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Designing Efficient Spaced Seeds for SOLiD Read Mapping.

Laurent Noé , Marta Gîrdea , Gregory Kucherov
Advances in Bioinformatics, 2010, ⟨10.1155/2010/708501⟩
Article dans une revue inria-00527029v1

Conservation of the glycogen metabolism pathway underlines a pivotal function of storage polysaccharides in Chlamydiae

Matthieu Colpaert , Derifa Kadouche , Mathieu Ducatez , Trestan Pillonel , Carole Kebbi-Beghdadi et al.
Communications Biology, 2021, 4 (1), ⟨10.1038/s42003-021-01794-y⟩
Article dans une revue hal-03174571v1
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Iterative Spaced Seed Hashing: Closing the Gap Between Spaced Seed Hashing and k-mer Hashing

Enrico Petrucci , Laurent Noé , Cinzia Pizzi , Matteo Comin
15th International Symposium on Bioinformatics Research and Applications (ISBRA), Jun 2019, Barcelona, Spain. pp.208-219, ⟨10.1007/978-3-030-20242-2_18⟩
Communication dans un congrès hal-02146404v1 a repository of interoperable open-source code for many-core bioinformatics

Jean-Frédéric Berthelot , Charles Deltel , Mathieu Giraud , Stéphane Janot , Laetitia Jourdan et al.
JOBIM 2011, Jul 2011, Paris, France
Communication dans un congrès hal-00637847v1
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Vidjil: A Web Platform for Analysis of High-Throughput Repertoire Sequencing

Marc Duez , Mathieu Giraud , Ryan Herbert , Tatiana Rocher , Mikael Salson et al.
PLoS ONE, 2016, 11 (11), ⟨10.1371/journal.pone.0166126⟩
Article dans une revue hal-01397079v1
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Norine, Florine, s2m : powerful bioinformatics resource and tools for the discovery of novel nonribosomal peptides, natural metabolites with versatile activities

Qassim Esmaeel , Yoann Dufresne , Areski Flissi , Maude Pupin , Philippe Jacques et al.
FEMS 2017 - 7th congress of Federation of European Microbiology societies, Jul 2017, Valencia, Spain
Poster de conférence hal-01888999v1
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Prediction and pattern matching algorithms for RNA multi-structures

Azadeh Saffarian
Data Structures and Algorithms [cs.DS]. Université des Sciences et Technologie de Lille - Lille I, 2011. English. ⟨NNT : ⟩
Thèse tel-00832700v1
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Bioinformatics Sequence Comparisons on Manycore Processors

Tuan Tu Tran
Data Structures and Algorithms [cs.DS]. Université des Sciences et Technologie de Lille - Lille I, 2012. English. ⟨NNT : ⟩
Thèse tel-00832663v1
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Read indexing

Nicolas Philippe , Mikael Salson , Thierry Lecroq , Martine Léonard , Thérèse Commes et al.
EMBnet.journal, 2011, 17 (Supplement B), pp.1. ⟨10.14806/ej.17.B.289⟩
Article dans une revue lirmm-00757983v1

Structural and content diversity of mitochondrial genome in beet: a comparative genomic analysis

Aude Darracq , Jean-Stéphane Varré , Laurence Maréchal-Drouard , Adeline Courseaux , Vincent Castric et al.
Genome Biology and Evolution, 2011, 3, pp.723-736. ⟨10.1093/gbe/evr042⟩
Article dans une revue hal-00616508v1

Improved search heuristics find 20 000 new alignments between human and mouse genomes.

Martin Frith , Laurent Noé
Nucleic Acids Research, 2014, 42 (7), pp.e59. ⟨10.1093/nar/gku104⟩
Article dans une revue hal-00958207v1

Assembly scaffolding with PE-contaminated mate-pair libraries

Kristoffer Sahlin , Rayan Chikhi , Lars Arvestad
Bioinformatics, 2016, 32 (13), pp.1925 - 1932. ⟨10.1093/bioinformatics/btw064⟩
Article dans une revue hal-01396904v1
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ProCARs: Progressive Reconstruction of Ancestral Gene Orders

Amandine Perrin , Jean-Stéphane Varré , Samuel Blanquart , Aïda Ouangraoua
BMC Genomics, 2015, 16 (Suppl 5), pp.S6. ⟨10.1186/1471-2164-16-S5-S6⟩
Article dans une revue hal-01217311v1
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AllSome Sequence Bloom Trees

Chen Sun , Robert S. Harris , Rayan Chikhi , Paul Medvedev
RECOMB 2017 - 21st Annual International Conference on Research in Computational Molecular Biology, May 2017, Hong Kong, China. ⟨10.1007/978-3-319-56970-3_17⟩
Communication dans un congrès hal-01575350v1

Nonribosomal peptides and polyketides of Burkholderia: new compounds potentially implicated in biocontrol and pharmaceuticals

Qassim Esmaeel , Maude Pupin , Philippe Jacques , Valérie Leclère
Environmental Science and Pollution Research, 2017, ⟨10.1007/s11356-017-9166-3⟩
Article dans une revue hal-01548616v1

Giraffe genome sequence reveals clues to its unique morphology and physiology

Morris Agaba , Edson Ishengoma , Webb Colby Miller , Barbara C. Mcgrath , Chelsea N. Hudson et al.
Nature Communications, 2016, 7, ⟨10.1038/ncomms11519⟩
Article dans une revue hal-01395703v1
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Diversity of monomers in nonribosomal peptides: towards the prediction of origin and biological activity.

Ségolène Caboche , Valérie Leclère , Maude Pupin , Gregory Kucherov , Philippe Jacques et al.
Journal of Bacteriology, 2010, 192 (19), pp.5143-50. ⟨10.1128/JB.00315-10⟩
Article dans une revue hal-00641488v1

Efficient alternatives to PSI-BLAST

Michal Startek , Slawomir Lasota , Maciej Sykulski , Adam Bulak , Laurent Noé et al.
Bulletin of the Polish Academy of Sciences: Technical Sciences, 2012, 60 (3), pp.495-505. ⟨10.2478/v10175-012-0063-0⟩
Article dans une revue hal-00749016v1
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Structure, biosynthesis, and properties of kurstakins, nonribosomal lipopeptides from Bacillus spp.

Max Béchet , Thibault Caradec , Walaa Hussein , Ahmed Abderrahmani , Marlène Chollet et al.
Applied Microbiology and Biotechnology, 2012, 95 (3), pp.593-600. ⟨10.1007/s00253-012-4181-2⟩
Article dans une revue hal-00749819v1

Frugal alignment-free identification of FLT3-internal tandem duplications with FiLT3r

Augustin Boudry , Sasha Darmon , Nicolas Duployez , Martin Figeac , Sandrine Geffroy et al.
BMC Bioinformatics, 2022, 23 (1), pp.448. ⟨10.1186/s12859-022-04983-6⟩
Article dans une revue hal-03920854v1
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High-throughput sequencing in acute lymphoblastic leukemia: Follow-up of minimal residual disease and emergence of new clones

Mikael Salson , Mathieu Giraud , Aurélie Caillault , Nathalie Grardel , Nicolas Duployez et al.
Leukemia Research, 2017, 53, pp.1-7. ⟨10.1016/j.leukres.2016.11.009⟩
Article dans une revue hal-01404817v1
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Improved Sensitivity And Reliability Of Anchor Based Genome Alignment

Raluca Uricaru , Célia Michotey , Laurent Noé , Hélène Chiapello , Eric Rivals et al.
JOBIM'09 : Journées Ouvertes en Biologie, Informatique et Mathématiques, Jun 2009, Nantes, France. pp.31-36
Communication dans un congrès lirmm-00407215v1

Using Minimum Path Cover to Boost Dynamic Programming on DAGs: Co-Linear Chaining Extended

Anna Kuosmanen , Topi Paavilainen , Travis Gagie , Rayan Chikhi , Alexandru Ioan Tomescu et al.
RECOMB 2018 - 22nd Annual International Conference on Research in Computational Molecular Biology, Apr 2018, Paris, France
Communication dans un congrès hal-01935568v1
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Efficient dynamic range minimum query

Alice Héliou , Martine Léonard , Laurent Mouchard , Mikael Salson
Theoretical Computer Science, 2016, 656, pp.108-117. ⟨10.1016/j.tcs.2016.07.002⟩
Article dans une revue hal-01255499v2

RecoverY: k-mer-based read classification for Y-chromosome-specific sequencing and assembly

Samarth Rangavittal , Robert Harris , Monika Cechova , Marta Tomaszkiewicz , Rayan Chikhi et al.
Article dans une revue hal-01729744v1

Les séquenceurs à haut débit

Mathieu Giraud , Mikaël Salson
Interstices, 2011
Article dans une revue hal-01350176v1

The predictive strength of next-generation sequencing MRD detection for relapse compared with current methods in childhood ALL.

Michaela Kotrova , Katerina Muzikova , Ester Mejstrikova , Michaela Novakova , Violeta Bakardjieva-Mihaylova et al.
Blood, 2015, 126 (8), pp.1045-7. ⟨10.1182/blood-2015-07-655159⟩
Article dans une revue hal-01241663v1
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Querying Large Read Collections in Main Memory: A Versatile data Structure

Nicolas Philippe , Mikael Salson , Thierry Lecroq , Martine Léonard , Thérèse Commes et al.
BMC Bioinformatics, 2011, 12, pp.242-258. ⟨10.1186/1471-2105-12-242⟩
Article dans une revue lirmm-00632958v1
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NRPS toolbox for the discovery of new nonribosomal peptides and synthetases

Maude Pupin , Malika Smaïl-Tabbone , Philippe Jacques , Marie-Dominique Devignes , Valérie Leclère et al.
Journées Ouvertes en Biologie, l'Informatique et les Mathématiques - JOBIM 2012, Jul 2012, Rennes, France. pp.89-93
Communication dans un congrès hal-00734312v1
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Structural pattern matching of nonribosomal peptides.

Ségolène Caboche , Maude Pupin , Valérie Leclère , Philippe Jacques , Gregory Kucherov et al.
BMC Structural Biology, 2009, 9 (15), ⟨10.1186/1472-6807-9-15⟩
Article dans une revue hal-00641486v1