Bjarne Knudsen

Summary

Affiliation: University of Aarhus
Country: Denmark

Publications

  1. pmc Using equilibrium frequencies in models of sequence evolution
    Bjarne Knudsen
    Department of Zoology, Box 118525, University of Florida, Gainesville, FL 32611 8525, USA
    BMC Evol Biol 5:21. 2005
  2. pmc A likelihood ratio test for evolutionary rate shifts and functional divergence among proteins
    B Knudsen
    Bioinformatics Research Center, University of Aarhus, Høegh Guldbergsgade 10, Building 090, DK 8000 Arhus C, Denmark
    Proc Natl Acad Sci U S A 98:14512-7. 2001
  3. ncbi Sequence alignments and pair hidden Markov models using evolutionary history
    Bjarne Knudsen
    Department of Zoology, Box 118525, University of Florida, Gainesville, FL 32611 8525, USA
    J Mol Biol 333:453-60. 2003
  4. pmc Pfold: RNA secondary structure prediction using stochastic context-free grammars
    Bjarne Knudsen
    BiRC Bioinformatics Research Center, University of Aarhus, Høegh Guldbergsgade 10, Building 090, 8000 Arhus C, Denmark
    Nucleic Acids Res 31:3423-8. 2003
  5. pmc Semiautomated improvement of RNA alignments
    Ebbe S Andersen
    Department of Molecular Biology, University of Aarhus, Arhus C, Denmark
    RNA 13:1850-9. 2007
  6. pmc Incorporating experimental design and error into coalescent/mutation models of population history
    Bjarne Knudsen
    Department of Zoology, University of Florida, Gainesville, FL 32611 8525, USA
    Genetics 176:2335-42. 2007
  7. pmc Characterising RNA secondary structure space using information entropy
    Zsuzsanna Sükösd
    Bioinformatics Research Center, Aarhus University, Aarhus, Denmark
    BMC Bioinformatics 14:S22. 2013
  8. pmc Using evolutionary rates to investigate protein functional divergence and conservation. A case study of the carbonic anhydrases
    Bjarne Knudsen
    Bioinformatics Research Center, University of Aarhus, 8000 Aarhus C, Denmark
    Genetics 164:1261-9. 2003
  9. pmc Neuronal transcriptome of Aplysia: neuronal compartments and circuitry
    Leonid L Moroz
    The Whitney Laboratory for Marine Bioscience, University of Florida, 9505 Ocean Shore Boulevard, St Augustine, FL 32080, USA
    Cell 127:1453-67. 2006
  10. doi Structure of nanoscale truncated octahedral DNA cages: variation of single-stranded linker regions and influence on assembly yields
    Cristiano Luis Pinto Oliveira
    Department of Chemistry and Interdisciplinary Nanoscience Center iNANO, University of Aarhus, 8000 Aarhus C, Denmark
    ACS Nano 4:1367-76. 2010

Collaborators

Detail Information

Publications23

  1. pmc Using equilibrium frequencies in models of sequence evolution
    Bjarne Knudsen
    Department of Zoology, Box 118525, University of Florida, Gainesville, FL 32611 8525, USA
    BMC Evol Biol 5:21. 2005
    ..In this study, we derive an expected value for f, starting from a nearly neutral model of weak selection, and then assess the biological interpretation of this factor with evolutionary simulations...
  2. pmc A likelihood ratio test for evolutionary rate shifts and functional divergence among proteins
    B Knudsen
    Bioinformatics Research Center, University of Aarhus, Høegh Guldbergsgade 10, Building 090, DK 8000 Arhus C, Denmark
    Proc Natl Acad Sci U S A 98:14512-7. 2001
    ..The results are compared with an earlier Bayesian method, thereby highlighting the advantages of the new likelihood ratio tests...
  3. ncbi Sequence alignments and pair hidden Markov models using evolutionary history
    Bjarne Knudsen
    Department of Zoology, Box 118525, University of Florida, Gainesville, FL 32611 8525, USA
    J Mol Biol 333:453-60. 2003
    ..Human alpha and beta-hemoglobin sequences are aligned, as an illustration of the potential utility of this pair HMM approach...
  4. pmc Pfold: RNA secondary structure prediction using stochastic context-free grammars
    Bjarne Knudsen
    BiRC Bioinformatics Research Center, University of Aarhus, Høegh Guldbergsgade 10, Building 090, 8000 Arhus C, Denmark
    Nucleic Acids Res 31:3423-8. 2003
    ..The method improves a previous algorithm based on an explicit evolutionary model and a probabilistic model of structures. Predictions can be done on a web server at http://www.daimi.au.dk/~compbio/pfold...
  5. pmc Semiautomated improvement of RNA alignments
    Ebbe S Andersen
    Department of Molecular Biology, University of Aarhus, Arhus C, Denmark
    RNA 13:1850-9. 2007
    ..The open architecture of the SARSE editor makes it a flexible tool to improve all RNA alignments with relatively little human intervention. Online documentation and software are available at (http://sarse.ku.dk)...
  6. pmc Incorporating experimental design and error into coalescent/mutation models of population history
    Bjarne Knudsen
    Department of Zoology, University of Florida, Gainesville, FL 32611 8525, USA
    Genetics 176:2335-42. 2007
    ..It is currently implemented as a maximum-likelihood method, but this model may also serve as the basis for the development of Bayesian approaches that incorporate experimental design and error...
  7. pmc Characterising RNA secondary structure space using information entropy
    Zsuzsanna Sükösd
    Bioinformatics Research Center, Aarhus University, Aarhus, Denmark
    BMC Bioinformatics 14:S22. 2013
    ..We also discuss interpretations and applications of this quantity, including how it can clarify reasons for low prediction reliability scores. PPfold and its source code are available from http://birc.au.dk/software/ppfold/...
  8. pmc Using evolutionary rates to investigate protein functional divergence and conservation. A case study of the carbonic anhydrases
    Bjarne Knudsen
    Bioinformatics Research Center, University of Aarhus, 8000 Aarhus C, Denmark
    Genetics 164:1261-9. 2003
    ..As illustrated by the CAs, these LRTs, in combination with other biological evidence, offer a powerful and cost-effective approach for testing hypotheses, making predictions, and designing experiments in protein functional studies...
  9. pmc Neuronal transcriptome of Aplysia: neuronal compartments and circuitry
    Leonid L Moroz
    The Whitney Laboratory for Marine Bioscience, University of Florida, 9505 Ocean Shore Boulevard, St Augustine, FL 32080, USA
    Cell 127:1453-67. 2006
    ....
  10. doi Structure of nanoscale truncated octahedral DNA cages: variation of single-stranded linker regions and influence on assembly yields
    Cristiano Luis Pinto Oliveira
    Department of Chemistry and Interdisciplinary Nanoscience Center iNANO, University of Aarhus, 8000 Aarhus C, Denmark
    ACS Nano 4:1367-76. 2010
    ..A linker length of two thymidines represents a sharp cutoff abolishing cage assembly. This is supported by energy minimization calculations suggesting substantial hydrogen bond deformation in a cage with linkers of two thymidines...
  11. ncbi Role of the trans-activation response element in dimerization of HIV-1 RNA
    Ebbe S Andersen
    Department of Molecular Biology, Bioinformatics Research Center, University of Aarhus, DK 8000 Aarhus C, Denmark
    J Biol Chem 279:22243-9. 2004
    ..The unique structure of the TAR-TAR dimer renders it an intriguing therapeutic target for the treatment of HIV-1 infection...
  12. ncbi Evolutionary divergence of thyrotropin receptor structure
    Bjarne Knudsen
    Bioinformatics Research Center, University of Aarhus, 8000 Aarhus C, Denmark
    Mol Genet Metab 81:322-34. 2004
    ..Rate shift analyses have identified residues whose manipulation in the human TSHR may lead to better understanding of receptor functions and help in the creation of designer analogues...
  13. ncbi RNA interactions in the 5' region of the HIV-1 genome
    Christian Kroun Damgaard
    Department of Molecular Biology, University of Aarhus, C F Møllers Alle, Building 130, DK 8000 C, Arhus, Denmark
    J Mol Biol 336:369-79. 2004
    ..To obtain information about tertiary interactions we applied an intramolecular UV-crosslinking strategy and identified a novel tertiary interaction within the PBS hairpin structure...
  14. pmc Assembly and structural analysis of a covalently closed nano-scale DNA cage
    Felicie F Andersen
    Department of Molecular Biology and Interdisciplinary Nanoscience Center iNANO, University of Aarhus, C F Møllers Alle, Bldg 1130, 8000 Aarhus C, Denmark
    Nucleic Acids Res 36:1113-9. 2008
    ....
  15. ncbi Complete DNA sequence of the mitochondrial genome of the sea-slug, Aplysia californica: conservation of the gene order in Euthyneura
    Bjarne Knudsen
    Department of Zoology, University of Florida, 223 Bartram Hall, Gainesville, 32611, USA
    Mol Phylogenet Evol 38:459-69. 2006
    ..The Aplysia mitochondrial genome sequenced here will serve as an important platform in both comparative and neurobiological studies using this model organism...
  16. ncbi Statistical alignment: computational properties, homology testing and goodness-of-fit
    J Hein
    Department of Genetics and Ecology The Institute of Biological Science, University of Aarhus, Building 540, Ny Munkegade, Arhus C, 8000, Denmark
    J Mol Biol 302:265-79. 2000
    ....
  17. ncbi Evolutionary rate variation and RNA secondary structure prediction
    B Knudsen
    Bioinformatics Research Center, Høegh Guldbergsgade 10, University of Aarhus, DK 8000 Arhus C, Denmark
    Comput Biol Chem 28:219-26. 2004
    ..We find that changes within a fairly large range still produce reliable predictions and conclude that using rates from a limited set of RNA sequences is valid over a broader range of sequences...
  18. pmc tmRDB (tmRNA database)
    B Knudsen
    Department of Genetics and Ecology, The Institute of Biological Sciences, University of Aarhus, Building 540, Ny Munkegade, DK 8000 Aarhus C, Denmark
    Nucleic Acids Res 29:171-2. 2001
    ..The alignments with their corresponding structural annotation can be obtained in various formats, including a new column format designed to improve and simplify computational usability of the data...
  19. ncbi Functional divergence of the circadian clock proteins in prokaryotes
    Volodymyr Dvornyk
    Osteoporosis Research Center and Department of Biomedical Sciences, Creighton University, 601 N 30th St, Ste 6767, Omaha, NE 68131, USA
    Genetica 124:247-54. 2005
    ..Rate shift analyses have identified residues whose manipulation in the Kai proteins may lead to better understanding of their functions in the two different types of the cyanobacterial circadian system...
  20. pmc tmRDB (tmRNA database)
    Christian Zwieb
    Department of Molecular Biology, The University of Texas Health Science Center at Tyler, 11937 US Highway 271, Tyler, TX 75708 3154, USA
    Nucleic Acids Res 31:446-7. 2003
    ..Three-dimensional models of the tmRNAs and their associated proteins in PDB format give evidence for the recent progress that has been made in the understanding of tmRNP structure and function...
  21. ncbi Evolution of the thyrotropin receptor: a G protein coupled receptor with an intrinsic capacity to dimerize
    Viktoria Kaczur
    Kenézy Teaching Hospital of Debrecen, Laboratory for Endocrinology and Human Genetics and Third Department of Internal Medicine, Debrecen, Hungary
    Mol Genet Metab 78:275-90. 2003
    ..We highlight the value of evolutionary informatics and set the stage for dissecting out potential subtle differences in TSHR function associated with structural variations...
  22. pmc SRPDB: Signal Recognition Particle Database
    Magnus Alm Rosenblad
    Department of Medical Biochemistry, University of Goteborg, Box 440, SE 405 30 Goteborg, Sweden
    Nucleic Acids Res 31:363-4. 2003
    ....
  23. ncbi Identification of functional amino acids in the Nramp family by a combination of evolutionary analysis and biophysical studies of metal and proton cotransport in vivo
    Roman Chaloupka
    Institut National de la Recherche Scientifique, INRS Institut Armand Frappier, 531, Bd des prairies, Laval, Quebec, Canada H7V 1B7
    Biochemistry 44:726-33. 2005
    ..It is proposed that co-occurrence of these four Nramp-specific transmembrane residues may have contributed to the emergence of this family of metal and proton cotransporters...