Detectability of Sequence Homology by DNA Hybridization. - Ralf Bundschuh; Terence Hwa (German Conference on Bioinformatics, 1998)

Rapid Assessment of Extremal Statistics for Gapped Local Alignment. - Rolf Olsen; Ralf Bundschuh; Terence Hwa (ISMB, 1999)

An analytic approach to significance assessment in local sequence alignment with gaps. - Ralf Bundschuh (RECOMB, 2000)

An analytic study of the phase transition line in local sequence alignment with gaps. - Ralf Bundschuh; Terence Hwa (Discret. Appl. Math., 2000)

Hybrid alignment: high-performance with universal statistics. - Yi-Kuo Yu; Ralf Bundschuh; Terence Hwa (Bioinform., 2002)

Rapid Significance Estimation in Local Sequence Alignment with Gaps. - Ralf Bundschuh (J. Comput. Biol., 2002)

Computational prediction of RNA editing sites. - Ralf Bundschuh (Bioinform., 2004)

Using hybrid alignment for iterative sequence database searches. - Yuheng Li; Mario Lauria; Ralf Bundschuh (Concurr. Pract. Exp., 2004)

Suboptimal Alignments Improve the Detection of Weak Homologs in Sequence Database Searches. - Yuheng Li; Mario Lauria; Ralf Bundschuh (BIBE, 2005)

Alignment Statistics for Long-Range Correlated Genomic Sequences. - Philipp W. Messer; Ralf Bundschuh; Martin Vingron; Peter F. Arndt (RECOMB, 2006)

A Practical Approach to Significance Assessment in Alignment with Gaps. - Nicholas Chia; Ralf Bundschuh (J. Comput. Biol., 2006)

Large scale genotype-phenotype correlation analysis based on phylogenetic trees. - Farhat Habib; Andrew D. Johnson; Ralf Bundschuh; Daniel Janies (Bioinform., 2007)

Effects of Long-Range Correlations in DNA on Sequence Alignment Score Statistics. - Philipp W. Messer; Ralf Bundschuh; Martin Vingron; Peter F. Arndt (J. Comput. Biol., 2007)

Genome annotation in the presence of insertional RNA editing. - Christina Beargie; Tsunglin Liu; Mark Corriveau; Ha Youn Lee; Jonatha Gott; Ralf Bundschuh (Bioinform., 2008)

Simple is beautiful: a straightforward approach to improve the delineation of true and false positives in PSI-BLAST searches. - Marianne M. Lee; Michael K. Chan; Ralf Bundschuh (Bioinform., 2008)

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

Modeling the interplay of single-stranded binding proteins and nucleic acid secondary structure. - Robert A. Forties; Ralf Bundschuh (Bioinform., 2010)

A scalable, flexible workflow for MethylCap-seq data analysis. - 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; et al. (GENSiPS, 2011)

A performance enhanced PSI-BLAST based on hybrid alignment. - Yuheng Li; Nicholas Chia; Mario Lauria; Ralf Bundschuh (Bioinform., 2011)

Comparison of Insertional RNA Editing in Myxomycetes. - Cai Chen; David Frankhouser; Ralf Bundschuh (PLoS Comput. Biol., 2012)

PrEMeR-CG: inferring nucleotide level DNA methylation values from MethylCap-seq data. - 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 (Bioinform., 2014)

The search for the determinants of insertional RNA editing in Physarum polycephalum mitochondrial RNAs. - Ralf Bundschuh (BICT, 2015)

Statistical methods for detecting differentially methylated regions based on MethylCap-seq data. - Deepak Nag Ayyala; David E. Frankhouser; Javkhlan-Ochir Ganbat; Guido Marcucci; Ralf Bundschuh; Pearlly Yan; Shili Lin (Briefings Bioinform., 2016)

RiboProP: a probabilistic ribosome positioning algorithm for ribosome profiling. - Dengke Zhao; William D. Baez; Kurt Fredrick; Ralf Bundschuh (Bioinform., 2019)

A model of pulldown alignments from SssI-treated DNA improves DNA methylation prediction. - Blythe S. Moreland; Kenji M. Oman; Ralf Bundschuh (BMC Bioinform., 2019)

Single nucleotide polymorphisms affect RNA-protein interactions at a distance through modulation of RNA secondary structures. - Elan Shatoff; Ralf Bundschuh (PLoS Comput. Biol., 2020)

dsRBPBind: modeling the effect of RNA secondary structure on double-stranded RNA-protein binding. - Elan Shatoff; Ralf Bundschuh (Bioinform., 2022)