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

  28. Published

    Dominance of a clonal green sulfur bacterial population in a stratified lake

    Gregersen, Lea Haarup, Habicht, K. S., Peduzzi, S., Tonolla, M., Canfield, D. E., Miller, M., Cox, R. P. & Frigaard, Niels-Ulrik, 2009, In: FEMS Microbiology Ecology. 70, 1, p. 30-41 12 p.

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

  29. Published

    Effect of energy metabolism on protein motility in the bacterial outer membrane

    Ryder, T. W., Xu, L., Berg-Sørensen, K., Brown, Stanley & Oddershede, L. B., 2009, In: Biophysical Journal. 97, 5, p. 1305-1312 8 p.

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

  30. Published

    Genetic variant near IRS1 is associated with type 2 diabetes, insulin resistance and hyperinsulinemia

    Rung, J., Cauchi, S., Albrechtsen, A., Shen, L., Rocheleau, G., Cavalcanti-Proença, C., Bacot, F., Balkau, B., Belisle, A., Borch-Johnsen, K., Charpentier, G., Dina, C., Durand, E., Elliott, P., Hadjadj, S., Järvelin, M-R., Laitinen, J., Lauritzen, T., Marre, M., Mazur, A. & 20 others, Meyre, D., Montpetit, A., Pisinger, C., Posner, B., Poulsen, P., Pouta, A., Prentki, M., Ribel-Madsen, R., Ruokonen, A., Sandbaek, A., Serre, D., Tichet, J., Vaxillaire, M., Wojtaszewski, Jørgen F P, Vaag, Allan, Hansen, T., Polychronakos, C., Pedersen, Oluf Borbye, Froguel, P. & Sladek, R., 2009, In: Nature Genetics. 41, 10, p. 1110-1115 6 p.

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

  31. Published

    In defense of statistical methods for detecting positive selection

    Yang, Z., Nielsen, Rasmus & Goldman, N., 2009, In: Proceedings of the National Academy of Science of the United States of America. 106, 36, p. E95

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

  32. Published

    Inference of historical changes in migration rate from the lengths of migrant tracts

    Pool, J. E. & Nielsen, Rasmus, 2009, In: Genetics. 181, 2, p. 711-9 8 p.

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

  33. Published

    Maximum likelihood estimation of weight matrices for targeted homology search

    Menzel, P., Gorodkin, Jan & Stadler, P. F., 2009, Proceedings of the German Conference on Bioinformatics 2009. Grosse, I., Neumann, S., Posch, S., Schreiber, F. & Stadler, P. (eds.). Gesellschaft für Informatik, p. 211-220 10 p. (Lecture Notes in Informatics).

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

  34. Published

    Mutational analysis of three bchH paralogs in (bacterio-)chlorophyll biosynthesis in Chlorobaculum tepidum

    Gomez Maqueo Chew, A., Frigaard, Niels-Ulrik & Bryant, D. A., 2009, In: Photosynthesis Research. 101, 1, p. 21-34 13 p.

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

  35. Published

    Probabilistic models and machine learning in structural bioinformatics

    Hamelryck, Thomas Wim, 2009, In: Statistical Methods in Medical Research. 18, 5, p. 505-26 21 p.

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

  36. Published

    Radiation of extant Cetaceans Driven by Restructuring of the Oceans

    Steeman, M. E., Hebsgaard, M. B., Fordyce, J., Syw, H., Rabovsky, D., Nielsen, Rasmus, Rahbek, Carsten, Glenner, Henrik, Sørensen, Martin Vinther & Willerslev, Eske, 2009, In: Systematic Biology. 58, p. 573-585 12 p.

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

  37. Published

    Relatedness mapping and tracts of relatedness for genome-wide data in the presence of linkage disequilibrium

    Albrechtsen, Anders, Korneliussen, Thorfinn Sand, Moltke, Ida, van Overseem Hansen, T., Nielsen, Finn Cilius & Nielsen, Rasmus, 2009, In: Genetic Epidemiology. 33, 3, p. 266-274

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

  38. Published

    Statistical inferences in phylogeography

    Nielsen, Rasmus & Beaumont, M. A., 2009, In: Molecular Ecology. 18, 6, p. 1034-47 13 p.

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

  39. Published

    Structural and kinetic studies of the allosteric transition in Sulfolobus solfataricus uracil phosphoribosyltransferase: Permanent activation by engineering of the C-terminus

    Christoffersen, S., Kadziola, Anders, Johansson, E., Rasmussen, M., Willemoës, Martin & Jensen, K. F., 2009, In: Journal of Molecular Biology. 393, 2, p. 464-477

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

  40. Published

    Structural profiles of human miRNA families from pairwise clustering

    Kaczkowski, B., Þórarinsson, E., Reiche, K., Havgaard, Jakob Hull, Stadler, P. F. & Gorodkin, Jan, 2009, In: Bioinformatics. 25, 3, p. 291-294 4 p.

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

  41. Published

    Structure of PhnP: a phosphodiesterase of the carbon-phosphorous lyase pathway for phosphonate degradation

    Podzelinska, K., He, S., Wathier, M., Yakunin, A., Proudfoot, M., Hove-Jensen, B., Zechel, D. L. & Jia, Z., 2009, In: Journal of Biological Chemistry. 284, 25, p. 17216-17226

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

  42. Published

    Targets of balancing selection in the human genome

    Andrés, A. M., Hubisz, M. J., Indap, A., Torgerson, D. G., Degenhardt, J. D., Boyko, A. R., Gutenkunst, R. N., White, T. J., Green, E. D., Bustamante, C. D., Clark, A. G. & Nielsen, Rasmus, 2009, In: Molecular Biology and Evolution. 26, 12, p. 2755-64 9 p.

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

  43. Published

    The tedious task of finding homologous noncoding RNA genes

    Menzel, K. P., Gorodkin, Jan & Stadler, P. F., 2009, In: RNA: A publication of the RNA Society. 15, 12, p. 2075-2082 8 p.

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

  44. Published

    Uncovering commensal bacteria-plant interaction: characterisation of bacterial endophytes and their population structures in the model plant Arabidopsis thaliana

    Paiva, D. S., Klepac-Ceraj, V., Lemon, K., Kolter, R., Frigaard, Niels-Ulrik, Gautier, L. & Sakuragi, Y., 2009.

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

  45. Published

    Large BRCA1 and BRCA2 genomic rearrangements in Danish high risk breast-ovarian cancer families

    Hansen, Thomas van Overeem, Jønson, L., Albrechtsen, Anders, Andersen, M. K., Ejlertsen, Bent Laursen & Nielsen, Finn Cilius, May 2009, In: Breast Cancer Research and Treatment. 115, 2, p. 315-323 9 p.

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

  46. Published

    MicroRNA expression analysis by LNA enhanced microarrays

    Søkilde, R., Kaczkowski, B., Barken, K. B., Mouritzen, P., Møller, Søren & Litman, Thomas, 1 Oct 2009, MicroRNA Profiling in Cancer: A Bioinformatics Perspective. Pan Stanford Publishing Pte. Ltd., p. 23-46 24 p.

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

  47. 2010
  48. Published

    3-methylcholanthrene induces differential recruitment of aryl hydrocarbon receptor to human promoters

    Pansoy, A., Ahmed, S., Valen, E., Sandelin, Albin Gustav & Matthews, J., 2010, In: Toxicological Sciences. 117, 1, p. 90-100 11 p.

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

  49. Published

    A long-standing Pleistocene refugium in southern Africa and a mosaic of refugia in East Africa: insights from mtDNA and the common eland antelope

    Lorenzen, Eline, Masembe, C., Arctander, P. & Siegismund, Hans Redlef, 2010, In: Journal of Biogeography. 37, 3, p. 571-581 11 p.

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

  50. Published

    A simple procedure for routine RNA extraction and miRNA array analyses from a single thyroid in vivo fine needle aspirate

    Rossing, M., Kaczkowski, B., Futoma-Kazmierczak, E., Glud, M., Klausen, M., Faber, Jens, Nygaard, Birte, Kiss, K., Sørensen, C. H., Nielsen, Finn Cilius, Bennedbæk, F. N. & Friis-Hansen, Lennart Jan, 2010, In: Scandinavian Journal of Clinical & Laboratory Investigation. 70, 8, p. 529-534 6 p.

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

  51. Published

    Accumulation of intermediates of the carbon-phosphorus lyase pathway for phosphonate degradation in phn mutants of Escherichia coli

    Hove-Jensen, B., Rosenkrantz, T. J., Zechel, D. L. & Willemoës, Martin, 2010, In: Journal of Bacteriology. 192, 1, p. 370-374

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

  52. Published

    Antibodies against foot-and-mouth disease (FMD) virus in African buffalos (Syncerus caffer) in selected National Parks in Uganda (2001-2003)

    Ayebazibwe, C., Mwiine, F. N., Balinda, S. N., Tjørnehøj, K., Masembe, C., Muwanika, V. B., Okurut, A. R. A., Siegismund, Hans Redlef & Alexandersen, S., 2010, In: Transboundary and Emerging Diseases. 57, 4, p. 286-92 6 p.

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

  53. Published

    Bioinformatical approaches to RNA structure prediction & Sequencing of an ancient human genome

    Lindgreen, S., 2010, Biologisk Institut: Museum Tusculanum. 111 p.

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

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