Fiche membre | Laboratoire des Sciences du Numérique de Nantes

Géraldine JEAN

ENSEIGNANT-CHERCHEUR

: Geraldine.Jeanatls2n.fr

Adresse :

Université de Nantes - faculté des Sciences et Techniques ( FST )
Petit Port
2 Chemin de la Houssinière
BP 92208
44322 Nantes Cedex 3

Batiment 34, étage 3, bureau 304

Publications référencées sur HAL

Revues internationales avec comité de lecture (ART_INT)

[1] A. Alexandrino, A. Oliveira, G. Jean, G. Fertin, U. Dias, Z. Dias. Reversal and Transposition Distance on Unbalanced Genomes Using Intergenic Information. In Journal of Computational Biology ; éd. Mary Ann Liebert, 2023, vol. 30, num. 8.
https://hal.science/hal-04416210

[2] A. Oliveira, A. Alexandrino, G. Jean, G. Fertin, U. Dias, Z. Dias. Approximation algorithms for sorting by k-cuts on signed permutations. In Journal of Combinatorial Optimization ; éd. Springer Verlag, 2022, vol. 45, num. 6.
https://hal.science/hal-04416193

[3] A. Oliveira, G. Jean, G. Fertin, K. Brito, U. Dias, Z. Dias. Sorting Permutations by Intergenic Operations. In IEEE/ACM Transactions on Computational Biology and Bioinformatics ; éd. Institute of Electrical and Electronics Engineers, 2021.
https://hal.science/hal-03346838

[4] L. Bulteau, G. Fertin, G. Jean, C. Komusiewicz. Sorting by Multi-Cut Rearrangements. In Algorithms ; éd. MDPI, 2021, vol. 14, num. 6.
https://hal.science/hal-03388451

[5] G. Fertin, J. Fradin, G. Jean. The Maximum Colorful Arborescence problem: How (computationally) hard can it be?. In Theoretical Computer Science ; éd. Elsevier, 2021, vol. 852.
https://hal.science/hal-03346859

[6] A. Oliveira, G. Jean, G. Fertin, K. Brito, L. Bulteau, U. Dias, Z. Dias. Sorting Signed Permutations by Intergenic Reversals. In IEEE/ACM Transactions on Computational Biology and Bioinformatics ; éd. Institute of Electrical and Electronics Engineers, 2020.
https://hal.science/hal-02901617

[7] K. Brito, G. Jean, G. Fertin, A. Oliveira, U. Dias, Z. Dias. Sorting by Genome Rearrangements on Both Gene Order and Intergenic Sizes. In Journal of Computational Biology ; éd. Mary Ann Liebert, 2020, vol. 27, num. 2.
https://hal.science/hal-02482109

[8] A. Oliveira, G. Jean, G. Fertin, U. Dias, Z. Dias. Super short operations on both gene order and intergenic sizes. In Algorithms for Molecular Biology ; éd. BioMed Central, 2019, vol. 14, num. 1.
https://hal.science/hal-02481196

[9] G. Fertin, L. Jankowiak, G. Jean. Prefix and suffix reversals on strings. In Discrete Applied Mathematics ; éd. Elsevier, 2018, vol. 246.
https://hal.science/hal-01911089

[10] D. Mandakovic, C. Rojas, J. Maldonado, M. Latorre, D. Travisany, E. Delage, A. Bihouee, G. Jean, F. Diaz, B. Fernández-Gómez, P. Cabrera, A. Gaete, C. Latorre, R. Gutierrez, A. Maass, V. Cambiazo, S. Navarrete, D. Eveillard, M. Gonzalez. Structure and co-occurrence patterns in microbial communities under acute environmental stress reveal ecological factors fostering resilience. In Scientific Reports ; éd. Nature Publishing Group, 2018, vol. 8, num. 1.
https://hal.science/hal-01774624

[11] G. Fertin, G. Jean, E. Tannier. Algorithms for computing the double cut and join distance on both gene order and intergenic sizes. In Algorithms for Molecular Biology ; éd. BioMed Central, 2017, vol. 12.
https://hal.science/hal-01533200

[12] G. Fertin, G. Jean, A. Radulescu, I. Rusu. Hybrid de novo tandem repeat detection using short and long reads. In BMC Medical Genomics ; éd. BioMed Central, 2015, vol. 8, num. Suppl 3.
https://hal.science/hal-01214038

[13] V. Sreedharan, S. Schultheiss, G. Jean, A. Kahles, R. Bohnert, P. Drewe, P. Mudrakarta, N. Görnitz, G. Zeller, G. Rätsch. Oqtans: the RNA-seq workbench in the cloud for complete and reproducible quantitative transcriptome analysis.. In Bioinformatics ; éd. Oxford University Press (OUP), 2014.
https://hal.science/hal-00965351

[14] M. Dubin, P. Zhang, D. Meng, M. Remigereau, E. Osborne, F. Paolo Casale, P. Drewe, A. Kahles, G. Jean, B. Vilhjálmsson, J. Jagoda, S. Irez, V. Voronin, Q. Song, Q. Long, G. Rätsch, O. Stegle, R. Clark, M. Nordborg. DNA methylation in Arabidopsis has a genetic basis and shows evidence of local adaptation.. In eLife ; éd. eLife Sciences Publication, 2014, vol. 4.
https://hal.science/hal-01162697

[15] N. Renseigné, T. Alioto, J. Behr, R. Bohnert, D. Campagna, C. Davis, A. Dobin, P. Engström, T. Gingeras, G. Grant, G. Jean, A. Kahles, P. Kosarev, S. Li, J. Liu, C. Mason, V. Molodtsov, Z. Ning, H. Ponstingl, J. Prins, P. Ribeca, I. Seledtsov, B. Sipos, V. Solovyev, T. Steijger, G. Valle, N. Vitulo, K. Wang, T. Wu, G. Zeller, G. Rätsch, N. Goldman, T. Hubbard, J. Harrow, R. Guigó, P. Bertone. Systematic evaluation of spliced alignment programs for RNA-seq data.. In Nature Methods ; éd. Nature Publishing Group, 2013.
https://hal.science/hal-00909047

[16] T. Steijger, J. Abril, P. Engström, F. Kokocinski, M. Akerman, T. Alioto, G. Ambrosini, S. Antonarakis, J. Behr, P. Bertone, R. Bohnert, P. Bucher, N. Cloonan, T. Derrien, S. Djebali, J. Du, S. Dudoit, M. Gerstein, T. Gingeras, D. Gonzalez, S. Grimmond, R. Guigó, L. Habegger, J. Harrow, T. Hubbard, C. Iseli, G. Jean, A. Kahles, J. Lagarde, J. Leng, G. Lefebvre, S. Lewis, A. Mortazavi, P. Niermann, G. Rätsch, A. Reymond, P. Ribeca, H. Richard, J. Rougemont, J. Rozowsky, M. Sammeth, A. Sboner, M. Schulz, S. Searle, N. Solorzano, V. Solovyev, M. Stanke, B. Stevenson, H. Stockinger, A. Valsesia, D. Weese, S. White, B. Wold, J. Wu, T. Wu, G. Zeller, D. Zerbino, M. Zhang. Assessment of transcript reconstruction methods for RNA-seq.. In Nature Methods ; éd. Nature Publishing Group, 2013, vol. 10, num. 12.
https://hal.science/hal-00909081

[17] G. Jean, M. Nikolski. SyDiG: uncovering Synteny in Distant Genomes. In Int. J. of Bioinformatics Research and Applications. 2011
https://hal.science/hal-00737390

[18] X. Gan, O. Stegle, J. Behr, J. Steffen, P. Drewe, K. Hildebrand, R. Lyngsoe, S. Schultheiss, E. Osborne, V. Sreedharan, A. Kahles, R. Bohnert, G. Jean, P. Derwent, P. Kersey, E. Belfield, N. Harberd, E. Kemen, C. Toomajian, P. Kover, R. Clark, G. Rätsch, R. Mott. Multiple reference genomes and transcriptomes for Arabidopsis thaliana.. In Nature ; éd. Nature Publishing Group, 2011, vol. 477, num. 7365.
https://hal.science/hal-00909088

[19] G. Jean, A. Kahles, V. Sreedharan, F. de Bona, G. Rätsch. RNA-Seq read alignments with PALMapper.. In Curr Protoc Bioinformatics, vol. Chapter 11. 12-2010
https://hal.science/hal-00909100

[20] G. Jean, D. Sherman, M. Nikolski. Mining the semantics of genome super-blocks to infer ancestral architectures. In Journal of Computational Biology ; éd. Mary Ann Liebert, 2009, vol. 16, num. 9.
https://inria.hal.science/inria-00414692

[21] J. Souciet, B. Dujon, C. Gaillardin, M. Johnston, P. Baret, P. Cliften, D. Sherman, J. Weissenbach, E. Westhof, P. Wincker, C. Jubin, J. Poulain, V. Barbe, B. Ségurens, F. Artiguenave, V. Anthouard, B. Vacherie, M. Val, R. Fulton, P. Minx, R. Wilson, P. Durrens, G. Jean, C. Marck, T. Martin, M. Nikolski, T. Rolland, M. Seret, S. Casaregola, L. Despons, C. Fairhead, G. Fischer, I. Lafontaine, V. Leh, M. Lemaire, J. de Montigny, C. Neuvéglise, A. Thierry, I. Blanc-Lenfle, C. Bleykasten, J. Diffels, E. Fritsch, L. Frangeul, A. Goeffon, N. Jauniaux, R. Kachouri-Lafond, C. Payen, S. Potier, L. Pribylova, C. Ozanne, G. Richard, C. Sacerdot, M. Straub, E. Talla. Comparative genomics of protoploid Saccharomycetaceae. In Genome Research ; éd. Cold Spring Harbor Laboratory Press, 2009, vol. 19.
https://inria.hal.science/inria-00407511

[22] G. Jean, M. Nikolski. Genome rearrangements: a correct algorithm for optimal capping. In Information Processing Letters ; éd. Elsevier, 2007, vol. 104, num. 1.
https://inria.hal.science/inria-00274291

Conférences internationales avec comité de lecture et actes (COMM_INT)

[23] G. Siqueira, A. Oliveira Alexandrino, A. Rodrigues Oliveira, G. Jean, G. Fertin, Z. Dias. Approximating Rearrangement Distances with Replicas and Flexible Intergenic Regions. In International Symposium on Bioinformatics Research and Applications (ISBRA 2023), octobre 2023, Wrocław, Pologne.In Springer (éds.), . Springer Nature, 2023.
https://hal.science/hal-04418179

[24] E. Benoist, G. Fertin, G. Jean. L'Inférence de Protéines à travers le Modèle Peptide Quantity Assignment. In 23ème congrès annuel de la Société Française de Recherche Opérationnelle et d'Aide à la Décision, février 2022, Villeurbanne - Lyon, France.
https://hal.science/hal-03595308

[25] G. Fertin, O. Fontaine, G. Jean, S. Vialette. The Maximum Zero-Sum Partition Problem. In 25th International Computer Symposium, ICS 2022, décembre 2022, Taoyuan, Taïwan.
https://hal.science/hal-04293802

[26] A. Rodrigues Oliveira, A. Oliveira Alexandrino, G. Jean, G. Fertin, U. Dias, Z. Dias. Sorting by k-Cuts on Signed Permutations. In Comparative Genomics 19th International Conference, RECOMB-CG 2022, mai 2022, La Jolla, états-Unis.In Springer Verlag (éds.), . Springer International Publishing, 2022.
https://hal.science/hal-03959780

[27] E. Benoist, G. Fertin, G. Jean. The Exact Subset MultiCover Problem. In Theory and Applications of Models of Computation. TAMC 2022, septembre 2022, Tianjin, Chine.In Springer Verlag (éds.), . Springer International Publishing, 2022.
https://hal.science/hal-03958441

[28] G. Fertin, G. Jean, A. Labarre. Sorting Genomes by Prefix Double-Cut-and-Joins. In String Processing and Information Retrieval, 29th International Symposium, SPIRE 2022, novembre 2022, Concepcion, Chili.In Springer Verlag (éds.), . Springer International Publishing, 2022.
https://hal.science/hal-03958465

[29] A. Oliveira Alexandrino, A. Rodrigues Oliveira, G. Jean, G. Fertin, U. Dias, Z. Dias. Transposition Distance Considering Intergenic Regions for Unbalanced Genomes. In Bioinformatics Research and Applications 18th International Symposium, ISBRA 2022, novembre 2022, Haifa, Israël.In Springer Verlag (éds.), . Springer Nature Switzerland, 2022.
https://hal.science/hal-03958480

[30] L. Bulteau, G. Fertin, G. Jean, C. Komusiewicz. Sorting by Multi-cut Rearrangements. In SOFSEM 2021, janvier 2021, Bolzano-Bozen, Italie.
https://hal.science/hal-03346830

[31] A. Oliveira, G. Jean, G. Fertin, K. Brito, U. Dias, Z. Dias. A 3.5-Approximation Algorithm for Sorting by Intergenic Transpositions. In 7th International Conference, AlCoB 2020 (Algorithms for Computational Biology ), avril 2020, Missoula, états-Unis.
https://hal.science/hal-02528304

[32] K. Brito, G. Jean, G. Fertin, A. Oliveira, U. Dias, Z. Dias. Sorting by Reversals, Transpositions, and Indels on Both Gene Order and Intergenic Sizes. In International Symposium on Bioinformatics Research and Applications ISBRA 2019, juin 2019, Barcelona, Espagne.
https://hal.science/hal-02304027

[33] A. Rodrigues Oliveira, G. Jean, G. Fertin, U. Dias, Z. Dias. Super Short Reversals on Both Gene Order and Intergenic Sizes. In Advances in Bioinformatics and Computational Biology - 11th Brazilian Symposium on Bioinformatics -- BSB 2018, octobre 2018, Niteroi, Brésil.In Springer (éds.), . , 2018.
https://hal.science/hal-02081164

[34] G. Fertin, J. Fradin, G. Jean. Algorithmic Aspects of the Maximum Colorful Arborescence Problem. In Theory and Applications of Models of Computation - 14th Annual Conference, avril 2017, Berne, Suisse.
https://hal.science/hal-01524069

[35] G. Fertin, G. Jean, E. Tannier. Genome Rearrangements on both Gene Order and Intergenic Regions. In WABI 2016, 2016, Aarhus, Danemark.
https://hal.science/hal-01334942

[36] G. Fertin, G. Jean, A. Radulescu, I. Rusu. DExTaR: Detection of Exact Tandem Repeats based on the de Bruijn graph. In IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2014), novembre 2014, Belfast, Irlande.
https://hal.science/hal-01117967

[37] S. Schultheiss, G. Jean. Oqtans: Quantitative transcriptome analysis in the cloud I. In Meeting on Advances and Challenges of RNA-seq Analysis, juin 2012, Halle, Allemagne.
https://hal.science/hal-01172014

[38] S. Schultheiss, G. Jean, J. Behr, R. Bohnert, P. Drewe, N. Görnitz, A. Kahles, P. Mudrakarta, V. Sreedharan, G. Zeller, G. Rätsch. Oqtans: a Galaxy-integrated workflow for quantitative transcriptome analysis from NGS Data. In Seventh International Society for Computational Biology (ISCB) Student Council Symposium 2011, juillet 2011, , Autriche.In BMC Bioinformatics ; éd. BioMed Central, 2011.
https://hal.science/hal-00914308

[39] G. Jean. Reconstruction and visualization of genome rearrangements within the Kluyveromyces. In First German / French / European Meeting on Yeast and Filamentous Fungi, mai 2008, Strasbourg, France.
https://inria.hal.science/inria-00350613

[40] G. Jean, D. Sherman, M. Nikolski. Reconstruction and visualization of genome rearrangements within the Kuyveromyces. In ESF-EMBO Symposium on Comparative Genomics of Eukaryotic Microorganisms, octobre 2007, San Feliu de Guixols, Espagne.
https://inria.hal.science/inria-00350567

[41] G. Jean. Reconstruction of ancestral genomes within Hemiascomycetes. In Yeast Genome 10th Anniversary, septembre 2006, Brussels, Belgique.
https://inria.hal.science/inria-00407497

Conférences nationales avec comité de lecture et actes (COMM_NAT)

[42] G. Jean. Méthode in silico pour la reconstruction d'une architecture ancestrale de génome. In JOBIM satellite meeting, juillet 2007, Marseille, France.
https://inria.hal.science/inria-00352587

Ouvrages - Chapitres d‘ouvrages et directions d‘ouvrages (OUV)

[43] G. Jean, A. Radulescu, I. Rusu. The Contig Assembly Problem and Its Algorithmic Solutions. In Algorithms for Next-Generation Sequencing Data, pp. 267-298. 2017
https://hal.science/hal-01819204

Theses et HDR (THESE)

[44] G. Jean. In silico methods for genome rearrangement analysis: from identification of common markers to ancestral reconstruction.. Thèses : Université Sciences et Technologies - Bordeaux I.
https://theses.hal.science/tel-00350900v2

Autres publications (AUTRES)

[45] A. Lysiak, G. Fertin, G. Jean, D. Tessier. Detection of multiple modifications in mass spectra without any a priori. In 69th ASMS Conference on Mass Spectrometry and Allied Topics, octobre 2021, Philadelphia (PA), états-Unis.
https://hal.science/hal-03959810

[46] A. Benoiston, E. Eveillard, S. Chaffron, S. Ayata, C. Bowler, L. Guidi, E. Delage, G. Jean, L. Bittner, T. Corrdinators. Biological pump processes are driven by microbial networks in the global oligotrophic ocean. In ISME17, août 2018, Leipzig, Allemagne.
https://hal.science/hal-04021817