Ralf Bundschuh

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Detectability of Sequence Homology by DNA Hybridization

Terence Hwa, Ralf Bundschuh, 1998, German Conference on Bioinformatics.

Modeling the interplay of single-stranded binding proteins and nucleic acid secondary structure

Ralf Bundschuh, Robert A. Forties, R. Bundschuh, 2010, Bioinform..

Effects of Long-Range Correlations in DNA on Sequence Alignment Score Statistics

Martin Vingron, Ralf Bundschuh, Philipp W. Messer, 2007, J. Comput. Biol..

Statistical methods for detecting differentially methylated regions based on MethylCap-seq data

Pearlly Yan, Ralf Bundschuh, Shili Lin, 2016, Briefings Bioinform..

Computational prediction of RNA editing sites

Ralf Bundschuh, R. Bundschuh, 2004, Bioinform..

SIB-BLAST: a web server for improved delineation of true and false positives in PSI-BLAST searches

Ralf Bundschuh, Marianne M. Lee, Michael K. Chan, 2009, Nucleic Acids Res..

Simple is beautiful: a straightforward approach to improve the delineation of true and false positives in PSI-BLAST searches

Ralf Bundschuh, Marianne M. Lee, Michael K. Chan, 2008, Bioinform..

Single nucleotide polymorphisms affect RNA-protein interactions at a distance through modulation of RNA secondary structures

Ralf Bundschuh, Elan Shatoff, R. Bundschuh, 2020, PLoS Comput. Biol..

Large scale genotype-phenotype correlation analysis based on phylogenetic trees

Ralf Bundschuh, Andrew D. Johnson, Daniel Janies, 2007, Bioinform..

PrEMeR-CG: inferring nucleotide level DNA methylation values from MethylCap-seq data

Pearlly Yan, Ralf Bundschuh, Shili Lin, 2014, Bioinform..

A Practical Approach to Significance Assessment in Alignment with Gaps

Ralf Bundschuh, Nicholas Chia, R. Bundschuh, 2005, RECOMB.

An analytic approach to significance assessment in local sequence alignment with gaps

Ralf Bundschuh, R. Bundschuh, 2000, RECOMB '00.

Alignment Statistics for Long-Range Correlated Genomic Sequences

Martin Vingron, Ralf Bundschuh, Philipp W. Messer, 2006, RECOMB.

A performance enhanced PSI-BLAST based on hybrid alignment

Mario Lauria, Ralf Bundschuh, Nicholas Chia, 2011, Bioinform..

Suboptimal alignments improve the detection of weak homologs in sequence database searches

Mario Lauria, Ralf Bundschuh, Yuheng Li, 2005, Fifth IEEE Symposium on Bioinformatics and Bioengineering (BIBE'05).

Rapid significance estimation in local sequence alignment with gaps

Ralf Bundschuh, R. Bundschuh, 2001, RECOMB.

A model of pulldown alignments from SssI-treated DNA improves DNA methylation prediction

Ralf Bundschuh, Blythe S. Moreland, Kenji M. Oman, 2019, BMC Bioinformatics.

RiboProP: a probabilistic ribosome positioning algorithm for ribosome profiling

Ralf Bundschuh, Dengke Zhao, William D. Baez, 2018, Bioinform..

RBPBind: Quantitative Prediction of Protein-RNA Interactions.

Ralf Bundschuh, Jeff Gaither, Yi-Hsuan Lin, 2016, Journal of molecular biology.

A Practical Approach to Significance Assessment in Alignment with Gaps

Ralf Bundschuh, Nicholas Chia, 2005, RECOMB.

Using hybrid alignment for iterative sequence database searches

Mario Lauria, Ralf Bundschuh, Yuheng Li, 2003, Proceedings International Parallel and Distributed Processing Symposium.

Genome annotation in the presence of insertional RNA editing

Ha Youn Lee, Ralf Bundschuh, Tsunglin Liu, 2008, Bioinform..

Using hybrid alignment for iterative sequence database searches: Research Articles

Mario Lauria, Ralf Bundschuh, Yuheng Li, 2004 .

Rapid Significance Estimation in Local Sequence Alignment with Gaps

Ralf Bundschuh, 2002, J. Comput. Biol..

A scalable, flexible workflow for MethylCap-seq data analysis

Pearlly Yan, Ralf Bundschuh, Michael Trimarchi, 2011, 2011 IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS).

Rapid Assessment of Extremal Statistics for Gapped Local Alignment

Rolf Olsen, Terence Hwa, Ralf Bundschuh, 1999, ISMB.

The search for the determinants of insertional RNA editing in Physarum polycephalum mitochondrial RNAs

Ralf Bundschuh, 2015, BICT.

An analytic study of the phase transition line in local sequence alignment with gaps

Terence Hwa, Ralf Bundschuh, 2000, Discret. Appl. Math..

Comparison of Insertional RNA Editing in Myxomycetes

Ralf Bundschuh, Cai Chen, David Frankhouser, 2012, PLoS Comput. Biol..

Using hybrid alignment for iterative sequence database searches

Mario Lauria, Ralf Bundschuh, Yuheng Li, 2004, Concurr. Pract. Exp..

Quality Control for RNA-Seq (QuaCRS): An Integrated Quality Control Pipeline

Pearlly Yan, Ralf Bundschuh, Karl W. Kroll, 2014, Cancer informatics.

dsRBPBind: modeling the effect of RNA secondary structure on double-stranded RNA-protein binding

Ralf Bundschuh, Elan Shatoff, 2022, Bioinform..

Computational approaches to insertional RNA editing.

Ralf Bundschuh, 2007, Methods in enzymology.

Correlation of Klebsiella pneumoniae Comparative Genetic Analyses with Virulence Profiles in a Murine Respiratory Disease Model

Pearlly Yan, Ralf Bundschuh, R. Bundschuh, 2014, PloS one.

Statistical significance and extremal ensemble of gapped local hybrid alignment

Terence Hwa, Ralf Bundschuh, Yi-Kuo Yu, 2002 .

Short-read, high-throughput sequencing technology for STR genotyping.

Ralf Bundschuh, Pearlly S Yan, Seth A Faith, 2012, BioTechniques. Rapid dispatches.

The Physarum polycephalum Genome Reveals Extensive Use of Prokaryotic Two-Component and Metazoan-Type Tyrosine Kinase Signaling

Takamasa Suzuki, John J. Tyson, Wolfgang Marwan, 2015, Genome biology and evolution.

Discovery of new genes and deletion editing in Physarum mitochondria enabled by a novel algorithm for finding edited mRNAs

Ralf Bundschuh, R. Bundschuh, N. Parimi, 2005, Nucleic acids research.

Contribution of ribosomal residues to P-site tRNA binding

Ralf Bundschuh, Kurt Fredrick, R. Bundschuh, 2009, Nucleic acids research.

Quantification of the differences between quenched and annealed averaging for RNA secondary structures.

Ralf Bundschuh, Tsunglin Liu, Tsunglin Liu, 2005, Physical review. E, Statistical, nonlinear, and soft matter physics.

Epigenetics meets genetics in acute myeloid leukemia: clinical impact of a novel seven-gene score.

Pearlly Yan, Ralf Bundschuh, David Frankhouser, 2014, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

Methods for high-throughput MethylCap-Seq data analysis

Pearlly Yan, Ralf Bundschuh, David Frankhouser, 2012, BMC Genomics.

Genome-wide methylation profiling in decitabine-treated patients with acute myeloid leukemia.

Pearlly Yan, Ralf Bundschuh, David Frankhouser, 2012, Blood.

Small RNAs in tomato fruit and leaf development.

Ralf Bundschuh, Richard S Nelson, Je-Gun Joung, 2008, Biochimica et biophysica acta.

The flexibility of locally melted DNA

Michael G. Poirier, Ralf Bundschuh, Robert A. Forties, 2009, Nucleic acids research.

Enrichment-based DNA methylation analysis using next-generation sequencing: sample exclusion, estimating changes in global methylation, and the contribution of replicate lanes

Pearlly Yan, Ralf Bundschuh, David Frankhouser, 2012, BMC Genomics.

Physical Biology of the Cell

Ralf Bundschuh, 2008 .