Zobrazeno 1 - 10
of 36
pro vyhledávání: '"Vladimir Reinharz"'
Publikováno v:
RNA Biology, Vol 19, Iss 1, Pp 1208-1227 (2022)
This study investigates the importance of the structural context in the formation of a type I/II A-minor motif. This very frequent structural motif has been shown to be important in the spatial folding of RNA molecules. We developed an automated meth
Externí odkaz:
https://doaj.org/article/64ec346cb700473c8866de84e464cfcf
Autor:
Adequate Mhlanga, Rami Zakh, Alexander Churkin, Vladimir Reinharz, Jeffrey S. Glenn, Ohad Etzion, Scott J. Cotler, Cihan Yurdaydin, Danny Barash, Harel Dahari
Publikováno v:
Mathematics, Vol 10, Iss 20, p 3917 (2022)
Hepatitis D virus is an infectious subviral agent that can only propagate in people infected with hepatitis B virus. In this study, we modified and further developed a recent model for early hepatitis D virus and hepatitis B virus kinetics to better
Externí odkaz:
https://doaj.org/article/cb8b09866b0c414cb31b22035b1ee4ec
Publikováno v:
Mathematics, Vol 10, Iss 12, p 2136 (2022)
Mathematical models, some of which incorporate both intracellular and extracellular hepatitis C viral kinetics, have been advanced in recent years for studying HCV–host dynamics, antivirals mode of action, and their efficacy. The standard ordinary
Externí odkaz:
https://doaj.org/article/830ddf4d44534b6da9196a595b686045
Finding recurrent RNA structural networks with fast maximal common subgraphs of edge-colored graphs.
Publikováno v:
PLoS Computational Biology, Vol 17, Iss 5, p e1008990 (2021)
RNA tertiary structure is crucial to its many non-coding molecular functions. RNA architecture is shaped by its secondary structure composed of stems, stacked canonical base pairs, enclosing loops. While stems are precisely captured by free-energy mo
Externí odkaz:
https://doaj.org/article/79e2fe16a9cc4cc6b12cd4a833b36af4
Publikováno v:
BMC Genomics, Vol 17, Iss S10, Pp 175-186 (2016)
Abstract Background Secondary structures form the scaffold of multiple sequence alignment of non-coding RNA (ncRNA) families. An accurate reconstruction of ancestral ncRNAs must use this structural signal. However, the inference of ancestors of a sin
Externí odkaz:
https://doaj.org/article/1f49b4a2f930420893e73c6b2220e434
Publikováno v:
Mathematics, Vol 8, Iss 9, p 1483 (2020)
Parameter estimation in mathematical models that are based on differential equations is known to be of fundamental importance. For sophisticated models such as age-structured models that simulate biological agents, parameter estimation that addresses
Externí odkaz:
https://doaj.org/article/0e279718c6e84832b30f28e75a035d52
Publikováno v:
Frontiers in Applied Mathematics and Statistics, Vol 3 (2017)
The multiscale model of hepatitis C virus (HCV) dynamics, which includes intracellular viral RNA (vRNA) replication, has been formulated in recent years in order to provide a new conceptual framework for understanding the mechanism of action of a var
Externí odkaz:
https://doaj.org/article/10139ae7b89441adbc6e88487c4cf09c
Autor:
Yann Ponty, Vladimir Reinharz
Publikováno v:
From Sequences to Graphs. :185-231
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::e07dca796c42355473c9cb6297852df2
https://doi.org/10.1002/9781394169641.ch6
https://doi.org/10.1002/9781394169641.ch6
Autor:
Gabriel Loyer, Vladimir Reinharz
The prediction of RNA structure canonical base pairs from a single sequence, especially pseudoknotted ones, remains challenging in a thermodynamic models that approximates the energy of the local 3D motifs joining canonical stems. It has become more
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::09f300bec76ed4341bf440cf7903d04f
https://doi.org/10.1101/2023.03.09.531928
https://doi.org/10.1101/2023.03.09.531928
AlphaFold2 (AF) is a promising tool, but is it accurate enough to predict single mutation effects? Here, we report that a measure for localized structural deformation between protein pairs differing by only 1-3 mutations is correlated across 4,645 ex
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::c531844108471de321df986914b03a80
https://doi.org/10.1101/2022.04.14.488301
https://doi.org/10.1101/2022.04.14.488301