A quantitative model for a nanoscale switch accurately predicts thermal actuation behavior

Authors: Crocker, Kyle, Johnson, Joshua, Pfeifer, Wolfgang, Castro, Carlos, Bundschuh, Ralf

Subject Terms: Quantitative Biology - Biomolecules, Physics - Biological Physics

Access URL: http://arxiv.org/abs/2101.07935

Potential evolutionary advantage of a dissociative search mechanism in DNA mismatch repair

Authors: Crocker, Kyle, London, James, Medina, Andrés, Fishel, Richard, Bundschuh, Ralf

Source: Phys. Rev. E 103, 052404 (2021)

Subject Terms: Quantitative Biology - Subcellular Processes, Physics - Biological Physics

Access URL: http://arxiv.org/abs/2012.09844

On the behavior of random RNA secondary structures near the glass transition

Authors: Baez, William D., Wiese, Kay Jörg, Bundschuh, Ralf

Source: Phys. Rev. E 99, 022415 (2019)

Subject Terms: Quantitative Biology - Biomolecules, Condensed Matter - Disordered Systems and Neural Networks, Condensed Matter - Statistical Mechanics

Access URL: http://arxiv.org/abs/1808.02351

The exon junction complex undergoes a compositional switch that alters mRNP structure and nonsense-mediated mRNA decay activity

Authors: Mabin, Justin W., Woodward, Lauren A., Patton, Robert, Yi, Zhongxia, Jia, Mengxuan, Wysocki, Vicki, Bundschuh, Ralf, Singh, Guramrit

Subject Terms: Quantitative Biology - Genomics

Access URL: http://arxiv.org/abs/1807.00789

CLEAR: Coverage-based Limiting-cell Experiment Analysis for RNA-seq

Authors: Walker, Logan A, Sovic, Michael G, Chiang, Chi-Ling, Hu, Eileen, Denninger, Jiyeon K, Chen, Xi, Kirby, Elizabeth D, Byrd, John C, Muthusamy, Natarajan, Bundschuh, Ralf, Yan, Pearlly

Subject Terms: Quantitative Biology - Genomics, Quantitative Biology - Quantitative Methods

Access URL: http://arxiv.org/abs/1806.03142

PP2A is a therapeutically targetable driver of cell fate decisions via a c-Myc/p21 axis in human and murine acute myeloid leukemia

Authors: Goswami, Swagata, Mani, Rajeswaran, Nunes, Jessica, Chiang, Chi-Ling, Zapolnik, Kevan, Hu, Eileen, Frissora, Frank, Mo, Xiaokui, Walker, Logan A., Yan, Pearlly, Bundschuh, Ralf, Beaver, Larry, Devine, Raymond, Tsai, Yo-Ting, Ventura, Ann, Xie, Zhiliang, Chen, Min, Lapalombella, Rosa, Walker, Alison, Mims, Alice, Larkin, Karilyn, Grieselhuber, Nicole, Bennett, Chad, Phelps, Mitch, Hertlein, Erin, Behbehani, Gregory, Vasu, Sumithira, Byrd, John C., Muthusamy, Natarajan

Source: Blood. 139(9):1340-1358

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100183245068.0x000001&indx=1&recIds=ETOCvdc_100183245068.0x000001

High-Force Application by a Nanoscale DNA Force Spectrometer

Authors: Darcy, Michael, Crocker, Kyle, Wang, Yuchen, Le, Jenny V., Mohammadiroozbahani, Golbarg, Abdelhamid, Mahmoud A. S., Craggs, Timothy D., Castro, Carlos E., Bundschuh, Ralf, Poirier, Michael G.

Source: ACS nano. 16(4):5682-5695

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCRN629236592&indx=1&recIds=ETOCRN629236592

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

Authors: Shatoff, Elan, Bundschuh, Ralf

Source: Bioinformatics. 38(3):687-693

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100139037178.0x000001&indx=1&recIds=ETOCvdc_100139037178.0x000001

Leukemia-initiating HSCs in chronic lymphocytic leukemia reveal clonal leukemogenesis and differential drug sensitivity

Authors: Chiang, Chi-Ling, Hu, Eileen Y., Chang, Lingqian, Labanowska, Jadwiga, Zapolnik, Kevan, Mo, Xiaokui, Shi, Junfeng, Doong, Tzyy-Jye, Lozanski, Arletta, Yan, Pearlly S., Bundschuh, Ralf, Walker, Logan A., Gallego-Perez, Daniel, Lu, Wu, Long, Meixiao, Kim, Sanggu, Heerema, Nyla A., Lozanski, Gerard, Woyach, Jennifer A., Byrd, John C., Lee, Ly James, Muthusamy, Natarajan

Source: In Cell Reports 19 July 2022 40(3)

Dietary omega-3 fatty acid intake impacts peripheral blood DNA methylation -anti-inflammatory effects and individual variability in a pilot study

Authors: Frankhouser, David E, Steck, Sarah, Sovic, Michael G, Belury, Martha A, Wang, Qianben, Clinton, Steven K, Bundschuh, Ralf, Yan, Pearlly S, Yee, Lisa D

Source: In The Journal of Nutritional Biochemistry January 2022 99

A scalable, flexible workflow for MethylCap-seq data analysis

Authors: Rodriguez, Benjamin, Tam, Hok-Hei, Frankhouser, David, Trimarchi, Michael, Murphy, Mark, Kuo, Chris, Parikh, Deval, Ball, Bryan, Schwind, Sebastian, Curfman, John, Blum, William, Marcucci, Guido, Yan, Pearlly, Bundschuh, Ralf

Source: 2011 IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS) Genomic Signal Processing and Statistics (GENSIPS), 2011 IEEE International Workshop on. :1-4 Dec, 2011

Relation: 2011 IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS)

Targeting OCT3 attenuates doxorubicin-induced cardiac injury

Authors: Huang, Kevin M., Thomas, Megan Zavorka, Magdy, Tarek, Eisenmann, Eric D., Uddin, Muhammad Erfan, DiGiacomo, Duncan F., Pan, Alexander, Keiser, Markus, Otter, Marcus, Xia, Sherry H., Li, Yang, Jin, Yan, Fu, Qiang, Gibson, Alice A., Bonilla, Ingrid M., Carnes, Cynthia A., Corps, Kara N., Coppola, Vincenzo, Smith, Sakima A., Addison, Daniel, Nies, Anne T., Bundschuh, Ralf, Chen, Taosheng, Lustberg, Maryam B., Wang, Joanne, Oswald, Stefan, Campbell, Moray J., Yan, Pearlly S., Baker, Sharyn D., Hu, Shuiying, Burridge, Paul W., Sparreboom, Alex

Source: Proceedings of the National Academy of Sciences of the United States of America, 2021 Feb 01. 118(5), 1-9.

Access URL: https://www.jstor.org/stable/27006166

RBPBind: Quantitative prediction of Protein-RNA Interactions

Authors: Gaither, Jeff, Lin, Yi-Hsuan, Bundschuh, Ralf

Subject Terms: Quantitative Biology - Biomolecules

Access URL: http://arxiv.org/abs/1611.01245

Maturation of 23S rRNA includes removal of helix H1 in many bacteria

Authors: Shatoff, Elan A., Gemler, Bryan T., Bundschuh, Ralf, Fredrick, Kurt

Source: RNA biology. 18(S2):856-865

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100139436733.0x000001&indx=1&recIds=ETOCvdc_100139436733.0x000001

A quantitative model for a nanoscale switch accurately predicts thermal actuation behaviorElectronic supplementary information (ESI) available. See DOI: 10.1039/d1nr02873a

Authors: Crocker, Kyle, Johnson, Joshua, Pfeifer, Wolfgang, Castro, Carlos, Bundschuh, Ralf

Source: Nanoscale. 13(32):13746-13757

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100128085632.0x000001&indx=1&recIds=ETOCvdc_100128085632.0x000001

Functional Analysis of BipA in E. coli Reveals the Natural Plasticity of 50S Subunit Assembly

Authors: Gibbs, Michelle R., Moon, Kyung-Mee, Warner, Benjamin R., Chen, Menglin, Bundschuh, Ralf, Foster, Leonard J., Fredrick, Kurt

Source: In Journal of Molecular Biology 4 September 2020 432(19):5259-5272

RNA structure generates natural cooperativity between single-stranded RNA binding proteins targeting 5' and 3'UTRs

Authors: Lin, Yi-Hsuan, Bundschuh, Ralf

Source: Nucl. Acids Res. (30 January 2015) 43 (2): 1160-1169

Subject Terms: Quantitative Biology - Biomolecules

Access URL: http://arxiv.org/abs/1410.5319

Interplay between single-stranded binding proteins on RNA secondary structure

Authors: Lin, Yi-Hsuan, Bundschuh, Ralf

Source: Phys. Rev. E 88, 052707 (2013)

Subject Terms: Quantitative Biology - Biomolecules

Access URL: http://arxiv.org/abs/1310.5778

Quantitative Modeling of Nucleosome Unwrapping from Both Ends

Authors: Zhao, Dengke, Le, Jenny V., Darcy, Michael A., Crocker, Kyle, Poirier, Michael G., Castro, Carlos, Bundschuh, Ralf

Source: In Biophysical Journal 3 December 2019 117(11):2204-2216

RNA Secondary Structure Prediction in the Presence of Single-Stranded Binding Proteins

Authors: Forties, Robert A., Bundschuh, Ralf

Source: 2009 Ohio Collaborative Conference on Bioinformatics Bioinformatics, 2009. OCCBIO '09. Ohio Collaborative Conference on. :57-57 Jun, 2009

Relation: 2009 Ohio Collaborative Conference on Bioinformatics (OCCBIO)