Random versus Deterministic Descent in RNA Energy Landscape Analysis

Autor: Andreas Alexander Albrecht, Luke Day, Kathleen Steinhöfel, Ouala Abdelhadi Ep Souki

Publikováno v: Day, L J, Abdelhadi Ep Souki, O, Albrecht, A & Steinhofel, K K 2016, ' Random versus Deterministic Descent in RNA Energy Landscape Analysis ', Advances in Bioinformatics . https://doi.org/10.1155/2016/9654921
Advances in Bioinformatics, Vol 2016 (2016)
Advances in Bioinformatics

Identifying sets of metastable conformations is a major research topic in RNA energy landscape analysis, and recently several methods have been proposed for finding local minima in landscapes spawned by RNA secondary structures. An important and time

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::1b76ddad95fac83269c277975f8cc062
https://doi.org/10.1155/2016/9654921

CRISPR/Cas9 editing reveals novel mechanisms of clustered microRNA regulation and function

Autor: Anna Zampetaki, Simon M. Hughes, Manuel Mayr, Lazaros Lataniotis, Clinton A. L. Monfries, Andreas Alexander Albrecht, Fatma O. Kok, Kathleen Steinhöfel, Lorena Benedetti, Nathan D. Lawson

Publikováno v: Scientific Reports
Scientific Reports, Vol 7, Iss 1, Pp 1-14 (2017)
Lataniotis, L, Albrecht, A, Kok, F O, Monfries, C A L, Benedetti, L, Lawson, N D, Hughes, S, Steinhofel, K, Mayr, M & Zampetaki, A 2017, ' CRISPR/Cas9 editing reveals novel mechanisms of clustered microRNA regulation and function ', Scientific Reports, vol. 7, no. 1, pp. 8585 . https://doi.org/10.1038/s41598-017-09268-0

MicroRNAs (miRNAs) are important regulators of diverse physiological and pathophysiological processes. MiRNA families and clusters are two key features in miRNA biology. Here we explore the use of CRISPR/Cas9 as a powerful tool to delineate the funct

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::445d89980fadf2a151f761b931a9cd79
http://europepmc.org/articles/PMC5561095

Accessibility of microRNA binding sites in metastable RNA secondary structures in the presence of SNPs

Autor: Andreas Alexander Albrecht, Ouala Abdelhadi Ep Souki, Kathleen Steinhöfel, Luke Day

Publikováno v: Bioinformatics. 30:343-352

Motivation: We study microRNA (miRNA) bindings to metastable RNA secondary structures close to minimum free energy conformations in the context of single nucleotide polymorphisms (SNPs) and messenger RNA (mRNA) concentration levels, i.e. whether feat

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::7c0d462c112376da97f201f181f3db5a
https://doi.org/10.1093/bioinformatics/btt695

Uphill unfolding of native protein conformations in cubic lattices

Autor: Andreas Alexander Albrecht, Leonidas Kapsokalivas, Kathleen Steinhöfel

Publikováno v: Journal of Computational Science. 1:6-12

We present results from simulations of unfolding in cubic lattices with two types of simplified energy functions, namely the Miyazawa–Jernigan (MJ) energy function and the hydrophobic-polar (HP) model. The simulations are executed on six benchmark

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::1e74702a84e86a160e57b59c70268854
https://doi.org/10.1016/j.jocs.2010.01.001

Population-based local search for protein folding simulation in the MJ energy model and cubic lattices

Autor: Leonidas Kapsokalivas, Kathleen Steinhöfel, Andreas Alexander Albrecht, Xiangchao Gan

Publikováno v: Computational Biology and Chemistry. 33:283-294

We present experimental results on benchmark problems in 3D cubic lattice structures with the Miyazawa-Jernigan energy function for two local search procedures that utilise the pull-move set: (i) population-based local search (PLS) that traverses the

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::d24a87736cb82cb637ed8eb4f79c69f4
https://doi.org/10.1016/j.compbiolchem.2009.06.006