Ryan R. Cheng

Assistant Professor of Chemistry

University of Kentucky

Biography

Ryan R. Cheng is an assistant professor of chemistry at the University of Kentucky. His research focuses on using computer simulations, biopolymer theory, statistical mechanics, and machine learning to address biophysical problems, particularly in the area of structural genomics.

Interests

Biophysics
Computational and Theoretical Chemistry

Education

Postdoc/Research Scientist, 2022
Center for Theoretical Biological Physics, Rice University
Ph.D. in Theoretical Chemistry, 2012
University of Texas at Austin
B.S. in Chemistry, 2007
Carnegie Mellon University

The Team

Aleena Javaid, Undergraduate Researcher

Aleena is currently a 3rd year chemistry student at UKY.

Devilal Dahal, Postdoctoral Researcher

Devilal received his Ph.D. in Computational Physics from the University of Southern Mississippi under the supervision of Professor Parthapratim Biswas. His research currently focuses on the mechanics of the genome.

Matheus Mello, Graduate Student

Matheus is currently a Ph.D. student at Rice University under the supervision of Professor Jose Onuchic. We are currently collaborating on the analysis of imaging data!

Mayu Shibata, Graduate Student

Mayu is currently a Ph.D. student at Ochanomizu University under the supervision of Professor Kei Yura. We are collaborating on a project focusing on amino acid co-evolution!

Sasindu Gunasinghe, Graduate Student

Sasindu received his bachelors degree in Chemistry from the Institute of Chemistry Ceylon in Sri Lanka. His research will focus on the role of epigenetics in cell differentiation and disease states.

Projects

Genome mechanics

We are currently exploring how mechanical stress modulates the structural ensembles and dynamics of the genome.

Genome organization

We explore the 3D structures of chromatin and the relationship of those structures to biological functions, such as transcriptional regulation.

Protein sequence analysis

Amino acid coevolution is used to predict spatial contacts that have been maintained over the course of natural selection.

Gallery

Publications

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

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.

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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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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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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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