Ralf Bundschuh

31 papers A 2B 4C 1Journal 21Unranked 3
YearRankTypeTitle / Venue / Authors
2025 J jnl
The structural effects of indel polymorphisms outside the binding site on RNA-protein interactions are shaped by selection.
PLoS Comput. Biol.
Carlos Owusu-Ansah, Elan Shatoff, Ralf Bundschuh
2022 J jnl
dsRBPBind: modeling the effect of RNA secondary structure on double-stranded RNA-protein binding.
Bioinform.
Elan Shatoff, Ralf Bundschuh
2020 J jnl
Single nucleotide polymorphisms affect RNA-protein interactions at a distance through modulation of RNA secondary structures.
PLoS Comput. Biol.
Elan Shatoff, Ralf Bundschuh
2019 J jnl
A model of pulldown alignments from SssI-treated DNA improves DNA methylation prediction.
BMC Bioinform.
Blythe S. Moreland, Kenji M. Oman, Ralf Bundschuh
2019 J jnl
RiboProP: a probabilistic ribosome positioning algorithm for ribosome profiling.
Bioinform.
Dengke Zhao, William D. Baez, Kurt Fredrick, Ralf Bundschuh
2016 J jnl
Statistical methods for detecting differentially methylated regions based on MethylCap-seq data.
Briefings Bioinform.
Deepak Nag Ayyala, David E. Frankhouser, Javkhlan-Ochir Ganbat, Guido Marcucci, Ralf Bundschuh, Pearlly Yan, Shili Lin
2015 — conf
The search for the determinants of insertional RNA editing in Physarum polycephalum mitochondrial RNAs.
BICT
Ralf Bundschuh
2014 J jnl
PrEMeR-CG: inferring nucleotide level DNA methylation values from MethylCap-seq data.
Bioinform.
David E. Frankhouser, Mark Murphy, James S. Blachly, Jincheol Park, Mike W. Zoller, Javkhlan-Ochir Ganbat, John Curfman, John C. Byrd, Shili Lin, Guido Marcucci, Pearlly Yan, Ralf Bundschuh
2012 J jnl
Comparison of Insertional RNA Editing in
PLoS Comput. Biol.
Cai Chen, David Frankhouser, Ralf Bundschuh
2011 J jnl
A performance enhanced PSI-BLAST based on hybrid alignment.
Bioinform.
Yuheng Li, Nicholas Chia, Mario Lauria, Ralf Bundschuh
2011 — conf
A scalable, flexible workflow for MethylCap-seq data analysis.
GENSiPS
Benjamin Rodriguez, Hok-Hei Tam, David Frankhouser, Michael Trimarchi, Mark Murphy, Chris Kuo, Deval Parikh, Bryan Ball, Sebastian Schwind, John Curfman, William Blum, Guido Marcucci, Pearlly Yan, Ralf Bundschuh
2010 J jnl
Modeling the interplay of single-stranded binding proteins and nucleic acid secondary structure.
Bioinform.
Robert A. Forties, Ralf Bundschuh
2009 J jnl
SIB-BLAST: a web server for improved delineation of true and false positives in PSI-BLAST searches.
Nucleic Acids Res.
Marianne M. Lee, Michael K. Chan, Ralf Bundschuh
2008 J jnl
Genome annotation in the presence of insertional RNA editing.
Bioinform.
Christina Beargie, Tsunglin Liu, Mark Corriveau, Ha Youn Lee, Jonatha Gott, Ralf Bundschuh
2008 J jnl
Simple is beautiful: a straightforward approach to improve the delineation of true and false positives in PSI-BLAST searches.
Bioinform.
Marianne M. Lee, Michael K. Chan, Ralf Bundschuh
2007 J jnl
Effects of Long-Range Correlations in DNA on Sequence Alignment Score Statistics.
J. Comput. Biol.
Philipp W. Messer, Ralf Bundschuh, Martin Vingron, Peter F. Arndt
2007 J jnl
Large scale genotype-phenotype correlation analysis based on phylogenetic trees.
Bioinform.
Farhat Habib, Andrew D. Johnson, Ralf Bundschuh, Daniel Janies
2006 J jnl
A Practical Approach to Significance Assessment in Alignment with Gaps.
J. Comput. Biol.
Nicholas Chia, Ralf Bundschuh
2006 B conf
Alignment Statistics for Long-Range Correlated Genomic Sequences.
RECOMB
Philipp W. Messer, Ralf Bundschuh, Martin Vingron, Peter F. Arndt
2005 B conf
A Practical Approach to Significance Assessment in Alignment with Gaps.
RECOMB
Nicholas Chia, Ralf Bundschuh
2005 C conf
Suboptimal Alignments Improve the Detection of Weak Homologs in Sequence Database Searches.
BIBE
Yuheng Li, Mario Lauria, Ralf Bundschuh
2004 J jnl
Computational prediction of RNA editing sites.
Bioinform.
Ralf Bundschuh
2004 J jnl
Using hybrid alignment for iterative sequence database searches.
Concurr. Pract. Exp.
Yuheng Li, Mario Lauria, Ralf Bundschuh
2003 A conf
Using Hybrid Alignment for Iterative Sequence Database Searches.
IPDPS
Yuheng Li, Mario Lauria, Ralf Bundschuh
2002 J jnl
Hybrid alignment: high-performance with universal statistics.
Bioinform.
Yi-Kuo Yu, Ralf Bundschuh, Terence Hwa
2002 J jnl
Rapid Significance Estimation in Local Sequence Alignment with Gaps.
J. Comput. Biol.
Ralf Bundschuh
2001 B conf
Rapid significance estimation in local sequence alignment with gaps.
RECOMB
Ralf Bundschuh
2000 B conf
An analytic approach to significance assessment in local sequence alignment with gaps.
RECOMB
Ralf Bundschuh
2000 J jnl
An analytic study of the phase transition line in local sequence alignment with gaps.
Discret. Appl. Math.
Ralf Bundschuh, Terence Hwa
1999 A conf
Rapid Assessment of Extremal Statistics for Gapped Local Alignment.
ISMB
Rolf Olsen, Ralf Bundschuh, Terence Hwa
1998 — conf
Detectability of Sequence Homology by DNA Hybridization.
German Conference on Bioinformatics
Ralf Bundschuh, Terence Hwa