Rolf Backofen

Personal Home Page

http://www.bioinf.uni-freiburg.de/~backofen/

Articles in Scholarly Journals [Incomplete List]

  1. Variations on RNA folding and alignment: lessons from Benasque
    Journal of Mathematical Biology, vol. 56, no. 1-2, pp. 129–144, 2007
  2. Fast detection of common sequence structure patterns in RNAs
    Journal of Discrete Algorithms, vol. 5, no. 2, pp. 212–228, 2007
  3. Locality and Gaps in RNA Comparison
    Journal of Computational Biology, vol. 14, no. 8, pp. 1074–1087, 2007
  4. TassDB: a database of alternative tandem splice sites
    Nucleic Acids Research, vol. 35, no. Database, pp. D188–D192, 2007
  5. INFO-RNA--a server for fast inverse RNA folding satisfying sequence constraints
    Nucleic Acids Research, vol. 35, no. Web Server, pp. W310–W313, 2007
  6. BioBayesNet: a web server for feature extraction and Bayesian network modeling of biological sequence data
    Nucleic Acids Research, vol. 35, no. Web Server, pp. W688–W693, 2007
  7. Exploring the lower part of discrete polymer model energy landscapes
    Europhysics Letters (EPL), vol. 74, no. 4, pp. 726–732, 2007
  8. Inferring Noncoding RNA Families and Classes by Means of Genome-Scale Structure-Based Clustering
    PLoS Computational Biology, vol. 3, no. 4, p. e65, 2007
  9. Alternative Splicing at NAGNAG Acceptors: Simply Noise or Noise and More?
    PLoS Genetics, vol. 2, no. 11, p. e207, 2006
  10. Using RNA secondary structures to guide sequence motif finding towards single-stranded regions
    Nucleic Acids Research, vol. 34, no. 17, pp. e117–e117, 2006
  11. Genome Biology, vol. 7, no. 7, p. R65, 2006
  12. Single-Nucleotide Polymorphisms in NAGNAG Acceptors Are Highly Predictive for Variations of Alternative Splicing
    The American Journal of Human Genetics, vol. 78, no. 2, pp. 291–302, 2006
  13. INFO-RNA--a fast approach to inverse RNA folding
    Bioinformatics, vol. 22, no. 15, pp. 1823–1831, 2006
  14. Sequencing errors or SNPs at splice-acceptor guanines in dbSNP?
    Nature Biotechnology, vol. 24, no. 9, Article ID nbt0906-1068b, 2 pages, 2006
  15. A Constraint-Based Approach to Fast and Exact Structure Prediction in Three-Dimensional Protein Models
    Constraints, vol. 11, no. 1, pp. 5–30, 2006
  16. Corrigendum: Widespread occurrence of alternative splicing at NAGNAG acceptors contributes to proteome plasticity
    Nature Genetics, vol. 37, no. 1, Article ID ng0105-106c, 1 pages, 2005
  17. Non-EST based prediction of exon skipping and intron retention events using Pfam information
    Nucleic Acids Research, vol. 33, no. 17, pp. 5611–5621, 2005
  18. A multiple-feature framework for modelling and predicting transcription factor binding sites
    Bioinformatics, vol. 21, no. 14, pp. 3082–3088, 2005
  19. SECISDesign: a server to design SECIS-elements within the coding sequence
    Bioinformatics, vol. 21, no. 15, pp. 3312–3313, 2005
  20. MARNA: multiple alignment and consensus structure prediction of RNAs based on sequence structure comparisons
    Bioinformatics, vol. 21, no. 16, pp. 3352–3359, 2005
  21. Journal of Bioinformatics and Computational Biology, vol. 2, no. 4, p. 681, 2004
  22. Widespread occurrence of alternative splicing at NAGNAG acceptors contributes to proteome plasticity
    Nature Genetics, vol. 36, no. 12, Article ID ng1469, 2 pages, 2004
  23. A polynomial time upper bound for the number of contacts in the HP-model on the face-centered-cubic lattice (FCC)
    Journal of Discrete Algorithms, vol. 2, no. 2, pp. 161–206, 2004
  24. Constraints, vol. 7, no. 3/4, pp. 333–349, 2002
  25. Constraints, vol. 6, no. 2/3, pp. 141–156, 2001
  26. Constraints, vol. 6, no. 2/3, pp. 223–255, 2001
  27. Constraints, vol. 6, no. 2/3, pp. 139–139, 2001
  28. How to Win a Game with Features,
    Information and Computation, vol. 142, no. 1, pp. 76–101, 1998
  29. A first-order axiomatization of the theory of finite trees
    Journal of Logic, Language and Information, vol. 4, no. 1, pp. 5–39, 1995
  30. A complete and recursive feature theory
    Theoretical Computer Science, vol. 146, no. 1-2, pp. 243–268, 1995
  31. A complete axiomatization of a theory with feature and arity constraints,
    The Journal of Logic Programming, vol. 24, no. 1-2, pp. 37–71, 1995
  32. Regular Path Expressions in Feature Logic
    Journal of Symbolic Computation, vol. 17, no. 5, pp. 421–455, 1994