Publications | Biophysics Graduate Program

[1]	Ariel Robbins, Hazen Hildebolt, Michael Neuhoff, Peter Beshay, Jessica O Winter, Carlos E Castro, Ralf Bundschuh, and Michael G Poirier "Cooperative control of a DNA origami force sensor." Sci Rep 14, 4132 (2024).
[2]	Fawwaz M Naeem, Bryan T Gemler, Zakkary A McNutt, Ralf Bundschuh, and Kurt Fredrick "Analysis of programmed frameshifting during translation of " RNA 30, 136-148 (2024).
[3]	Zakkary A McNutt, Bappaditya Roy, Bryan T Gemler, Elan A Shatoff, Kyung-Mee Moon, Leonard J Foster, Ralf Bundschuh, and Kurt Fredrick "Ribosomes lacking bS21 gain function to regulate protein synthesis in Flavobacterium johnsoniae." Nucleic Acids Res 51, 1927-1942 (2023).
[4]	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).
[5]	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).
[6]	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).
[7]	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).
[8]	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).
[9]	Dengke Zhao, William D Baez, Kurt Fredrick, and Ralf Bundschuh "RiboProP: a probabilistic ribosome positioning algorithm for ribosome profiling." Bioinformatics 35, 1486-1493 (2019).
[10]	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).
[11]	Cai Chen and Ralf Bundschuh "Quantitative models for accelerated protein dissociation from nucleosomal DNA." Nucleic Acids Res. 42, 9753-60 (2014).
[12]	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).
[13]	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).
[14]	Cai Chen, David Frankhouser, and Ralf Bundschuh "Comparison of insertional RNA editing in Myxomycetes." PLoS Comput. Biol. 8, e1002400 (2012).
[15]	Cai Chen and Ralf Bundschuh "Systematic investigation of insertional and deletional RNA-DNA differences in the human transcriptome." BMC Genomics 13, 616 (2012).
[16]	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).
[17]	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).

Publications (co-)authored by Ralf Bundschuh with students in the Biophysics program