R Bundschuh

Summary

Affiliation: The Ohio State University
Country: USA

Publications

  1. ncbi request reprint Unified approach to partition functions of RNA secondary structures
    Ralf Bundschuh
    Departments of Physics, Chemistry and Biochemistry, Center for RNA Biology, The Ohio State University, 191 West Woodruff Avenue, Columbus, OH, 43210 1117, USA
    J Math Biol 69:1129-50. 2014
  2. pmc Comparison of insertional RNA editing in Myxomycetes
    Cai Chen
    Biophysics Graduate Program, The Ohio State University, Columbus, Ohio, United States of America
    PLoS Comput Biol 8:e1002400. 2012
  3. pmc A quantitative model of nucleosome dynamics
    Robert A Forties
    Department of Physics, The Ohio State University, 191 West Woodruff Avenue, Columbus, Ohio 43210 1117, USA
    Nucleic Acids Res 39:8306-13. 2011
  4. pmc SIB-BLAST: a web server for improved delineation of true and false positives in PSI-BLAST searches
    Marianne M Lee
    The Ohio State Biophysics Program, Ohio State University, Columbus, OH 43210 1117, USA
    Nucleic Acids Res 37:W53-6. 2009
  5. pmc Enrichment-based DNA methylation analysis using next-generation sequencing: sample exclusion, estimating changes in global methylation, and the contribution of replicate lanes
    Michael P Trimarchi
    Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio, USA
    BMC Genomics 13:S6. 2012
  6. pmc Methods for high-throughput MethylCap-Seq data analysis
    Benjamin A T Rodriguez
    The Ohio State University Comprehensive Cancer Center, Columbus, Ohio, USA
    BMC Genomics 13:S14. 2012
  7. pmc Systematic investigation of insertional and deletional RNA-DNA differences in the human transcriptome
    Cai Chen
    Biophysics Graduate Program, The Ohio State University, Columbus, OH, USA
    BMC Genomics 13:616. 2012
  8. ncbi request reprint Computational prediction of RNA editing sites
    R Bundschuh
    Department of Physics, The Ohio State University, 174 West 18th Avenue, Columbus, OH 43210 1106, USA
    Bioinformatics 20:3214-20. 2004
  9. ncbi request reprint The role of dimerization in noise reduction of simple genetic networks
    R Bundschuh
    Department of Physics, The Ohio State University, Columbus, OH 43210 1106, U S A
    J Theor Biol 220:261-9. 2003
  10. pmc Complete characterization of the edited transcriptome of the mitochondrion of Physarum polycephalum using deep sequencing of RNA
    R Bundschuh
    Department of Physics, Department of Biochemistry and Center for RNA Biology, Ohio State University, Columbus, OH 43210, USA
    Nucleic Acids Res 39:6044-55. 2011

Collaborators

  • F Hayot
  • U Gerland
  • Richard Fishel
  • Cai Chen
  • D M Layton
  • J M Gott
  • Benjamin A T Rodriguez
  • Guido Marcucci
  • Pearlly Yan
  • David Frankhouser
  • Michael P Trimarchi
  • John Curfman
  • Mark Murphy
  • Robert A Forties
  • Marianne M Lee
  • Bryan Ball
  • William Blum
  • Hok Hei Tam
  • Deval Parikh
  • Sebastian Schwind
  • Rita Huang
  • Michael W Y Chan
  • Hung Cheng Lai
  • Michael Trimarchi
  • Michael G Poirier
  • Justin A North
  • Sarah Javaid
  • Omar P Tabbaa
  • Michael K Chan

Detail Information

Publications16

  1. ncbi request reprint Unified approach to partition functions of RNA secondary structures
    Ralf Bundschuh
    Departments of Physics, Chemistry and Biochemistry, Center for RNA Biology, The Ohio State University, 191 West Woodruff Avenue, Columbus, OH, 43210 1117, USA
    J Math Biol 69:1129-50. 2014
    ..Then, we show that this approach can be applied to the study of the molten-native transition, denaturation of RNA molecules, as well as to studies of the glass phase of random RNA sequences. ..
  2. pmc Comparison of insertional RNA editing in Myxomycetes
    Cai Chen
    Biophysics Graduate Program, The Ohio State University, Columbus, Ohio, United States of America
    PLoS Comput Biol 8:e1002400. 2012
    ..Beyond revealing interesting properties of insertional RNA editing in Myxomycetes, our work suggests possible approaches to be used when finding sequence motifs for any biological process fails...
  3. pmc A quantitative model of nucleosome dynamics
    Robert A Forties
    Department of Physics, The Ohio State University, 191 West Woodruff Avenue, Columbus, Ohio 43210 1117, USA
    Nucleic Acids Res 39:8306-13. 2011
    ..This model's precise agreement with current experiments suggests that it can be applied more generally to provide important mechanistic understanding of the numerous nucleosome alterations that occur during DNA processing...
  4. pmc SIB-BLAST: a web server for improved delineation of true and false positives in PSI-BLAST searches
    Marianne M Lee
    The Ohio State Biophysics Program, Ohio State University, Columbus, OH 43210 1117, USA
    Nucleic Acids Res 37:W53-6. 2009
    ..Notably, this improvement to PSI-BLAST comes at minimal computational cost as SIB-BLAST utilizes existing results already produced in a PSI-BLAST search...
  5. pmc Enrichment-based DNA methylation analysis using next-generation sequencing: sample exclusion, estimating changes in global methylation, and the contribution of replicate lanes
    Michael P Trimarchi
    Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio, USA
    BMC Genomics 13:S6. 2012
    ....
  6. pmc Methods for high-throughput MethylCap-Seq data analysis
    Benjamin A T Rodriguez
    The Ohio State University Comprehensive Cancer Center, Columbus, Ohio, USA
    BMC Genomics 13:S14. 2012
    ..Currently there is a lack of workflows for efficient analysis of large, MethylCap-seq datasets containing multiple sample groups...
  7. pmc Systematic investigation of insertional and deletional RNA-DNA differences in the human transcriptome
    Cai Chen
    Biophysics Graduate Program, The Ohio State University, Columbus, OH, USA
    BMC Genomics 13:616. 2012
    ..Here, we provide the first study to examine the possibility of genome-wide indel RNA-DNA differences in one human individual, NA12878, whose RNA and matching genome have been deeply sequenced...
  8. ncbi request reprint Computational prediction of RNA editing sites
    R Bundschuh
    Department of Physics, The Ohio State University, 174 West 18th Avenue, Columbus, OH 43210 1106, USA
    Bioinformatics 20:3214-20. 2004
    ..Nevertheless, knowledge of these editing sites is crucial for understanding the editing machinery of these organisms...
  9. ncbi request reprint The role of dimerization in noise reduction of simple genetic networks
    R Bundschuh
    Department of Physics, The Ohio State University, Columbus, OH 43210 1106, U S A
    J Theor Biol 220:261-9. 2003
    ..This difference in the ability to reduce fluctuations may be of importance in the design of genetic networks...
  10. pmc Complete characterization of the edited transcriptome of the mitochondrion of Physarum polycephalum using deep sequencing of RNA
    R Bundschuh
    Department of Physics, Department of Biochemistry and Center for RNA Biology, Ohio State University, Columbus, OH 43210, USA
    Nucleic Acids Res 39:6044-55. 2011
    ..Curiously, one of the latter mRNAs contains no editing sites...
  11. pmc Fluctuations and slow variables in genetic networks
    R Bundschuh
    Department of Physics, The Ohio State University, Columbus 43210 1106, USA
    Biophys J 84:1606-15. 2003
    ..This approach ought to be applicable to a wide range of genetic networks...
  12. ncbi request reprint Dynamics of intramolecular recognition: base-pairing in DNA/RNA near and far from equilibrium
    R Bundschuh
    Department of Physics, The Ohio State University, Columbus, OH 43210 1117, USA
    Eur Phys J E Soft Matter 19:319-29. 2006
    ..Here, we review different theoretical approaches to the study of base-pairing thermodynamics and kinetics, and illustrate the rich phenomenology with several examples that use these approaches...
  13. ncbi request reprint A puzzle in DNA biophysics
    R Bundschuh
    Department of Physics, The Ohio State University, 191 W Woodruff Avenue, Columbus, OH 43210 1117, USA
    Eur Phys J E Soft Matter 19:347-9; discussion 351-2. 2006
    ..As this puzzle questions our basic understanding of DNA, it must be resolved, most likely by a combination of additional experiments and new theoretical work...
  14. pmc A statistical analysis of RNA folding algorithms through thermodynamic parameter perturbation
    D M Layton
    Department of Physics, The Ohio State University 174 W 18th Avenue, Columbus, OH 43210 1106, USA
    Nucleic Acids Res 33:519-24. 2005
    ..Here, a new measure of stability using parameter perturbation is proposed, and its limitations are discussed...
  15. ncbi request reprint Asymmetric exclusion process and extremal statistics of random sequences
    R Bundschuh
    Department of Physics, University of California at San Diego, La Jolla, California 92093 0319, USA
    Phys Rev E Stat Nonlin Soft Matter Phys 65:031911. 2002
    ..The statistical significance of sequence alignments is characterized through studying the total hopping current of the discrete time and space version of the asymmetric exclusion process...
  16. ncbi request reprint Statistical mechanics of secondary structures formed by random RNA sequences
    R Bundschuh
    Department of Physics, University of California at San Diego, 9500 Gilman Drive, La Jolla, California 92093 0319, USA
    Phys Rev E Stat Nonlin Soft Matter Phys 65:031903. 2002
    ..It is revealed by a change in the coefficient of the logarithmic excitation energy, from being disorder dominated to being entropy dominated...