Topological language for RNA

@article{Huang2016TopologicalLF,
  title={Topological language for RNA},
  author={Fenix W. D. Huang and Christian M. Reidys},
  journal={Mathematical biosciences},
  year={2016},
  volume={282},
  pages={
          109-120
        }
}

Fatgraph models of RNA structure

This review paper discusses minimum free energy folding of pk-structures and combines these above results outlining how to obtain an inverse folding algorithm for PK structures.

Statistics of topological RNA structures

A new bivariate generating function is derived whose singular expansion allows for analysis of the distributions of arcs, stacks, hairpin- , interior- and multi-loops and H-type pseudoknots, kissing hairpins and their respective expectation values.

Statistics of topological RNA structures

In this paper we study properties of topological RNA structures, i.e. RNA contact structures with cross-serial interactions that are filtered by their topological genus. RNA secondary structures

Sequence‐structure relations of biopolymers

It is illustrated that there are multiple sequences in the partition function of a fixed structure, each having nearly the same mutual information, that are nevertheless poorly aligned, indicating the possibility of the existence of relevant patterns embedded in the sequences that are not discoverable using alignments.

Structural relation matching: an algorithm to identify structural patterns into RNAs and their interactions

The problem of identifying a given structural pattern into secondary structures or the associated cores or shadow of both RNAs and RNA–RNA interactions, characterized by arbitrary pseudoknots, is faced and these abstractions are mapped into a matrix, whose elements represent the relations among loops.

Topological Classification of RNA Structures via Intersection Graph

An abstract algebraic representation of RNA secondary structures as a composition of hairpins, considered as basic loops, and a novel methodology to classify RNA structures based on two topological invariants, the genus and the crossing number are proposed.

Michael Waterman's Contributions to Computational Biology and Bioinformatics

On the occasion of Dr. Michael Waterman's 80th birthday, a review of his major contributions to the field of computational biology and bioinformatics including the famous Smith-Waterman algorithm for sequence alignment and algorithms for sequence assembly are reviewed.

A reappraisal of the form – function problem. Theory and phenomenology

It is argued that form has an organizing power, hence a causal action, in the sense that it enables to induce functional events during different biological processes, at the supramolecular, cellular, and organismal levels of organization, and clearly topological forms must be matched with specific kinetic and dynamical parameters to have a functional effectiveness in living systems.

Loop homology of bi-secondary structures II

In this paper, we analyze the homology of the simplicial complex induced by a given pair of RNA secondary structures, R=(S,T)\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym}

Input–output maps are strongly biased towards simple outputs

A practical bound is provided on the probability that a randomly generated computer program produces a given output of a given complexity and this upper bound is applied to RNA folding and financial trading algorithms.

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