[PubMed search]
[arXiv search]
[ORCID - 0000-0002-6699-8614]

[137] Jeff Gaither, Yi-Hsuan Lin, and Ralf Bundschuh
"RBPBind: Quantitative Prediction of Protein-RNA Interactions."
J Mol Biol 434, 167515 (2022).
[Journal] [PubMed] 
[136] Zhongxia Yi, René M Arvola, Sean Myers, Corinne N Dilsavor, Rabab Abu Alhasan, Bayley N Carter, Robert D Patton, Ralf Bundschuh, and Guramrit Singh
"Mammalian UPF3A and UPF3B can activate nonsense-mediated mRNA decay independently of their exon junction complex binding."
EMBO J 41, e109202 (2022).
[Journal (open access)] [PubMed] 
[135] Ahmed A Zayed, James M Wainaina, Guillermo Dominguez-Huerta, Eric Pelletier, Jiarong Guo, Mohamed Mohssen, Funing Tian, Akbar Adjie Pratama, Benjamin Bolduc, Olivier Zablocki, Dylan Cronin, Lindsey Solden, Erwan Delage, Adriana Alberti, Jean-Marc Aury, Quentin Carradec, Corinne da Silva, Karine Labadie, Julie Poulain, Hans-Joachim Ruscheweyh, Guillem Salazar, Elan Shatoff, , Ralf Bundschuh, Kurt Fredrick, Laura S Kubatko, Samuel Chaffron, Alexander I Culley, Shinichi Sunagawa, Jens H Kuhn, Patrick Wincker, Matthew B Sullivan, Silvia G Acinas, Marcel Babin, Peer Bork, Emmanuel Boss, Chris Bowler, Guy Cochrane, Colomban de Vargas, Gabriel Gorsky, Lionel Guidi, Nigel Grimsley, Pascal Hingamp, Daniele Iudicone, Olivier Jaillon, Stefanie Kandels, Lee Karp-Boss, Eric Karsenti, Fabrice Not, Hiroyuki Ogata, Nicole Poulton, Stéphane Pesant, Christian Sardet, Sabrinia Speich, Lars Stemmann, Matthew B Sullivan, Shinichi Sungawa, and Patrick Wincker
"Cryptic and abundant marine viruses at the evolutionary origins of Earths RNA virome."
Science 376, 156-162 (2022).
[Journal] [PubMed] 
[134] Swagata Goswami, Rajeswaran Mani, Jessica Nunes, Chi-Ling Chiang, Kevan Zapolnik, Eileen Hu, Frank Frissora, Xiaokui Mo, Logan A Walker, Pearlly Yan, Ralf Bundschuh, Larry Beaver, Raymond Devine, Yo-Ting Tsai, Ann Ventura, Zhiliang Xie, Min Chen, Rosa Lapalombella, Alison Walker, Alice Mims, Karilyn Larkin, Nicole Grieselhuber, Chad Bennett, Mitch Phelps, Erin Hertlein, Gregory Behbehani, Sumithira Vasu, John C Byrd, and Natarajan Muthusamy
"PP2A is a therapeutically targetable driver of cell fate decisions via a c-Myc/p21 axis in human and murine acute myeloid leukemia."
Blood 139, 1340-1358 (2022).
[Journal] [PubMed] 
[133] Jiyeon K Denninger, Logan A Walker, Xi Chen, Altan Turkoglu, Alex Pan, Zoe Tapp, Sakthi Senthilvelan, Raina Rindani, Olga N Kokiko-Cochran, Ralf Bundschuh, Pearlly Yan, and Elizabeth D Kirby
"Robust Transcriptional Profiling and Identification of Differentially Expressed Genes With Low Input RNA Sequencing of Adult Hippocampal Neural Stem and Progenitor Populations."
Front Mol Neurosci 15, 810722 (2022).
[Journal (open access)] [PubMed] 
[132] Elan A Shatoff, Bryan T Gemler, Ralf Bundschuh, and Kurt Fredrick
"Maturation of 23S rRNA includes removal of helix H1 in many bacteria."
RNA Biol 18, 856-865 (2021).
[Journal (open access)] [PubMed] 
[131] Kyle Crocker, Joshua Johnson, Wolfgang Pfeifer, Carlos Castro, and Ralf Bundschuh
"A quantitative model for a nanoscale switch accurately predicts thermal actuation behavior."
Nanoscale 13, 13746-13757 (2021).
[Journal] [PubMed] 
[130] David E Frankhouser, Sarah Steck, Michael G Sovic, Martha A Belury, Qianben Wang, Steven K Clinton, Ralf Bundschuh, Pearlly S Yan, and Lisa D Yee
"Dietary omega-3 fatty acid intake impacts peripheral blood DNA methylation -anti-inflammatory effects and individual variability in a pilot study."
J Nutr Biochem 99, 108839 (2021).
[Journal] [PubMed] 
[129] Huiling He, Sandya Liyanarachchi, Wei Li, Daniel F Comiskey, Pearlly Yan, Ralf Bundschuh, Altan M Turkoglu, Pamela Brock, Matthew D Ringel, and Albert de la Chapelle
"Transcriptome analysis discloses dysregulated genes in normal appearing tumor-adjacent thyroid tissues from patients with papillary thyroid carcinoma."
Sci Rep 11, 14126 (2021).
[Journal (open access)] [PubMed] 
[128] Kyle Crocker, James London, Andrés Medina, Richard Fishel, and Ralf Bundschuh
"Evolutionary advantage of a dissociative search mechanism in DNA mismatch repair."
Phys Rev E 103, 052404 (2021).
[Journal] [PubMed] 
[127] Kevin M Huang, Megan Zavorka Thomas, Tarek Magdy, Eric D Eisenmann, Muhammad Erfan Uddin, Duncan F DiGiacomo, Alexander Pan, Markus Keiser, Marcus Otter, Sherry H Xia, Yang Li, Yan Jin, Qiang Fu, Alice A Gibson, Ingrid M Bonilla, Cynthia A Carnes, Kara N Corps, Vincenzo Coppola, Sakima A Smith, Daniel Addison, Anne T Nies, Ralf Bundschuh, Taosheng Chen, Maryam B Lustberg, Joanne Wang, Stefan Oswald, Moray J Campbell, Pearlly S Yan, Sharyn D Baker, Shuiying Hu, Paul W Burridge, and Alex Sparreboom
"Targeting OCT3 attenuates doxorubicin-induced cardiac injury."
Proc Natl Acad Sci U S A 118, e2020168118 (2021).
[Journal] [PubMed] 
[126] Vikash Jha, Bappaditya Roy, Dushyant Jahagirdar, Zakkary A McNutt, Elan A Shatoff, Bethany L Boleratz, Dean E Watkins, Ralf Bundschuh, Kaustuv Basu, Joaquin Ortega, and Kurt Fredrick
"Structural basis of sequestration of the anti-Shine-Dalgarno sequence in the Bacteroidetes ribosome."
Nucleic Acids Res 49, 547-567 (2021).
[Journal (open access)] [PubMed] 
[125] Yuchen Wang, Jenny V Le, Kyle Crocker, Michael A Darcy, Patrick D Halley, Dengke Zhao, Nick Andrioff, Cassie Croy, Michael G Poirier, Ralf Bundschuh, and Carlos E Castro
"A nanoscale DNA force spectrometer capable of applying tension and compression on biomolecules."
Nucleic Acids Res 49, 8987-8999 (2021).
[Journal (open access)] [PubMed] 
[124] Zakkary A McNutt, Mai D Gandhi, Elan A Shatoff, Bappaditya Roy, Aishwarya Devaraj, Ralf Bundschuh, and Kurt Fredrick
"Comparative Analysis of anti-Shine- Dalgarno Function in "
Front Mol Biosci 8, 787388 (2021).
[123] Michelle R Gibbs, Kyung-Mee Moon, Benjamin R Warner, Menglin Chen, Ralf Bundschuh, Leonard J Foster, and Kurt Fredrick
"Functional Analysis of BipA in E. coli Reveals the Natural Plasticity of 50S Subunit Assembly."
J Mol Biol 432, S0022-28362030460-5 (2020).
[Journal] [PubMed] 
[122] Robert D Patton, Manu Sanjeev, Lauren A Woodward, Justin W Mabin, Ralf Bundschuh, and Guramrit Singh
"Chemical crosslinking enhances RNA immunoprecipitation for efficient identification of binding sites of proteins that photo-crosslink poorly with RNA."
RNA 26, 1216-1233 (2020).
[Journal (open access)] [PubMed] 
[121] Pooja Gangras, Thomas L Gallagher, Michael A Parthun, Zhongxia Yi, Robert D Patton, Kiel T Tietz, Natalie C Deans, Ralf Bundschuh, Sharon L Amacher, and Guramrit Singh
"Zebrafish rbm8a and magoh mutants reveal EJC developmental functions and new 3UTR intron-containing NMD targets."
PLoS Genet. 16, e1008830 (2020).
[Journal (open access)] [PubMed] 
[120] Elan Shatoff and Ralf Bundschuh
"Single nucleotide polymorphisms affect RNA-protein interactions at a distance through modulation of RNA secondary structures."
PLoS Comput. Biol. 16, e1007852 (2020).
[Journal (open access)] [PubMed] 
[119] Daniel Del Valle Morales, Jackson B Trotman, Ralf Bundschuh, and Daniel R Schoenberg
"Inhibition of cytoplasmic cap methylation identifies 5 TOP mRNAs as recapping targets and reveals recapping sites downstream of native 5 ends."
Nucleic Acids Res. 48, 3806-3815 (2020).
[Journal (open access)] [PubMed] 
[118] Logan A Walker, Michael G Sovic, Chi-Ling Chiang, Eileen Hu, Jiyeon K Denninger, Xi Chen, Elizabeth D Kirby, John C Byrd, Natarajan Muthusamy, Ralf Bundschuh, and Pearlly Yan
"CLEAR: coverage-based limiting-cell experiment analysis for RNA-seq."
J Transl Med 18, 63 (2020).
[Journal (open access)] [PubMed] 
[117] Maximillian Westphal, David Frankhouser, Carmine Sonzone, Peter G Shields, Pearlly Yan, and Ralf Bundschuh
"SMaSH: Sample matching using SNPs in humans."
BMC Genomics 20, 1001 (2019).
[Journal (open access)] [PubMed] 
[116] Dengke Zhao, Jenny V Le, Michael A Darcy, Kyle Crocker, Michael G Poirier, Carlos Castro, and Ralf Bundschuh
"Quantitative Modeling of Nucleosome Unwrapping from Both Ends."
Biophys. J. 117, S0006-34951930880-X (2019).
[Journal] [PubMed] 
[115] William D Baez, Bappaditya Roy, Zakkary A McNutt, Elan A Shatoff, Shicheng Chen, Ralf Bundschuh, and Kurt Fredrick
"Global analysis of protein synthesis in Flavobacterium johnsoniae reveals the use of Kozak-like sequences in diverse bacteria."
Nucleic Acids Res. 47, 10477-10488 (2019).
[Journal (open access)] [PubMed] 
[114] Alexander Pan, Lianbo Yu, Justin Breitbach, Ralf Bundschuh, Virginia M Goettl, Zachary A Hing, Parviz Kanga, Rose Mantel, Deepa Sampath, Lisa L Smith, Ronni Wasmuth, Danielle K White, Pearlly Yan, John C Byrd, and Jennifer A Woyach
"Eμ-TCL1xMyc: A Novel Mouse Model for Concurrent CLL and B-Cell Lymphoma."
Clin. Cancer Res. 25, 6260-6273 (2019).
[Journal] [PubMed] [free in PubMed central] 
[113] Blythe S Moreland, Kenji M Oman, and Ralf Bundschuh
"A model of pulldown alignments from SssI-treated DNA improves DNA methylation prediction."
BMC Bioinformatics 20, 431 (2019).
[Journal (open access)] [PubMed] 
[112] Chi-Ling Chiang, Swagata Goswami, Frank W Frissora, Zhiliang Xie, Pearlly S Yan, Ralf Bundschuh, Logan A Walker, Xiaomeng Huang, Rajeswaran Mani, Xiaokui M Mo, Sivasubramanian Baskar, Christoph Rader, Mitch A Phelps, Guido Marcucci, John C Byrd, L James Lee, and Natarajan Muthusamy
"ROR1-targeted delivery of miR-29b induces cell cycle arrest and therapeutic benefit in vivo in a CLL mouse model."
Blood 134, 432-444 (2019).
[Journal] [PubMed] 
[111] Kyle Caution, Alexander Pan, Kathrin Krause, Asmaa Badr, Kaitlin Hamilton, Anup Vaidya, Hawin Gosu, Kylene Daily, Shady Estfanous, Mikhail A Gavrilin, Mark E Drew, Estelle Cormet-Boyaka, Xi Chen, David E Frankhouser, Ralf Bundschuh, Pearlly Yan, Duaa Dakhlallah, and Amal O Amer
"Methylomic correlates of autophagy activity in cystic fibrosis."
J. Cyst. Fibros. 18, 491-500 (2019).
[Journal (open access)] [PubMed] 
[110] Matthew Brehove, Elan Shatoff, Benjamin T Donovan, Caroline M Jipa, Ralf Bundschuh, and Michael G Poirier
"DNA sequence influences hexasome orientation to regulate DNA accessibility."
Nucleic Acids Res. 47, 5617-5633 (2019).
[Journal (open access)] [PubMed] 
[109] Samantha Dodbele, Blythe Moreland, Spencer M Gardner, Ralf Bundschuh, and Jane E Jackman
"5'-End sequencing in Saccharomyces cerevisiae offers new insights into 5'-ends of tRNAHis and snoRNAs."
FEBS Lett. 593, 971-981 (2019).
[Journal] [PubMed] 
[108] Dengke Zhao, William D Baez, Kurt Fredrick, and Ralf Bundschuh
"RiboProP: a probabilistic ribosome positioning algorithm for ribosome profiling."
Bioinformatics 35, 1486-1493 (2019).
[Journal] [PubMed] 
[107] Luke K Genutis, Jerneja Tomsic, Ralf A Bundschuh, Pamela L Brock, Michelle D Williams, Sameek Roychowdhury, Julie W Reeser, Wendy L Frankel, Mohammed Alsomali, Mark J Routbort, Russell R Broaddus, Paul E Wakely, John E Phay, Christopher J Walker, and Albert de la Chapelle
"Microsatellite Instability Occurs in a Subset of Follicular Thyroid Cancers."
Thyroid 29, 523-529 (2019).
[Journal] [PubMed] 
[106] Carol J Huseby, Ralf Bundschuh, and Jeff Kuret
"The role of annealing and fragmentation in human tau aggregation dynamics."
J. Biol. Chem. 294, 4728-4737 (2019).
[Journal] [PubMed] [free in PubMed central] 
[105] William D Baez, Kay Jörg Wiese, and Ralf Bundschuh
"Behavior of random RNA secondary structures near the glass transition."
Phys Rev E 99, 022415 (2019).
[Journal] [PubMed] 
[104] Justin W Mabin, Lauren A Woodward, Robert D Patton, Zhongxia Yi, Mengxuan Jia, Vicki H Wysocki, Ralf Bundschuh, and Guramrit Singh
"The Exon Junction Complex Undergoes a Compositional Switch that Alters mRNP Structure and Nonsense-Mediated mRNA Decay Activity."
Cell Rep 25, 2431-2446.e7 (2018).
[Journal (open access)] [PubMed] 
[103] Jeungphill Hanne, Brooke M Britton, Jonghyun Park, Jiaquan Liu, Juana Martín-López, Nathan Jones, Matthew Schoffner, Piotr Klajner, Ralf Bundschuh, Jong-Bong Lee, and Richard Fishel
"MutS homolog sliding clamps shield the DNA from binding proteins."
J. Biol. Chem. 293, 14285-14294 (2018).
[Journal] [PubMed] 
[102] Huiling He, Wei Li, Pearlly Yan, Ralf Bundschuh, Jackson A Killian, Jadwiga Labanowska, Pamela Brock, Rulong Shen, Nyla A Heerema, and Albert de la Chapelle
"Identification of a Recurrent LMO7-BRAF Fusion in Papillary Thyroid Carcinoma."
Thyroid 28, 748-754 (2018).
[Journal] [PubMed] 
[101] Daniel L Kiss, William D Baez, Kay Huebner, Ralf Bundschuh, and Daniel R Schoenberg
"Loss of fragile histidine triad Fhit protein expression alters the translation of cancer-associated mRNAs."
BMC Res Notes 11, 178 (2018).
[Journal (open access)] [PubMed] 
[100] Jackson A Killian, Taha M Topiwala, Alex R Pelletier, David E Frankhouser, Pearlly S Yan, and Ralf Bundschuh
"FuSpot: a web-based tool for visual evaluation of fusion candidates."
BMC Genomics 19, 139 (2018).
[Journal (open access)] [PubMed] 
[99] Daniel L Kiss, William Baez, Kay Huebner, Ralf Bundschuh, and Daniel R Schoenberg
"Impact of FHIT loss on the translation of cancer-associated mRNAs."
Mol. Cancer 16, 179 (2017).
[Journal (open access)] [PubMed] 
[98] 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] 
[97] 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] 
[96] 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] 
[95] 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] 
[94] 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] 
[93] 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] 
[92] 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] 
[91] 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] 
[90] 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] 
[89] 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] 
[88] Christopher J Walker, Mario A Miranda, Matthew J OHern, Joseph P McElroy, Kevin R Coombes, Ralf Bundschuh, David E Cohn, David G Mutch, and Paul J Goodfellow
"Patterns of CTCF and ZFHX3 Mutation and Associated Outcomes in Endometrial Cancer."
J. Natl. Cancer Inst. 107, djv249 (2015).
[Journal] [PubMed] [free in PubMed central] 
[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).
[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).
[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).
[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).
[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).
[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).
[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).
[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).
[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).
[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).
[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).