TangleSolve: topological analysis of site-specific recombination. - Yuki Saka; Mariel Vázquez (Bioinform., 2002)

Comparing DNA Damage-Processing Pathways by Computer Analysis of Chromosome Painting Data. - Dan Levy; Mariel Vázquez; Michael Cornforth; Bradford Loucas; Rainer K. Sachs; Javier Arsuaga (J. Comput. Biol., 2004)

SCHIP: statistics for chromosome interphase positioning based on interchange data. - Sergi Vives; Bradford Loucas; Mariel Vázquez; David J. Brenner; Rainer K. Sachs; Lynn Hlatky; Michael Cornforth; Javier Arsuaga (Bioinform., 2005)

Site-Specific Recombination Modeled as a Band Surgery: Applications to Xer Recombination. - Kai Ishihara; Koya Shimokawa; Mariel Vázquez (Discrete and Topological Models in Molecular Biology, 2014)

A Symmetry Motivated Link Table. - Shawn Witte; Michelle Flanner; Mariel Vázquez (Symmetry, 2018)

Tree polynomials identify a link between co-transcriptional R-loops and nascent RNA folding. - Pengyu Liu 003; Jacob Lusk; Natasa Jonoska; Mariel Vázquez (PLoS Comput. Biol., 2024)