2 citations · 4 across the 9 of their papers we have counts for
13 papers
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…
On an enhancement of RNA probing data using Information Theory
Thomas J. X. Li, Christian M. Reidys
Identifying the secondary structure of an RNA is crucial for understanding its diverse regulatory functions. This paper focuses on how to enhance target identification in a Boltzma…
The block spectrum of RNA pseudoknot structures
Thomas J. X. Li, Christina S. Burris, Christian M. Reidys
In this paper we analyze the length-spectrum of blocks in -structures. -structures are a class of RNA pseudoknot structures that plays a key role in the context of polynomial…
The rainbow-spectrum of RNA secondary structures
Thomas J. X. Li, Christian M. Reidys
In this paper we analyze the length-spectrum of rainbows in RNA secondary structures. A rainbow in a secondary structure is a maximal arc with respect to the partial order induced…
From unicellular fatgraphs to trees
Thomas J. X. Li, Christian M. Reidys
In this paper we study the minimum number of reversals needed to transform a unicellular fatgraph into a tree. We consider reversals acting on boundary components, having the natur…
Statistics of topological RNA structures
Thomas J. X. Li, Christian M. Reidys
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 second…
RNA secondary structures having a compatible sequence of certain nucleotide ratios
Christopher L. Barrett, Thomas J. X. Li, Christian M. Reidys
Given a random RNA secondary structure, , we study RNA sequences having fixed ratios of nuclotides that are compatible with . We perform this analysis for RNA secondary struc…
A combinatorial interpretation of the coefficients
Thomas J. X. Li, Christian M. Reidys
Studying the virtual Euler characteristic of the moduli space of curves, Harer and Zagier compute the generating function of unicellular maps of genus . They furthermor…
The topological filtration of -structures
Thomas J. X. Li, Christian M. Reidys
In this paper we study -structures filtered by topological genus. -structures are a class of RNA pseudoknot structures that plays a key role in the context of polynomial time…
Combinatorics of -structures
Hillary S. W. Han, Thomas J. X. Li, Christian M. Reidys
In this paper we study canonical -structures, a class of RNA pseudoknot structures that plays a key role in the context of polynomial time folding of RNA pseudoknot structures.…
Combinatorial analysis of interacting RNA molecules
Thomas J. X. Li, Christian M. Reidys
Recently several minimum free energy (MFE) folding algorithms for predicting the joint structure of two interacting RNA molecules have been proposed. Their folding targets are inte…
Combinatorics of RNA-RNA interaction
Thomas J. X. Li, Christian M. Reidys
RNA-RNA binding is an important phenomenon observed for many classes of non-coding RNAs and plays a crucial role in a number of regulatory processes. Recently several MFE folding a…