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authIdHal_s : geraldine-jean
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The Maximum Colorful Arborescence problem: How (computationally) hard can it be?

Guillaume Fertin , Julien Fradin , Géraldine Jean
Theoretical Computer Science, 2021, 852, pp.104-120. ⟨10.1016/j.tcs.2020.11.021⟩
Journal articles hal-03346859v1

Prefix and suffix reversals on strings

Guillaume Fertin , Loïc Jankowiak , Géraldine Jean
Discrete Applied Mathematics, 2018, 246, pp.140 - 153. ⟨10.1016/j.dam.2017.07.031⟩
Journal articles hal-01911089v1

Super Short Reversals on Both Gene Order and Intergenic Sizes

Andre Rodrigues Oliveira , Géraldine Jean , Guillaume Fertin , Ulisses Dias , Zanoni Dias et al.
Advances in Bioinformatics and Computational Biology - 11th Brazilian Symposium on Bioinformatics -- BSB 2018, Oct 2018, Niteroi, Brazil. pp.14--25
Conference papers hal-02081164v1

Systematic evaluation of spliced alignment programs for RNA-seq data.

Non Renseigné , Tyler Alioto , Jonas Behr , Regina Bohnert , Davide Campagna et al.
Nature Methods, 2013, epub ahead of print. ⟨10.1038/nmeth.2722⟩
Journal articles hal-00909047v1

Transposition Distance Considering Intergenic Regions for Unbalanced Genomes

Alexsandro Oliveira Alexandrino , Andre Rodrigues Oliveira , Géraldine Jean , Guillaume Fertin , Ulisses Dias et al.
Bioinformatics Research and Applications 18th International Symposium, ISBRA 2022, Nov 2022, Haifa, Israel. pp.100-113, ⟨10.1007/978-3-031-23198-8_10⟩
Conference papers hal-03958480v1

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 et al.
International Symposium on Bioinformatics Research and Applications ISBRA 2019, Jun 2019, Barcelona, Spain. pp.28-39, ⟨10.1007/978-3-030-20242-2_3⟩
Conference papers hal-02304027v1

Sorting Signed Permutations by Intergenic Reversals

Andre Rodrigues Oliveira , Géraldine Jean , Guillaume Fertin , Klairton Lima Brito , Laurent Bulteau et al.
IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2020, ⟨10.1109/TCBB.2020.2993002⟩
Journal articles hal-02901617v1

Reconstruction and visualization of genome rearrangements within the Kluyveromyces

Géraldine Jean
First German / French / European Meeting on Yeast and Filamentous Fungi, May 2008, Strasbourg, France
Conference papers inria-00350613v1

DExTaR: Detection of Exact Tandem Repeats based on the de Bruijn graph

Guillaume Fertin , Géraldine Jean , Andreea Radulescu , Irena Rusu
IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2014), Nov 2014, Belfast, Ireland. pp.90-93, ⟨10.1109/BIBM.2014.6999134⟩
Conference papers hal-01117967v1
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Sorting by Multi-Cut Rearrangements

Laurent Bulteau , Guillaume Fertin , Géraldine Jean , Christian Komusiewicz
Algorithms, 2021, 14 (6), pp.169. ⟨10.3390/a14060169⟩
Journal articles hal-03388451v1

Assessment of transcript reconstruction methods for RNA-seq.

Tamara Steijger , Josep F Abril , Pär G Engström , Felix Kokocinski , Martin Akerman et al.
Nature Methods, 2013, 10 (12), pp.1177-1184. ⟨10.1038/nmeth.2714⟩
Journal articles hal-00909081v1
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Structure and co-occurrence patterns in microbial communities under acute environmental stress reveal ecological factors fostering resilience

Dinka Mandakovic , Claudia Rojas , Jonathan Maldonado , Mauricio Latorre , Dante Travisany et al.
Scientific Reports, 2018, 8 (1), pp.5875. ⟨10.1038/s41598-018-23931-0⟩
Journal articles hal-01774624v1

Multiple reference genomes and transcriptomes for Arabidopsis thaliana.

Xiangchao Gan , Oliver Stegle , Jonas Behr , Joshua G Steffen , Philipp Drewe et al.
Nature, 2011, 477 (7365), pp.419-23. ⟨10.1038/nature10414⟩
Journal articles hal-00909088v1

Sorting Genomes by Prefix Double-Cut-and-Joins

Guillaume Fertin , Géraldine Jean , Anthony Labarre
String Processing and Information Retrieval, 29th International Symposium, SPIRE 2022, Nov 2022, Concepcion, Chile. pp.178-190, ⟨10.1007/978-3-031-20643-6_13⟩
Conference papers hal-03958465v1

Genome Rearrangements on both Gene Order and Intergenic Regions

Guillaume Fertin , Géraldine Jean , Eric Tannier
WABI 2016, 2016, Aarhus, Denmark. pp.162-173
Conference papers hal-01334942v1
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Algorithms for computing the double cut and join distance on both gene order and intergenic sizes

Guillaume Fertin , Géraldine Jean , Eric Tannier
Algorithms for Molecular Biology, 2017, 12, 16 (11 p.). ⟨10.1186/s13015-017-0107-y⟩
Journal articles hal-01533200v1
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Comparative genomics of protoploid Saccharomycetaceae

Jean-Luc Souciet , Bernard Dujon , Claude Gaillardin , Mark Johnston , Philippe V Baret et al.
Genome Research, 2009, 19, pp.1696-1709. ⟨10.1101/gr.091546.109⟩
Journal articles inria-00407511v1

Genome rearrangements: a correct algorithm for optimal capping

Géraldine Jean , Macha Nikolski
Information Processing Letters, 2007, 104 (1), pp.14-20. ⟨10.1016/j.ipl.2007.04.011⟩
Journal articles istex inria-00274291v1
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L'Inférence de Protéines à travers le Modèle Peptide Quantity Assignment

Emile Benoist , Guillaume Fertin , Géraldine Jean
23ème congrès annuel de la Société Française de Recherche Opérationnelle et d'Aide à la Décision, INSA Lyon, Feb 2022, Villeurbanne - Lyon, France
Conference papers hal-03595308v1

RNA-Seq read alignments with PALMapper.

Géraldine Jean , André Kahles , Vipin T Sreedharan , Fabio de Bona , Gunnar Rätsch et al.
Curr Protoc Bioinformatics, 2010, Chapter 11, pp.Unit 11.6. ⟨10.1002/0471250953.bi1106s32⟩
Journal articles hal-00909100v1

Reconstruction and visualization of genome rearrangements within the Kuyveromyces

Géraldine Jean , David James Sherman , Macha Nikolski
ESF-EMBO Symposium on Comparative Genomics of Eukaryotic Microorganisms, Oct 2007, San Feliu de Guixols, Spain. pp.44
Conference papers inria-00350567v1

Hybrid de novo tandem repeat detection using short and long reads

Guillaume Fertin , Géraldine Jean , Andreea Radulescu , Irena Rusu
BMC Medical Genomics, 2015, 8 (Suppl 3), pp.S5. ⟨10.1186/1755-8794-8-S3-S5⟩
Journal articles hal-01214038v1

DNA methylation in Arabidopsis has a genetic basis and shows evidence of local adaptation.

Manu J Dubin , Pei Zhang , Dazhe Meng , Marie-Stanislas Remigereau , Edward J Osborne et al.
eLife, 2014, 4, pp.4:e05255
Journal articles hal-01162697v1

Sorting by Multi-cut Rearrangements

Laurent Bulteau , Guillaume Fertin , Géraldine Jean , Christian Komusiewicz
International Conference on Current Trends in Theory and Practice of Informatics (SOFSEM 2021), pp.593-607, 2021, ⟨10.1007/978-3-030-67731-2_43⟩
Book sections hal-03346830v1

SpecGlob: rapid and accurate alignment of mass spectra differing from their peptide models by several unknown modifications

Albane Lysiak , Guillaume Fertin , Géraldine Jean , Dominique Tessier
2022
Preprints, Working Papers, ... hal-03959826v1

Detection of multiple modifications in mass spectra without any a priori

Albane Lysiak , Guillaume Fertin , Géraldine Jean , Dominique Tessier
69th ASMS Conference on Mass Spectrometry and Allied Topics, Oct 2021, Philadelphia (PA), United States
Poster communications hal-03959810v1

The Contig Assembly Problem and Its Algorithmic Solutions

Géraldine Jean , Andreea Radulescu , Irena Rusu
Algorithms for Next-Generation Sequencing Data, pp. 267-298, 2017
Book sections hal-01819204v1

A 3.5-Approximation Algorithm for Sorting by Intergenic Transpositions

Andre Rodrigues Oliveira , Géraldine Jean , Guillaume Fertin , Klairton Lima Brito , Ulisses Dias et al.
7th International Conference, AlCoB 2020 (Algorithms for Computational Biology ), Apr 2020, Missoula, United States. pp.16-28, ⟨10.1007/978-3-030-42266-0_2⟩
Conference papers hal-02528304v1

Super short operations on both gene order and intergenic sizes

Andre Oliveira , Géraldine Jean , Guillaume Fertin , Ulisses Dias , Zanoni Dias et al.
Algorithms for Molecular Biology, 2019, 14 (1), ⟨10.1186/s13015-019-0156-5⟩
Journal articles hal-02481196v1

Mining the semantics of genome super-blocks to infer ancestral architectures

Géraldine Jean , David James Sherman , Macha Nikolski
Journal of Computational Biology, 2009, 16 (9), pp.1267-1284. ⟨10.1089/cmb.2008.0046⟩
Journal articles inria-00414692v1