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Géraldine Jean

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Books and Theses

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2008
[b1]
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Géraldine Jean:
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). University of Bordeaux, France, 2008

Journal Articles

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2025
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Guillaume Fertin, Géraldine Jean, Anthony Labarre:
Sorting genomes by prefix double-cut-and-joins. Theor. Comput. Sci. 1024: 114909 (2025)
2024
[j20]
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Gabriel Siqueira, Andre Rodrigues Oliveira, Alexsandro Oliveira Alexandrino, Géraldine Jean, Guillaume Fertin, Zanoni Dias:
Assignment of orthologous genes in unbalanced genomes using cycle packing of adjacency graphs. J. Heuristics 30(5): 269-289 (2024)
[j19]
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Guillaume Fertin, Oscar Fontaine, Géraldine Jean, Stéphane Vialette:
The Maximum Zero-Sum Partition problem. Theor. Comput. Sci. 1019: 114811 (2024)
2023
[j18]
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Grégoire Prunier, Mehdi Cherkaoui, Albane Lysiak, Olivier Langella, Mélisande Blein-Nicolas, Virginie Lollier, Emile Benoist, Géraldine Jean, Guillaume Fertin, Hélène Rogniaux, Dominique Tessier:
Fast alignment of mass spectra in large proteomics datasets, capturing dissimilarities arising from multiple complex modifications of peptides. BMC Bioinform. 24(1): 421 (2023)
[j17]
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Alexsandro Oliveira Alexandrino, Andre Rodrigues Oliveira, Géraldine Jean, Guillaume Fertin, Ulisses Dias, Zanoni Dias:
Reversal and Transposition Distance on Unbalanced Genomes Using Intergenic Information. J. Comput. Biol. 30(8): 861-876 (2023)
[j16]
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Andre Rodrigues Oliveira, Alexsandro Oliveira Alexandrino, Géraldine Jean, Guillaume Fertin, Ulisses Dias, Zanoni Dias:
Approximation algorithms for sorting by k-cuts on signed permutations. J. Comb. Optim. 45(1): 6 (2023)
2021
[j15]
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Laurent Bulteau, Guillaume Fertin, Géraldine Jean, Christian Komusiewicz:
Sorting by Multi-Cut Rearrangements. Algorithms 14(6): 169 (2021)
[j14]
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Albane Lysiak, Guillaume Fertin, Géraldine Jean, Dominique Tessier:
Evaluation of open search methods based on theoretical mass spectra comparison. BMC Bioinform. 22-S(2): 65 (2021)
[j13]
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Andre Rodrigues Oliveira, Géraldine Jean, Guillaume Fertin, Klairton Lima Brito, Ulisses Dias, Zanoni Dias:
Sorting Permutations by Intergenic Operations. IEEE ACM Trans. Comput. Biol. Bioinform. 18(6): 2080-2093 (2021)
[j12]
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Andre Rodrigues Oliveira, Géraldine Jean, Guillaume Fertin, Klairton Lima Brito, Laurent Bulteau, Ulisses Dias, Zanoni Dias:
Sorting Signed Permutations by Intergenic Reversals. IEEE ACM Trans. Comput. Biol. Bioinform. 18(6): 2870-2876 (2021)
[j11]
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Guillaume Fertin, Julien Fradin, Géraldine Jean:
The Maximum Colorful Arborescence problem: How (computationally) hard can it be? Theor. Comput. Sci. 852: 104-120 (2021)
2020
[j10]
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Klairton Lima Brito, Géraldine Jean, Guillaume Fertin, Andre Rodrigues Oliveira, Ulisses Dias, Zanoni Dias:
Sorting by Genome Rearrangements on Both Gene Order and Intergenic Sizes. J. Comput. Biol. 27(2): 156-174 (2020)
2019
[j9]
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Andre Rodrigues Oliveira, Géraldine Jean, Guillaume Fertin, Ulisses Dias, Zanoni Dias:
Super short operations on both gene order and intergenic sizes. Algorithms Mol. Biol. 14(1): 21:1-21:17 (2019)
2018
[j8]
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Guillaume Fertin, Loïc Jankowiak, Géraldine Jean:
Prefix and suffix reversals on strings. Discret. Appl. Math. 246: 140-153 (2018)
2017
[j7]
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Guillaume Fertin, Géraldine Jean, Eric Tannier:
Algorithms for computing the double cut and join distance on both gene order and intergenic sizes. Algorithms Mol. Biol. 12(1): 16:1-16:11 (2017)
2014
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Vipin T. Sreedharan, Sebastian J. Schultheiß, Géraldine Jean, André Kahles, Regina Bohnert, Philipp Drewe, Pramod Mudrakarta, Nico Görnitz, Georg Zeller, Gunnar Rätsch:
Oqtans: the RNA-seq workbench in the cloud for complete and reproducible quantitative transcriptome analysis. Bioinform. 30(9): 1300-1301 (2014)
[j5]
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Vipin T. Sreedharan, Sebastian J. Schultheiß, Géraldine Jean, André Kahles, Regina Bohnert, Philipp Drewe, Pramod Mudrakarta, Nico Görnitz, Georg Zeller, Gunnar Rätsch:
Oqtans: a multifunctional workbench for RNA-seq data analysis. BMC Bioinform. 15(S-3): A7 (2014)
2011
[j4]
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Sebastian J. Schultheiß, Géraldine Jean, Jonas Behr, Regina Bohnert, Philipp Drewe, Nico Görnitz, André Kahles, Pramod Mudrakarta, Vipin T. Sreedharan, Georg Zeller, Gunnar Rätsch:
Oqtans: a Galaxy-integrated workflow for quantitative transcriptome analysis from NGS Data. BMC Bioinform. 12(S-11): A7 (2011)
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Géraldine Jean, Macha Nikolski:
SyDiG: uncovering Synteny in Distant Genomes. Int. J. Bioinform. Res. Appl. 7(1): 43-62 (2011)
2009
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Géraldine Jean, David James Sherman, Macha Nikolski:
Mining the Semantics of Genome Super-Blocks to Infer Ancestral Architectures. J. Comput. Biol. 16(9): 1267-1284 (2009)
2007
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Géraldine Jean, Macha Nikolski:
Genome rearrangements: a correct algorithm for optimal capping. Inf. Process. Lett. 104(1): 14-20 (2007)

Conference and Workshop Papers

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2023
[c14]
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Gabriel Siqueira, Alexsandro Oliveira Alexandrino, Andre Rodrigues Oliveira, Géraldine Jean, Guillaume Fertin, Zanoni Dias:
Approximating Rearrangement Distances with Replicas and Flexible Intergenic Regions. ISBRA 2023: 241-254
2022
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Guillaume Fertin, Oscar Fontaine, Géraldine Jean, Stéphane Vialette:
The Maximum Zero-Sum Partition Problem. ICS 2022: 73-85
[c12]
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Alexsandro Oliveira Alexandrino, Andre Rodrigues Oliveira, Géraldine Jean, Guillaume Fertin, Ulisses Dias, Zanoni Dias:
Transposition Distance Considering Intergenic Regions for Unbalanced Genomes. ISBRA 2022: 100-113
[c11]
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Andre Rodrigues Oliveira, Alexsandro Oliveira Alexandrino, Géraldine Jean, Guillaume Fertin, Ulisses Dias, Zanoni Dias:
Sorting by k-Cuts on Signed Permutations. RECOMB-CG 2022: 189-204
[c10]
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Guillaume Fertin, Géraldine Jean, Anthony Labarre:
Sorting Genomes by Prefix Double-Cut-and-Joins. SPIRE 2022: 178-190
[c9]
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Emile Benoist, Guillaume Fertin, Géraldine Jean:
The Exact Subset MultiCover Problem. TAMC 2022: 189-200
2021
[c8]
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Laurent Bulteau, Guillaume Fertin, Géraldine Jean, Christian Komusiewicz:
Sorting by Multi-cut Rearrangements. SOFSEM 2021: 593-607
2020
[c7]
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Andre Rodrigues Oliveira, Géraldine Jean, Guillaume Fertin, Klairton Lima Brito, Ulisses Dias, Zanoni Dias:
A 3.5-Approximation Algorithm for Sorting by Intergenic Transpositions. AlCoB 2020: 16-28
2019
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Klairton Lima Brito, Géraldine Jean, Guillaume Fertin, Andre Rodrigues Oliveira, Ulisses Dias, Zanoni Dias:
Sorting by Reversals, Transpositions, and Indels on Both Gene Order and Intergenic Sizes. ISBRA 2019: 28-39
2018
[c5]
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Andre Rodrigues Oliveira, Géraldine Jean, Guillaume Fertin, Ulisses Dias, Zanoni Dias:
Super Short Reversals on Both Gene Order and Intergenic Sizes. BSB 2018: 14-25
2017
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Guillaume Fertin, Julien Fradin, Géraldine Jean:
Algorithmic Aspects of the Maximum Colorful Arborescence Problem. TAMC 2017: 216-230
2016
[c3]
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Guillaume Fertin, Géraldine Jean, Eric Tannier:
Genome Rearrangements on Both Gene Order and Intergenic Regions. WABI 2016: 162-173
2015
[c2]
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Guillaume Fertin, Loïc Jankowiak, Géraldine Jean:
Prefix and Suffix Reversals on Strings. SPIRE 2015: 165-176
2014
[c1]
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Guillaume Fertin, Géraldine Jean, Andreea Radulescu, Irena Rusu:
DExTaR: Detection of exact tandem repeats based on the de Bruijn graph. BIBM 2014: 90-93

Parts in Books or Collections

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2017
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Géraldine Jean, Andreea Radulescu, Irena Rusu:
The Contig Assembly Problem and Its Algorithmic Solutions. Algorithms for Next-Generation Sequencing Data 2017: 267-298

Informal and Other Publications

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2022
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Guillaume Fertin, Géraldine Jean, Anthony Labarre:
Sorting Genomes by Prefix Double-Cut-and-Joins. CoRR abs/2208.14315 (2022)

Coauthor Index

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