Publications and Preprints

The Topological Properties of the Protein Universe. Joint with C.D.Madsen, S.Y.Zhang, L.Ham, A.Davis, D.Pires and M.P.H.Stumpf, 2023, bioaRxiv, Nature Communications

Topological Optimal Transport for Geometric Cycle Matching. Joint with S.Y.Zhang, M.P.H.Stumpf and T.Needham, 2025,  J. Appl. Comput. Topol. , ArXiv

Topology in soft and biological matter. EUTOPIA collaboration, 2024, Physics Reports

GridPyM: a Python module to handle grid diagrams. Joint with D.Celoria, 2022, ArXiv , J. Softw. Alg. Geom..  

Homology of Homologous Knotted proteins. Joint with K.Benjamin, L.Mukta, G.Moryoussef, C.Uren, H.A.Harrington and U.Tillmann, 2022,  ArXiv  Royal Society Interface 

A topological selection of folding pathways from native states of knotted proteins. Joint with N.Yerolemou,O.Vipond, B.I.Mahler, P.Dabrowski-Tumanski and D.Goundaroulis, 2021. Symmetry. Symmetry  ArXiv

F-distance of knotoids and protein structure. Joint with D.Goundaroulis. Proceedings of the Royal Society A, 2021.  PRSA  ArXiv 

Grid diagrams as tools to investigate knot spaces and topoisomerase-mediated simplification of DNA topology. Joint with D.Celoria, H.A.Harrington, A.Stasiak and D.Buck, Science Advances,2020 .  ScienceAdvances  ArXiv

Double branched cover of knotoids. Joint with D.Buck, H.A.Harrington, M.Lackenby, 2019 ArXiv   Communications in Analysis & Geometry 

 The Reidemeister graph is a complete knot invariant. Joint with D.Celoria, Algebraic & Geometric Topology, 2018.  AGT  ArXiv

An exploration of low crossing and chiral cosmetic bands with grid diagrams. Joint with D.Celoria, C.Ktenidis 2025, ArXiv

Topologically Directed Simulations Reveal the Impact of Geometric Constraints on Knotted Proteins. Joint with A.Klotz and D.Goundaroulis, 2025, ArXiv 

Geometry of the Space of Partitioned Networks: A Unified Theoretical and Computational Framework. Joint with S.Y.Zhang, F.Lan, Y.Zhou, B.Wang, M.P.H.Stumpf and T.Needham, 2024, ArXiv

Knot intensity distribution: a local measure of entanglement. Joint with D.Celoria, 2022, ArXiv

Hypergraphs for multiscale cycles in structured data. Joint with H. Yoon, C.D. Madsen, D.O.  Ajayi, M.P.H. Stumpf, H.A. Harrington, 2022,  ArXiv