Mathematical Biocomplexity
Mathematical Biocomplexity

Publications

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Our Scholarly Work

Search our numerous publications, which reflect our research expertise and scholarly work. Publications are searchable by topic area or keyword, such as an author’s last name, publication, year, etc.

All Publications

Mathematical Biocomplexity
Preprint/Prospective Article

Garden-of-Eden states and fixed points of monotone dynamical systems

Chen R; Mortveit H; Reidys C . arXiv preprint arXiv:1805.03163. arxiv.org. 2018;
Mathematical Biocomplexity
Article

Linear sequential dynamical systems, incidence algebras, and Möbius functions

Chen R; Reidys C . Linear Algebra and its Applications. Elsevier. 2018; 553:270-291
Mathematical Biocomplexity
Preprint/Prospective Article

Network tomography: a new structure spectrum for studying network dynamics

Chen R; Reidys C; Bura A . arXiv preprint arXiv:1810.07004. arxiv.org. 2018;
Mathematical Biocomplexity
Article

A Combinatorial Identity Concerning Plane Colored Trees and its Applications.

Chen R; Reidys C . J. Integer Seq.. Amser. 2017; 20
Mathematical Biocomplexity
Article

Fatgraph models of RNA structure

Huang F; Reidys C; Rezazadegan R . Molecular Based Mathematical Biology. Directory of Open Access Journals. 2017; 5(1):44216
Mathematical Biocomplexity
Part of Book

Geometric combinatorics and computational molecular biology: branching polytopes for RNA sequences

Drellich E; Gainer-Dewar A; Harrington H; He Q; Heitsch C; Poznanovic S . Algebraic and Geometric Methods in Discrete Mathematics. American Mathematical Soc.. 2017; 685:137-154
Mathematical Biocomplexity
Article

Sequence–structure relations of biopolymers

Barrett C; Huang F; Reidys C . Bioinformatics. Oxford University Press. 2017; 33(3):382-389
Mathematical Biocomplexity
Article

Statistics of topological RNA structure

Li T; Reidys C . Journal of Mathematical Biology. Springer Berlin Heidelberg. 2017;
Mathematical Biocomplexity
Article

Statistics of topological RNA structures

Li, T; Reidys C . Journal of mathematical biology. Springer. 2017; 74(7):1793-1821
Mathematical Biocomplexity
Article

A topological framework for signed permutations

Huang F; Reidys C . Discrete Mathematics. Elsevier. 2017; 340(9):2161-2182
Mathematical Biocomplexity
Research Paper

Algebraic geometry arising from discrete models of gene regulatory networks

He Q 2016;
Mathematical Biocomplexity
Preprint/Prospective Article

On a lower bound for sorting signed permutations by reversals

Bura A; Chen R; Reidys C . arXiv preprint arXiv:1602.00778. arxiv.org. 2016;
Mathematical Biocomplexity
Article

Plane Permutations and Applications to a Result of Zagier--Stanley and Distances of Permutations

Chen R; Reidys C . SIAM Journal on Discrete Mathematics. SIAM. 2016;
Mathematical Biocomplexity
Article

Stratification and enumeration of boolean functions by canalizing depth

He Q; Macauley M . Physica D: Nonlinear Phenomena. Elsevier. 2016; 314:44204
Mathematical Biocomplexity
Preprint/Prospective Article

The boundary length and point spectrum enumeration of partial chord diagrams using cut and join recursion

Andersen J; Fuji H; Penner R; Reidys C . arXiv preprint arXiv …. arxiv.org. 2016;
Mathematical Biocomplexity
Preprint/Prospective Article

On the local genus distribution of graph embeddings

Chen R; Reidys C . arXiv preprint arXiv:1601.02574. arxiv.org. 2016;
Mathematical Biocomplexity
Article

Topological language for RNA

Huang F; Reidys C . Mathematical biosciences. Elsevier. 2016; 282:109-120
Mathematical Biocomplexity
Preprint/Prospective Article

Another combinatorial proof of a result of Zagier and Stanley

Chen R; Reidys C . arXiv preprint arXiv:1502.07674. arxiv.org. 2015;
Mathematical Biocomplexity
Part of Book

Dynamics of Complex Boolean Networks: Canalization, Stability, and Criticality

He Q; Macauley M; Davies R . Algebraic and Discrete Mathematical Methods for Modern Biology. Elsevier. 2015; :93-119
Mathematical Biocomplexity
Preprint/Prospective Article

New formulas counting one-face maps and Chapuy's recursion

Chen R; Reidys C . arXiv preprint arXiv:1510.05038. arxiv.org. 2015;
Mathematical Biocomplexity
Article

RNA Secondary Structures: An Approach Through Pseudoknots and Fatgraphs

Reidys C . Algebraic and Discrete Mathematical Methods for …. Elsevier. 2015; :347-362
Mathematical Biocomplexity
Part of Book

RNA Secondary Structures: Combinatorial Models and Folding Algorithms

He Q; Macauley M; Davies R . Algebraic and Discrete Mathematical Methods for Modern Biology. Elsevier. 2015; :321-345
Mathematical Biocomplexity
Article

On RNA–RNA interaction structures of fixed topological genus

Fu B; Han H; Reidys C . Mathematical Biosciences. Elsevier. 2015; 262:88-104
Mathematical Biocomplexity
Article

Shapes of topological RNA structures

Huang F; Reidys C . Mathematical biosciences. Elsevier. 2015; 270:57-65
Mathematical Biocomplexity
Preprint/Prospective Article

A simple framework on sorting permutations

Chen R; Reidys C . arXiv preprint arXiv:1502.07971. arxiv.org. 2015;