Center for RNA Biology Publications

Publications by Ralf Bundschuh since 2000

• Robert A Forties, Ralf Bundschuh, and Michael G Poirier
  "The flexibility of locally melted DNA."
  Nucleic Acids Res. 37, 4580-6 (2009).

• Shinichiro Shoji, Nimo M Abdi, Ralf Bundschuh, and Kurt Fredrick
  "Contribution of ribosomal residues to P-site tRNA binding."
  Nucleic Acids Res. 37, 4033-42 (2009).

• Marianne M Lee, Michael K Chan, and Ralf Bundschuh
  "SIB-BLAST: a web server for improved delineation of true and false positives in PSI-BLAST searches."
  Nucleic Acids Res. 37, W53-6 (2009).

• Malcolm McCauley, Robert Forties, Ulrich Gerland, and Ralf Bundschuh
  "Anomalous scaling in nanopore translocation of structured heteropolymers."
  Physical biology 6, 036006 (2009).

• Christina Beargie, Tsunglin Liu, Mark Corriveau, Ha Youn Lee, Jonatha Gott, and Ralf Bundschuh
  "Genome annotation in the presence of insertional RNA editing."
  Bioinformatics 24, 2571-8 (2008).

• Marko Djordjevic and Ralf Bundschuh
  "Formation of the open complex by bacterial RNA polymerase--a quantitative model."
  Biophys. J. 94, 4233-48 (2008).

• Marianne M Lee, Michael K Chan, and Ralf Bundschuh
  "Simple is beautiful a straightforward approach to improve the delineation of true and false positives in PSI-BLAST searches."
  Bioinformatics 24, 1339-43 (2008).

• Marianne M Lee, Ralf Bundschuh, and Michael K Chan
  "Distant homology detection using a LEngth and STructure-based sequence Alignment Tool LESTAT."
  Proteins 71, 1409-19 (2008).

• Ralf Bundschuh and Robijn Bruinsma
  "Melting of branched RNA molecules."
  Phys. Rev. Lett. 100, 148101 (2008).

• Asuka Itaya, Ralf Bundschuh, Anthony J Archual, Je-Gun Joung, Zhangjun Fei, Xinbin Dai, Patrick X Zhao, Yuhong Tang, Richard S Nelson, and Biao Ding
  "Small RNAs in tomato fruit and leaf development."
  Biochim. Biophys. Acta 1779, 99-107 (2008).

• Philipp W Messer, Ralf Bundschuh, Martin Vingron, and Peter F Arndt
  "Effects of long-range correlations in DNA on sequence alignment score statistics."
  J. Comput. Biol. 14, 655-68 (2007).

• Farhat Habib, Andrew D Johnson, Ralf Bundschuh, and Daniel Janies
  "Large scale genotype-phenotype correlation analysis based on phylogenetic trees."
  Bioinformatics 23, 785-8 (2007).

• Asuka Itaya, Xuehua Zhong, Ralf Bundschuh, Yijun Qi, Ying Wang, Ryuta Takeda, Ann R Harris, Carlos Molina, Richard S Nelson, and Biao Ding
  "A structured viroid RNA serves as a substrate for dicer-like cleavage to produce biologically active small RNAs but is resistant to RNA-induced silencing complex-mediated degradation."
  J. Virol. 81, 2980-94 (2007).

• Ralf Bundschuh
  "Computational approaches to insertional RNA editing."
  Meth. Enzymol. 424, 173-95 (2007).

• R Bundschuh and U Gerland
  "A puzzle in DNA biophysics."
  The European physical journal. E, Soft matter 19, 347-9; discussion 351-2 (2006).

• R Bundschuh and U Gerland
  "Dynamics of intramolecular recognition base-pairing in DNA/RNA near and far from equilibrium."
  The European physical journal. E, Soft matter 19, 319-29 (2006).

• Nicholas Chia and Ralf Bundschuh
  "A practical approach to significance assessment in alignment with gaps."
  J. Comput. Biol. 13, 429-41 (2006).

• Vishwesha Guttal and Ralf Bundschuh
  "Model for folding and aggregation in RNA secondary structures."
  Phys. Rev. Lett. 96, 018105 (2006).

• Tsunglin Liu and Ralf Bundschuh
  "Quantification of the differences between quenched and annealed averaging for RNA secondary structures."
  Physical review. E, Statistical, nonlinear, and soft matter physics 72, 061905 (2005).

• Ralf Bundschuh and Ulrich Gerland
  "Coupled dynamics of RNA folding and nanopore translocation."
  Phys. Rev. Lett. 95, 208104 (2005).

• Nicholas Chia and Ralf Bundschuh
  "Numerical method for accessing the universal scaling function for a multiparticle discrete time asymmetric exclusion process."
  Physical review. E, Statistical, nonlinear, and soft matter physics 72, 051102 (2005).

• Farhat Habib and Ralf Bundschuh
  "Modeling DNA unzipping in the presence of bound proteins."
  Physical review. E, Statistical, nonlinear, and soft matter physics 72, 031906 (2005).

• Tsunglin Liu and Ralf Bundschuh
  "Model for codon position bias in RNA editing."
  Phys. Rev. Lett. 95, 088101 (2005).

• D M Layton and R Bundschuh
  "A statistical analysis of RNA folding algorithms through thermodynamic parameter perturbation."
  Nucleic Acids Res. 33, 519-24 (2005).

• Jonatha M Gott, Neeta Parimi, and Ralf Bundschuh
  "Discovery of new genes and deletion editing in Physarum mitochondria enabled by a novel algorithm for finding edited mRNAs."
  Nucleic Acids Res. 33, 5063-72 (2005).

• R Bundschuh
  "Computational prediction of RNA editing sites."
  Bioinformatics 20, 3214-20 (2004).

• Nicholas Chia and Ralf Bundschuh
  "Finite width model sequence comparison."
  Physical review. E, Statistical, nonlinear, and soft matter physics 70, 021906 (2004).

• Ulrich Gerland, Ralf Bundschuh, and Terence Hwa
  "Translocation of structured polynucleotides through nanopores."
  Physical biology 1, 19-26 (2004).

• Tsunglin Liu and Ralf Bundschuh
  "Analytical description of finite size effects for RNA secondary structures."
  Physical review. E, Statistical, nonlinear, and soft matter physics 69, 061912 (2004).

• Ulrich Gerland, Ralf Bundschuh, and Terence Hwa
  "Mechanically probing the folding pathway of single RNA molecules."
  Biophys. J. 84, 2831-40 (2003).

• R Bundschuh, F Hayot, and C Jayaprakash
  "Fluctuations and slow variables in genetic networks."
  Biophys. J. 84, 1606-15 (2003).

• R Bundschuh, F Hayot, and C Jayaprakash
  "The role of dimerization in noise reduction of simple genetic networks."
  J. Theor. Biol. 220, 261-9 (2003).

• Ralf Bundschuh and Michael Lässig
  "Delocalization transitions of semiflexible manifolds."
  Physical review. E, Statistical, nonlinear, and soft matter physics 65, 061502 (2002).

• Yi-Kuo Yu, Ralf Bundschuh, and Terence Hwa
  "Hybrid alignment high-performance with universal statistics."
  Bioinformatics 18, 864-72 (2002).

• R Bundschuh
  "Asymmetric exclusion process and extremal statistics of random sequences."
  Physical review. E, Statistical, nonlinear, and soft matter physics 65, 031911 (2002).

• R Bundschuh and T Hwa
  "Statistical mechanics of secondary structures formed by random RNA sequences."
  Physical review. E, Statistical, nonlinear, and soft matter physics 65, 031903 (2002).

• Ralf Bundschuh
  "Rapid significance estimation in local sequence alignment with gaps."
  J. Comput. Biol. 9, 243-60 (2002).

• U Gerland, R Bundschuh, and T Hwa
  "Force-induced denaturation of RNA."
  Biophys. J. 81, 1324-32 (2001).

• S F Altschul, R Bundschuh, R Olsen, and T Hwa
  "The estimation of statistical parameters for local alignment score distributions."
  Nucleic Acids Res. 29, 351-61 (2001).