C. E. Heitsch Publications

The common denominator in my work is the field of combinatorics on words, an area at the juncture of mathematics and computer science with increasingly important biological applications.

Preprints and available Reprints

C. E. Heitsch, Kreweras Complementation and Orbits in Catalan Lattices, submitted to the Journal of Combinatorial Theory, Series A.
Preprint (34 pages)
C. E. Heitsch, Combinatorics on Plane Trees, Motivated by RNA Secondary Structure Reconfigurations, submitted to the SIAM Journal on Discrete Mathematics.
Preprint (47 pages)
C. E. Heitsch, Intractability of the Reductive Decision Procedure for Unavoidability Testing, a Special Case of Generalized Pattern Matching, submitted to Journal of Algorithms.
Preprint (39 pages)
C. E. Heitsch, Insufficiency of Four Known Necessary Conditions on String Unavoidability, Journal of Algorithms, 56(2):96-123, 2005.
Preprint (37 pages) Online reprint from Science Direct
C. E. Heitsch, A. E. Condon, H. H. Hoos, From RNA Secondary Structure to Coding Theory: A Combinatorial Approach, in Proceedings of the Eighth International Meeting on DNA Based Computers (DNA8), Lecture Notes in Computer Science, Springer-Verlag, Sapporo, Japan, June 2002.
Preprint (14 pages) Online reprint from SpringerLink
C. E. Heitsch, Exact Distribution of Deletion Sizes for Unavoidable Strings, in Proceedings of the 8th International Symposium on String Processing and Information Retrieval (SPIRE'01), IEEE Computer Society Press, Laguna de San Rafael, Chile, November 2001.
Preprint (8 pages)
C. E. Heitsch, Generalized Pattern Matching and the Computational Complexity of Unavoidability Testing, in Proceedings of the 12th Annual Symposium on Combinatorial Pattern Matching (CPM 2001), Lecture Notes in Computer Science, Springer-Verlag, Jerusalem, Israel, July 2001.
Preprint (12 pages) Online reprint from SpringerLink

Forthcoming Papers

C. E. Heitsch, Combinatorial Insights Into RNA Secondary Structure, in preparation for the Journal of Computational Biology.
C. E. Heitsch, Enumerating Pseudoknotted RNA Secondary Structures and Dual Graphs, in preparation.
C. E. Heitsch, A. E. Condon, H. H. Hoos, The Limits of Simplicity: a Combinatorial Solution to RNA Secondary Structure Design, in progress.
C. E. Heitsch, Random De Bruijn Sequences and the Design of DNA Codewords, in progress.

Abstracts for Poster Presentations

Analyzing the Branching Degree of RNA Viral Genomes: A Hepatitis C Case Study. The Ninth Annual International Conference on Research in Computational Molecular Biology (RECOMB 2005), Cambridge, MA, May 17 - 18, 2005.
Abstract and poster handout.
Biochemical Properties of Random de Bruijn Sequences, with M. Li and R. Corn. Digital Biology: The Emerging Paradigm, Biomedical Information Science and Technology Initiative (BISTI) Symposium, National Institutes of Health, Bethesda, MD, November 6-7, 2003.
Abstract and poster handout.
Towards the Design of RNA Molecules with A. E. Condon and H. H. Hoos. Mathematics and Molecular Biology VII: Modeling Across the Scales -- Atoms to Organisms, Santa Fe, NM, January 9, 2002.
Abstract and poster handout.

Christine E. Heitsch
Last modified 21.01.05