Affiliation: The Ohio State University
- Unified approach to partition functions of RNA secondary structuresRalf 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. ..
- Comparison of insertional RNA editing in MyxomycetesCai 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...
- A quantitative model of nucleosome dynamicsRobert 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...
- SIB-BLAST: a web server for improved delineation of true and false positives in PSI-BLAST searchesMarianne 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...
- Enrichment-based DNA methylation analysis using next-generation sequencing: sample exclusion, estimating changes in global methylation, and the contribution of replicate lanesMichael P Trimarchi
Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio, USA
BMC Genomics 13:S6. 2012....
- Methods for high-throughput MethylCap-Seq data analysisBenjamin 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...
- Systematic investigation of insertional and deletional RNA-DNA differences in the human transcriptomeCai 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...
- Complete characterization of the edited transcriptome of the mitochondrion of Physarum polycephalum using deep sequencing of RNAR 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...
- Dynamics of intramolecular recognition: base-pairing in DNA/RNA near and far from equilibriumR 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...
- A puzzle in DNA biophysicsR 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...
- Computational prediction of RNA editing sitesR 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...
- Fluctuations and slow variables in genetic networksR 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...
- The role of dimerization in noise reduction of simple genetic networksR 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...
- A statistical analysis of RNA folding algorithms through thermodynamic parameter perturbationD 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...
- Asymmetric exclusion process and extremal statistics of random sequencesR 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...
- Statistical mechanics of secondary structures formed by random RNA sequencesR 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...
- Rapid assessment of extremal statistics for gapped local alignmentR Olsen
Department of Physics, University of California at San Diego, La Jolla 92093 0319, USA
Proc Int Conf Intell Syst Mol Biol . 1999..The availability of a rapid and accurate significance estimation method gives one the flexibility to fine tune scoring parameters to detect weakly homologous sequences and obtain optimal alignment fidelity...