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Ryan R Cheng, Ph.D. - Publications

Affiliations: 
2013-2022 Center for Theoretical Biological Physics Rice University, Houston, TX 
 2022- Chemistry University of Kentucky, Lexington, KY 
Area:
Biophysics
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26 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2024 Shibata M, Lin X, Onuchic JN, Yura K, Cheng RR. Residue coevolution and mutational landscape for OmpR and NarL response regulator subfamilies. Biophysical Journal. PMID 38291753 DOI: 10.1016/j.bpj.2024.01.028  0.695
2023 Ruben BS, Brahmachari S, Contessoto VG, Cheng RR, Oliveira Junior AB, Di Pierro M, Onuchic JN. Structural Reorganization and Relaxation Dynamics of Axially Stressed Chromosomes. Biophysical Journal. PMID 36960531 DOI: 10.1016/j.bpj.2023.03.029  0.409
2022 Contessoto VG, Cheng RR, Onuchic JN. Uncovering the statistical physics of 3D chromosomal organization using data-driven modeling. Current Opinion in Structural Biology. 75: 102418. PMID 35839701 DOI: 10.1016/j.sbi.2022.102418  0.452
2021 Mehrabiani KM, Cheng RR, Onuchic JN. Expanding Direct Coupling Analysis to Identify Heterodimeric Interfaces from Limited Protein Sequence Data. The Journal of Physical Chemistry. B. PMID 34618469 DOI: 10.1021/acs.jpcb.1c07145  0.589
2020 Cheng RR, Contessoto V, Lieberman-Aiden E, Wolynes PG, Di Pierro M, Onuchic JN. Exploring chromosomal structural heterogeneity across multiple cell lines. Elife. 9. PMID 33047670 DOI: 10.7554/eLife.60312  0.474
2020 Contessoto VG, Cheng RR, Hajitaheri A, Dodero-Rojas E, Mello MF, Lieberman-Aiden E, Wolynes PG, Di Pierro M, Onuchic JN. The Nucleome Data Bank: web-based resources to simulate and analyze the three-dimensional genome. Nucleic Acids Research. PMID 33021634 DOI: 10.1093/nar/gkaa818  0.456
2019 Mandic A, Hayes RL, Lammert H, Cheng RR, Onuchic JN. Structure-Based Model of RNA Pseudoknot Captures Magnesium-dependent Folding Thermodynamics. The Journal of Physical Chemistry. B. PMID 30676755 DOI: 10.1021/Acs.Jpcb.8B10791  0.462
2018 Krepel D, Cheng RR, Di Pierro M, Onuchic JN. Deciphering the structure of the condensin protein complex. Proceedings of the National Academy of Sciences of the United States of America. PMID 30385633 DOI: 10.1073/Pnas.1812770115  0.547
2018 Vian L, Pękowska A, Rao SSP, Kieffer-Kwon KR, Jung S, Baranello L, Huang SC, El Khattabi L, Dose M, Pruett N, Sanborn AL, Canela A, Maman Y, Oksanen A, Resch W, ... ... Cheng RR, et al. The Energetics and Physiological Impact of Cohesin Extrusion. Cell. 175: 292-294. PMID 30241609 DOI: 10.1016/j.cell.2018.09.002  0.34
2018 Cheng RR, Haglund E, Tiee NS, Morcos F, Levine H, Adams JA, Jennings PA, Onuchic JN. Designing bacterial signaling interactions with coevolutionary landscapes. Plos One. 13: e0201734. PMID 30125296 DOI: 10.1371/Journal.Pone.0201734  0.54
2018 Vian L, Pękowska A, Rao SSP, Kieffer-Kwon KR, Jung S, Baranello L, Huang SC, El Khattabi L, Dose M, Pruett N, Sanborn AL, Canela A, Maman Y, Oksanen A, Resch W, ... ... Cheng RR, et al. The Energetics and Physiological Impact of Cohesin Extrusion. Cell. PMID 29706548 DOI: 10.1016/J.Cell.2018.03.072  0.434
2017 Di Pierro M, Cheng RR, Lieberman Aiden E, Wolynes PG, Onuchic JN. De novo prediction of human chromosome structures: Epigenetic marking patterns encode genome architecture. Proceedings of the National Academy of Sciences of the United States of America. PMID 29087948 DOI: 10.1016/J.Bpj.2017.11.3265  0.468
2016 Bai F, Morcos F, Cheng RR, Jiang H, Onuchic JN. Elucidating the druggable interface of protein-protein interactions using fragment docking and coevolutionary analysis. Proceedings of the National Academy of Sciences of the United States of America. PMID 27911825 DOI: 10.1073/Pnas.1615932113  0.65
2015 Cheng RR, Raghunathan M, Noel JK, Onuchic JN. Constructing sequence-dependent protein models using coevolutionary information. Protein Science : a Publication of the Protein Society. PMID 26223372 DOI: 10.1002/Pro.2758  0.717
2014 Morcos F, Schafer NP, Cheng RR, Onuchic JN, Wolynes PG. Coevolutionary information, protein folding landscapes, and the thermodynamics of natural selection. Proceedings of the National Academy of Sciences of the United States of America. 111: 12408-13. PMID 25114242 DOI: 10.1073/Pnas.1413575111  0.526
2014 Cheng RR, Morcos F, Levine H, Onuchic JN. Toward rationally redesigning bacterial two-component signaling systems using coevolutionary information. Proceedings of the National Academy of Sciences of the United States of America. 111: E563-71. PMID 24449878 DOI: 10.1073/Pnas.1323734111  0.529
2013 Cheng RR, Hawk AT, Makarov DE. Exploring the role of internal friction in the dynamics of unfolded proteins using simple polymer models. The Journal of Chemical Physics. 138: 074112. PMID 23445002 DOI: 10.1063/1.4792206  0.621
2012 Soranno A, Buchli B, Nettels D, Cheng RR, Müller-Späth S, Pfeil SH, Hoffmann A, Lipman EA, Makarov DE, Schuler B. Quantifying internal friction in unfolded and intrinsically disordered proteins with single-molecule spectroscopy. Proceedings of the National Academy of Sciences of the United States of America. 109: 17800-6. PMID 22492978 DOI: 10.1073/Pnas.1117368109  0.618
2012 Madsen JA, Cheng RR, Kaoud TS, Dalby KN, Makarov DE, Brodbelt JS. Charge-site-dependent dissociation of hydrogen-rich radical peptide cations upon vacuum UV photoexcitation. Chemistry (Weinheim An Der Bergstrasse, Germany). 18: 5374-83. PMID 22431222 DOI: 10.1002/Chem.201103534  0.478
2011 Cone CW, Cheng RR, Makarov DE, Vanden Bout DA. Molecular weight effect on the formation of β phase poly(9,9'-dioctylfluorene) in dilute solutions. The Journal of Physical Chemistry. B. 115: 12380-5. PMID 21899310 DOI: 10.1021/Jp2061078  0.476
2011 Cheng RR, Makarov DE. Failure of one-dimensional Smoluchowski diffusion models to describe the duration of conformational rearrangements in floppy, diffusive molecular systems: a case study of polymer cyclization. The Journal of Chemical Physics. 134: 085104. PMID 21361559 DOI: 10.1063/1.3556750  0.536
2010 Cheng RR, Uzawa T, Plaxco KW, Makarov DE. Universality in the timescales of internal loop formation in unfolded proteins and single-stranded oligonucleotides. Biophysical Journal. 99: 3959-68. PMID 21156138 DOI: 10.1016/J.Bpj.2010.11.017  0.627
2010 Uzawa T, Cheng RR, White RJ, Makarov DE, Plaxco KW. A mechanistic study of electron transfer from the distal termini of electrode-bound, single-stranded DNAs. Journal of the American Chemical Society. 132: 16120-6. PMID 20964337 DOI: 10.1021/Ja106345D  0.502
2010 Cheng RR, Makarov DE. End-to-surface reaction dynamics of a single surface-attached DNA or polypeptide. The Journal of Physical Chemistry. B. 114: 3321-9. PMID 20151703 DOI: 10.1021/Jp910669D  0.502
2009 Cheng RR, Uzawa T, Plaxco KW, Makarov DE. The rate of intramolecular loop formation in DNA and polypeptides: the absence of the diffusion-controlled limit and fractional power-law viscosity dependence. The Journal of Physical Chemistry. B. 113: 14026-34. PMID 19780594 DOI: 10.1021/Jp902291N  0.541
2009 Uzawa T, Cheng RR, Cash KJ, Makarov DE, Plaxco KW. The length and viscosity dependence of end-to-end collision rates in single-stranded DNA. Biophysical Journal. 97: 205-10. PMID 19580758 DOI: 10.1016/J.Bpj.2009.04.036  0.539
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