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Intégration de donnéesModélisation de systèmes / problèmes / donnéesOptimisation combinatoire / discrète

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BioinformatiqueBiologie des SystèmesMétagénomiqueModélisation Biologique

Géraldine Jean

Enseignant chercheur / Enseignante chercheuse – Maître / maîtresse de conférences

Equipe :

Employeur : Nantes Université

Expertises :

BioinformatiqueAlgorithmique combinatoireComplexité algorithmiqueGénomique comparativeProtéomique

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Publications déposées sur HAL

Nombre de publications retournées : 55

Revues internationales avec comité de lecture

[1] G. Jean, M. Nikolski. Genome rearrangements: a correct algorithm for optimal capping, in Information Processing Letters, vol. 104, no. 1, pp. 14-20, DOI

[2] G. Jean, D. Sherman, M. Nikolski. Mining the semantics of genome super-blocks to infer ancestral architectures, in Journal of Computational Biology, vol. 16, no. 9, pp. 1267-1284, DOI

[3] 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-Louis, 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, vol. 19, pp. 1696-1709, DOI

[4] G. Jean, A. Kahles, V. Sreedharan, F. de Bona, G. Rätsch. RNA-Seq read alignments with PALMapper., in Curr Protoc Bioinformatics, vol. Chapter 11, pp. Unit 11.6, DOI

[5] G. Jean, M. Nikolski. , in Int. J. of Bioinformatics Research and Applications, pp. 43-62, DOI

[6] 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, vol. 477, no. 7365, pp. 419-23, DOI

[7] 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, pp. epub ahead of print, DOI

[8] 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, vol. 10, no. 12, pp. 1177-1184, DOI

[9] 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, pp. epub ahead of print, DOI

[10] 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, vol. 4, pp. 4:e05255,

[11] G. Fertin, G. Jean, A. Radulescu, I. Rusu. Hybrid de novo tandem repeat detection using short and long reads, in BMC Medical Genomics, vol. 8, no. Suppl 3, pp. S5, DOI

[12] 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, vol. 12, pp. 16 (11 pages), DOI

[13] G. Fertin, L. Jankowiak, G. Jean. Prefix and suffix reversals on strings, in Discrete Applied Mathematics, vol. 246, pp. 140 – 153, DOI

[14] D. Mandakovic, C. Rojas, J. Maldonado, M. Latorre, D. Travisany, E. Delage, A. Bihouée, 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, vol. 8, no. 1, pp. 5875, DOI

[15] 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, vol. 14, no. 1, DOI

[16] 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, DOI

[17] 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, vol. 27, no. 2, pp. 156-174, DOI

[18] 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, pp. 1-1, DOI

[19] L. Bulteau, G. Fertin, G. Jean, C. Komusiewicz. Sorting by Multi-Cut Rearrangements, in Algorithms, vol. 14, no. 6, pp. 169, DOI

[20] G. Fertin, J. Fradin, G. Jean. The Maximum Colorful Arborescence problem: How (computationally) hard can it be?, in Theoretical Computer Science, vol. 852, pp. 104-120, DOI

[21] 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, vol. 45, no. 6, DOI

[22] 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, vol. 30, no. 8, pp. 861-876, DOI

[23] G. Siqueira, A. Oliveira, A. Alexandrino, G. Jean, G. Fertin, Z. Dias. Assignment of orthologous genes in unbalanced genomes using cycle packing of adjacency graphs, in Journal of Heuristics, vol. 30, no. 5-6, pp. 269-289, DOI

[24] G. Fertin, G. Jean, A. Labarre. Sorting genomes by prefix double-cut-and-joins, in Theoretical Computer Science, vol. 1024, pp. 114909, DOI

[25] G. Fertin, O. Fontaine, G. Jean, S. Vialette. The Maximum Zero-Sum Partition problem, in Theoretical Computer Science, vol. 1019, pp. 114811, DOI

[26] É. Benoist, G. Jean, H. Rogniaux, G. Fertin, D. Tessier. SpecPeptidOMS Directly and Rapidly Aligns Mass Spectra on Whole Proteomes and Identifies Peptides That Are Not Necessarily Tryptic : Implications for Peptidomics, in Journal of Proteome Research, vol. 24, no. 4, pp. 2159-2172, DOI

Conférences internationales avec comité de lecture et actes

[27] G. Jean. Reconstruction of ancestral genomes within Hemiascomycetes, in Yeast Genome 10th Anniversary, Brussels, Belgique,

[28] 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, San Feliu de Guixols, Espagne,

[29] G. Jean. Reconstruction and visualization of genome rearrangements within the Kluyveromyces, in First German / French / European Meeting on Yeast and Filamentous Fungi, Strasbourg, France,

[30] 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 BMC Bioinformatics, pp. 12(Suppl 11):A7, in Seventh International Society for Computational Biology (ISCB) Student Council Symposium 2011, Autriche, DOI

[31] S. Schultheiss, G. Jean. Oqtans: Quantitative transcriptome analysis in the cloud I, in Meeting on Advances and Challenges of RNA-seq Analysis, Halle, Allemagne,

[32] 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), Belfast, Irlande, DOI

[33] G. Fertin, G. Jean, E. Tannier. Genome Rearrangements on both Gene Order and Intergenic Regions, in WABI 2016, Aarhus, Danemark,

[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, Berne, Suisse, DOI

[35] 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, Niteroi, Brésil, DOI

[36] 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, Barcelona, Espagne, DOI

[37] 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 ), Missoula, états-Unis, DOI

[38] L. Bulteau, G. Fertin, G. Jean, C. Komusiewicz. Sorting by Multi-cut Rearrangements, in SOFSEM 2021, Bolzano-Bozen, Italie, DOI

[39] 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, Villeurbanne – Lyon, France,

[40] 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, La Jolla, états-Unis, DOI

[41] E. Benoist, G. Fertin, G. Jean. The Exact Subset MultiCover Problem, in Theory and Applications of Models of Computation. TAMC 2022, Tianjin, Chine, DOI

[42] 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, Concepcion, Chili, DOI

[43] 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, Haifa, Israël, DOI

[44] G. Fertin, O. Fontaine, G. Jean, S. Vialette. The Maximum Zero-Sum Partition Problem, in 25th International Computer Symposium, ICS 2022, Taoyuan, Taïwan, DOI

[45] 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), Wrocław, Pologne, DOI

[46] A. Berthier, É. Benoist, G. Fertin, G. Jean. GSI: A New Approach to the Protein Inference Problem, in 26th International Conference on Algorithms for Bioinformatics (WABI 2026), L'Aquila, Italie, DOI

Autres publications

[50] 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, Leipzig, Allemagne,

[51] 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, Philadelphia (PA), états-Unis,

[52] A. Lysiak, G. Fertin, G. Jean, D. Tessier. SpecGlob: rapid and accurate alignment of mass spectra differing from their peptide models by several unknown modifications, DOI

[53] G. Jean, C. Lemaitre, M. Salson. SeqBIM 2025 Abstracts and Proceedings, in SeqBIM 2025, Nantes, France,

[54] A. Berthier, E. Benoist, G. Fertin, G. Jean, H. Rogniaux. Global Spectrum Interpretation (GSI): A global, integrative approach for the protein inference problem, in EuPA 2025, Saint-Malo, France,

[55] E. Benoist, G. Jean, H. Rogniaux, G. Fertin, D. Tessier. SpecPeptidOMS allows fast and without a priori peptide identification in a peptidomics context., in EuPA conference, Saint-Malo, France,

PeptidOMS – Approches numériques innovantes en peptidomique : le pari des stratégies OMS

Pas de plateformes référencées pour l’instant

Pas de logiciels de référencés pour l’instant