Computational and RNA Biology

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  1. 2001
  2. Published

    Implications of secondary structure prediction and amino acid sequence comparison of class I and class II phosphoribosyl diphosphate synthases on catalysis, regulation, and quaternary structure.

    Krath, B. N. & Hove-Jensen, B., 2001, In: Protein Science. 10, 11, p. 2317-24 7 p.

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

  3. Published

    On the total number of genes and their length distribution in complete microbial genomes

    Skovgaard, M., Jensen, Lars Juhl, Brunak, Søren, Ussery, D. & Krogh, Anders, 2001, In: Trends in Genetics. 17, 8, p. 425-8 4 p.

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

  4. Published

    The remarkable chlorosome

    Frigaard, Niels-Ulrik, Vassilieva, E. V., Li, H., Milks, K. J., Zhao, J. & Bryant, D. A., 2001, Proceedings of the 12th International Congress on Photosynthesis. CSIRO Publishing, p. S1-003 6 p.

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

  5. 2002
  6. Published

    Chlorobium tepidum mutant lacking bacteriochlorophyll c made by inactivation of the bchK gene, encoding bacteriochlorophyll c synthase

    Frigaard, Niels-Ulrik, Voigt, G. D. & Bryant, D. A., 2002, In: Journal of Bacteriology. 184, 12, p. 3368-3376 8 p.

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

  7. Published

    E. coli dihydroorotate dehydrogenase reveals structural and functional distinctions between different classes of dihydroorotate dehydrogenases.

    Nørager, S., Jensen, K. F., Björnberg, O. & Larsen, Sine, 2002, In: Structure. 10, p. 1211-1223

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

  8. Published

    Molecular identification of the insect adipokinetic hormone receptors.

    Staubli, F., Jørgensen, T. J. D., Cazzamali, G., Williamson, M., Lenz, C., Søndergaard, Leif, Roepstorff, P. & Grimmelikhuijzen, Cornelis (Cok), 2002, In: Proceedings of the National Academy of Science of the United States of America. 99, 6, p. 3446-51 5 p.

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

  9. Published

    Selective Protein Extraction from Chlorobium tepidum Chlorosomes Using Detergents. Evidence That CsmA Forms Multimers and Binds Bacteriochlorophyll a

    Bryant, D. A., Vassilieva, E. V., Frigaard, Niels-Ulrik & Li, H., 2002, In: Biochemistry. 41, 48, p. 14403-14411 9 p.

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

  10. Published

    Selective advantage of ray florets in Scalesia affinis and S. pedunculata (Asteraceae), two endemic species from the Galápagos

    Nielsen, Lene Rostgaard, Philipp, M. & Siegismund, Hans Redlef, 2002, In: Evolutionary Ecology. 16, 2, p. 139-153 15 p.

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

  11. Published

    Subcellular localization of chlorosome proteins in Chlorobium tepidum and characterization of three new chlorosome proteins: CsmF, CsmH, and CsmX

    Vassilieva, E. V., Stirewalt, V. L., Jakobs, C. U., Frigaard, Niels-Ulrik, Inoue-Sakamoto, K., Baker, M. A., Sotak, A. & Bryant, D. A., 2002, In: Biochemistry. 41, p. 4358-4370 13 p.

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

  12. Published

    The Motion of a Single Molecule, the Lambda-Receptor, in the Bacterial Outer Membrane

    Oddershede, L., Dreyer, J. K., Grego, S., Brown, Stanley & Berg-Sørensen, K., 2002, In: Biophysical Journal. 83, 6, p. 3152-61 9 p.

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

  13. 2003
  14. Published

    Chlorobium Tepidum: Insights into the Structure, Physiology, and Metabolism of a Green Sulfur Bacterium Derived from the Complete Genome Sequence

    Frigaard, Niels-Ulrik, Chew, A. G. M., Li, H., Maresca, J. A. & Bryant, D. A., 2003, In: Photosynthesis Research. 78, 2, p. 93-117 24 p.

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

  15. Published

    EasyGene - a prokaryotic gene finder that ranks ORFs by statistical significance

    Larsen, T. S. & Krogh, Anders, 2003, In: BMC Bioinformatics. 4(1), p. 21

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

  16. Published

    Escherichia coli phnN, encoding ribose 1,5-bisphosphokinase activity (phosphoribosyl diphosphate forming): dual role in phosphonate degradation and NAD biosynthesis pathways.

    Hove-Jensen, B., Rosenkrantz, T. J., Haldimann, A. & Wanner, B. L., 2003, In: Journal of Bacteriology. 185, 9, p. 2793-801 8 p.

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

  17. Published

    Gene flow from oilseed rape (Brassica napus) and beet (Beta vulgaris) to wild relatives: Effects of herbicide tolerant cultivars

    J�rgensen, R. B., Hauser, T. P., Hansen, L. B., Siegismund, Hans Redlef, Andersen, B., Lelley, T., Balazs, E. & Tepfer, M., 2003, Ecological impact of GMO dissemination in agro-ecosystems.

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

  18. Published

    Molecular cloning, functional expression, and gene silencing of two Drosophila receptors for the Drosophila neuropeptide pyrokinin-2.

    Rosenkilde, C., Cazzamali, G., Williamson, M., Hauser, Frank, Søndergaard, Leif, DeLotto, R. & Grimmelikhuijzen, Cornelis (Cok), 2003, In: Biochemical and Biophysical Research Communications. 309, 2, p. 485-94 9 p.

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

  19. Published

    Prediction of lipoprotein signal peptides in Gram-negative bacteria.

    Juncker, A. S., Willenbrock, H., Heijne, G. V., Nielsen, H. & Krogh, Anders, 2003, In: Protein Science. 12(8), p. 1652-1662

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

  20. Published

    Reliability measures for membrane protein topology prediction algorithms

    Melén, K., Krogh, Anders & Heijne, G. V., 2003, In: Journal of Molecular Biology. 327(3), p. 735-744

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

  21. Published

    RpoD promoters in Campylobacter jejuni exhibit a strong periodic signal instead of a -35 box

    Petersen, L., Larsen, T. S., Ussery, D. W., On, S. L. W. & Krogh, Anders, 2003, In: Journal of Molecular Biology. 326(5), p. 1361-1372

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

  22. Published

    Single-cell Analysis of Lambda Immunity Regulation

    Bæk, K. T., Svenningsen, Sine Lo, Eisen, H., Sneppen, Kim & Brown, Stanley, 2003, In: Journal of Molecular Biology. 334, 3, p. 363-372 10 p.

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

  23. Published

    Partial self-incompatibility in the polyploid endemic species Scalesia affinis (Asteraceae) from the Galápagos: remnants of a self-incompatibility system?

    Nielsen, Lene Rostgaard, Siegismund, Hans Redlef & PHILIPP, M., 1 May 2003, In: Botanical Journal of the Linnean Society. 142, 1, p. 93-101 9 p.

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

  24. Published

    Morphometric, AFLP and plastid microsatellite variation in populations of Scalesia divisa and S. incisa (Asteraceae) from the Galápagos Islands

    Nielsen, Lene Rostgaard, Cowan, R. S., Siegismund, Hans Redlef, Adsersen, Henning Emil, PHILIPP, M. & Fay, M. F., 1 Nov 2003, In: Botanical Journal of the Linnean Society. 143, 3, p. 243-254 12 p.

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

  25. 2004
  26. Published

    A Combined Transmembrane Topology and Signal Peptide Prediction Method

    Kall, L., Krogh, Anders & Sonnhammer, E. L., 2004, In: Journal of Molecular Biology. Vol. 338 (5), p. 1027-36

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

  27. Published

    A New Paradigm for General Architecture Routing

    Paluszewski, M., Winter, Pawel & Zachariasen, M., 2004, Proceedings of the 14th ACM Great Lakes Symposium on VLSI. New York, NY, USA: Association for Computing Machinery, p. 202-207

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

  28. Published

    Adaptive evolution of cytochrome c oxidase: Infrastructure for a carnivorous plant radiation

    Jobson, R. W., Nielsen, Rasmus, Laakkonen, L., Wikström, M. & Albert, V. A., 2004, In: Proceedings of the National Academy of Sciences of the United States of America. 101, 52, p. 18064-18068 5 p.

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

  29. Published

    Dwarfism and impaired gut development in insulin-like growth factor II mRNA-binding protein 1-deficient mice

    Hansen, Thomas van Overeem, Hammer, N. A., Nielsen, J., Madsen, Mette, Dalbaeck, C., Wewer, Ulla M., Christiansen, Jan & Nielsen, Finn Cilius, 2004, In: Molecular and Cellular Biology. 24, 10, p. 4448-64 17 p.

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

  30. Published

    Gene Inactivation in the Cyanobacterium Synechococcus sp. PCC 7002 and the Green Sulfur Bacterium Chlorobium tepidum Using In Vitro-Made DNA Constructs and Natural Transformation

    Frigaard, Niels-Ulrik, Sakuragi, Y. & Bryant, D. A., 2004, In: Methods in Molecular Biology. 274, p. 325-340 15 p.

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

  31. Published

    Genetic manipulation of carotenoid biosynthesis in the green sulfur bacterium Chlorobium tepidum

    Frigaard, Niels-Ulrik, Maresca, J. A., Yunker, C. E., Jones, A. D. & Bryant, D. A., 2004, In: Journal of Bacteriology. 186, 16, p. 5210-5220 10 p.

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

  32. Published

    Heterooligomeric phosphoribosyl diphosphate synthase of Saccharomyces cerevisiae: Combinatorial expression of the five PRS genes in Escherichia coli

    Hove-Jensen, B., 2004, In: Journal of Biological Chemistry. 279, 39, p. 40345-50 5 p.

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

  33. Published

    Nine mutants of Chlorobium tepidum each unable to synthesize a different chlorosome protein still assemble functional chlorosomes

    Frigaard, Niels-Ulrik, Li, H., Milks, K. J. & Bryant, D. A., 2004, In: Journal of Bacteriology. 186, 3, p. 646-653 7 p.

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

  34. Published

    Seeing green bacteria in a new light: genomics-enabled studies of the photosynthetic apparatus in green sulfur bacteria and filamentous anoxygenic phototrophic bacteria

    Frigaard, Niels-Ulrik & Bryant, D. A., 2004, In: Archives of Microbiology. 182, 4, p. 265-276 12 p.

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

  35. Published

    Structural, kinetic, and mutational studies of the zinc ion environment in tetrameric cytidine deaminase

    Johansson, E., Neuhard, J., Willemoës, Martin & Larsen, Sine, 2004, In: Biochemistry. 43, 20, p. 6020-9 9 p.

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

  36. Published

    Surface exposed amino acid differences between mesophilic and thermophilic phosphoribosyl diphosphate synthase.

    Hove-Jensen, B. & McGuire, J. N., 2004, In: European Journal of Biochemistry. 271, 22, p. 4526-33 7 p.

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

  37. 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

  38. Published

    The bchU gene of Chlorobium tepidum encodes the C-20 methyltransferase in bacteriochlorophyll c biosynthesis

    Maresca, J. A., Gomez Maqueo Chew, A., Ponsatí, M. R., Frigaard, Niels-Ulrik, Ormerod, J. G. & Bryant, D. A., 2004, In: Journal of Bacteriology. 186, 9, p. 2558-2566 9 p.

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

  39. 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

  40. Published

    The fission yeast heterochromatin protein Rik1 is required for telomere clustering during meiosis

    Tuzon, C. T., Borgstrøm, B., Weilguny, D., Egel, Richard, Cooper, J. P. & Nielsen, Olaf, 2004, In: Journal of Cell Biology. 165, 6, p. 759-65 6 p.

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

  41. 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

  42. 2005
  43. Published

    Allosteric regulation and communication between subunits in uracil phosphoribosyltransferase from Sulfolobus solfataricus

    Arent, S., Harris, P., Jensen, K. F. & Larsen, Sine, 2005, In: Biochemistry. 44, 3, p. 883-892

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

  44. Published

    Catalytic residues Lys197 and Arg199 of Bacillus subtilis phosphoribosyl diphosphate synthase. Alanine-scanning mutagenesis of the flexible catalytic loop.

    Hove-Jensen, B., Bentsen, A. K. & Harlow, K. W., 2005, In: FEBS Journal. 272, 14, p. 3631-9 8 p.

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

  45. Published

    Characterization of different crystal forms of the a-glucosidase MalA from Sulfolobus solfataricus

    Ernst, H. A., Willemoës, Martin, Lo Leggio, Leila, Leonard, G., Blum, P. & Larsen, Sine, 2005, In: Acta Crystallographica Section F. 61, p. 1039-1042

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

  46. Published

    Characterization of different crystal forms of the alpha-glucosidase MalA from Sulfolobus solfataricus

    Ernst, H. A., Willemoës, Martin, Lo Leggio, Leila, Leonard, G., Blum, P. & Larsen, Sine, 2005, In: Acta Crystallographica. Section F : Structural Biology and Crystallization Communications. 61, Pt 12, p. 1039-42 3 p.

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

  47. 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

  48. Published

    Expression of IGF-II mRNA-binding proteins (IMPs) in gonads and testicular cancer

    Hammer, N. A., Hansen, Thomas van Overeem, Byskov, A. G., Rajpert-De Meyts, E., Grøndahl, M. L., Bredkjaer, H. E., Wewer, Ulla M., Christiansen, Jan & Nielsen, Finn Cilius, 2005, In: Reproduction. 130, 2, p. 203-12 10 p.

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

  49. Published

    Full cyclic coordinate descent: solving the protein loop closure problem in Cα space

    Boomsma, Wouter & Hamelryck, Thomas Wim, 2005, In: BMC Bioinformatics. 6, 10 p., 159.

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

  50. Published

    Isolation and Characterization of Carotenosomes from a Bacteriochlorophyll c-less Mutant of Chlorobium tepidum

    Frigaard, Niels-Ulrik, Li, H., Martinsson, P., Das, S. K., Frank, H. A., Aartsma, T. J. & Bryant, D. A., 2005, In: Photosynthesis Research. 86, 1-2, p. 101-11 10 p.

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

  51. Published

    Novel class III phosphoribosyl diphosphate synthase: structure and properties of the tetrameric, phosphate-activated, non-allosterically inhibited enzyme from Methanocaldococcus jannaschii.

    Kadziola, Anders, Jepsen, C. H., Johansson, E., McGuire, J., Larsen, Sine & Hove-Jensen, B., 2005, In: Journal of Molecular Biology. 354, 4, p. 815-28 13 p.

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

  52. Published

    Når enzymer tøver - CTP - biosyntesen i mælkesyrebakterier

    Martinussen, J., Willemoës, Martin, Kilstrup, M., Jensen, P. R. & Hammer, K., 2005, In: Dansk Kemi. 86, 8, p. 20-22

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

  53. Published

    Structures of dCTP deaminase from Escherichia coli with bound substrate and product: reaction mechanism and determinants of mono- and bifunctionality for a family of enzymes

    Johansson, E., Fanø, M., Bynck, J. H., Neuhard, J., Larsen, S., Sigurskjold, B. W., Christensen, U. & Willemoës, Martin, 2005, In: Journal of Biological Chemistry. 280, 4, p. 3051-9 8 p.

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

  54. 2006
  55. Published

    A hidden Markov model approach for determining expression from genomic tiling micro arrays

    Terkelsen, K. M., Gardner, P. P., Arctander, P. & Krogh, Anders, 2006, In: BMC Bioinformatics. 7, 239

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

  56. Published

    Community genomics among stratified microbial assemblages in the ocean's interior

    DeLong, E. F., Preston, C. M., Mincer, T., Rich, V., Hallam, S. J., Frigaard, Niels-Ulrik, Martinez, A., Sullivan, M. B., Edwards, R., Brito, B. R., Chisholm, S. W. & Karl, D. M., 2006, In: Science. 311, 5760, p. 496-503 7 p.

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

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