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).
