Genome rearrangements: a correct algorithm for optimal capping. - Géraldine Jean; Macha Nikolski (Inf. Process. Lett., 2007)

In silico methods for genome rearrangement analysis: from identification of common markers to ancestral reconstruction. (Méthodes in silico pour l'étude des réarrangements génomiques : de l'identification de marqueurs communs à la reconstruction ancestrale). - Géraldine Jean (2008)

Mining the Semantics of Genome Super-Blocks to Infer Ancestral Architectures. - Géraldine Jean; David James Sherman; Macha Nikolski (J. Comput. Biol., 2009)

Oqtans: a Galaxy-integrated workflow for quantitative transcriptome analysis from NGS Data. - Sebastian J. Schultheiß; Géraldine Jean; Jonas Behr; Regina Bohnert; Philipp Drewe; Nico Görnitz; André Kahles; Pramod Mudrakarta; Vipin T. Sreedharan; Georg Zeller; Gunnar Rätsch (BMC Bioinform., 2011)

SyDiG: uncovering Synteny in Distant Genomes. - Géraldine Jean; Macha Nikolski (Int. J. Bioinform. Res. Appl., 2011)

DExTaR: Detection of exact tandem repeats based on the de Bruijn graph. - Guillaume Fertin; Géraldine Jean; Andreea Radulescu; Irena Rusu (BIBM, 2014)

Oqtans: the RNA-seq workbench in the cloud for complete and reproducible quantitative transcriptome analysis. - Vipin T. Sreedharan; Sebastian J. Schultheiß; Géraldine Jean; André Kahles; Regina Bohnert; Philipp Drewe; Pramod Mudrakarta; Nico Görnitz; Georg Zeller; Gunnar Rätsch (Bioinform., 2014)

Oqtans: a multifunctional workbench for RNA-seq data analysis. - Vipin T. Sreedharan; Sebastian J. Schultheiß; Géraldine Jean; André Kahles; Regina Bohnert; Philipp Drewe; Pramod Mudrakarta; Nico Görnitz; Georg Zeller; Gunnar Rätsch (BMC Bioinform., 2014)

Genome Rearrangements on Both Gene Order and Intergenic Regions. - Guillaume Fertin; Géraldine Jean; Eric Tannier (WABI, 2016)

The Contig Assembly Problem and Its Algorithmic Solutions. - Géraldine Jean; Andreea Radulescu; Irena Rusu (Algorithms for Next-Generation Sequencing Data, 2017)

Algorithmic Aspects of the Maximum Colorful Arborescence Problem. - Guillaume Fertin; Julien Fradin; Géraldine Jean (TAMC, 2017)

Algorithms for computing the double cut and join distance on both gene order and intergenic sizes. - Guillaume Fertin; Géraldine Jean; Eric Tannier (Algorithms Mol. Biol., 2017)

Super Short Reversals on Both Gene Order and Intergenic Sizes. - Andre Rodrigues Oliveira; Géraldine Jean; Guillaume Fertin; Ulisses Dias; Zanoni Dias (BSB, 2018)

Prefix and suffix reversals on strings. - Guillaume Fertin; Loïc Jankowiak; Géraldine Jean (Discret. Appl. Math., 2018)

Sorting by Reversals, Transpositions, and Indels on Both Gene Order and Intergenic Sizes. - Klairton Lima Brito; Géraldine Jean; Guillaume Fertin; Andre Rodrigues Oliveira; Ulisses Dias; Zanoni Dias (ISBRA, 2019)

Super short operations on both gene order and intergenic sizes. - Andre Rodrigues Oliveira; Géraldine Jean; Guillaume Fertin; Ulisses Dias; Zanoni Dias (Algorithms Mol. Biol., 2019)

A 3.5-Approximation Algorithm for Sorting by Intergenic Transpositions. - Andre Rodrigues Oliveira; Géraldine Jean; Guillaume Fertin; Klairton Lima Brito; Ulisses Dias; Zanoni Dias (AlCoB, 2020)

Sorting by Genome Rearrangements on Both Gene Order and Intergenic Sizes. - Klairton Lima Brito; Géraldine Jean; Guillaume Fertin; Andre Rodrigues Oliveira; Ulisses Dias; Zanoni Dias (J. Comput. Biol., 2020)

Sorting by Multi-Cut Rearrangements. - Laurent Bulteau; Guillaume Fertin; Géraldine Jean; Christian Komusiewicz (Algorithms, 2021)

Evaluation of open search methods based on theoretical mass spectra comparison. - Albane Lysiak; Guillaume Fertin; Géraldine Jean; Dominique Tessier (BMC Bioinform., 2021)

Sorting Signed Permutations by Intergenic Reversals. - Andre Rodrigues Oliveira; Géraldine Jean; Guillaume Fertin; Klairton Lima Brito; Laurent Bulteau; Ulisses Dias; Zanoni Dias (IEEE ACM Trans. Comput. Biol. Bioinform., 2021)

Sorting Permutations by Intergenic Operations. - Andre Rodrigues Oliveira; Géraldine Jean; Guillaume Fertin; Klairton Lima Brito; Ulisses Dias; Zanoni Dias (IEEE ACM Trans. Comput. Biol. Bioinform., 2021)

The Maximum Colorful Arborescence problem: How (computationally) hard can it be? - Guillaume Fertin; Julien Fradin; Géraldine Jean (Theor. Comput. Sci., 2021)

Transposition Distance Considering Intergenic Regions for Unbalanced Genomes. - Alexsandro Oliveira Alexandrino; Andre Rodrigues Oliveira; Géraldine Jean; Guillaume Fertin; Ulisses Dias; Zanoni Dias (ISBRA, 2022)

Sorting by k-Cuts on Signed Permutations. - Andre Rodrigues Oliveira; Alexsandro Oliveira Alexandrino; Géraldine Jean; Guillaume Fertin; Ulisses Dias; Zanoni Dias (RECOMB-CG, 2022)

Approximating Rearrangement Distances with Replicas and Flexible Intergenic Regions. - Gabriel Siqueira; Alexsandro Oliveira Alexandrino; Andre Rodrigues Oliveira; Géraldine Jean; Guillaume Fertin; Zanoni Dias (ISBRA, 2023)

Approximation algorithms for sorting by k-cuts on signed permutations. - Andre Rodrigues Oliveira; Alexsandro Oliveira Alexandrino; Géraldine Jean; Guillaume Fertin; Ulisses Dias; Zanoni Dias (J. Comb. Optim., 2023)

Reversal and Transposition Distance on Unbalanced Genomes Using Intergenic Information. - Alexsandro Oliveira Alexandrino; Andre Rodrigues Oliveira; Géraldine Jean; Guillaume Fertin; Ulisses Dias; Zanoni Dias (J. Comput. Biol., 2023)

Fast alignment of mass spectra in large proteomics datasets, capturing dissimilarities arising from multiple complex modifications of peptides. - Grégoire Prunier; Mehdi Cherkaoui; Albane Lysiak; Olivier Langella; Mélisande Blein-Nicolas; Virginie Lollier; Emile Benoist; Géraldine Jean; Guillaume Fertin; Hélène Rogniaux; Dominique Tessier (BMC Bioinform., 2023)

The Maximum Zero-Sum Partition problem. - Guillaume Fertin; Oscar Fontaine; Géraldine Jean; Stéphane Vialette (Theor. Comput. Sci., 2024)

Assignment of orthologous genes in unbalanced genomes using cycle packing of adjacency graphs. - Gabriel Siqueira; Andre Rodrigues Oliveira; Alexsandro Oliveira Alexandrino; Géraldine Jean; Guillaume Fertin; Zanoni Dias (J. Heuristics, 2024)

The Exact Subset MultiCover problem. - Emile Benoist; Guillaume Fertin; Géraldine Jean (Theor. Comput. Sci., 2025)

Sorting genomes by prefix double-cut-and-joins. - Guillaume Fertin; Géraldine Jean; Anthony Labarre (Theor. Comput. Sci., 2025)