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On the readability of overlap digraphs

Rayan Chikhi , Paul Medvedev , Martin Milanič , Sofya Raskhodnikova
Discrete Applied Mathematics, 2016, 205, pp.35-44. ⟨10.1016/j.dam.2015.12.009⟩
Article dans une revue hal-01729749v1
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Algorithmique pour la recherche de motifs approchée et application à la recherche de cibles de microARN

Christophe Vroland
Bio-informatique [q-bio.QM]. Université Lille 1 Sciences et technologies, 2016. Français. ⟨NNT : ⟩
Thèse tel-01576433v1

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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Burkholderia genome mining for nonribosomal peptide synthetases reveals a great potential for novel siderophores and lipopeptides synthesis

Qassim Esmaeel , Maude Pupin , Nam Phuong Kieu , Gabrielle Chataigné , Max Béchet et al.
MicrobiologyOpen, 2016, 5 (3), pp.512 - 526. ⟨10.1002/mbo3.347⟩
Article dans une revue hal-01398944v1
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Compter les globules blancs, analyser les partitions

Mathieu Giraud
Informatique [cs]. Université de Lille 1 – Sciences et Technologies, 2016
HDR tel-01577763v1
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On the Levenshtein Automaton and the Size of the Neighborhood of a Word

Hélène Touzet
LATA 2016 - 10th International Conference on Language and Automata Theory and Applications, Mar 2016, Prague, Czech Republic. pp.207-218, ⟨10.1007/978-3-319-30000-9_16⟩
Communication dans un congrès hal-01360482v1

A time- and cost-effective strategy to sequence mammalian Y Chromosomes: an application to the de novo assembly of gorilla Y

Marta Tomaszkiewicz , Samarth Rangavittal , Monika Cechova , Rebeca Campos Sanchez , Howard William Fescemyer et al.
Genome Research, 2016, 26 (4), pp.530 - 540. ⟨10.1101/gr.199448.115⟩
Article dans une revue hal-01395702v1

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

Bioinformatics Tools for the Discovery of New Nonribosomal Peptides

Valérie Leclère , Tilmann Weber , Philippe Jacques , Maude Pupin
Bradley S. Evans. Nonribosomal Peptide and Polyketide Biosynthesis, 1401, Humana Press, pp.209-232, 2016, Methods in Molecular Biology, 978-1-4939-3373-0 978-1-4939-3375-4. ⟨10.1007/978-1-4939-3375-4_14⟩
Chapitre d'ouvrage hal-01398960v1
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Assisted transcriptome reconstruction and splicing orthology

Samuel Blanquart , Jean-Stéphane Varré , Paul Guertin , Amandine Perrin , Anne Bergeron et al.
BMC Genomics, 2016, Proceedings of the 14th Annual Research in Computational Molecular Biology (RECOMB) Comparative Genomics Satellite Workshop: genomics, 17 (Suppl 10), pp.786. ⟨10.1186/s12864-016-3103-6⟩
Article dans une revue hal-01396410v1
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Multi-loci diagnosis of acute lymphoblastic leukaemia with high-throughput sequencing and bioinformatics analysis

Yann Ferret , Aurélie Caillault , Shéhérazade Sebda , Marc Duez , Nathalie Grardel et al.
British Journal of Haematology, 2016, 173 (3), pp.413-420. ⟨10.1111/bjh.13981⟩
Article dans une revue hal-01279160v1

Nonribosomal peptide synthetase with a unique iterative-alternative-optional mechanism catalyzes amonabactin synthesis in Aeromonas

Qassim Esmaeel , Mickael Chevalier , Gabrielle Chataigne , Rathinasamy Subashkumar , Philippe Jacques et al.
Applied Microbiology and Biotechnology, 2016, 100 (19), pp.8453-8463. ⟨10.1007/s00253-016-7773-4⟩
Article dans une revue hal-01601408v1

Traitement des données - introduction

Iovka Boneva , Héléne Touzet
Les Big Data à découvert, 2016
Chapitre d'ouvrage hal-01574692v1

A dataset of sequences with manually curated V(D)J designations

Mikael Salson , Aurélie Caillault , Marc Duez , Yann Ferret , Alice Fievet et al.
2016
Autre publication scientifique hal-01331556v1
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Approximate search of short patterns with high error rates using the 01⁎0 lossless seeds

Christophe Vroland , Mikael Salson , Sébastien Bini , Hélène Touzet
Journal of Discrete Algorithms, 2016, 37, pp.3-16. ⟨10.1016/j.jda.2016.03.002⟩
Article dans une revue hal-01360485v1
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Smiles2Monomers: a link between chemical and biological structures for polymers

Yoann Dufresne , Laurent Noé , Valérie Leclère , Maude Pupin
Journal of Cheminformatics, 2015, 7, ⟨10.1186/s13321-015-0111-5⟩
Article dans une revue hal-01250619v1
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Norine: a powerful resource for novel nonribosomal peptide discovery

Maude Pupin , Qassim Esmaeel , Areski Flissi , Yoann Dufresne , Philippe Jacques et al.
Synthetic and Systems Biotechnology, 2015, ⟨10.1016/j.synbio.2015.11.001⟩
Article dans une revue hal-01250614v1

Algorithms for bioinformatics

Hélène Touzet
Mihai Pop; Hélène Touzet. WABI, Sep 2015, Atlanta, United States. 9289, Springer Verlag, 2015, 15th International Workshop, WABI 2015, Atlanta, GA, USA, September 10-12, 2015, Proceedings, ⟨10.1007/978-3-662-48221-6⟩
Proceedings/Recueil des communications hal-01228138v1

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

Finding and analysing microRNAs in plant genomes with miRkwood

Isabelle Guigon , Sylvain Legrand , Jean-Frédéric Berthelot , Mohcen Benmounah , Helene Touzet et al.
JOBIM 2015, Jul 2015, Clermont-Ferrand, France
Communication dans un congrès hal-01247604v1

Modeling alternate RNA structures in genomic sequences.

Azadeh Saffarian , Mathieu Giraud , Hélène Touzet
Journal of Computational Biology, 2015, 22 (3), pp.190-204
Article dans une revue hal-01228130v1

Genome scaffolding with PE-contaminated mate-pair libraries

Kristoffer Sahlin , Rayan Chikhi , Lars Arvestad.
WABI 2015, 2015, Atlanta, United States. ⟨10.1101/025650⟩
Communication dans un congrès hal-01236176v1

Perfect Hashing Structures for Parallel Similarity Searches

Tuan Tu Tran , Mathieu Giraud , Jean-Stéphane Varré
International Workshop on High Performance Computational Biology (HiCOMB 2015) / International Parallel and Distributed Processing Symposium (IPDPS 2015), 2015, Hyderabad, India. pp.332-341, ⟨10.1109/IPDPSW.2015.105⟩
Communication dans un congrès hal-01153893v1
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Norine, the knowledgebase dedicated to non-ribosomal peptides, is now open to crowdsourcing

Areski Flissi , Yoann Dufresne , Juraj Michalik , Laurie Tonon , Stéphane Janot et al.
Nucleic Acids Research, 2015, ⟨10.1093/nar/gkv1143⟩
Article dans une revue hal-01235996v1

Deciphering metatranscriptomic data

Evguenia Kopylova , Laurent Noé , Corinne da Silva , Jean-Frédéric Berthelot , Adriana A. Alberti et al.
Methods in Molecular Biology, 1269, Springer, pp.279-291, 2015, RNA Bioinformatics, 978-1-4939-2290-1. ⟨10.1007/978-1-4939-2291-8_17⟩
Chapitre d'ouvrage hal-01104015v1
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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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A Coverage Criterion for Spaced Seeds and Its Applications to Support Vector Machine String Kernels and $k$-Mer Distances

Laurent Noé , Donald E. K. Martin
Journal of Computational Biology, 2014, 21 (12), pp.28. ⟨10.1089/cmb.2014.0173⟩
Article dans une revue hal-01083204v1
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ProCARs: Progressive Reconstruction of Ancestral Gene Orders

Amandine Perrin , Jean-Stéphane Varré , Samuel Blanquart , Aïda Ouangraoua
ISCB-Latin America, Oct 2014, Belo Horizonte, Brazil
Communication dans un congrès hal-01083841v1
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Lossless seeds for searching short patterns with high error rates

Christophe Vroland , Mikaël Salson , Hélène Touzet
International Workshop On Combinatorial Algorithms, Oct 2014, Duluth, United States
Communication dans un congrès hal-01079840v1
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Searching for alternate RNA structures in genomic sequences

Azadeh Saffarian , Mathieu Giraud , Hélène Touzet
Computational Methods for Structural RNAs, CMSR'14, Sep 2014, Strasbourg, France. pp.13-24, ⟨10.15455/CMSR.2014.0002⟩
Communication dans un congrès hal-01084319v1