Publications

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.

Cite

Sumitabha Brahmachari, Benjamin Ruben, Vinicius Contessoto, Ryan Cheng, Antonio Oliviera Jr, Michele Di Pierro, Jose Onuchic (2023). Structural Integrity and Relaxation Dynamics of Axially Stressed Chromosomes. Bulletin of the American Physical Society.

Cite

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

Cite

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.

Cite

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.

Cite

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.

Cite

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.

Cite

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.

Cite

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.

Cite

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.

Cite

Michele Di Pierro, Ryan R Cheng, Bin Zhang, José N Onuchic, Peter G Wolynes (2019). Learning genomic energy landscapes from experiments. Modeling the 3D Conformation of Genomes.

Cite

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.

Cite

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.

Cite

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.

Cite

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.

Cite

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.

Cite

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.

Cite

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.

Cite

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

Cite

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.

Cite

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

Cite

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.

Cite

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.

Cite

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.

Cite

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.

Cite

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.

Cite

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.

Cite

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.

Cite

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.

Cite

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.

Cite

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.

Cite

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.

Cite

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.

Cite

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.

Cite

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.

Cite

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.

Cite

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.

Cite