5 citations · 8 across the 7 of their papers we have counts for
8 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…
Loop Homology of Bi-secondary Structures II
Andrei C. Bura, Qijun He, Christian M. Reidys
In this paper we further describe the features of the topological space obtained from the loop nerve of , for a bi-secondary structure. We will first identify c…
Loop Homology of Bi-secondary Structures
Andrei C. Bura, Qijun He, Christian M. Reidys
In this paper we compute the loop homology of bi-secondary structures. Bi-secondary structures were introduced by Haslinger and Stadler and are pairs of RNA secondary structures, i…
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…
Small Groebner Fans of Ideals of Points
Elena Dimitrova, Qijun He, Lorenzo Robbiano +1
In the context of modeling biological systems, it is of interest to generate ideals of points with a unique reduced Groebner basis, and the first main goal of this paper is to iden…
Geometric combinatorics and computational molecular biology: branching polytopes for RNA sequences
Elizabeth Drellich, Andrew Gainer-Dewar, Heather A. Harrington +3
Questions in computational molecular biology generate various discrete optimization problems, such as DNA sequence alignment and RNA secondary structure prediction. However, the op…
Stratification and enumeration of Boolean functions by canalizing depth
Qijun He, Matthew Macauley
Boolean network models have gained popularity in computational systems biology over the last dozen years. Many of these networks use canalizing Boolean functions, which has led to…