Publications

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[ORCID - 0000-0002-6699-8614]


[97] Dimitrios Papaioannou, Deedra Nicolet, Stefano Volinia, Krzysztof Mrózek, Pearlly Yan, Ralf Bundschuh, Andrew J Carroll, Jessica Kohlschmidt, William Blum, Bayard L Powell, Geoffrey L Uy, Jonathan E Kolitz, Eunice S Wang, Ann-Kathrin Eisfeld, Shelley J Orwick, David M Lucas, Michael A Caligiuri, Richard M Stone, John C Byrd, Ramiro Garzon, and Clara D Bloomfield
"Prognostic and biologic significance of long non-coding RNA profiling in younger adults with cytogenetically normal acute myeloid leukemia."
Haematologica 102, 1391-1400 (2017).
[Journal (open access)] [PubMed] 
 
[96] C J Walker, A-K Eisfeld, L K Genutis, M Bainazar, J Kohlschmidt, K Mrózek, A J Carroll, J E Kolitz, B L Powell, E S Wang, R M Stone, R Bundschuh, A de la Chapelle, and C D Bloomfield
"No evidence for microsatellite instability in acute myeloid leukemia."
Leukemia 31, 1474-1476 (2017).
[Journal] [PubMed] 
 
[95] Daniel L Kiss, Catherine E Waters, Iman M Ouda, Joshua C Saldivar, Jenna R Karras, Zaynab A Amin, Seham Mahrous, Teresa Druck, Ralf A Bundschuh, Daniel R Schoenberg, and Kay Huebner
"Identification of Fhit as a post-transcriptional effector of Thymidine Kinase 1 expression."
Biochim. Biophys. Acta 1860, 374-382 (2017).
[Journal] [PubMed] 
 
[94] Michael P Trimarchi, Pearlly Yan, Joanna Groden, Ralf Bundschuh, and Paul J Goodfellow
"Identification of endometrial cancer methylation features using combined methylation analysis methods."
PLoS ONE 12, e0173242 (2017).
[Journal (open access)] [PubMed] 
 
[93] Blythe Moreland, Kenji Oman, John Curfman, Pearlly Yan, and Ralf Bundschuh
"Methyl-CpG/MBD2 Interaction Requires Minimum Separation and Exhibits Minimal Sequence Specificity."
Biophys. J. 111, 2551-2561 (2016).
[free journal link] [PubMed] 
 
[92] Deepak N Ayyala, David E Frankhouser, Javkhlan-Ochir Ganbat, Guido Marcucci, Ralf Bundschuh, Pearlly Yan, and Shili Lin
"Statistical methods for detecting differentially methylated regions based on MethylCap-seq data."
Brief. Bioinformatics 17, 926-937 (2016).
[Journal] [PubMed] 
 
[91] Christopher J Walker, Mario A Miranda, Matthew J OHern, James S Blachly, Cassandra L Moyer, Jennifer Ivanovich, Karl W Kroll, Ann-Kathrin Eisfeld, Caroline E Sapp, David G Mutch, David E Cohn, Ralf Bundschuh, and Paul J Goodfellow
"MonoSeq Variant Caller Reveals Novel Mononucleotide Run Indel Mutations in Tumors with Defective DNA Mismatch Repair."
Hum. Mutat. 37, 1004-12 (2016).
[Journal] [PubMed] [free in PubMed central] 
 
[90] Sandya Liyanarachchi, Wei Li, Pearlly Yan, Ralf Bundschuh, Pamela Brock, Leigha Senter, Matthew D Ringel, Albert de la Chapelle, and Huiling He
"Genome-wide expression screening discloses long noncoding RNAs involved in thyroid carcinogenesis."
J. Clin. Endocrinol. Metab., jc20161991 (2016).
[Journal] [PubMed] 
 
[89] Daniel L Kiss, Kenji M Oman, Julie A Dougherty, Chandrama Mukherjee, Ralf Bundschuh, and Daniel R Schoenberg
"Cap homeostasis is independent of polyA tail length."
Nucleic Acids Res. 44, 304-14 (2016).
[Journal (open access)] [PubMed] 
 
[88] Kristine E Yoder and Ralf Bundschuh
"Host Double Strand Break Repair Generates HIV-1 Strains Resistant to CRISPR/Cas9."
Sci Rep 6, 29530 (2016).
[Journal (open access)] [PubMed] 
 
[87] C Niederwieser, J Kohlschmidt, S Volinia, S P Whitman, K H Metzeler, A-K Eisfeld, K Maharry, P Yan, D Frankhouser, H Becker, S Schwind, A J Carroll, D Nicolet, J H Mendler, J P Curfman, Y-Z Wu, M R Baer, B L Powell, J E Kolitz, J O Moore, T H Carter, R Bundschuh, R A Larson, R M Stone, K Mrózek, G Marcucci, and C D Bloomfield
"Prognostic and biologic significance of DNMT3B expression in older patients with cytogenetically normal primary acute myeloid leukemia."
Leukemia 29, 567-75 (2015).
[Journal] [PubMed] 
 
[86] Yi-Hsuan Lin and Ralf Bundschuh
"RNA structure generates natural cooperativity between single-stranded RNA binding proteins targeting 5 and 3UTRs."
Nucleic Acids Res. 43, 1160-9 (2015).
[Journal (open access)] [PubMed] 
 
[85] Daniel L Kiss, Kenji Oman, Ralf Bundschuh, and Daniel R Schoenberg
"Uncapped 5 ends of mRNAs targeted by cytoplasmic capping map to the vicinity of downstream CAGE tags."
FEBS Lett. 589, 279-284 (2015).
[Journal] [PubMed] 
 
[84] Pauline Schaap, Israel Barrantes, Pat Minx, Narie Sasaki, Roger W Anderson, Marianne Bénard, Kyle K Biggar, Nicolas E Buchler, Ralf Bundschuh, Xiao Chen, Catrina Fronick, Lucinda Fulton, Georg Golderer, Niels Jahn, Volker Knoop, Laura F Landweber, Chrystelle Maric, Dennis Miller, Angelika A Noegel, Rob Peace, Gérard Pierron, Taeko Sasaki, Mareike Schallenberg-Rüdinger, Michael Schleicher, Reema Singh, Thomas Spaller, Kenneth B Storey, Takamasa Suzuki, Chad Tomlinson, John J Tyson, Wesley C Warren, Ernst R Werner, Gabriele Werner-Felmayer, Richard K Wilson, Thomas Winckler, Jonatha M Gott, Gernot Glöckner, and Wolfgang Marwan
"The Physarum polycephalum Genome Reveals Extensive Use of Prokaryotic Two-Component and Metazoan-Type Tyrosine Kinase Signaling."
Genome Biol Evol 8, 109-25 (2015).
[Journal (open access)] [PubMed] 
 
[83] 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, and Ralf Bundschuh
"PrEMeR-CG: inferring nucleotide level DNA methylation values from MethylCap-seq data."
Bioinformatics 30, 3567-74 (2014).
[PubMed] 
 
[82] Rohan Balakrishnan, Kenji Oman, Shinichiro Shoji, Ralf Bundschuh, and Kurt Fredrick
"The conserved GTPase LepA contributes mainly to translation initiation in Escherichia coli."
Nucleic Acids Res. 42, 13370-83 (2014).
[Journal (open access)] [PubMed] 
 
[81] Cai Chen and Ralf Bundschuh
"Quantitative models for accelerated protein dissociation from nucleosomal DNA."
Nucleic Acids Res. 42, 9753-60 (2014).
[Journal (open access)] [PubMed] 
 
[80] Ralf Bundschuh
"Unified approach to partition functions of RNA secondary structures."
J Math Biol 69, 1129-50 (2014).
[Journal] [PubMed] 
 
[79] Bhaskara R Madina, Vikas Kumar, Richard Metz, Blaine H M Mooers, Ralf Bundschuh, and Jorge Cruz-Reyes
"Native mitochondrial RNA-binding complexes in kinetoplastid RNA editing differ in guide RNA composition."
RNA 20, 1142-52 (2014).
[PubMed] 
 
[78] Guido Marcucci, Pearlly Yan, Kati Maharry, David Frankhouser, Deedra Nicolet, Klaus H Metzeler, Jessica Kohlschmidt, Krzysztof Mrózek, Yue-Zhong Wu, Donna Bucci, John P Curfman, Susan P Whitman, Ann-Kathrin Eisfeld, Jason H Mendler, Sebastian Schwind, Heiko Becker, Constance Bär, Andrew J Carroll, Maria R Baer, Meir Wetzler, Thomas H Carter, Bayard L Powell, Jonathan E Kolitz, John C Byrd, Christoph Plass, Ramiro Garzon, Michael A Caligiuri, Richard M Stone, Stefano Volinia, Ralf Bundschuh, and Clara D Bloomfield
"Epigenetics meets genetics in acute myeloid leukemia: clinical impact of a novel seven-gene score."
J. Clin. Oncol. 32, 548-56 (2014).
[Journal] [PubMed] 
 
[77] Geoffrey R Bennett, Ryan Peters, Xiao-Hong Wang, Jeungphill Hanne, Robert W Sobol, Ralf Bundschuh, Richard Fishel, and Kristine E Yoder
"Repair of Oxidative DNA Base Damage in the Host Genome Influences the HIV Integration Site Sequence Preference."
PLoS ONE 9, e103164 (2014).
[PubMed] 
 
[76] Ramy A Fodah, Jacob B Scott, Hok-Hei Tam, Pearlly Yan, Tia L Pfeffer, Ralf Bundschuh, and Jonathan M Warawa
"Correlation of Klebsiella pneumoniae Comparative Genetic Analyses with Virulence Profiles in a Murine Respiratory Disease Model."
PLoS ONE 9, e107394 (2014).
[Journal (open access)] [PubMed] 
 
[75] Karl W Kroll, Nima E Mokaram, Alexander R Pelletier, David E Frankhouser, Maximillian S Westphal, Paige A Stump, Cameron L Stump, Ralf Bundschuh, James S Blachly, and Pearlly Yan
"Quality Control for RNA-Seq QuaCRS: An Integrated Quality Control Pipeline."
Cancer Inform 13, 7-14 (2014).
[Journal (open access)] [PubMed] 
 
[74] K M Bernot, R F Siebenaler, S P Whitman, N A Zorko, G G Marcucci, R Santhanam, E H Ahmed, M Ngangana, K K McConnell, J S Nemer, D L Brook, S K Kulp, C S Chen, D Frankhouser, P Yan, R Bundschuh, X Zhang, A M Dorrance, K E Dickerson, D Jarjoura, W Blum, G Marcucci, and M A Caligiuri
"Toward personalized therapy in AML: in vivo benefit of targeting aberrant epigenetics in MLL-PTD-associated AML."
Leukemia 27, 2379-82 (2013).
[Journal] [PubMed] 
 
[73] Yi-Hsuan Lin and Ralf Bundschuh
"Interplay between single-stranded binding proteins on RNA secondary structure."
Phys Rev E Stat Nonlin Soft Matter Phys 88, 052707 (2013).
[Journal] [PubMed] [PDF] 
 
[72] Cai Chen and Ralf Bundschuh
"Systematic investigation of insertional and deletional RNA-DNA differences in the human transcriptome."
BMC Genomics 13, 616 (2012).
[Journal (open access)] [PubMed] 
 
[71] Justin A North, John C Shimko, Sarah Javaid, Alex M Mooney, Matthew A Shoffner, Sean D Rose, Ralf Bundschuh, Richard Fishel, Jennifer J Ottesen, and Michael G Poirier
"Regulation of the nucleosome unwrapping rate controls DNA accessibility."
Nucleic Acids Res. 40, 10215-27 (2012).
[Journal (open access)] [PubMed] 
 
[70] Benjamin At Rodriguez, David Frankhouser, Mark Murphy, Michael Trimarchi, Hok-Hei Tam, John Curfman, Rita Huang, Michael Wy Chan, Hung-Cheng Lai, Deval Parikh, Bryan Ball, Sebastian Schwind, William Blum, Guido Marcucci, Pearlly Yan, and Ralf Bundschuh
"Methods for high-throughput MethylCap-Seq data analysis."
BMC Genomics 13, S14 (2012).
[Journal (open access)] [PubMed] 
 
[69] Chandrama Mukherjee, Deepak P Patil, Brian A Kennedy, Baskar Bakthavachalu, Ralf Bundschuh, and Daniel R Schoenberg
"Identification of cytoplasmic capping targets reveals a role for cap homeostasis in translation and mRNA stability."
Cell Rep 2, 674-84 (2012).
[Journal (open access)] [PubMed] 
 
[68] Pearlly Yan, David Frankhouser, Mark Murphy, Hok-Hei Tam, Benjamin Rodriguez, John Curfman, Michael Trimarchi, Susan Geyer, Yue-Zhong Wu, Susan P Whitman, Klaus Metzeler, Alison Walker, Rebecca Klisovic, Samson Jacob, Michael R Grever, John C Byrd, Clara D Bloomfield, Ramiro Garzon, William Blum, Michael A Caligiuri, Ralf Bundschuh, and Guido Marcucci
"Genome-wide methylation profiling in decitabine-treated patients with acute myeloid leukemia."
Blood 120, 2466-74 (2012).
[Journal] [PubMed] 
 
[67] Daniel M Bornman, Mark E Hester, Jared M Schuetter, Manjula D Kasoji, Angela Minard-Smith, Curt A Barden, Scott C Nelson, Gene D Godbold, Christine H Baker, Boyu Yang, Jacquelyn E Walther, Ivan E Tornes, Pearlly S Yan, Benjamin Rodriguez, Ralf Bundschuh, Michael L Dickens, Brian A Young, and Seth A Faith
"Short-read, high-throughput sequencing technology for STR genotyping."
Biotech Rapid Dispatches 2012, 1-6 (2012).
[Journal] [PubMed] [free in PubMed central] 
 
[66] Ravindra Amunugama, Yujiong He, Smaranda Willcox, Robert A Forties, Kang-Sup Shim, Ralf Bundschuh, Yu Luo, Jack Griffith, and Richard Fishel
"RAD51 Protein ATP Cap Regulates Nucleoprotein Filament Stability."
J. Biol. Chem. 287, 8724-36 (2012).
[PubMed] 
 
[65] Cai Chen, David Frankhouser, and Ralf Bundschuh
"Comparison of insertional RNA editing in myxomycetes."
PLoS Comput. Biol. 8, e1002400 (2012).
[Journal (open access)] [PubMed] 
 
[64] Michael P Trimarchi, Mark Murphy, David Frankhouser, Benjamin At Rodriguez, John Curfman, Guido Marcucci, Pearlly Yan, and Ralf Bundschuh
"Enrichment-based DNA methylation analysis using next-generation sequencing: sample exclusion, estimating changes in global methylation, and the contribution of replicate lanes."
BMC Genomics 13, S6 (2012).
[PubMed] 
 
[63] Robert A Forties, Justin A North, Sarah Javaid, Omar P Tabbaa, Richard Fishel, Michael G Poirier, and Ralf Bundschuh
"A quantitative model of nucleosome dynamics."
Nucleic Acids Res. 39, 8306-13 (2011).
[Journal (open access)] [PubMed] 
 
[62] R Bundschuh and P Bundschuh
"Distribution of Fibonacci and Lucas Numbers Modulo 3^k"
The Fibonacci Quarterly 49, 201-210 (2011).
[Journal] [PDF] 
 
[61] R Bundschuh, J Altmüller, C Becker, P Nürnberg, and J M Gott
"Complete characterization of the edited transcriptome of the mitochondrion of Physarum polycephalum using deep sequencing of RNA."
Nucleic Acids Res. 39, 6044-55 (2011).
[Journal (open access)] [PubMed] 
 
[60] Yuheng Li, Nicholas Chia, Mario Lauria, and Ralf Bundschuh
"A performance enhanced PSI-BLAST based on hybrid alignment."
Bioinformatics Oxford, England 27, 31-37 (2011).
[free journal link] [PubMed] 
 
[59] 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, and Ralf Bundschuh
"A Scalable, Flexible Workflow for MethylCap-Seq Data Analysis."
IEEE International Workshop on Genomic Signal Processing and Statistics : proceedings. IEEE International Workshop on Genomic Signal Processing and Statistics, 1-4 (2011).
[PubMed] 
 
[58] P Bundschuh and R Bundschuh
"The sequence of Lucas numbers is not stable modulo 2 and 5"
Uniform Distribution Theory 6, 113-130 (2010).
[Journal] [PDF] 
 
[57] Robert A Forties and Ralf Bundschuh
"Modeling the interplay of single-stranded binding proteins and nucleic acid secondary structure."
Bioinformatics 26, 61-7 (2010).
[free journal link] [PubMed] 
 
[56] Robert A Forties, Ralf Bundschuh, and Michael G Poirier
"The flexibility of locally melted DNA."
Nucleic Acids Res. 37, 4580-6 (2009).
[Journal (open access)] [PubMed] 
 
[55] Marianne M Lee, Michael K Chan, and Ralf Bundschuh
"SIB-BLAST: a web server for improved delineation of true and false positives in PSI-BLAST searches."
Nucleic Acids Res. 37, W53-6 (2009).
[Journal (open access)] [PubMed] 
 
[54] Shinichiro Shoji, Nimo M Abdi, Ralf Bundschuh, and Kurt Fredrick
"Contribution of ribosomal residues to P-site tRNA binding."
Nucleic Acids Res. 37, 4033-42 (2009).
[Journal (open access)] [PubMed] 
 
[53] Malcolm McCauley, Robert Forties, Ulrich Gerland, and Ralf Bundschuh
"Anomalous scaling in nanopore translocation of structured heteropolymers."
Physical biology 6, 036006 (2009).
[Journal] [PubMed] [PDF] 
 
[52] Christina Beargie, Tsunglin Liu, Mark Corriveau, Ha Youn Lee, Jonatha Gott, and Ralf Bundschuh
"Genome annotation in the presence of insertional RNA editing."
Bioinformatics 24, 2571-8 (2008).
[free journal link] [PubMed] 
 
[51] Marianne M Lee, Michael K Chan, and Ralf Bundschuh
"Simple is beautiful: a straightforward approach to improve the delineation of true and false positives in PSI-BLAST searches."
Bioinformatics 24, 1339-43 (2008).
[free journal link] [PubMed] 
 
[50] Marko Djordjevic and Ralf Bundschuh
"Formation of the open complex by bacterial RNA polymerase--a quantitative model."
Biophys. J. 94, 4233-48 (2008).
[Journal] [PubMed] [free in PubMed central] 
 
[49] Marianne M Lee, Ralf Bundschuh, and Michael K Chan
"Distant homology detection using a LEngth and STructure-based sequence Alignment Tool LESTAT."
Proteins 71, 1409-19 (2008).
[Journal] [PubMed] 
 
[48] Ralf Bundschuh and Robijn Bruinsma
"Melting of branched RNA molecules."
Phys. Rev. Lett. 100, 148101 (2008).
[Journal] [PubMed] [PDF] 
 
[47] Asuka Itaya, Ralf Bundschuh, Anthony J Archual, Je-Gun Joung, Zhangjun Fei, Xinbin Dai, Patrick X Zhao, Yuhong Tang, Richard S Nelson, and Biao Ding
"Small RNAs in tomato fruit and leaf development."
Biochim. Biophys. Acta 1779, 99-107 (2008).
[Journal] [PubMed] 
 
[46] Philipp W Messer, Ralf Bundschuh, Martin Vingron, and Peter F Arndt
"Effects of long-range correlations in DNA on sequence alignment score statistics."
J. Comput. Biol. 14, 655-68 (2007).
[Journal] [PubMed] 
 
[45] Farhat Habib, Andrew D Johnson, Ralf Bundschuh, and Daniel Janies
"Large scale genotype-phenotype correlation analysis based on phylogenetic trees."
Bioinformatics 23, 785-8 (2007).
[free journal link] [PubMed] 
 
[44] Asuka Itaya, Xuehua Zhong, Ralf Bundschuh, Yijun Qi, Ying Wang, Ryuta Takeda, Ann R Harris, Carlos Molina, Richard S Nelson, and Biao Ding
"A structured viroid RNA serves as a substrate for dicer-like cleavage to produce biologically active small RNAs but is resistant to RNA-induced silencing complex-mediated degradation."
J. Virol. 81, 2980-94 (2007).
[Journal] [PubMed] [free in PubMed central] 
 
[43] Ralf Bundschuh
"Computational approaches to insertional RNA editing."
Meth. Enzymol. 424, 173-95 (2007).
[Journal] [PubMed] 
 
[42] Philipp W Messer, Ralf Bundschuh, Martin Vingron, and Peter F Arndt
"Alignment Statistics for Long-Range Correlated Genomic Sequences"
Lecture Notes in Computer Science 3909, 426-440 (2006).
[Journal] 
 
[41] Nicholas Chia and Ralf Bundschuh
"A practical approach to significance assessment in alignment with gaps."
J. Comput. Biol. 13, 429-41 (2006).
[Journal] [PubMed] [PDF] 
 
[40] R Bundschuh and U Gerland
"Dynamics of intramolecular recognition: base-pairing in DNA/RNA near and far from equilibrium."
The European physical journal. E, Soft matter 19, 319-29 (2006).
[Journal] [PubMed] [PDF] 
 
[39] R Bundschuh and U Gerland
"A puzzle in DNA biophysics."
The European physical journal. E, Soft matter 19, 347-9; discussion 351-2 (2006).
[Journal] [PubMed] [PDF] 
 
[38] Vishwesha Guttal and Ralf Bundschuh
"Model for folding and aggregation in RNA secondary structures."
Phys. Rev. Lett. 96, 018105 (2006).
[Journal] [PubMed] [PDF] 
 
[37] Tsunglin Liu and Ralf Bundschuh
"Quantification of the differences between quenched and annealed averaging for RNA secondary structures."
Physical review. E, Statistical, nonlinear, and soft matter physics 72, 061905 (2005).
[Journal] [PubMed] [PDF] 
 
[36] Ralf Bundschuh and Ulrich Gerland
"Coupled dynamics of RNA folding and nanopore translocation."
Phys. Rev. Lett. 95, 208104 (2005).
[Journal] [PubMed] [PDF] 
 
[35] Nicholas Chia and Ralf Bundschuh
"Numerical method for accessing the universal scaling function for a multiparticle discrete time asymmetric exclusion process."
Physical review. E, Statistical, nonlinear, and soft matter physics 72, 051102 (2005).
[Journal] [PubMed] [PDF] 
 
[34] Yuheng Li, Mario Lauria, and Ralf Bundschuh
"Suboptimal Alignments Improve the Detection of Weak Homologs in Sequence Database Searches"
Proceedings of BIBE05, 135-160 (2005).
[PDF] 
 
[33] Farhat Habib and Ralf Bundschuh
"Modeling DNA unzipping in the presence of bound proteins."
Physical review. E, Statistical, nonlinear, and soft matter physics 72, 031906 (2005).
[Journal] [PubMed] [PDF] 
 
[32] Tsunglin Liu and Ralf Bundschuh
"Model for codon position bias in RNA editing."
Phys. Rev. Lett. 95, 088101 (2005).
[Journal] [PubMed] [PDF] 
 
[31] Jonatha M Gott, Neeta Parimi, and Ralf Bundschuh
"Discovery of new genes and deletion editing in Physarum mitochondria enabled by a novel algorithm for finding edited mRNAs."
Nucleic Acids Res. 33, 5063-72 (2005).
[Journal (open access)] [PubMed] 
 
[30] D M Layton and R Bundschuh
"A statistical analysis of RNA folding algorithms through thermodynamic parameter perturbation."
Nucleic Acids Res. 33, 519-24 (2005).
[Journal (open access)] [PubMed] 
 
[29] R Bundschuh
"Computational prediction of RNA editing sites."
Bioinformatics 20, 3214-20 (2004).
[free journal link] [PubMed] 
 
[28] Nicholas Chia and Ralf Bundschuh
"Finite width model sequence comparison."
Physical review. E, Statistical, nonlinear, and soft matter physics 70, 021906 (2004).
[Journal] [PubMed] [PDF] 
 
[27] Yuheng Li, Mario Lauria, and Ralf Bundschuh
"Using Hybrid Alignment for Iterative Sequence Database Searches"
Concurr. Comp. Pract. Exp. 16, 841-853 (2004).
[Journal] [PDF] 
 
[26] Ulrich Gerland, Ralf Bundschuh, and Terence Hwa
"Translocation of structured polynucleotides through nanopores."
Physical biology 1, 19-26 (2004).
[Journal] [PubMed] [PDF] 
 
[25] Tsunglin Liu and Ralf Bundschuh
"Analytical description of finite size effects for RNA secondary structures."
Physical review. E, Statistical, nonlinear, and soft matter physics 69, 061912 (2004).
[Journal] [PubMed] [PDF] 
 
[24] Ulrich Gerland, Ralf Bundschuh, and Terence Hwa
"Mechanically probing the folding pathway of single RNA molecules."
Biophys. J. 84, 2831-40 (2003).
[Journal] [PubMed] [PDF] 
 
[23] R Bundschuh, F Hayot, and C Jayaprakash
"Fluctuations and slow variables in genetic networks."
Biophys. J. 84, 1606-15 (2003).
[Journal] [PubMed] [PDF] 
 
[22] R Bundschuh, F Hayot, and C Jayaprakash
"The role of dimerization in noise reduction of simple genetic networks."
J. Theor. Biol. 220, 261-9 (2003).
[Journal] [PubMed] [PDF] 
 
[21] R Bundschuh and T Hwa
"Phases of the secondary structures of RNA sequences"
Europhys. Lett. 59, 903-909 (2002).
[Journal] [PDF] 
 
[20] Yi-Kuo Yu, Ralf Bundschuh, and Terence Hwa
"Hybrid alignment: high-performance with universal statistics."
Bioinformatics 18, 864-72 (2002).
[Journal] [PubMed] [PDF] 
 
[19] Ralf Bundschuh and Michael Lässig
"Delocalization transitions of semiflexible manifolds."
Physical review. E, Statistical, nonlinear, and soft matter physics 65, 061502 (2002).
[Journal] [PubMed] [PDF] 
 
[18] R Bundschuh and T Hwa
"Statistical mechanics of secondary structures formed by random RNA sequences."
Physical review. E, Statistical, nonlinear, and soft matter physics 65, 031903 (2002).
[Journal] [PubMed] [PDF] 
 
[17] R Bundschuh
"Asymmetric exclusion process and extremal statistics of random sequences."
Physical review. E, Statistical, nonlinear, and soft matter physics 65, 031911 (2002).
[Journal] [PubMed] [PDF] 
 
[16] Y.-K. Yu, R. Bundschuh, and T. Hwa
"Statistical Significance and Extreme Ensemble of Gapped Local Hybrid Alignment"
Biological Evolution and Statistical Physics, M. Lässig and A. Valeriani, eds., 3-22 (2002).
[Journal] [PDF] 
 
[15] Ralf Bundschuh
"Rapid significance estimation in local sequence alignment with gaps."
J. Comput. Biol. 9, 243-60 (2002).
[Journal] [PubMed] [PDF] 
 
[14] U Gerland, R Bundschuh, and T Hwa
"Force-induced denaturation of RNA."
Biophys. J. 81, 1324-32 (2001).
[Journal] [PubMed] [PDF] 
 
[13] Ralf Bundschuh
"High precision simulations of the longest common subsequence problem"
Europ. Phys. J. B 22, 533-541 (2001).
[Journal] [PDF] 
 
[12] S F Altschul, R Bundschuh, R Olsen, and T Hwa
"The estimation of statistical parameters for local alignment score distributions."
Nucleic Acids Res. 29, 351-61 (2001).
[Journal] [PubMed] [PDF] 
 
[11] R Bundschuh, M Lässig, and R Lipowsky
"Semi-flexible polymers with attractive interactions"
Europ. Phys. J. E 3, 295-306 (2000).
[Journal] 
 
[10] Ralf Bundschuh and Terence Hwa
"An analytic study of the phase transition line in local sequence alignment with gaps"
Discrete Applied Mathematics 104, 113-142 (2000).
[Journal] [PDF] 
 
[9] Ralf Bundschuh
"An analytic approach to significance assessment in local sequence alignment with gaps"
Proceedings of the fourth annual international conference on computational molecular biology (RECOMB2000), S. Istrail et al., eds., ACM press, (New York, NY, 2000), 86-95 (2000).
[PDF] 
 
[8] Ralf Bundschuh and Terence Hwa
"RNA secondary structure formation: a solvable model of heteropolymer folding"
Phys. Rev. Lett. 83, 1479-1482 (1999).
[Journal] [PDF] 
 
[7] Ralf Bundschuh, Carlos Cassanello, Didina Serban, and Martin R Zirnbauer
"Weak localization of disordered quasiparticles in the mixed superconducting state"
Phys. Rev. B 59, 4382-4389 (1999).
[Journal] [PDF] 
 
[6] R Olsen, R Bundschuh, and T Hwa
"Rapid assessment of extremal statistics for gapped local alignment."
Proc Int Conf Intell Syst Mol Biol, 211-22 (1999).
[PubMed] [PDF] 
 
[5] Ralf Bundschuh, Carlos Cassanello, Didina Serban, and Martin R Zirnbauer
"Localization of quasiparticles in a disordered vortex"
Nucl. Phys. B 532, 689-732 (1998).
[Journal] [PDF] 
 
[4] Ralf Bundschuh and Michael Lässig
"Directed polymers in high dimensions"
Phys. Rev. E 54, 304-320 (1996).
[Journal] [PDF] 
 
[3] Ralf Bundschuh and Michael Lässig
"Comment on "Simplest possible self-organized critical system""
Phys. Rev. Lett. 77, 4273 (1996).
[Journal] [PDF] 
 
[2] R Everaers, R Bundschuh, and K Kremer
"Fluctuations and stiffness of double-stranded polymers: railway-track model"
Europhys. Lett. 54, 263-268 (1995).
[Journal] [PDF] 
 
[1] U Fastenrath, G Adams, R Bundschuh, T Hermes, B Raab, I Schlosser, T Wehner, and T Wichmann
"Universality in the 2D localization problem"
Physica A 54, 302-308 (1991).
[Journal]