33 citations · 161 across the 71 of their papers we have counts for
83 papers
Exact enumeration of RNA secondary structures by helices and loops
Ricky X. F. Chen, Christian M. Reidys, Michael S. Waterman
Enumerative studies of RNA secondary structures were initiated four decades ago by Waterman and his coworkers. Since then, RNA secondary structures have been explored according to…
The site linkage spectrum of data arrays
Christopher Barrett, Andrei Bura, Fenix Huang +1
A new perspective is introduced regarding the analysis of Multiple Sequence Alignments (MSA), representing aligned data defined over a finite alphabet of symbols. The framework is…
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…
A computational framework for weighted simplicial homology
Andrei C. Bura, Neelav S. Dutta, Thomas J. X. Li +1
We provide a bottom up construction of torsion generators for weighted homology of a weighted complex over a discrete valuation ring . This is achieved by starti…
On Weighted Simplicial Homology
Thomas J. X. Li, Christian M. Reidys
We develop a framework for computing the homology of weighted simplicial complexes with coefficients in a discrete valuation ring. A weighted simplicial complex, , introduce…
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…