# Publications

### 2017

• Maximum likelihood estimates of pairwise rearrangement distances

• Enumerating Transformation Semigroups

• Computing Finite Semigroups

### 2016

• Finite Computational Structures and Implementations

• On the atoms of algebraic lattices arising in $q$-theory

### 2015

• Symmetries of Automata

• Algebraic double cut and join - A group-theoretic approach to the operator on multichromosomal genomes

• Symmetry structure in discrete models of biochemical systems: natural subsystems and the weak control hierarchy in a new model of computation driven by interactions

• Computational Understanding and Manipulation of Symmetries

### 2014

• SgpDec: Cascade (De)Compositions of Finite Transformation Semigroups and Permutation Groups

• Bacterial Genomics and Computational Group Theory: The BioGAP Package for GAP

• Group-theoretic models of the inversion process in bacterial genomes

### 2013

• Exploring the concept of interaction computing through the discrete algebraic analysis of the Belousov–Zhabotinsky reaction

### 2012

• BIOMICS Project: Biological and Mathematical Basis of Interaction Computing

• Algebraic Analysis of the Computation in the Belousov-Zhabotinksy Reaction

### 2011

• How to Solve it? - The Tsumego Session

• Symmetries of Automata (extended abstract)

• Algorithms for the Efficient Calculation of the Holonomy Decomposition (extended abstract)

• Book Review: Applications of Automata Theory and Algebra via the Mathematical Theory of Complexity to Biology, Physics, Psychology, Philosophy, and Games by John Rhodes

### 2010

• On the Skeleton of a Transformation Semigroup

• On Straight Words and Minimal Permutators in Finite Transformation Semigroups

• Transformation Semigroups as Constructive Dynamical Spaces

### 2008

• Automatic Analysis of Computation in BioChemical Reactions

• Algebraic Properties of Automata Associated to Petri Nets and Applications to Computation in Intermediary Metabolism

• Hierachical Coordinate Systems for Understanding Complexity and its Evolution with Applications to Genetic Regulatory Networks

### 2007

• Finite residue class rings of integers modulo $n$ from the viewpoint of global semigroup theory

• [HUN] Mesterséges élet és megértés

• Mirroring, Deixis, and Interaction Topology in the Emergence of Shared Vocabularies

### 2006

• Making Sense of the Sensory Data - Coordinate Systems by Hierarchical Decomposition

### 2005

• Cycle Structure in Automata and the Holonomy Decomposition

### 2004

• [HUN] A spirálok szépségéről

• Algebraic Hierarchical Decomposition of Finite State Automata: Comparison of Implementations for Krohn-Rhodes Theory

### 2003

• Evolvability of the Genotype-Phenotype Relation in Populations of Self-Replicating Digital Organisms in a Tierra-like System

• [HUN] Digitális evolúció

### 1997

• [HUN] A lét értelmére vonatkozó kérdés ismételt felvetése - Túl misztikán és logikán