Publications

Mayu Shibata, Xingcheng Lin, José N Onuchic, Kei Yura, Ryan R Cheng (2024). Residue coevolution and mutational landscape for OmpR and NarL response regulator subfamilies. Biophysical Journal.

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Benjamin S Ruben, Sumitabha Brahmachari, Vinı́cius G Contessoto, Ryan R Cheng, Antonio B Oliveira Junior, Michele Di Pierro, José N Onuchic (2023). Structural reorganization and relaxation dynamics of axially stressed chromosomes. Biophysical Journal.

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Amit Das, Ryan Cheng, Davit Potoyan, Michele Di Pierro (2023). 3D genome architecture regulates the traffic of transcription factors throughout human chromosomes. Biophysical Journal.

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Vinı́cius G Contessoto, Ryan R Cheng, José N Onuchic (2022). Uncovering the statistical physics of 3D chromosomal organization using data-driven modeling. Current Opinion in Structural Biology.

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Vinı́cius G Contessoto, Ryan R Cheng, Arya Hajitaheri, Esteban Dodero-Rojas, Matheus F Mello, Erez Lieberman Aiden, Peter G Wolynes, Michele Di Pierro, José N Onuchic (2021). The Nucleome Data Bank: web-based resources to simulate and analyze the three-dimensional genome. Nucleic Acids Research.

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Kareem M Mehrabiani, Ryan R Cheng, José N Onuchic (2021). Expanding direct coupling analysis to identify heterodimeric interfaces from limited protein sequence data. The Journal of Physical Chemistry B.

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Ryan R Cheng, Esteban Dodero-Rojas, Michele Di Pierro, José N Onuchic (2021). Evolutionary differences in the ACE2 reveals the molecular origins of COVID-19 susceptibility. bioRxiv.

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Ryan R Cheng, Vinicius G Contessoto, Erez Lieberman Aiden, Peter G Wolynes, Michele Di Pierro, José N Onuchic (2020). Exploring chromosomal structural heterogeneity across multiple cell lines. Elife.

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Mayu Shibata, Xingcheng Lin, Ryan R Cheng, Kei Yura, José N Onuchic (2020). Comparative Analysis of the Residue Co-Evolution of the DNA-Binding Response Regulator Subfamilies. Biophysical Journal.

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Ana Mandic, Ryan L Hayes, Heiko Lammert, Ryan R Cheng, José N Onuchic (2019). Structure-based model of RNA pseudoknot captures magnesium-dependent folding thermodynamics. The Journal of Physical Chemistry B.

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Laura Vian, Aleksandra Pękowska, Suhas SP Rao, Kyong-Rim Kieffer-Kwon, Seolkyoung Jung, Laura Baranello, Su-Chen Huang, Laila El Khattabi, Marei Dose, Nathanael Pruett, others (2018). The energetics and physiological impact of cohesin extrusion. Cell.

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Carlos A Bueno, Davit A Potoyan, Ryan R Cheng, Peter G Wolynes (2018). Prediction of changes in protein folding stability upon single residue mutations. Biophysical Journal.

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Ryan R Cheng, Ellinor Haglund, Nicholas S Tiee, Faruck Morcos, Herbert Levine, Joseph A Adams, Patricia A Jennings, José N Onuchic (2018). Designing bacterial signaling interactions with coevolutionary landscapes. PloS one.

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Dana Krepel, Ryan R Cheng, Michele Di Pierro, José N Onuchic (2018). Deciphering the structure of the condensin protein complex. Proceedings of the National Academy of Sciences.

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Michele Di Pierro, Ryan R Cheng, Erez Lieberman Aiden, Peter G Wolynes, José N Onuchic (2018). De novo prediction of human chromosome structures: Epigenetic marking patterns encode genome architecture. Biophysical Journal.

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Ryan R Cheng, Ellinor Haglund, Nicholas Tiee, Faruck Morcos, Herbert Levine, Joseph A Adams, Patricia A Jennings, José N Onuchic (2017). Guiding the design of bacterial signaling interactions using a coevolutionary landscape. bioRxiv.

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Michele Di Pierro, Ryan R Cheng, Erez Lieberman Aiden, Peter G Wolynes, José N Onuchic (2017). De novo prediction of human chromosome structures: Epigenetic marking patterns encode genome architecture. Proceedings of the National Academy of Sciences.

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Ryan R Cheng (2017). Connecting the Sequence-Space of Bacterial Signaling Proteins to Phenotypes using Coevolutionary Landscapes. Biophysical Journal.

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Fang Bai, Faruck Morcos, Ryan R Cheng, Hualiang Jiang, José N Onuchic (2016). Elucidating the druggable interface of protein- protein interactions using fragment docking and coevolutionary analysis. Proceedings of the National Academy of Sciences.

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Ryan R Cheng, Mohit Raghunathan, Jeffrey K Noel, José N Onuchic (2016). Constructing sequence-dependent protein models using coevolutionary information. Protein Science.

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Ryan R Cheng, Olle Nordesjö, Ryan L Hayes, Herbert Levine, Samuel C Flores, José N Onuchic, Faruck Morcos (2016). Connecting the sequence-space of bacterial signaling proteins to phenotypes using coevolutionary landscapes. Molecular Biology and Evolution.

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Joseph S Boyd, Ryan R Cheng, Mark L Paddock, Cigdem Sancar, Faruck Morcos, Susan S Golden (2016). A combined computational and genetic approach uncovers network interactions of the cyanobacterial circadian clock. Journal of Bacteriology.

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Ryan R Cheng, Faruck Morcos, Herbert Levine, José N Onuchic (2014). Toward rationally redesigning bacterial two-component signaling systems using coevolutionary information. Proceedings of the National Academy of Sciences.

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Faruck Morcos, Nicholas P Schafer, Ryan R Cheng, José N Onuchic, Peter G Wolynes (2014). Coevolutionary information, protein folding landscapes, and the thermodynamics of natural selection. Proceedings of the National Academy of Sciences.

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Ryan R Cheng, Alexander T Hawk, Dmitrii E Makarov (2013). Exploring the role of internal friction in the dynamics of unfolded proteins using simple polymer models. The Journal of Chemical Physics.

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Andrea Soranno, Brigitte Buchli, Daniel Nettels, Ryan R Cheng, Sonja Müller-Späth, Shawn H Pfeil, Armin Hoffmann, Everett A Lipman, Dmitrii E Makarov, Benjamin Schuler (2012). Quantifying internal friction in unfolded and intrinsically disordered proteins with single-molecule spectroscopy. Proceedings of the National Academy of Sciences.

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James A Madsen, Ryan R Cheng, Tamer S Kaoud, Kevin N Dalby, Dmitrii E Makarov, Jennifer S Brodbelt (2012). Charge-Site Dependent Dissociation of Hydrogen-Rich Radical Peptide Cations upon Vacuum UV Photoexcitation. Chemistry-A European Journal.

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Craig W Cone, Ryan R Cheng, Dmitrii E Makarov, David A Vanden Bout (2011). Molecular Weight Effect on the formation of $β$ Phase Poly (9, 9′-dioctylfluorene) in Dilute Solutions. The Journal of Physical Chemistry B.

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Ryan R Cheng, Dmitrii E Makarov (2011). 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. Journal of Chemical Physics.

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Ryan R Cheng, Takanori Uzawa, Kevin W Plaxco, Dmitrii E Makarov (2010). Universality in the timescales of internal loop formation in unfolded proteins and single-stranded oligonucleotides. Biophysical journal.

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Ryan R Cheng, Dmitrii E Makarov (2010). End-to-surface reaction dynamics of a single surface-attached DNA or polypeptide. The Journal of Physical Chemistry B.

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Gizelle A Sherwood, Ryan Cheng, Kelly Chacon-Madrid, Timothy M Smith, Linda A Peteanu, Jurjen Wildeman (2010). Chain Length and Substituent Effects on the Formation of Excimer-Like States in Nanoaggregates of CN-PPV Model Oligomers. The Journal of Physical Chemistry C.

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Takanori Uzawa, Ryan R Cheng, Ryan J White, Dmitrii E Makarov, Kevin W Plaxco (2010). A mechanistic study of electron transfer from the distal termini of electrode-bound, single-stranded DNAs. Journal of the American Chemical Society.

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Ryan R Cheng, Takanori Uzawa, Kevin W Plaxco, Dmitrii E Makarov (2009). 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.

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Takanori Uzawa, Ryan R Cheng, Kevin J Cash, Dmitrii E Makarov, Kevin W Plaxco (2009). The length and viscosity dependence of end-to-end collision rates in single-stranded DNA. Biophysical journal.

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Gizelle A Sherwood, Ryan Cheng, Timothy M Smith, James H Werner, Andrew P Shreve, Linda A Peteanu, Jurjen Wildeman (2009). Aggregation effects on the emission spectra and dynamics of model oligomers of MEH-PPV. The Journal of Physical Chemistry C.

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