Zobrazeno 1 - 10
of 75
pro vyhledávání: '"Ryan R Cheng"'
Autor:
Ryan R Cheng, Vinicius G Contessoto, Erez Lieberman Aiden, Peter G Wolynes, Michele Di Pierro, Jose N Onuchic
Publikováno v:
eLife, Vol 9 (2020)
Using computer simulations, we generate cell-specific 3D chromosomal structures and compare them to recently published chromatin structures obtained through microscopy. We demonstrate using machine learning and polymer physics simulations that epigen
Externí odkaz:
https://doaj.org/article/dcd8f4691c724d23a58e834aec515630
Autor:
Ryan R Cheng, Ellinor Haglund, Nicholas S Tiee, Faruck Morcos, Herbert Levine, Joseph A Adams, Patricia A Jennings, José N Onuchic
Publikováno v:
PLoS ONE, Vol 13, Iss 8, p e0201734 (2018)
Selecting amino acids to design novel protein-protein interactions that facilitate catalysis is a daunting challenge. We propose that a computational coevolutionary landscape based on sequence analysis alone offers a major advantage over expensive, t
Externí odkaz:
https://doaj.org/article/7dd888a3f09141b8a676ed9ee40d1100
Autor:
Benjamin S. Ruben, Sumitabha Brahmachari, Vinícius G. Contessoto, Ryan R. Cheng, Antonio B. Oliveira Junior, Michele Di Pierro, José N. Onuchic
Publikováno v:
Biophysical Journal. 122:1633-1645
Micromechanical studies of mitotic chromosomes have revealed them to be remarkably extensible objects and informed early models of mitotic chromosome organization. We use a data-driven, coarsegrained polymer modeling approach, capable of generating e
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::0604331ddb37ee411b69537199138df3
https://doi.org/10.1016/j.bpj.2023.03.029
https://doi.org/10.1016/j.bpj.2023.03.029
Autor:
Ryan R. Cheng, Arya Hajitaheri, Erez Lieberman Aiden, Esteban Dodero-Rojas, Matheus F. Mello, Vinícius G. Contessoto, José N. Onuchic, Peter G. Wolynes, Michele Di Pierro
Publikováno v:
Scopus
Repositório Institucional da UNESP
Universidade Estadual Paulista (UNESP)
instacron:UNESP
Nucleic Acids Research
Repositório Institucional da UNESP
Universidade Estadual Paulista (UNESP)
instacron:UNESP
Nucleic Acids Research
Made available in DSpace on 2021-06-25T10:15:21Z (GMT). No. of bitstreams: 0 Previous issue date: 2021-01-08 Welch Foundation National Science Foundation We introduce the Nucleome Data Bank (NDB), a web-based platform to simulate and analyze the thre
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::2ea3d12f47e421a07f1286fa79b28a57
https://doi.org/10.1093/nar/gkaa818
https://doi.org/10.1093/nar/gkaa818
Publikováno v:
The journal of physical chemistry. B. 125(41)
Direct coupling analysis (DCA) is a global statistical approach that uses information encoded in protein sequence data to predict spatial contacts in a three-dimensional structure of a folded protein. DCA has been widely used to predict the monomeric
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::0c5039c87900b431411085bdb5fbeb2e
https://pubmed.ncbi.nlm.nih.gov/34618469
https://pubmed.ncbi.nlm.nih.gov/34618469
Publikováno v:
The Journal of Physical Chemistry B. 123:1505-1511
We develop a simple, coarse-grained approach for simulating the folding of the Beet Western Yellow Virus (BWYV) pseudoknot toward the goal of creating a transferable model that can be used to study other small RNA molecules. This approach combines a
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::5cca0d4f6678b5baed86ac7faed8ffb9
https://doi.org/10.1021/acs.jpcb.8b10791
https://doi.org/10.1021/acs.jpcb.8b10791
Publikováno v:
Current Opinion in Structural Biology. 75:102418
In recent years, much effort has been devoted to understanding the three-dimensional (3D) organization of the genome and how genomic structure mediates nuclear function. The development of experimental techniques that combine DNA proximity ligation w
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::b45095d5a3afdf6654476125360d2af0
https://doi.org/10.1016/j.sbi.2022.102418
https://doi.org/10.1016/j.sbi.2022.102418
We explore the energetic frustration patterns associated with the binding between the SARS-CoV-2 spike protein and the ACE2 receptor protein in a broad selection of animals. Using energy landscape theory and the concept of energy frustration—theore
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::e40b6be7af53f73b815b8ef381b64a33
https://doi.org/10.1101/2021.03.25.437113
https://doi.org/10.1101/2021.03.25.437113
Autor:
Vinícius G. Contessoto, Ryan R. Cheng, Michele Di Pierro, Erez Lieberman Aiden, Peter G. Wolynes, José N. Onuchic
Publikováno v:
eLife, Vol 9 (2020)
eLife
eLife
We study the structural ensembles of human chromosomes across different cell types. Using computer simulations, we generate cell-specific 3D chromosomal structures and compare them to recently published chromatin structures obtained through microscop
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::6f01d1f63c8edfbe4e6a92abd7a7c642
https://elifesciences.org/articles/60312
https://elifesciences.org/articles/60312