Vincent Moulton

Theor. Comput. Sci., 2025

Is this network proper forest-based?

[BibT_eX]

[DOI]

Inf. Process. Lett., 2025

2024

Orienting undirected phylogenetic networks.

[BibT_eX]

[DOI]

J. Comput. Syst. Sci., March, 2024

Shared Ancestry Graphs and Symbolic Arboreal Maps.

[BibT_eX]

[DOI]

Guillaume E. Scholz

SIAM J. Discret. Math., 2024

Spaces of ranked tree-child networks.

[BibT_eX]

[DOI]

CoRR, 2024

Encoding Semi-Directed Phylogenetic Networks with Quarnets.

[BibT_eX]

[DOI]

Leonie Veenema-Nipius

CoRR, 2024

Phylogenetic Trees Defined by at Most Three Characters.

[BibT_eX]

[DOI]

Electron. J. Comb., 2024

2023

Diversities and the Generalized Circumradius.

[BibT_eX]

[DOI]

Discret. Comput. Geom., December, 2023

Polynomial invariants for cactuses.

[BibT_eX]

[DOI]

Leo van Iersel

Yukihiro Murakami

Inf. Process. Lett., August, 2023

Injective Split Systems.

[BibT_eX]

[DOI]

Graphs Comb., August, 2023

Planar median graphs and cubesquare-graphs.

[BibT_eX]

[DOI]

Discret. Appl. Math., May, 2023

Planar Rooted Phylogenetic Networks.

[BibT_eX]

[DOI]

IEEE ACM Trans. Comput. Biol. Bioinform., 2023

Computing consensus networks for collections of 1-nested phylogenetic networks.

[BibT_eX]

[DOI]

J. Graph Algorithms Appl., 2023

Encoding and ordering X-cactuses.

[BibT_eX]

[DOI]

Adv. Appl. Math., 2023

2022

Degradome Assisted Plant MicroRNA Prediction Under Alternative Annotation Criteria.

[BibT_eX]

[DOI]

Salma Alzahrani

Christopher Applegate

IEEE ACM Trans. Comput. Biol. Bioinform., 2022

Posets and Spaces of $k$-Noncrossing RNA Structures.

[BibT_eX]

[DOI]

SIAM J. Discret. Math., 2022

Order Distances and Split Systems.

[BibT_eX]

[DOI]

Order, 2022

An algorithm for reconstructing level-2 phylogenetic networks from trinets.

[BibT_eX]

[DOI]

Inf. Process. Lett., 2022

Overlaid species forests.

[BibT_eX]

[DOI]

Guillaume E. Scholz

Discret. Appl. Math., 2022

Level-2 networks from shortest and longest distances.

[BibT_eX]

[DOI]

Discret. Appl. Math., 2022

2021

Optimal realizations and the block decomposition of a finite metric space.

[BibT_eX]

[DOI]

Discret. Appl. Math., 2021

2020

Recognizing and realizing cactus metrics.

[BibT_eX]

[DOI]

Inf. Process. Lett., 2020

Weakly displaying trees in temporal tree-child network.

[BibT_eX]

[DOI]

Simone Linz

Miguel Sautie Castellanos

CoRR, 2020

Evolution through segmental duplications and losses: a Super-Reconciliation approach.

[BibT_eX]

[DOI]

Algorithms Mol. Biol., 2020

Reconstructibility of unrooted level-k phylogenetic networks from distances.

[BibT_eX]

[DOI]

Leo van Iersel

Yukihiro Murakami

Adv. Appl. Math., 2020

2019

The complexity of comparing multiply-labelled trees by extending phylogenetic-tree metrics.

[BibT_eX]

[DOI]

Theor. Comput. Sci., 2019

The polytopal structure of the tight-span of a totally split-decomposable metric.

[BibT_eX]

[DOI]

Discret. Math., 2019

Rooting for phylogenetic networks.

[BibT_eX]

[DOI]

CoRR, 2019

Hierarchies from Lowest Stable Ancestors in Nonbinary Phylogenetic Networks.

[BibT_eX]

[DOI]

J. Classif., 2019

Three-Way Symbolic Tree-Maps and Ultrametrics.

[BibT_eX]

[DOI]

Guillaume E. Scholz

J. Classif., 2019

2018

UPGMA and the normalized equidistant minimum evolution problem.

[BibT_eX]

[DOI]

Theor. Comput. Sci., 2018

Leaf-Reconstructibility of Phylogenetic Networks.

[BibT_eX]

[DOI]

Leo van Iersel

Miguel Sautie Castellanos

SIAM J. Discret. Math., 2018

Geometric medians in reconciliation spaces of phylogenetic trees.

[BibT_eX]

[DOI]

Inf. Process. Lett., 2018

The UEA sRNA Workbench (version 4.4): a comprehensive suite of tools for analyzing miRNAs and sRNAs.

[BibT_eX]

[DOI]

Bioinform., 2018

SPECTRE: a suite of phylogenetic tools for reticulate evolution.

[BibT_eX]

[DOI]

Bioinform., 2018

Combinatorial properties of triplet covers for binary trees.

[BibT_eX]

[DOI]

Adv. Appl. Math., 2018

Reconstructing the History of Syntenies Through Super-Reconciliation.

[BibT_eX]

[DOI]

Proceedings of the Comparative Genomics - 16th International Conference, 2018

2017

A cubic-time algorithm for computing the trinet distance between level-1 networks.

[BibT_eX]

[DOI]

James Oldman

Inf. Process. Lett., 2017

Recovering tree-child networks from shortest inter-taxa distance information.

[BibT_eX]

[DOI]

CoRR, 2017

Quarnet inference rules for level-1 networks.

[BibT_eX]

[DOI]

CoRR, 2017

Binets: fundamental building blocks for phylogenetic networks.

[BibT_eX]

[DOI]

CoRR, 2017

Tree-based unrooted phylogenetic networks.

[BibT_eX]

[DOI]

Andrew R. Francis

CoRR, 2017

miRCat2: accurate prediction of plant and animal microRNAs from next-generation sequencing datasets.

[BibT_eX]

[DOI]

Bioinform., 2017

Reconstructing Phylogenetic Level-1 Networks from Nondense Binet and Trinet Sets.

[BibT_eX]

[DOI]

Algorithmica, 2017

2016

Reduction rules for the maximum parsimony distance on phylogenetic trees.

[BibT_eX]

[DOI]

Theor. Comput. Sci., 2016

The minimum evolution problem is hard: a link between tree inference and graph clustering problems.

[BibT_eX]

[DOI]

Bioinform., 2016

Characterizing block graphs in terms of their vertex-induced partitions.

[BibT_eX]

[DOI]

Australas. J Comb., 2016

2015

Optimal realizations of two-dimensional, totally-decomposable metrics.

[BibT_eX]

[DOI]

Discret. Math., 2015

A parsimony-based metric for phylogenetic trees.

[BibT_eX]

[DOI]

Adv. Appl. Math., 2015

2014

Representing Partitions on Trees.

[BibT_eX]

[DOI]

SIAM J. Discret. Math., 2014

Fishing for minimum evolution trees with Neighbor-Nets.

[BibT_eX]

[DOI]

Sarah Bastkowski

Inf. Process. Lett., 2014

Computing the blocks of a quasi-median graph.

[BibT_eX]

[DOI]

Discret. Appl. Math., 2014

2013

SuperQ: Computing Supernetworks from Quartets.

[BibT_eX]

[DOI]

IEEE ACM Trans. Comput. Biol. Bioinform., 2013

Searching for realizations of finite metric spaces in tight spans.

[BibT_eX]

[DOI]

Discret. Optim., 2013

Obtaining splits from cut sets of tight spans.

[BibT_eX]

[DOI]

Discret. Appl. Math., 2013

Generating functions for multi-labeled trees.

[BibT_eX]

[DOI]

Discret. Appl. Math., 2013

Encoding and Constructing 1-Nested Phylogenetic Networks with Trinets.

[BibT_eX]

[DOI]

Algorithmica, 2013

2012

FiRePat - Finding Regulatory Patterns between sRNAs and Genes.

[BibT_eX]

[DOI]

WIREs Data Mining Knowl. Discov., 2012

Constructing and Drawing Regular Planar Split Networks.

[BibT_eX]

[DOI]

Binh T. Nguyen

IEEE ACM Trans. Comput. Biol. Bioinform., 2012

Injective optimal realizations of finite metric spaces.

[BibT_eX]

[DOI]

Discret. Math., 2012

Trees, tight-spans and point configurations.

[BibT_eX]

[DOI]

Maribel Hernandez-Rosales

Discret. Math., 2012

Recognizing Treelike k-Dissimilarities.

[BibT_eX]

[DOI]

J. Classif., 2012

From event-labeled gene trees to species trees.

[BibT_eX]

[DOI]

BMC Bioinform., 2012

The UEA sRNA workbench: a suite of tools for analysing and visualizing next generation sequencing microRNA and small RNA datasets.

[BibT_eX]

[DOI]

Bioinform., 2012

Computing evolutionary distinctiveness indices in large scale analysis.

[BibT_eX]

[DOI]

Algorithms Mol. Biol., 2012

Computational Modeling of the Regulatory Network Organizing the Wound Response in Arabidopsis thaliana.

[BibT_eX]

[DOI]

Artif. Life, 2012

The split decomposition of a k-dissimilarity map.

[BibT_eX]

[DOI]

Adv. Appl. Math., 2012

Computing a Consensus of Multilabeled Trees.

[BibT_eX]

[DOI]

Proceedings of the 14th Meeting on Algorithm Engineering & Experiments, 2012

Basic Phylogenetic Combinatorics.

[BibT_eX]

[DOI]

Cambridge University Press, ISBN: 978-0-521-76832-0, 2012

2011

Metrics on Multilabeled Trees: Interrelationships and Diameter Bounds.

[BibT_eX]

[DOI]

IEEE ACM Trans. Comput. Biol. Bioinform., 2011

Blocks and Cut Vertices of the Buneman Graph.

[BibT_eX]

[DOI]

SIAM J. Discret. Math., 2011

Identifying and Reconstructing Lateral Transfers from Distance Matrices by Combining the Minimum Contradiction Method and Neighbor-Net.

[BibT_eX]

[DOI]

Marc Thuillard

J. Bioinform. Comput. Biol., 2011

The 'Butterfly effect' in Cayley graphs, and its relevance for evolutionary genomics

[BibT_eX]

[DOI]

CoRR, 2011

2010

An Algorithm for Computing Cutpoints in Finite Metric Spaces.

[BibT_eX]

[DOI]

J. Classif., 2010

Finding sRNA generative locales from high-throughput sequencing data with NiBLS.

[BibT_eX]

[DOI]

Daniel MacLean

David J. Studholme

BMC Bioinform., 2010

RDP3: a flexible and fast computer program for analyzing recombination.

[BibT_eX]

[DOI]

Bioinform., 2010

Distinguishing between hot-spots and melting-pots of genetic diversity using haplotype connectivity.

[BibT_eX]

[DOI]

Algorithms Mol. Biol., 2010

2009

Refining Phylogenetic Trees Given Additional Data: An Algorithm Based on Parsimony.

[BibT_eX]

[DOI]

IEEE ACM Trans. Comput. Biol. Bioinform., 2009

Special Section: Phylogenetics.

[BibT_eX]

[DOI]

Daniel H. Huson

IEEE ACM Trans. Comput. Biol. Bioinform., 2009

Maximum Parsimony for Tree Mixtures.

[BibT_eX]

[DOI]

Stefan Grünewald

IEEE ACM Trans. Comput. Biol. Bioinform., 2009

Consistency of Topological Moves Based on the Balanced Minimum Evolution Principle of Phylogenetic Inference.

[BibT_eX]

[DOI]

IEEE ACM Trans. Comput. Biol. Bioinform., 2009

Optimal realizations of generic five-point metrics.

[BibT_eX]

[DOI]

Alice Lesser

Eur. J. Comb., 2009

Consistency of the QNet algorithm for generating planar split networks from weighted quartets.

[BibT_eX]

[DOI]

Stefan Grünewald

Discret. Appl. Math., 2009

Identifying recombinants in human and primate immunodeficiency virus sequence alignments using quartet scanning.

[BibT_eX]

[DOI]

BMC Bioinform., 2009

PADRE: a package for analyzing and displaying reticulate evolution.

[BibT_eX]

[DOI]

Bioinform., 2009

Phylogenetic diversity and the maximum coverage problem.

[BibT_eX]

[DOI]

Appl. Math. Lett., 2009

Barriers in metric spaces.

[BibT_eX]

[DOI]

Appl. Math. Lett., 2009

A graph-theoretical invariant of topological spaces.

[BibT_eX]

[DOI]

Appl. Math. Lett., 2009

Characterizing weak compatibility in terms of weighted quartets.

[BibT_eX]

[DOI]

Adv. Appl. Math., 2009

2008

Computing Phylogenetic Diversity for Split Systems.

[BibT_eX]

[DOI]

Binh T. Nguyen

IEEE ACM Trans. Comput. Biol. Bioinform., 2008

The Complexity of Deriving Multi-Labeled Trees from Bipartitions.

[BibT_eX]

[DOI]

J. Comput. Biol., 2008

Compatible decompositions and block realizations of finite metrics.

[BibT_eX]

[DOI]

Eur. J. Comb., 2008

Counting vertices and cubes in median graphs of circular split systems.

[BibT_eX]

[DOI]

Eur. J. Comb., 2008

Characterizing Cell-Decomposable Metrics.

[BibT_eX]

[DOI]

Electron. J. Comb., 2008

A toolkit for analysing large-scale plant small RNA datasets.

[BibT_eX]

[DOI]

Bioinform., 2008

Block realizations of finite metrics and the tight-span construction I: The embedding theorem.

[BibT_eX]

[DOI]

Appl. Math. Lett., 2008

Cut points in metric spaces.

[BibT_eX]

[DOI]

Appl. Math. Lett., 2008

A scoring matrix approach to detecting miRNA target sites.

[BibT_eX]

[DOI]

Simon Moxon

Jan T. Kim

Algorithms Mol. Biol., 2008

A regular decomposition of the edge-product space of phylogenetic trees.

[BibT_eX]

[DOI]

Adv. Appl. Math., 2008

Constructing Phylogenetic Supernetworks from Quartets.

[BibT_eX]

[DOI]

Proceedings of the Algorithms in Bioinformatics, 8th International Workshop, 2008

Time Series Data Mining Algorithms for Identifying Short RNA in Arabidopsis thaliana.

[BibT_eX]

Proceedings of the International Conference on Bioinformatics & Computational Biology, 2008

2007

RNAbor: a web server for RNA structural neighbors.

[BibT_eX]

[DOI]

Eva Freyhult

Peter Clote

Nucleic Acids Res., 2007

Two theorems concerning the Bannai-Ito conjecture.

[BibT_eX]

[DOI]

Sejeong Bang

Eur. J. Comb., 2007

Concerning the Relationship between Realizations and Tight Spans of Finite Metrics.

[BibT_eX]

[DOI]

Alice Lesser

Discret. Comput. Geom., 2007

Boltzmann probability of RNA structural neighbors and riboswitch detection.

[BibT_eX]

[DOI]

Eva Freyhult

Peter Clote

Bioinform., 2007

Consistency of the Neighbor-Net Algorithm.

[BibT_eX]

[DOI]

David Bryant

Algorithms Mol. Biol., 2007

An Algorithm for Computing Virtual Cut Points in Finite Metric Spaces.

[BibT_eX]

[DOI]

Proceedings of the Combinatorial Optimization and Applications, 2007

Phylogenetic networks.

[BibT_eX]

Proceedings of the Mathematics of Evolution and Phylogeny., 2007

2006

Parameter Reconstruction for Biochemical Networks Using Interval Analysis.

[BibT_eX]

[DOI]

Warwick Tucker

Reliab. Comput., 2006

On the structure of the tight-span of a totally split-decomposable metric.

[BibT_eX]

[DOI]

Eur. J. Comb., 2006

Imputing Supertrees and Supernetworks from Quartets.

[BibT_eX]

[DOI]

Proceedings of the Algorithms in Bioinformatics, 6th International Workshop, 2006

2005

Four Characters Suffice to Convexly Define a Phylogenetic Tree.

[BibT_eX]

[DOI]

Michael Anthony Steel

SIAM J. Discret. Math., 2005

The tight span of an antipodal metric space - Part I: : Combinatorial properties.

[BibT_eX]

[DOI]

Discret. Math., 2005

Delta additive and Delta ultra-additive maps, Gromov's trees, and the Farris transform.

[BibT_eX]

[DOI]

Discret. Appl. Math., 2005

Unbiased descriptor and parameter selection confirms the potential of proteochemometric modelling.

[BibT_eX]

[DOI]

BMC Bioinform., 2005

A comparison of RNA folding measures.

[BibT_eX]

[DOI]

Eva Freyhult

Paul P. Gardner

BMC Bioinform., 2005

Recovering a phylogenetic tree using pairwise closure operations.

[BibT_eX]

[DOI]

Appl. Math. Lett., 2005

Reconstructing Metabolic Networks Using Interval Analysis.

[BibT_eX]

[DOI]

Warwick Tucker

Proceedings of the Algorithms in Bioinformatics, 5th International Workshop, 2005

2004

The structure of spherical graphs.

[BibT_eX]

[DOI]

Dragan Stevanovic

Eur. J. Comb., 2004

The Tight Span of an Antipodal Metric Space: Part II--Geometrical Properties.

[BibT_eX]

[DOI]

Discret. Comput. Geom., 2004

Replacing cliques by stars in quasi-median graphs.

[BibT_eX]

[DOI]

Charles Semple

Discret. Appl. Math., 2004

VisRD--visual recombination detection.

[BibT_eX]

[DOI]

Kristoffer Forslund

Daniel H. Huson

Bioinform., 2004

Peeling phylogenetic 'oranges'.

[BibT_eX]

[DOI]

Adv. Appl. Math., 2004

2003

Maximal Energy Bipartite Graphs.

[BibT_eX]

[DOI]

Graphs Comb., 2003

Addendum to "on line arrangements in the hyperbolic plane" [European J. Combin.23 (2002) 549-557].

[BibT_eX]

[DOI]

Eur. J. Comb., 2003

A bound for the number of columns l(c, a, b) in the intersection array of a distance-regular graph.

[BibT_eX]

[DOI]

Sejeong Bang

Eur. J. Comb., 2003

A Search for H/ACA SnoRNAs in Yeast Using MFE Secondary Structure Prediction.

[BibT_eX]

[DOI]

Bioinform., 2003

Connectivity calculus.

[BibT_eX]

[DOI]

Appl. Math. Lett., 2003

Consensus Networks: A Method for Visualising Incompatibilities in Collections of Trees.

[BibT_eX]

[DOI]

Barbara R. Holland

Proceedings of the Algorithms in Bioinformatics, Third International Workshop, 2003

2002

On a Conjecture of Bannai and Ito: There are Finitely Many Distance-regular Graphs with Degree 5, 6 or 7.

[BibT_eX]

[DOI]

Eur. J. Comb., 2002

Hyperbolic Bridged Graphs.

[BibT_eX]

[DOI]

Eur. J. Comb., 2002

On Line Arrangements in the Hyperbolic Plane.

[BibT_eX]

[DOI]

Eur. J. Comb., 2002

Antipodal Metrics and Split Systems.

[BibT_eX]

[DOI]

Eur. J. Comb., 2002

The relation graph.

[BibT_eX]

[DOI]

Discret. Math., 2002

Quasi-median graphs from sets of partitions.

[BibT_eX]

[DOI]

Hans-Jürgen Bandelt

Discret. Appl. Math., 2002

NeighborNet: An Agglomerative Method for the Construction of Planar Phylogenetic Networks.

[BibT_eX]

[DOI]

David Bryant

Proceedings of the Algorithms in Bioinformatics, Second International Workshop, 2002

2001

Six Points Suffice: How to Check for Metric Consistency.

[BibT_eX]

[DOI]

Eur. J. Comb., 2001

Maximal Energy Graphs.

[BibT_eX]

[DOI]

Adv. Appl. Math., 2001

2000

Metrics on RNA Secondary Structures.

[BibT_eX]

[DOI]

J. Comput. Biol., 2000

A Classification of the Six-point Prime Metrics.

[BibT_eX]

[DOI]

Udo Tönges

Eur. J. Comb., 2000

On the tight span of an antipodal graph.

[BibT_eX]

[DOI]

Oliver Goodman

Discret. Math., 2000

Affine Maps That Induce Polyhedral Complex Isomorphisms.

[BibT_eX]

[DOI]

Discret. Comput. Geom., 2000

1999

Some new perspectives regarding sparse continuous models for discrete data structures.

[BibT_eX]

[DOI]

Electron. Notes Discret. Math., 1999

Retractions of Finite Distance Functions Onto Tree Metrics.

[BibT_eX]

[DOI]

Discret. Appl. Math., 1999

1998

The coherency index.

[BibT_eX]

[DOI]

Udo Tönges

Discret. Math., 1998

1997

DCA: an efficient implementation of the divide-and-conquer approach to simultaneous multiple sequence alignment.

[BibT_eX]

[DOI]

Jens Stoye

Comput. Appl. Biosci., 1997

1996

T-theory: An Overview.

[BibT_eX]

[DOI]

Werner F. Terhalle

Eur. J. Comb., 1996

Analyzing and Visualizing Sequence and Distance Data Using SplitsTree.

[BibT_eX]

[DOI]

Daniel H. Huson

Discret. Appl. Math., 1996

Dissimilarity maps and substitution models: Some new results.

[BibT_eX]

[DOI]