Zobrazeno 1 - 10
of 99
pro vyhledávání: '"Heitsch Christine"'
Publikováno v:
Computational and Mathematical Biophysics, Vol 7, Iss 1, Pp 48-63 (2019)
A riboswitch is a type of RNA molecule that regulates important biological functions by changing structure, typically under ligand-binding. We assess the extent that these ligand-bound structural alternatives are present in the Boltzmann sample, a st
Externí odkaz:
https://doaj.org/article/88395d15ff644c7fad20bb7d98f53a4c
Autor:
Hurley, Forrest, Heitsch, Christine
Understanding the base pairing of an RNA sequence provides insight into its molecular structure.By mining suboptimal sampling data, RNAprofiling 1.0 identifies the dominant helices in low-energy secondary structures as features, organizes them into p
Externí odkaz:
http://arxiv.org/abs/2303.15552
Autor:
Heitsch, Christine
The Kreweras complementation map is an anti-isomorphism on the lattice of noncrossing partitions. We consider an analogous operation for plane trees motivated by the molecular biology problem of RNA folding. In this context, we explicitly count the o
Externí odkaz:
http://arxiv.org/abs/2303.12240
The branching of an RNA molecule is an important structural characteristic yet difficult to predict correctly, especially for longer sequences. Using plane trees as a combinatorial model for RNA folding, we consider the thermodynamic cost, known as t
Externí odkaz:
http://arxiv.org/abs/2303.12227
A growing number of RNA sequences are now known to have distributions of multiple stable sequences. Recent algorithms use the list of nucleotides in a sequence and auxiliary experimental data to predict such distributions. Although the algorithms are
Externí odkaz:
http://arxiv.org/abs/1801.03055
The prevalent method for RNA secondary structure prediction for a single sequence is free energy minimization based on the nearest neighbor thermodynamic model (NNTM). One of the least well-developed parts of the model is the energy function assigned
Externí odkaz:
http://arxiv.org/abs/1708.05554
Autor:
Drellich, Elizabeth, Gainer-Dewar, Andrew, Harrington, Heather A., He, Qijun, Heitsch, Christine, Poznanović, Svetlana
Questions in computational molecular biology generate various discrete optimization problems, such as DNA sequence alignment and RNA secondary structure prediction. However, the optimal solutions are fundamentally dependent on the parameters used in
Externí odkaz:
http://arxiv.org/abs/1509.04090
We analyze the distribution of RNA secondary structures given by the Knudsen-Hein stochastic context-free grammar used in the prediction program Pfold. We prove that the distribution of base pairs, helices and various types of loops in RNA secondary
Externí odkaz:
http://arxiv.org/abs/1204.3670
Autor:
Cooper, Joshua, Heitsch, Christine E.
The skew of a binary string is the difference between the number of zeroes and the number of ones, while the length of the string is the sum of these two numbers. We consider certain suffixes of the lexicographically-least de Bruijn sequence at natur
Externí odkaz:
http://arxiv.org/abs/1003.5939
Autor:
Hower, Valerie, Heitsch, Christine E.
We extend recent methods for parametric sequence alignment to the parameter space for scoring RNA folds. This involves the construction of an RNA polytope. A vertex of this polytope corresponds to RNA secondary structures with common branching. We us
Externí odkaz:
http://arxiv.org/abs/0904.3700