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

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).

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).

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).

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).

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).

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).

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).

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).

Dengke Zhao, William D Baez, Kurt Fredrick, and Ralf Bundschuh
"RiboProP: a probabilistic ribosome positioning algorithm for ribosome profiling."
Bioinformatics 35, 1486-1493 (2019).

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).

Cai Chen and Ralf Bundschuh
"Quantitative models for accelerated protein dissociation from nucleosomal DNA."
Nucleic Acids Res. 42, 9753-60 (2014).

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).

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).

Cai Chen, David Frankhouser, and Ralf Bundschuh
"Comparison of insertional RNA editing in Myxomycetes."
PLoS Comput. Biol. 8, e1002400 (2012).

Cai Chen and Ralf Bundschuh
"Systematic investigation of insertional and deletional RNA-DNA differences in the human transcriptome."
BMC Genomics 13, 616 (2012).

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).

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).