Computational and RNA Biology

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  1. 2004
  2. 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

  3. 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

  4. 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

  5. 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

  6. 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

  7. 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

  8. 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

  9. 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

  10. 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

  11. 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

  12. 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

  13. 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

  14. 2005
  15. 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

  16. 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

  17. 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

  18. 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

  19. 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

  20. 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

  21. 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

  22. 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

  23. 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

  24. 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

  25. 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

  26. 2006
  27. 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

  28. 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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