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Irreducibility in RNA Structures [PDF]
Bulletin of Mathematical Biology, 2009 In this paper we study irreducibility in RNA structures. By RNA structure we mean RNA secondary as well as RNA pseudoknot structures. In our analysis we shall contrast random and minimum free energy (mfe) configurations. We compute various distributions: of the numbers of irreducible substructures, their locations and sizes, parameterized in terms of ...
Jin, Emma Y., Reidys, Christian M.
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RNA structure probing reveals the structural basis of Dicer binding and cleavage
Nature Communications, 2021 It is known that an RNA’s structure determines its biological function, yet current RNA structure probing methods only capture partial structure information.
Qingjun Luo +8 more
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Nature Communications, 2023 T-box riboswitches are unique riboregulators where gene regulation is mediated through interactions between two highly structured RNAs. Despite extensive structural insights, how RNA-RNA interactions drive the folding and structural transitions of T-box ...
Xiaolin Niu +5 more
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Recent Advances in Targeted Nanocarriers for the Management of Triple Negative Breast Cancer
Pharmaceutics, 2023 Triple-negative breast cancer (TNBC) is a life-threatening form of breast cancer which has been found to account for 15% of all the subtypes of breast cancer.
Rajesh Pradhan +5 more
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Canonical RNA Pseudoknot Structures [PDF]
Journal of Computational Biology, 2008 21 pages,7 ...
Ma, Gang, Reidys, Christian M.
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Cooperativity and Interdependency between RNA Structure and RNA–RNA Interactions
Non-Coding RNA, 2021 Complex RNA–RNA interactions are increasingly known to play key roles in numerous biological processes from gene expression control to ribonucleoprotein granule formation.
Ilias Skeparnias, Jinwei Zhang
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Viruses, 2020 The 3′-terminal stem-loop (3′SL) of the RNA genome of the flavivirus West Nile (WNV) harbors, in its stem, one of the sequence elements that are required for genome cyclization.
Alexandra Meyer +7 more
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RNA STRUCTURAL SEGMENTATION [PDF]
, 2009 We describe several dynamic programming segmentation algorithms to segment RNA secondary and tertiary structures into distinct domains. For this purpose, we consider fitness functions that variously depend on (i) base pairing probabilities in the Boltzmann low energy ensemble of structures, (ii) contact maps inferred from 3-dimensional structures, and (
Ivan, Dotú +3 more
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SS/SW BASE PAIRS ARE THE ONLY BASE PAIRS INVOLVED IN LONG-RANGE RNA TERTIARY MOTIFS
Journal of Bioinformatics and Genomics, 2020 The structure of noncoding RNAs largely determines their functions. With the rapid growth of experimental data on the RNA secondary structures, the task of predicting its spatial structure becomes the most urgent task of RNA bioinformatics.
Manakov, A.K. +2 more
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Fundamental Research, 2022 To enable diverse functions and precise regulation, an RNA sequence often folds into complex yet distinct structures in different cellular states. Probing RNA in its native environment is essential to uncovering RNA structures of biological contexts ...
Meiling Piao +12 more
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