A Distance-Based Block Searching Algorithm. - Marie-France Sagot; Alain Viari; Henry Soldano (ISMB, 1995)

Finding flexible patterns in a text: an application to three-dimensional molecular matching. - Marie-France Sagot; Alain Viari; Joël Pothier; Henry Soldano (Comput. Appl. Biosci., 1995)

A Double Combinatorial Approach to Discovering Patterns in Biological Sequences. - Marie-France Sagot; Alain Viari (CPM, 1996)

Flexible Identification of Structural Objects in Nucleic Acid Sequences: Palindromes, Mirror Repeats, Pseudoknots and Triple Helices. - Marie-France Sagot; Alain Viari (CPM, 1997)

Multiple Sequence Comparison - A Peptide Matching Approach. - Marie-France Sagot; Alain Viari; Henry Soldano (Theor. Comput. Sci., 1997)

Spelling Approximate Repeated or Common Motifs Using a Suffix Tree. - Marie-France Sagot (LATIN, 1998)

Identifying satellites in nucleic acid sequences. - Marie-France Sagot; Eugene W. Myers (RECOMB, 1998)

Identifying Satellites and Periodic Repetitions in Biological Sequences. - Marie-France Sagot; Eugene W. Myers (J. Comput. Biol., 1998)

Extracting structured motifs using a suffix tree - algorithms and application to promoter consensus identification. - Laurent Marsan; Marie-France Sagot (RECOMB, 2000)

Algorithms for Extracting Structured Motifs Using a Suffix Tree with an Application to Promoter and Regulatory Site Consensus Identification. - Laurent Marsan; Marie-France Sagot (J. Comput. Biol., 2000)

Some Approximation Results for the Maximum Agreement Forest Problem. - Estela Maris Rodrigues; Marie-France Sagot; Yoshiko Wakabayashi (RANDOM-APPROX, 2001)

Further Thoughts on the Syntenic Distance between Genomes. - Nadia Pisanti; Marie-France Sagot (Algorithmica, 2002)

Occurrence Probability of Structured Motifs in Random Sequences. - Stéphane Robin; Jean-Jacques Daudin; Hugues Richard; Marie-France Sagot; Sophie Schbath (J. Comput. Biol., 2002)

A Basis of Tiling Motifs for Generating Repeated Patterns and Its Complexity for Higher Quorum. - Nadia Pisanti; Maxime Crochemore; Roberto Grossi; Marie-France Sagot (MFCS, 2003)

Orphan gene finding - an exon assembly approach. - Philippe Blayo; Pierre Rouzé; Marie-France Sagot (Theor. Comput. Sci., 2003)

Sorting by Reversals in Subquadratic Time. - Eric Tannier; Marie-France Sagot (CPM, 2004)

Longest Repeats with a Block of Don't Cares. - Maxime Crochemore; Costas S. Iliopoulos; Manal Mohamed 001; Marie-France Sagot (LATIN, 2004)

A parallel algorithm for the extraction of structured motifs. - Alexandra M. Carvalho; Arlindo L. Oliveira; Ana T. Freitas; Marie-France Sagot (SAC, 2004)

Efficient Extraction of Structured Motifs Using Box-Links. - Alexandra M. Carvalho; Ana T. Freitas; Arlindo L. Oliveira; Marie-France Sagot (SPIRE, 2004)

Longest Motifs with a Functionally Equivalent Central Block. - Maxime Crochemore; Raffaele Giancarlo; Marie-France Sagot (SPIRE, 2004)

Novel Tree Edit Operations for RNA Secondary Structure Comparison. - Julien Allali; Marie-France Sagot (WABI, 2004)

A highly scalable algorithm for the extraction of CIS-regulatory regions. - Alexandra M. Carvalho; Ana T. Freitas; Arlindo L. Oliveira; Marie-France Sagot (APBC, 2005)

Perfect Sorting by Reversals. - Marie-France Sagot; Eric Tannier (COCOON, 2005)

A Pattern Extraction Algorithm for Abstract Melodic Representations that Allow Partial Overlapping of Intervallic Categories. - Emilios Cambouropoulos; Maxime Crochemore; Costas S. Iliopoulos; Manal Mohamed 001; Marie-France Sagot (ISMIR, 2005)

A Multiple Graph Layers Model with Application to RNA Secondary Structures Comparison. - Julien Allali; Marie-France Sagot (SPIRE, 2005)

Lossless Filter for Finding Long Multiple Approximate Repetitions Using a New Data Structure, the Bi-factor Array. - Pierre Peterlongo; Nadia Pisanti; Frédéric Boyer; Marie-France Sagot (SPIRE, 2005)

Reaction Motifs in Metabolic Networks. - Vincent Lacroix; Cristina G. Fernandes; Marie-France Sagot (WABI, 2005)

A first approach to finding common motifs with gaps. - Costas S. Iliopoulos; James A. M. McHugh; Pierre Peterlongo; Nadia Pisanti; Wojciech Rytter; Marie-France Sagot (Int. J. Found. Comput. Sci., 2005)

A New Distance for High Level RNA Secondary Structure Comparison. - Julien Allali; Marie-France Sagot (IEEE ACM Trans. Comput. Biol. Bioinform., 2005)

Bases of Motifs for Generating Repeated Patterns with Wild Cards. - Nadia Pisanti; Maxime Crochemore; Roberto Grossi; Marie-France Sagot (IEEE ACM Trans. Comput. Biol. Bioinform., 2005)

RISOTTO: Fast Extraction of Motifs with Mismatches. - Nadia Pisanti; Alexandra M. Carvalho; Laurent Marsan; Marie-France Sagot (LATIN, 2006)

The gapped-factor tree. - Pierre Peterlongo; Julien Allali; Marie-France Sagot (Stringology, 2006)

An Efficient Algorithm for the Identification of Structured Motifs in DNA Promoter Sequences. - Alexandra M. Carvalho; Ana T. Freitas; Arlindo L. Oliveira; Marie-France Sagot (IEEE ACM Trans. Comput. Biol. Bioinform., 2006)

Motif Search in Graphs: Application to Metabolic Networks. - Vincent Lacroix; Cristina G. Fernandes; Marie-France Sagot (IEEE ACM Trans. Comput. Biol. Bioinform., 2006)

Longest repeats with a block of k don't cares. - Maxime Crochemore; Costas S. Iliopoulos; Manal Mohamed 001; Marie-France Sagot (Theor. Comput. Sci., 2006)

Efficient Learning of Bayesian Network Classifiers. - Alexandra M. Carvalho; Arlindo L. Oliveira; Marie-France Sagot (Australian Conference on Artificial Intelligence, 2007)

The Solution Space of Sorting by Reversals. - Marília D. V. Braga; Marie-France Sagot; Céline Scornavacca; Eric Tannier (ISBRA, 2007)

Metabolic network visualization eliminating node redundance and preserving metabolic pathways. - Romain Bourqui; Ludovic Cottret; Vincent Lacroix; David Auber; Patrick Mary; Marie-France Sagot; Fabien Jourdan (BMC Syst. Biol., 2007)

Advances on sorting by reversals. - Eric Tannier; Anne Bergeron; Marie-France Sagot (Discret. Appl. Math., 2007)

All maximal-pairs in step-leap representation of melodic sequence. - Emilios Cambouropoulos; Maxime Crochemore; Costas S. Iliopoulos; Manal Mohamed 001; Marie-France Sagot (Inf. Sci., 2007)

Evolution under Reversals: Parsimony and Conservation of Common Intervals. - Yoan Diekmann; Marie-France Sagot; Eric Tannier (IEEE ACM Trans. Comput. Biol. Bioinform., 2007)

The maximum agreement forest problem: Approximation algorithms and computational experiments. - Estela Maris Rodrigues; Marie-France Sagot; Yoshiko Wakabayashi (Theor. Comput. Sci., 2007)

Efficient representation and P-value computation for high-order Markov motifs. - Paulo G. S. da Fonseca 001; Katia S. Guimarães; Marie-France Sagot (ECCB, 2008)

Enumerating Precursor Sets of Target Metabolites in a Metabolic Network. - Ludovic Cottret; Paulo Vieira Milreu; Vicente Acuña; Alberto Marchetti-Spaccamela; Fábio Viduani Martinez; Marie-France Sagot; Leen Stougie (WABI, 2008)

Precise detection of rearrangement breakpoints in mammalian chromosomes. - Claire Lemaitre; Eric Tannier; Christian Gautier; Marie-France Sagot (BMC Bioinform., 2008)

Indexing Gapped-Factors Using a Tree. - Pierre Peterlongo; Julien Allali; Marie-France Sagot (Int. J. Found. Comput. Sci., 2008)

Editorial. - Katia S. Guimarães; Marie-France Sagot (J. Discrete Algorithms, 2008)

Lossless filter for multiple repetitions with Hamming distance. - Pierre Peterlongo; Nadia Pisanti; Frédéric Boyer; Alair Pereira do Lago; Marie-France Sagot (J. Discrete Algorithms, 2008)

A multiple layer model to compare RNA secondary structures. - Julien Allali; Marie-France Sagot (Softw. Pract. Exp., 2008)

Exploring the Solution Space of Sorting by Reversals, with Experiments and an Application to Evolution. - Marília D. V. Braga; Marie-France Sagot; Céline Scornavacca; Eric Tannier (IEEE ACM Trans. Comput. Biol. Bioinform., 2008)

An Introduction to Metabolic Networks and Their Structural Analysis. - Vincent Lacroix; Ludovic Cottret; Patricia Thébault; Marie-France Sagot (IEEE ACM Trans. Comput. Biol. Bioinform., 2008)

A small trip in the untranquil world of genomes: A survey on the detection and analysis of genome rearrangement breakpoints. - Claire Lemaitre; Marie-France Sagot (Theor. Comput. Sci., 2008)

Multiple Alignment of Biological Networks: A Flexible Approach. - Yves-Pol Deniélou; Frédéric Boyer; Alain Viari; Marie-France Sagot (CPM, 2009)

An asymmetric approach to preserve common intervals while sorting by reversals. - Marília D. V. Braga; Christian Gautier; Marie-France Sagot (Algorithms Mol. Biol., 2009)

Lossless filter for multiple repeats with bounded edit distance. - Pierre Peterlongo; Gustavo Akio Tominaga Sacomoto; Alair Pereira do Lago; Nadia Pisanti; Marie-France Sagot (Algorithms Mol. Biol., 2009)

ISMB/ECCB 2009 Stockholm. - Marie-France Sagot; B. J. Morrison McKay; Gene Myers (Bioinform., 2009)

Modes and cuts in metabolic networks: Complexity and algorithms. - Vicente Acuña; Flavio Chierichetti; Vincent Lacroix; Alberto Marchetti-Spaccamela; Marie-France Sagot; Leen Stougie (Biosyst., 2009)

Assessing the Exceptionality of Coloured Motifs in Networks. - Sophie Schbath; Vincent Lacroix; Marie-France Sagot (EURASIP J. Bioinform. Syst. Biol., 2009)

New EIC Editorial. - Marie-France Sagot (IEEE ACM Trans. Comput. Biol. Bioinform., 2009)

EIC Editorial: Introducing New Associate Editors. - Marie-France Sagot (IEEE ACM Trans. Comput. Biol. Bioinform., 2009)

Mod/Resc Parsimony Inference. - Igor Nor; Danny Hermelin; Sylvain Charlat; Jan Engelstadter; Max Reuter; Olivier Duron; Marie-France Sagot (CPM, 2010)

Identifying SNPs without a Reference Genome by Comparing Raw Reads. - Pierre Peterlongo; Nicolas Schnel; Nadia Pisanti; Marie-France Sagot; Vincent Lacroix (SPIRE, 2010)

Enumerating Chemical Organisations in Consistent Metabolic Networks: Complexity and Algorithms. - Paulo Vieira Milreu; Vicente Acuña; Etienne Birmelé; Pierluigi Crescenzi; Alberto Marchetti-Spaccamela; Marie-France Sagot; Leen Stougie; Vincent Lacroix (WABI, 2010)

Cassis: detection of genomic rearrangement breakpoints. - Christian Baudet; Claire Lemaitre; Zanoni Dias; Christian Gautier; Eric Tannier; Marie-France Sagot (Bioinform., 2010)

A note on the complexity of finding and enumerating elementary modes. - Vicente Acuña; Alberto Marchetti-Spaccamela; Marie-France Sagot; Leen Stougie (Biosyst., 2010)

Repetition-free longest common subsequence. - Said Sadique Adi; Marília D. V. Braga; Cristina G. Fernandes; Carlos Eduardo Ferreira; Fábio Viduani Martinez; Marie-France Sagot; Marco Aurelio Stefanes; Christian Tjandraatmadja; Yoshiko Wakabayashi (Discret. Appl. Math., 2010)

MetExplore: a web server to link metabolomic experiments and genome-scale metabolic networks. - Ludovic Cottret; David Wildridge; Florence Vinson; Michael P. Barrett; Hubert Charles; Marie-France Sagot; Fabien Jourdan (Nucleic Acids Res., 2010)

Graph-Based Analysis of the Metabolic Exchanges between Two Co-Resident Intracellular Symbionts, Baumannia cicadellinicola and Sulcia muelleri, with Their Insect Host, Homalodisca coagulata. - Ludovic Cottret; Paulo Vieira Milreu; Vicente Acuña; Alberto Marchetti-Spaccamela; Leen Stougie; Hubert Charles; Marie-France Sagot (PLoS Comput. Biol., 2010)

Finding Long and Multiple Repeats with Edit Distance. - Maria Federico; Pierre Peterlongo; Nadia Pisanti; Marie-France Sagot (Stringology, 2011)

CycADS: an annotation database system to ease the development and update of BioCyc databases. - Augusto F. Vellozo; Amélie S. Véron; Patrice Baa-Puyoulet; Jaime Huerta-Cepas; Ludovic Cottret; Gérard Febvay; Federica Calevro; Yvan Rahbé; Angela E. Douglas; Toni Gabaldón; Marie-France Sagot; Hubert Charles; et al. (Database J. Biol. Databases Curation, 2011)

Bacterial syntenies: an exact approach with gene quorum. - Yves-Pol Deniélou; Marie-France Sagot; Frédéric Boyer; Alain Viari (BMC Bioinform., 2011)

Minimum Ratio Cover of Matrix Columns by Extreme Rays of Its Induced Cone. - Alexandre S. Freire; Vicente Acuña; Pilu Crescenzi; Carlos Eduardo Ferreira; Vincent Lacroix; Paulo Vieira Milreu; Eduardo Moreno 001; Marie-France Sagot (ISCO, 2012)

Efficient Bubble Enumeration in Directed Graphs. - Etienne Birmelé; Pierluigi Crescenzi; Rui A. Ferreira; Roberto Grossi; Vincent Lacroix; Andrea Marino 001; Nadia Pisanti; Gustavo Akio Tominaga Sacomoto; Marie-France Sagot (SPIRE, 2012)

BRASERO: A Resource for Benchmarking RNA Secondary Structure Comparison Algorithms. - Julien Allali; Cédric Saule; Cédric Chauve; Yves D'Aubenton-Carafa; Alain Denise; Christine Drevet; Pascal Ferraro; Daniel Gautheret; Claire Herrbach; Fabrice Leclerc; Antoine de Monte; Aïda Ouangraoua; et al. (Adv. Bioinformatics, 2012)

Sampling solution traces for the problem of sorting permutations by signed reversals. - Christian Baudet; Zanoni Dias; Marie-France Sagot (Algorithms Mol. Biol., 2012)

Algorithms and complexity of enumerating minimal precursor sets in genome-wide metabolic networks. - Vicente Acuña; Paulo Vieira Milreu; Ludovic Cottret; Alberto Marchetti-Spaccamela; Leen Stougie; Marie-France Sagot (Bioinform., 2012)

Navigating the unexplored seascape of pre-miRNA candidates in single-genome approaches. - Nuno D. Mendes; Steffen Heyne; Ana T. Freitas; Marie-France Sagot; Rolf Backofen (Bioinform., 2012)

KISSPLICE: de-novo calling alternative splicing events from RNA-seq data. - Gustavo Akio Tominaga Sacomoto; Janice Kielbassa; Rayan Chikhi; Raluca Uricaru; Pavlos Antoniou; Marie-France Sagot; Pierre Peterlongo; Vincent Lacroix (BMC Bioinform., 2012)

Optimal Listing of Cycles and st-Paths in Undirected Graphs - Etienne Birmelé; Rui A. Ferreira; Roberto Grossi; Andrea Marino 001; Nadia Pisanti; Romeo Rizzi; Gustavo Akio Tominaga Sacomoto; Marie-France Sagot (CoRR, 2012)

Mod/Resc Parsimony Inference: Theory and application. - Igor Nor; Danny Hermelin; Sylvain Charlat; Jan Engelstadter; Max Reuter; Olivier Duron; Marie-France Sagot (Inf. Comput., 2012)

EIC Editorial. - Marie-France Sagot (IEEE ACM Trans. Comput. Biol. Bioinform., 2012)

Telling stories: Enumerating maximal directed acyclic graphs with a constrained set of sources and targets. - Vicente Acuña; Etienne Birmelé; Ludovic Cottret; Pierluigi Crescenzi; Fabien Jourdan; Vincent Lacroix; Alberto Marchetti-Spaccamela; Andrea Marino 001; Paulo Vieira Milreu; Marie-France Sagot; Leen Stougie (Theor. Comput. Sci., 2012)

A Polynomial Delay Algorithm for the Enumeration of Bubbles with Length Constraints in Directed Graphs and Its Application to the Detection of Alternative Splicing in RNA-seq Data. - Gustavo Sacomoto; Vincent Lacroix; Marie-France Sagot (WABI, 2013)

Telling Stories Fast. - Michele Borassi; Pierluigi Crescenzi; Vincent Lacroix; Andrea Marino 001; Marie-France Sagot; Paulo Vieira Milreu (SEA, 2013)

Amortized Õ(|V|) -Delay Algorithm for Listing Chordless Cycles in Undirected Graphs. - Rui A. Ferreira; Roberto Grossi; Romeo Rizzi; Gustavo Sacomoto; Marie-France Sagot (ESA, 2014)

Efficiently Listing Bounded Length st-Paths. - Romeo Rizzi; Gustavo Sacomoto; Marie-France Sagot (IWOCA, 2014)

Navigating in a Sea of Repeats in RNA-seq without Drowning. - Gustavo Sacomoto; Blerina Sinaimeri; Camille Marchet; Vincent Miele; Marie-France Sagot; Vincent Lacroix (WABI, 2014)

Telling metabolic stories to explore metabolomics data: a case study on the yeast response to cadmium exposure. - Paulo Vieira Milreu; Cecilia Coimbra Klein; Ludovic Cottret; Vicente Acuña; Etienne Birmelé; Michele Borassi; Christophe Junot; Alberto Marchetti-Spaccamela; Andrea Marino 001; Leen Stougie; Fabien Jourdan; Pierluigi Crescenzi; et al. (Bioinform., 2014)

Rime: Repeat identification. - Maria Federico; Pierre Peterlongo; Nadia Pisanti; Marie-France Sagot (Discret. Appl. Math., 2014)

Incremental Complexity of a Bi-objective Hypergraph Transversal Problem. - Ricardo Andrade; Etienne Birmelé; Arnaud Mary; Thomas Picchetti; Marie-France Sagot (FCT, 2015)

EUCALYPT: efficient tree reconciliation enumerator. - Beatrice Donati; Christian Baudet; Blerina Sinaimeri; Pierluigi Crescenzi; Marie-France Sagot (Algorithms Mol. Biol., 2015)

A polynomial delay algorithm for the enumeration of bubbles with length constraints in directed graphs. - Gustavo Sacomoto; Vincent Lacroix; Marie-France Sagot (Algorithms Mol. Biol., 2015)

MeDuSa: a multi-draft based scaffolder. - Emanuele Bosi; Beatrice Donati; Marco Galardini; Sara Brunetti; Marie-France Sagot; Pietro Liò; Pierluigi Crescenzi; Renato Fani; Marco Fondi (Bioinform., 2015)

Mirinho: An efficient and general plant and animal pre-miRNA predictor for genomic and deep sequencing data. - Susan Higashi; Cyril Fournier; Christian Gautier; Christine Gaspin; Marie-France Sagot (BMC Bioinform., 2015)

Robustness of the Parsimonious Reconciliation Method in Cophylogeny. - Laura Urbini; Blerina Sinaimeri; Catherine Matias; Marie-France Sagot (AlCoB, 2016)

Computing and Listing st-Paths in Public Transportation Networks. - Katerina Böhmová; Matús Mihalák; Tobias Pröger; Gustavo Sacomoto; Marie-France Sagot (CSR, 2016)

On Maximal Chain Subgraphs and Covers of Bipartite Graphs. - Tiziana Calamoneri; Mattia Gastaldello; Arnaud Mary; Marie-France Sagot; Blerina Sinaimeri (IWOCA, 2016)

Enumeration of minimal stoichiometric precursor sets in metabolic networks. - Ricardo Andrade; Martin Wannagat; Cecilia Coimbra Klein; Vicente Acuña; Alberto Marchetti-Spaccamela; Paulo Vieira Milreu; Leen Stougie; Marie-France Sagot (Algorithms Mol. Biol., 2016)

DegreeCox - a network-based regularization method for survival analysis. - André Veríssimo; Arlindo Limede Oliveira; Marie-France Sagot; Susana Vinga (BMC Bioinform., 2016)

Tackling Big Data in the Life Sciences - Introduction to the Special Theme. - Roeland Merks; Marie-France Sagot (ERCIM News, 2016)

Extracting Few Representative Reconciliations with Host Switches. - Mattia Gastaldello; Tiziana Calamoneri; Marie-France Sagot (CIBB, 2017)

Playing hide and seek with repeats in local and global de novo transcriptome assembly of short RNA-seq reads. - Leandro Lima; Blerina Sinaimeri; Gustavo Sacomoto; Hélène Lopez-Maestre; Camille Marchet; Vincent Miele; Marie-France Sagot; Vincent Lacroix (Algorithms Mol. Biol., 2017)

Algorithmic Enumeration: Output-sensitive, Input-Sensitive, Parameterized, Approximative (Dagstuhl Seminar 18421). - Henning Fernau; Petr A. Golovach; Marie-France Sagot (Dagstuhl Reports, 2018)

Geometric medians in reconciliation spaces of phylogenetic trees. - Katharina T. Huber; Vincent Moulton; Marie-France Sagot; Blerina Sinaimeri (Inf. Process. Lett., 2018)

Computing and Listing st-Paths in Public Transportation Networks. - Katerina Böhmová; Luca Häfliger; Matús Mihalák; Tobias Pröger; Gustavo Sacomoto; Marie-France Sagot (Theory Comput. Syst., 2018)

Metabolic Games. - Taneli Pusa; Martin Wannagat; Marie-France Sagot (Frontiers Appl. Math. Stat., 2019)

Exploring the Robustness of the Parsimonious Reconciliation Method in Host-Symbiont Cophylogeny. - Laura Urbini; Blerina Sinaimeri; Catherine Matias; Marie-France Sagot (IEEE ACM Trans. Comput. Biol. Bioinform., 2019)

A Family of Tree-Based Generators for Bubbles in Directed Graphs. - Vicente Acuña; Leandro Lima; Giuseppe F. Italiano; Luca Pepè Sciarria; Marie-France Sagot; Blerina Sinaimeri (IWOCA, 2020)

On Bubble Generators in Directed Graphs. - Vicente Acuña; Roberto Grossi; Giuseppe Francesco Italiano; Leandro Lima; Romeo Rizzi; Gustavo Sacomoto; Marie-France Sagot; Blerina Sinaimeri (Algorithmica, 2020)

Algorithms for the quantitative Lock/Key model of cytoplasmic incompatibility. - Tiziana Calamoneri; Mattia Gastaldello; Arnaud Mary; Marie-France Sagot; Blerina Sinaimeri (Algorithms Mol. Biol., 2020)

MOOMIN - Mathematical explOration of 'Omics data on a MetabolIc Network. - Taneli Pusa; Mariana Galvao Ferrarini; Ricardo Andrade; Arnaud Mary; Alberto Marchetti-Spaccamela; Leen Stougie; Marie-France Sagot (Bioinform., 2020)

Capybara: equivalence ClAss enumeration of coPhylogenY event-BAsed ReconciliAtions. - Yishu Wang 002; Arnaud Mary; Marie-France Sagot; Blerina Sinaimeri (Bioinform., 2020)

MOMO - multi-objective metabolic mixed integer optimization: application to yeast strain engineering. - Ricardo Andrade; Mahdi Doostmohammadi; João L. Santos; Marie-France Sagot; Nuno P. Mira; Susana Vinga (BMC Bioinform., 2020)

Lazy listing of equivalence classes - A paper on dynamic programming and tropical circuits. - Yishu Wang 002; Arnaud Mary; Marie-France Sagot; Blerina Sinaimeri (CoRR, 2020)

Making Sense of a Cophylogeny Output: Efficient Listing of Representative Reconciliations. - Yishu Wang 002; Arnaud Mary; Marie-France Sagot; Blerina Sinaimeri (WABI, 2021)

A family of tree-based generators for bubbles in directed graphs. - Vicente Acuña; Leandro Ishi Soares de Lima; Giuseppe F. Italiano; Luca Pepè Sciarria; Marie-France Sagot; Blerina Sinaimeri (J. Graph Algorithms Appl., 2021)

Efficiently sparse listing of classes of optimal cophylogeny reconciliations. - Yishu Wang 002; Arnaud Mary; Marie-France Sagot; Blerina Sinaimeri (Algorithms Mol. Biol., 2022)

A General Framework for Enumerating Equivalence Classes of Solutions. - Yishu Wang 002; Arnaud Mary; Marie-France Sagot; Blerina Sinaimeri (Algorithmica, 2023)