5 citations · 7 across the 11 of their papers we have counts for
15 papers
The arithmetic topology of genetic alignments
Christopher Barrett, Andrei Bura, Qijun He +2
We propose a novel mathematical paradigm for the study of genetic variation in sequence alignments. This framework originates from extending the notion of pairwise relations, upon…
The energy-spectrum of bicompatible sequences
Fenix W. Huang, Christopher L. Barrett, Christian M. Reidys
Background: Genotype-phenotype maps provide a meaningful filtration of sequence space and RNA secondary structures are particular such phenotypes. Compatible sequences i.e.~sequenc…
Genetic robustness of let-7 miRNA sequence-structure pairs
Qijun He, Fenix W. Huang, Christopher Barrett +1
Genetic robustness, the preservation of evolved phenotypes against genotypic mutations, is one of the central concepts in evolution. In recent years a large body of work has focuse…
An efficient dual sampling algorithm with Hamming distance filtration
Fenix W. Huang, Qijun He, Christopher Barrett +1
Recently, a framework considering RNA sequences and their RNA secondary structures as pairs, led to some information-theoretic perspectives on how the semantics encoded in RNA sequ…
Topological language for RNA
Fenix W. D. Huang, Christian M. Reidys
In this paper we introduce a novel, context-free grammar, {\it RNAFeatures}, capable of generating any RNA structure including pseudoknot structures (pk-structure). We represen…
Sequence-structure relations of biopolymers
Christopher Barrett, Fenix W. Huang, Christian M. Reidys
Motivation: DNA data is transcribed into single-stranded RNA, which folds into specific molecular structures. In this paper we pose the question to what extent sequence- and struct…