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Article
RNA folding kinetics using Monte Carlo and Gillespie algorithms
RNA secondary structure folding kinetics is known to be important for the biological function of certain processes, such as the hok/sok system in E. coli. Although linear algebra provides an exact computational s...
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Article
Open AccessNew tools to analyze overlap** coding regions
Retroviruses transcribe messenger RNA for the overlap** Gag and Gag-Pol polyproteins, by using a programmed -1 ribosomal frameshift which requires a slippery sequence and an immediate downstream stem-loop se...
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Article
Open AccessRNAdualPF: software to compute the dual partition function with sample applications in molecular evolution theory
RNA inverse folding is the problem of finding one or more sequences that fold into a user-specified target structure s 0, i.e. whose minimum free energy secondary structure is identical...
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Article
Open AccessDesigning synthetic RNAs to determine the relevance of structural motifs in picornavirus IRES elements
The function of Internal Ribosome Entry Site (IRES) elements is intimately linked to their RNA structure. Viral IRES elements are organized in modular domains consisting of one or more stem-loops that harbor c...
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Article
RNA folding pathways and kinetics using 2D energy landscapes
RNA folding pathways play an important role in various biological processes, such as (i) the hok/sok (host-killing/suppression of killing) system in E. coli to check for sufficient plasmid copy number, (ii) the c...
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Article
Combinatorics of locally optimal RNA secondary structures
It is a classical result of Stein and Waterman that the asymptotic number of RNA secondary structures is $$1.104366 \cdot n^{-3/2} \cd...
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Article
Asymptotic Number of Hairpins of Saturated RNA Secondary Structures
In the absence of chaperone molecules, RNA folding is believed to depend on the distribution of kinetic traps in the energy landscape of all secondary structures. Kinetic traps in the Nussinov energy model are...
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Article
Open AccessAsymptotic structural properties of quasi-random saturated structures of RNA
RNA folding depends on the distribution of kinetic traps in the landscape of all secondary structures. Kinetic traps in the Nussinov energy model are precisely those secondary structures that are saturated, meani...
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Chapter and Conference Paper
Abstract: Using the Fast Fourier Transform to Accelerate the Computational Search for RNA Conformational Switches
We describe the broad outline of a new thermodynamics-based algorithm, FFTbor, that uses the fast Fourier transform to perform polynomial interpolation to compute the Boltzmann probability that secondary structur...
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Article
On the page number of RNA secondary structures with pseudoknots
Let \({\mathcal {S}}\) denote the set of (possibly noncanonical) base pairs {i, j} of an RNA tertiary structure; i.e....
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Article
Expected distance between terminal nucleotides of RNA secondary structures
In “The ends of a large RNA molecule are necessarily close”, Yoffe et al. (Nucleic Acids Res 39(1):292–299, 2011) used the programs $$...
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Article
Open AccessMaximum expected accuracy structural neighbors of an RNA secondary structure
Since RNA molecules regulate genes and control alternative splicing by allostery, it is important to develop algorithms to predict RNA conformational switches. Some tools, such as paRNAss, RNAshapes and RNAbor, c...
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Article
Introduction to special issue on RNA
In this introduction to the special issue on RNA, we provide a brief overview of some of the novel and exciting biological discoveries concerning diverse roles played by RNA, and subsequently we give a rapid s...
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Chapter and Conference Paper
Protein Structure Prediction with Large Neighborhood Constraint Programming Search
Protein structure predictions is regarded as a highly challenging problem both for the biology and for the computational communities. Many approaches have been developed in the recent years, moving to increasi...
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Article
Symmetric time war**, Boltzmann pair probabilities and functional genomics
Given two time series, possibly of different lengths, time war** is a method to construct an optimal alignment obtained by stretching or contracting time intervals. Unlike pairwise alignment of amino acid se...
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Article
Bioinformatik
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Chapter and Conference Paper
Protein Folding, the Levinthal Paradox and Rapidly Mixing Markov Chains
In [20,21], A. Šali, E. Shakhnovich and M. Karplus modeled protein folding using a 27-bead heteropolymer on a cubic lattice with normally distributed contact energies; i.e.
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Chapter and Conference Paper
Evolution as a computational engine
Given a finite set K of lethal genes, a starting genome x and a desired target genome y, is there a sequence of base insertions, deletions, and substitutions, which from x produces the desired genome y, and such ...
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Chapter and Conference Paper
A safe recursion scheme for exponential time
Using a function algebra characterization of exponential time due to Monien [5], in the style of Bellantoni-Cook [2], we characterize exponential time functions of linear growth via a safe course-of-values recurs...
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Article
Cutting planes, connectivity, and threshold logic
Originating from work in operations research the cutting plane refutation systemCP is an extension of resolution, where unsatisfiable propositional logic formulas in conjunctive normal form are recognized by show...
