Margherita Maria Ferrari’s research applies combinatorial and topological methods to analyze complex biomolecular processes, focusing on DNA self-assembly and DNA:RNA interactions. She develops mathematical models and graph-theoretical approaches—using graph invariants, edge-colorings, and decompositions—to optimize the design of DNA nanostructures from branched junctions. Her work also utilizes formal stochastic grammars and directed graphs to predict R-loop formations and investigate RNA-mediated DNA repair mechanisms. Furthermore, she employs graph algorithms for analyzing RNA secondary structures, building upon her expertise in discrete mathematics and graph theory.

Current trainees

Recent Publications (Past 5 Years)

A multipartite approach for the self-assembly of DNA graph structures

Simona Bonvicini , M. Ferrari
Natural Computing 2025-10-04
0 citations

The R-loop grammar predicts R-loop formation under different topological constraints

M. Ferrari , Svetlana Poznanovic , Manda Riehl , Jacob Lusk , Stella R. Hartono , Georgina Gonzalez-Isunza , F. Chédin , Mariel Vázquez , Nataša Jonoska
PLoS Comput. Biol. 2025-08-01
2 citations

RNA-mediated double-strand break repair by end-joining mechanisms

Youngkyu Jeon , Yilin Lu , M. Ferrari , Tejasvi Channagiri , Penghao Xu , Chance Meers , Yiqi Zhang , S. Balachander , Vivian S. Park , Stefania Marsili , Z. Pursell , Nataša Jonoska , F. Storici
Nature Communications 2024-09-11
15 citations

DSBplot: Indels in DNA Double-strand Break Repair Experiments.

Tejasvi Channagiri , M. Ferrari , Youngkyu Jeon , Penghao Xu , F. Storici , Natavsa Jonoska
arXiv.org 2023-12-29
0 citations
0 citations

RNA-mediated double-strand break repair in human cells

Youngkyu Jeon , M. Ferrari , Tejasvi Channagiri , Penghao Xu , S. Balachander , Vivian S. Park , Stefania Marsili , Z. Pursell , N. Jonoska , F. Storici
bioRxiv 2022-11-01
0 citations

On non-isomorphic biminimal pots realizing the cube

M. Ferrari , A. Pasotti , T. Traetta
2022-10-27
3 citations