PRODORIC: prokaryotic database of gene regulation. - Richard Münch; Karsten Hiller; Heiko Barg; Dana Heldt; Simone Linz; Edgar Wingender; Dieter Jahn (Nucleic Acids Res., 2003)

Hybridization in Nonbinary Trees. - Simone Linz; Charles Semple (IEEE ACM Trans. Comput. Biol. Bioinform., 2009)

Quantifying Hybridization in Realistic Time. - Joshua Collins; Simone Linz; Charles Semple (J. Comput. Biol., 2011)

A First Step Toward Computing All Hybridization Networks For Two Rooted Binary Phylogenetic Trees. - Céline Scornavacca; Simone Linz; Benjamin Albrecht (J. Comput. Biol., 2012)

Cycle Killer...Qu'est-ce que c'est? On the Comparative Approximability of Hybridization Number and Directed Feedback Vertex Set. - Steven Kelk; Leo van Iersel; Nela Lekic; Simone Linz; Céline Scornavacca; Leen Stougie (SIAM J. Discret. Math., 2012)

The Complexity of Finding Multiple Solutions to Betweenness and Quartet Compatibility. - Maria Luisa Bonet; Simone Linz; Katherine St. John (IEEE ACM Trans. Comput. Biol. Bioinform., 2012)

On the complexity of computing the temporal hybridization number for two phylogenies. - Peter J. Humphries; Simone Linz; Charles Semple (Discret. Appl. Math., 2013)

A quadratic kernel for computing the hybridization number of multiple trees. - Leo van Iersel; Simone Linz (Inf. Process. Lett., 2013)

Counting Trees in a Phylogenetic Network Is #P-Complete. - Simone Linz; Katherine St. John; Charles Semple (SIAM J. Comput., 2013)

Optimizing tree and character compatibility across several phylogenetic trees. - Simone Linz; Katherine St. John; Charles Semple (Theor. Comput. Sci., 2013)

Satisfying ternary permutation constraints by multiple linear orders or phylogenetic trees. - Leo van Iersel; Steven Kelk; Nela Lekic; Simone Linz (Theor. Comput. Sci., 2016)

Autumn Algorithm - Computation of Hybridization Networks for Realistic Phylogenetic Trees. - Daniel H. Huson; Simone Linz (IEEE ACM Trans. Comput. Biol. Bioinform., 2018)

On the existence of a cherry-picking sequence. - Janosch Döcker; Simone Linz (Theor. Comput. Sci., 2018)

Attaching leaves and picking cherries to characterise the hybridisation number for a set of phylogenies. - Simone Linz; Charles Semple (Adv. Appl. Math., 2019)

On the Subnet Prune and Regraft Distance. - Jonathan Klawitter; Simone Linz (Electron. J. Comb., 2019)

New reduction rules for the tree bisection and reconnection distance. - Steven Kelk; Simone Linz (CoRR, 2019)

Algorithms and Complexity in Phylogenetics (Dagstuhl Seminar 19443). - Magnus Bordewich; Britta Dorn; Simone Linz; Rolf Niedermeier (Dagstuhl Reports, 2019)

Deciding the existence of a cherry-picking sequence is hard on two trees. - Janosch Döcker; Leo van Iersel; Steven Kelk; Simone Linz (Discret. Appl. Math., 2019)

A Tight Kernel for Computing the Tree Bisection and Reconnection Distance between Two Phylogenetic Trees. - Steven Kelk; Simone Linz (SIAM J. Discret. Math., 2019)

Displaying trees across two phylogenetic networks. - Janosch Döcker; Simone Linz; Charles Semple (Theor. Comput. Sci., 2019)

Computing Close to Optimal Weighted Shortest Paths in Practice. - Nguyet Tran; Michael J. Dinneen; Simone Linz (ICAPS, 2020)

Close Weighted Shortest Paths on 3D Terrain Surfaces. - Nguyet Tran; Michael J. Dinneen; Simone Linz (SIGSPATIAL/GIS, 2020)

Caterpillars on three and four leaves are sufficient to reconstruct normal networks. - Simone Linz; Charles Semple (CoRR, 2020)

Weakly displaying trees in temporal tree-child network. - Katharina T. Huber; Simone Linz; Vincent Moulton (CoRR, 2020)

Placing quantified variants of 3-SAT and Not-All-Equal 3-SAT in the polynomial hierarchy. - Janosch Döcker; Britta Dorn; Simone Linz; Charles Semple (Theor. Comput. Sci., 2020)

Display Sets of Normal and Tree-Child Networks. - Janosch Döcker; Simone Linz; Charles Semple (Electron. J. Comb., 2021)

Reflections on kernelizing and computing unrooted agreement forests. - Rim van Wersch; Steven Kelk; Simone Linz; Georgios Stamoulis (Ann. Oper. Res., 2022)

Deep kernelization for the Tree Bisection and Reconnnect (TBR) distance in phylogenetics. - Steven Kelk; Simone Linz; Ruben Meuwese (CoRR, 2022)

Hypercubes and Hamiltonian Cycles of Display Sets of Rooted Phylogenetic Networks. - Janosch Döcker; Simone Linz; Charles Semple (CoRR, 2022)

Non-essential arcs in phylogenetic networks. - Simone Linz; Charles Semple (J. Comput. Syst. Sci., 2022)

On the Maximum Agreement Subtree Conjecture for Balanced Trees. - Magnus Bordewich; Simone Linz; Megan Owen; Katherine St. John; Charles Semple; Kristina Wicke (SIAM J. Discret. Math., 2022)

On the Complexity of Parameterized Local Search for the Maximum Parsimony Problem. - Christian Komusiewicz; Simone Linz; Nils Morawietz; Jannik Schestag (CPM, 2023)

Cyclic generators and an improved linear kernel for the rooted subtree prune and regraft distance. - Steven Kelk; Simone Linz; Ruben Meuwese (Inf. Process. Lett., 2023)

A QUBO formulation for the Tree Containment problem. - Michael J. Dinneen; Pankaj S. Ghodla; Simone Linz (Theor. Comput. Sci., 2023)

Phylogenetic Trees Defined by at Most Three Characters. - Katharina T. Huber; Simone Linz; Vincent Moulton; Charles Semple (Electron. J. Comb., 2024)

Deep kernelization for the Tree Bisection and Reconnection (TBR) distance in phylogenetics. - Steven Kelk; Simone Linz; Ruben Meuwese (J. Comput. Syst. Sci., 2024)

Hypercubes and Hamilton cycles of display sets of rooted phylogenetic networks. - Janosch Döcker; Simone Linz; Charles Semple (Adv. Appl. Math., 2024)

Cherry picking in forests: A new characterization for the unrooted hybrid number of two phylogenetic trees. - Katharina T. Huber; Simone Linz; Vincent Moulton (Discret. Math. Theor. Comput. Sci., 2025)

On the existence of funneled orientations for classes of rooted phylogenetic networks. - Janosch Döcker; Simone Linz (Theor. Comput. Sci., 2025)