 2009, In: Genetics. 181, 2, p. 701-10 9 p.

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

  27. Published

    Darwinian and demographic forces affecting human protein coding genes.

    Nielsen, Rasmus, Hubisz, M. J., Hellmann, I., Torgerson, D., Andres, A. M., Albrechtsen, Anders, Gutenkunst, R., Adams, M. D., Cargill, M., Boyko, A., Indap, A., Bustamante, C. D. & Clark, A. G., 2009, In: Genome Research. 19, 5, p. 838-49 12 p.

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

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