| Publication | Date of Publication | Type |
|---|
| A Sankoff-Rousseau-like algorithm for minimizing lateral gene transfers and losses on single origin characters | 2026-02-26 | Paper |
Forbidden configurations and dominating bicliques in undirected 2-quasi best match graphs
Discrete Applied Mathematics | 2026-02-24 | Paper |
Unstable cores are the source of instability in chemical reaction networks
Proceedings of the Royal Society of London. A. Mathematical, Physical and Engineering Sciences | 2025-10-08 | Paper |
Atom transition networks and isotope labeling patterns in large chemical reaction networks
MATCH - Communications in Mathematical and in Computer Chemistry | 2025-10-08 | Paper |
On the cut-vertex and the interval transit functions of hypergraphs
Graphs and Combinatorics | 2025-01-10 | Paper |
Core potentials: the consensus segmentation conjecture
Mathematics in Computer Science | 2024-12-17 | Paper |
Sorting signed permutations by tandem duplication random loss and inverse tandem duplication random loss
Advances in Applied Mathematics | 2024-10-09 | Paper |
Transit functions and pyramid-like binary clustering systems
Discrete Applied Mathematics | 2024-09-26 | Paper |
| Fitch graph completion | 2024-08-22 | Paper |
Chemically inspired Erdős-Rényi hypergraphs
Journal of Mathematical Chemistry | 2024-07-25 | Paper |
Forman-Ricci curvature for hypergraphs
Advances in Complex Systems | 2024-05-06 | Paper |
| Every atom-atom map can be explained by electron pushing diagrams | 2023-11-22 | Paper |
Optimisation via encodings: a renormalisation group perspective
Journal of Physics A: Mathematical and Theoretical | 2023-11-13 | Paper |
Orientation of Fitch Graphs and Reconciliation-Free Inference of Horizontal Gene Transfer in Gene Trees
SIAM Journal on Discrete Mathematics | 2023-10-13 | Paper |
| Unique Least Common Ancestors and Clusters in Directed Acyclic Graphs | 2023-09-24 | Paper |
Injective split systems
Graphs and Combinatorics | 2023-07-12 | Paper |
Comparison of Atom Maps
Match Communications in Mathematical and in Computer Chemistry | 2023-07-10 | Paper |
| Tailored machine learning models for functional RNA detection in genome-wide screens | 2023-07-06 | Dataset |
| Fitch Graph Completion | 2023-06-12 | Paper |
| The Theory of Gene Family Histories | 2023-04-24 | Paper |
Planar median graphs and cubesquare-graphs
Discrete Applied Mathematics | 2023-03-29 | Paper |
Quasi-best match graphs
Discrete Applied Mathematics | 2023-03-29 | Paper |
Efficient eigenvalue counts for tree-like networks
Journal of Complex Networks | 2023-03-10 | Paper |
Hamiltonicity in power graphs of a class of abelian groups
Journal of Algebraic Combinatorics | 2023-03-02 | Paper |
| Economic genome assembly from low coverage illumina and nanopore data | 2023-02-07 | Paper |
Hierarchical and modularly-minimal vertex colorings
The Art of Discrete and Applied Mathematics | 2022-12-19 | Paper |
| Transit Functions and Pyramid-Like Binary Clustering Systems | 2022-12-16 | Paper |
| Relative Timing Information and Orthology in Evolutionary Scenarios | 2022-12-05 | Paper |
Whitney's connectivity inequalities for directed hypergraphs
The Art of Discrete and Applied Mathematics | 2022-11-04 | Paper |
Generalized Fitch graphs. III: Symmetrized Fitch maps and sets of symmetric binary relations that are explained by unrooted edge-labeled trees
Discrete Mathematics & Theoretical Computer Science | 2022-09-30 | Paper |
Generalized Fitch graphs. III: Symmetrized Fitch maps and sets of symmetric binary relations that are explained by unrooted edge-labeled trees
Discrete Mathematics & Theoretical Computer Science | 2022-09-30 | Paper |
Least resolved trees for two-colored best match graphs
Journal of Graph Algorithms and Applications | 2022-06-28 | Paper |
Complete edge-colored permutation graphs
Advances in Applied Mathematics | 2022-06-13 | Paper |
| Clustering Systems of Phylogenetic Networks | 2022-04-28 | Paper |
Compatibility of partitions with trees, hierarchies, and split systems
Discrete Applied Mathematics | 2022-04-20 | Paper |
| Cut vertex transit functions of hypergraphs | 2022-03-24 | Paper |
From modular decomposition trees to rooted median graphs
Discrete Applied Mathematics | 2022-02-09 | Paper |
Compositional properties of alignments
Mathematics in Computer Science | 2022-01-28 | Paper |
| What makes a reaction network "chemical"? | 2022-01-05 | Paper |
Best match graphs with binary trees
(available as arXiv preprint) | 2021-12-21 | Paper |
Planar Median Graphs and Cubesquare-Graphs
(available as arXiv preprint) | 2021-10-18 | Paper |
Transit sets of \(k\)-point crossover operators
AKCE International Journal of Graphs and Combinatorics | 2021-10-05 | Paper |
Quasi-Best Match Graphs
(available as arXiv preprint) | 2021-09-21 | Paper |
| Rule composition in graph transformation models of chemical reactions | 2021-09-02 | Paper |
| Reachability, connectivity, and proximity in chemical spaces | 2021-09-02 | Paper |
| Towards mechanistic prediction of mass spectra using graph transformation | 2021-09-02 | Paper |
Indirect identification of horizontal gene transfer
Journal of Mathematical Biology | 2021-07-13 | Paper |
| Combining Orthology and Xenology Data in a Common Phylogenetic Tree | 2021-07-05 | Paper |
| A Simple Linear-Time Algorithm for the Common Refinement of Rooted Phylogenetic Trees on a Common Leaf Set | 2021-06-30 | Paper |
Corrigendum to: ``Best match graphs
Journal of Mathematical Biology | 2021-04-27 | Paper |
Complexity of modification problems for best match graphs
Theoretical Computer Science | 2021-04-08 | Paper |
Complete characterization of incorrect orthology assignments in best match graphs
Journal of Mathematical Biology | 2021-03-25 | Paper |
| Arc-Completion of 2-Colored Best Match Graphs to Binary-Explainable Best Match Graphs | 2021-03-11 | Paper |
| Heuristic Algorithms for Best Match Graph Editing | 2021-03-10 | Paper |
Transit sets of two-point crossover
The Art of Discrete and Applied Mathematics | 2021-02-19 | Paper |
A stochastic model for the evolution of transcription factor binding site abundance
Journal of Theoretical Biology | 2021-01-21 | Paper |
Alignments of mitochondrial genome arrangements: applications to metazoan phylogeny
Journal of Theoretical Biology | 2020-09-17 | Paper |
Cograph editing: Merging modules is equivalent to editing P_4s
The Art of Discrete and Applied Mathematics | 2020-09-15 | Paper |
Exact-2-relation graphs
Discrete Applied Mathematics | 2020-08-31 | Paper |
| Accelerated evolution of tissue-specific genes mediates divergence amidst gene flow in European green lizards | 2020-08-15 | Dataset |
Generalized Fitch graphs. II: Sets of binary relations that are explained by edge-labeled trees
Discrete Applied Mathematics | 2020-06-29 | Paper |
Forbidden time travel: characterization of time-consistent tree reconciliation maps
(available as arXiv preprint) | 2020-05-27 | Paper |
Centers of complex networks
Journal of Theoretical Biology | 2020-05-06 | Paper |
Quasi-independence, homology and the unity of type: a topological theory of characters
Journal of Theoretical Biology | 2020-05-06 | Paper |
| Convexity deficit of benzenoids | 2020-03-21 | Paper |
Best match graphs and reconciliation of gene trees with species trees
Journal of Mathematical Biology | 2020-03-05 | Paper |
Reciprocal best match graphs
Journal of Mathematical Biology | 2020-02-21 | Paper |
Complexity of modification problems for reciprocal best match graphs
Theoretical Computer Science | 2020-01-29 | Paper |
The short ruler on the torus
Journal of Difference Equations and Applications | 2019-12-17 | Paper |
Axiomatic characterization of transit functions of weak hierarchies
The Art of Discrete and Applied Mathematics | 2019-10-02 | Paper |
A short note on undirected Fitch graphs
The Art of Discrete and Applied Mathematics | 2019-10-02 | Paper |
Direct superbubble detection
Algorithms | 2019-07-08 | Paper |
| Hierarchical Colorings of Cographs | 2019-06-24 | Paper |
Best match graphs
Journal of Mathematical Biology | 2019-06-06 | Paper |
Chromatin computation: epigenetic inheritance as a pattern reconstruction problem
Journal of Theoretical Biology | 2019-05-14 | Paper |
Algebraic dynamic programming on trees
Algorithms | 2019-05-08 | Paper |
Innovation in gene regulation: the case of chromatin computation
Journal of Theoretical Biology | 2019-02-12 | Paper |
Reconstruction of pedigrees in clonal plant populations
Theoretical Population Biology | 2018-12-05 | Paper |
Mutate now, die later. Evolutionary dynamics with delayed selection
Journal of Theoretical Biology | 2018-11-26 | Paper |
Partially local multi-way alignments
Mathematics in Computer Science | 2018-11-05 | Paper |
Reconstructing gene trees from Fitch's xenology relation
Journal of Mathematical Biology | 2018-10-09 | Paper |
| Alignments as Compositional Structures | 2018-10-09 | Paper |
Cover-encodings of fitness landscapes
Bulletin of Mathematical Biology | 2018-09-25 | Paper |
The challenges and scope of theoretical biology
Journal of Theoretical Biology | 2018-09-17 | Paper |
Expansion of gene clusters, circular orders, and the shortest Hamiltonian path problem
Journal of Mathematical Biology | 2018-08-22 | Paper |
Temporal ordering of substitutions in RNA evolution: uncovering the structural evolution of the Human Accelerated Region 1
Journal of Theoretical Biology | 2018-05-24 | Paper |
Inferring phylogenetic trees from the knowledge of rare evolutionary events
Journal of Mathematical Biology | 2018-05-22 | Paper |
The short ruler on cones
Journal of Difference Equations and Applications | 2018-04-10 | Paper |
| Topological Representation of the Transit Sets of k-Point Crossover Operators | 2017-12-25 | Paper |
Oriented components and their separations
Applied General Topology | 2017-10-12 | Paper |
The mathematics of xenology: di-cographs, symbolic ultrametrics, 2-structures and tree-representable systems of binary relations
Journal of Mathematical Biology | 2017-08-11 | Paper |
Associativity and non-associativity of some hypergraph products
Mathematics in Computer Science | 2016-11-14 | Paper |
A software package for chemically inspired graph transformation
Graph Transformation | 2016-09-05 | Paper |
Automatic inference of graph transformation rules using the cyclic nature of chemical reactions
Graph Transformation | 2016-09-05 | Paper |
Algebraic dynamic programming for multiple context-free grammars
Theoretical Computer Science | 2016-06-30 | Paper |
Reconstruction of pedigrees in clonal plant populations
Theoretical Population Biology | 2016-06-22 | Paper |
Navigating the chemical space of HCN polymerization and hydrolysis: guiding graph grammars by mass spectrometry data
Entropy | 2016-05-10 | Paper |
Curve shortening by short rulers
Journal of Difference Equations and Applications | 2016-04-29 | Paper |
Curve shortening by short rulers
ESAIM: Proceedings and Surveys | 2016-02-02 | Paper |
Connectivity spaces
Mathematics in Computer Science | 2016-01-13 | Paper |
Spiders can be recognized by counting their legs
Mathematics in Computer Science | 2016-01-13 | Paper |
Rugged and elementary landscapes
Theory and Principled Methods for the Design of Metaheuristics | 2016-01-11 | Paper |
Spectral classes of regular, random, and empirical graphs
Linear Algebra and its Applications | 2015-11-17 | Paper |
RNA structures with pseudo-knots: graph-theoretical, combinatorial, and statistical properties
Bulletin of Mathematical Biology | 2015-10-27 | Paper |
Population dependent Fourier decomposition of fitness landscapes over recombination spaces: evolvability of complex characters
Bulletin of Mathematical Biology | 2015-10-27 | Paper |
Dynamics of autocatalytic replicator networks based on higher-order ligation reactions
Bulletin of Mathematical Biology | 2015-10-27 | Paper |
| The relaxed square property | 2015-09-23 | Paper |
The relaxed square property
(available as arXiv preprint) | 2015-09-23 | Paper |
50 Shades of Rule Composition
Formal Methods in Macro-Biology | 2015-08-06 | Paper |
The grid property and product-like hypergraphs
Graphs and Combinatorics | 2015-05-22 | Paper |
On the complexity of reconstructing chemical reaction networks
Mathematics in Computer Science | 2015-02-04 | Paper |
Convex cycle bases
Ars Mathematica Contemporanea | 2014-10-02 | Paper |
Relations between graphs
Ars Mathematica Contemporanea | 2014-05-14 | Paper |
Unique square property, equitable partitions, and product-like graphs
Discrete Mathematics | 2014-01-27 | Paper |
Regulatory Signals in Genomic Sequences
Networks: From Biology to Theory | 2013-07-31 | Paper |
A survey on hypergraph products
Mathematics in Computer Science | 2013-04-24 | Paper |
Minimum cycle bases of lexicographic products
Ars Mathematica Contemporanea | 2013-02-07 | Paper |
Orthology relations, symbolic ultrametrics, and cographs
Journal of Mathematical Biology | 2013-02-01 | Paper |
The Cartesian product of hypergraphs
Journal of Graph Theory | 2012-06-04 | Paper |
Diagonalized Cartesian products of \(S\)-prime graphs are \(S\)-prime
Discrete Mathematics | 2012-01-11 | Paper |
Symmetric circular matchings and RNA folding
Discrete Mathematics | 2012-01-11 | Paper |
Phylogenetic footprinting and consistent sets of local aligments
Combinatorial Pattern Matching | 2011-06-29 | Paper |
Local algorithms for the prime factorization of strong product graphs
Mathematics in Computer Science | 2011-02-19 | Paper |
Combinatorial vector fields and the valley structure of fitness landscapes
Journal of Mathematical Biology | 2010-11-11 | Paper |
Funnels in energy landscapes
The European Physical Journal B. Condensed Matter and Complex Systems | 2010-06-25 | Paper |
Funnels in energy landscapes
The European Physical Journal B. Condensed Matter and Complex Systems | 2010-06-25 | Paper |
A note on quasi-robust cycle bases
Ars Mathematica Contemporanea | 2010-04-15 | Paper |
| Target prediction and a statistical sampling algorithm for RNA-RNA interaction | 2009-08-05 | Paper |
A note on fundamental, non-fundamental, and robust cycle bases
Discrete Applied Mathematics | 2009-06-24 | Paper |
Discovering cis-regulatory modules by optimizing barbecues
Discrete Applied Mathematics | 2009-06-24 | Paper |
Approximate graph products
European Journal of Combinatorics | 2009-06-17 | Paper |
| RNA-RNA interaction prediction: partition function and base pair pairing probabilities | 2009-03-19 | Paper |
Variations on RNA folding and alignment: Lessons from Benasque
Journal of Mathematical Biology | 2008-08-18 | Paper |
| Visualization of barrier tree sequences revisited | 2008-04-14 | Paper |
Saddles and Barrier in Landscapes of Generalized Search Operators
Foundations of Genetic Algorithms | 2007-09-07 | Paper |
Laplacian eigenvectors of graphs. Perron-Frobenius and Faber-Krahn type theorems
Lecture Notes in Mathematics | 2007-08-16 | Paper |
A prime factor theorem for a generalized direct product
Discussiones Mathematicae Graph Theory | 2006-10-16 | Paper |
Evolving towards the hypercycle: a spatial model of molecular evolution
Physica D | 2006-06-30 | Paper |
| Nodal domain theorems and bipartite subgraphs | 2006-05-18 | Paper |
Minimum path bases and relevant paths
Networks | 2006-01-23 | Paper |
NEUTRAL NETWORKS OF INTERACTING RNA SECONDARY STRUCTURES
Advances in Complex Systems | 2006-01-09 | Paper |
Computational Science - ICCS 2004
Lecture Notes in Computer Science | 2005-12-23 | Paper |
Graph Laplacians, nodal domains, and hyperplane arrangements
Linear Algebra and its Applications | 2004-11-18 | Paper |
Circuit bases of strongly connected digraphs
Discussiones Mathematicae Graph Theory | 2004-10-27 | Paper |
Efficient computation of RNA folding dynamics
Journal of Physics A: Mathematical and General | 2004-08-23 | Paper |
MOLECULAR REPLICATOR DYNAMICS
Advances in Complex Systems | 2004-07-01 | Paper |
| scientific article; zbMATH DE number 2076525 (Why is no real title available?) | 2004-06-22 | Paper |
| scientific article; zbMATH DE number 1972808 (Why is no real title available?) | 2004-03-17 | Paper |
Minimum cycle bases of Halin graphs
Journal of Graph Theory | 2003-06-25 | Paper |
| scientific article; zbMATH DE number 1833092 (Why is no real title available?) | 2003-04-11 | Paper |
| scientific article; zbMATH DE number 1890109 (Why is no real title available?) | 2003-04-01 | Paper |
scientific article; zbMATH DE number 1887343 (Why is no real title available?)
Genetic Programming and Evolvable Machines | 2003-03-25 | Paper |
Landscapes on spaces of trees
Applied Mathematics and Computation | 2003-01-28 | Paper |
Landscapes and their correlation functions
Journal of Mathematical Chemistry | 2003-01-15 | Paper |
Autocatalytic replication in a CSTR and constant organization
Journal of Mathematical Biology | 2003-01-15 | Paper |
Discrete nodal domain theorems
Linear Algebra and its Applications | 2002-08-07 | Paper |
Fast Fourier transform for fitness landscapes
Applied and Computational Harmonic Analysis | 2002-07-04 | Paper |
Fractal geometry of spin-glass models
Journal of Physics A: Mathematical and General | 2002-06-11 | Paper |
Combinatorial landscapes
SIAM Review | 2002-04-15 | Paper |
Random field models for fitness landscapes
Journal of Mathematical Biology | 2002-04-08 | Paper |
The landscape of the traveling salesman problem
Physics Letters. A | 2002-02-18 | Paper |
Neutrality in fitness landscapes.
Applied Mathematics and Computation | 2001-04-25 | Paper |
Metastable states in short-rangedp-spin glasses
Journal of Physics A: Mathematical and General | 2001-03-26 | Paper |
Landscape statistics of the low-autocorrelation binary string problem
Journal of Physics A: Mathematical and General | 2001-03-05 | Paper |
RELEVANT CYCLES IN CHEMICAL REACTION NETWORKS
Advances in Complex Systems | 2001-01-01 | Paper |
GLASSY STATES IN A SHAKEN SANDBOX
Advances in Complex Systems | 2001-01-01 | Paper |
Interchangeability of relevant cycles in graphs
The Electronic Journal of Combinatorics | 2000-04-16 | Paper |
Interchangeability of relevant cycles in graphs
The Electronic Journal of Combinatorics | 2000-04-16 | Paper |
Amplitude Spectra of Fitness Landscapes
Advances in Complex Systems | 1999-12-16 | Paper |
Generic properties of combinatory maps: Neutral networks of RNA secondary structures
Bulletin of Mathematical Biology | 1999-10-18 | Paper |
Selection dynamics in autocatalytic systems: Templates replicating through binary ligation
Bulletin of Mathematical Biology | 1999-05-31 | Paper |
Combinatorics of RNA secondary structures
Discrete Applied Mathematics | 1999-03-22 | Paper |
The dynamics of locally adaptive parties under spatial voting
Journal of Economic Dynamics and Control | 1999-01-12 | Paper |
Minimal cycle bases of outerplanar graphs
The Electronic Journal of Combinatorics | 1998-04-01 | Paper |
Minimal cycle bases of outerplanar graphs
The Electronic Journal of Combinatorics | 1998-04-01 | Paper |
The supersymmetric particle spectrum in orbifold compactifications of string theory
Nuclear Physics B | 1998-02-26 | Paper |
Autocatalytic networks with intermediates. I: Irreversible reactions
Mathematical Biosciences | 1997-08-24 | Paper |
Autocatalytic networks with translation
Bulletin of Mathematical Biology | 1997-01-16 | Paper |
Permanence of sparse catalytic networks
Mathematical Biosciences | 1996-05-01 | Paper |
Random walks and orthogonal functions associated with highly symmetric graphs
Discrete Mathematics | 1996-04-22 | Paper |
Dynamics of small autocatalytic reaction networks. II: Replication, mutation and catalysis
Bulletin of Mathematical Biology | 1995-05-28 | Paper |
Immune networks modeled by replicator equations
Journal of Mathematical Biology | 1995-01-31 | Paper |
Landscapes: Complex optimization problems and biopolymer structures
Computers & Chemistry | 1994-12-18 | Paper |
The influence of mutation on autocatalytic reaction networks
Mathematical Biosciences | 1994-10-24 | Paper |
The probability of permanence
Mathematical Biosciences | 1993-06-29 | Paper |
Random catalytic reaction networks
Physica D | 1993-06-29 | Paper |
Mutation in autocatalytic reaction networks. An analysis based on perturbation theory
Journal of Mathematical Biology | 1992-09-27 | Paper |
Complementary replication
Mathematical Biosciences | 1992-06-28 | Paper |
Small autocatalytic reaction networks. III: Monotone growth functions
Bulletin of Mathematical Biology | 1992-06-25 | Paper |
Full characterization of a strange attractor. Chaotic dynamics in low- dimensional replicator systems
Physica D | 1991-01-01 | Paper |
Dynamics of small autocatalytic reaction networks. I: Bifurcations, permanence and exclusion
Bulletin of Mathematical Biology | 1990-01-01 | Paper |
