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Monomer structure fingerprints: an extension of the monomer composition version for peptide databases

Ammar Abdo , Eissa Ghaleb , Naser Alajmi , Maude Pupin
Journal of Computer-Aided Molecular Design, 2020, 34 (11), pp.1147-1156. ⟨10.1007/s10822-020-00336-8⟩
Article dans une revue hal-03081813v1

Palantir: a springboard for the analysis of secondary metabolite gene clusters in large-scale genome mining projects

Loïc Meunier , Pierre Tocquin , Luc Cornet , Damien Sirjacobs , Valérie Leclère et al.
Bioinformatics, 2020, 36 (15), pp.4345-4347. ⟨10.1093/bioinformatics/btaa517⟩
Article dans une revue hal-03081849v1
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REINDEER: efficient indexing of k-mer presence and abundance in sequencing datasets

Camille Marchet , Zamin Iqbal , Daniel Gautheret , Mikaël Salson , Rayan Chikhi et al.
Bioinformatics, 2020, 36 (Supplement_1), pp.i177-i185. ⟨10.1093/bioinformatics/btaa487⟩
Article dans une revue hal-03413006v1
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ELECTOR : evaluator for long reads correction methods

Camille Marchet , Pierre Morisse , Lolita Lecompte , Arnaud Lefebvre , Thierry Lecroq et al.
NAR Genomics and Bioinformatics, 2020, 2 (1), pp.1-12. ⟨10.1093/nargab/lqz015⟩
Article dans une revue hal-02371117v1

Iterative Spaced Seed Hashing: Closing the Gap Between Spaced Seed Hashing and k -mer Hashing

Enrico Petrucci , Laurent Noé , Cinzia Pizzi , Matteo Comin
Journal of Computational Biology, 2020, 27 (2), pp.223-233. ⟨10.1089/cmb.2019.0298⟩
Article dans une revue hal-02910076v1
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Use of whole-genome sequencing in the molecular investigation of care-associated HCoV-OC43 infections in a hematopoietic stem cell transplant unit

Delphine Beury , Léa Fléchon , Florence Maurier , Ségolène Caboche , Jean-Stéphane Varré et al.
Journal of Clinical Virology, 2020, 122, pp.104206. ⟨10.1016/j.jcv.2019.104206⟩
Article dans une revue hal-02403094v1
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Novel components at the periphery of long read genome assembly tools

Pierre Marijon
Computer Science [cs]. University of Lille, 2019. English. ⟨NNT : ⟩
Thèse tel-02441360v1
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miRkwood: a tool for the reliable identification of microRNAs in plant genomes

Isabelle Guigon , Sylvain Legrand , Jean-Frédéric Berthelot , Sébastien Bini , Delphine Lanselle et al.
BMC Genomics, 2019, 20 (1), ⟨10.1186/s12864-019-5913-9⟩
Article dans une revue hal-02265367v1
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rBAN: retro-biosynthetic analysis of nonribosomal peptides

Emma Ricart , Valérie Leclère , Areski Flissi , Markus Mueller , Maude Pupin et al.
Journal of Cheminformatics, 2019, 11 (1), pp.1-14. ⟨10.1186/s13321-019-0335-x⟩
Article dans une revue hal-02167433v1

Kendrick Mass Defect Approach Combined to NORINE Database for Molecular Formula Assignment of Nonribosomal Peptides

Mickael Chevalier , Emma Ricart , Emeline Hanozin , Maude Pupin , Philippe Jacques et al.
Journal of The American Society for Mass Spectrometry, 2019, 30 (12), pp.2608-2616. ⟨10.1007/s13361-019-02314-3⟩
Article dans une revue hal-02417587v1
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Predicting isoform transcripts: What does the comparison of known transcripts in human, mouse and dog tell us?

Nicolas Guillaudeux , Catherine Belleannée , Samuel Blanquart , Jean-Stéphane Varré
JOBIM 2019 - Journées Ouvertes Biologie, Informatique et Mathématiques, Jul 2019, Nantes, France. 8, pp.1, 2019, ⟨10.7490/f1000research.1117311.1⟩
Poster de conférence hal-02267357v1
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Comparative assessment of long-read error correction software applied to Nanopore RNA-sequencing data

Leandro Lima , Camille Marchet , Ségolène Caboche , Corinne da Silva , Benjamin Istace et al.
Briefings in Bioinformatics, 2019, pp.1-18. ⟨10.1093/bib/bbz058⟩
Article dans une revue hal-02394395v1
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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
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CONSENT: Scalable self-correction of long reads with multiple sequence alignment

Pierre Morisse , Camille Marchet , Antoine Limasset , Thierry Lecroq , Arnaud Lefebvre et al.
Recomb-Seq 2019 - 9th RECOMB Satellite Workshop on Massively Parallel Sequencing, May 2019, Washinton, United States. pp.1-9, ⟨10.1101/546630⟩
Communication dans un congrès hal-02435116v1
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Indexing De Bruijn graphs with minimizers

Camille Marchet , Maël Kerbiriou , Antoine Limasset
Recomb-Seq 2019 - 9th RECOMB Satellite Workshop on Massively Parallel Sequencing, May 2019, Whashinton, United States. pp.1-16, ⟨10.1101/546309⟩
Communication dans un congrès hal-02435086v1
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A complete protocol for whole-genome sequencing of virus from clinical samples: Application to coronavirus OC43

Florence Maurier , Delphine Beury , Léa Fléchon , Jean-Stéphane Varré , Hélène Touzet et al.
Virology, 2019, 531, pp.141-148. ⟨10.1016/j.virol.2019.03.006⟩
Article dans une revue hal-02167880v1
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Non-redundant sampling in RNA Bioinformatics

Juraj Michalik
Bioinformatics [q-bio.QM]. Université Paris Saclay (COmUE), 2019. English. ⟨NNT : 2019SACLX009⟩
Thèse tel-02124550v1

Graph analysis of fragmented long-read bacterial genome assemblies

Pierre Marijon , Rayan Chikhi , Jean-Stéphane Varré
Article dans une revue hal-02167175v1
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Toward perfect reads: self-correction of short reads via mapping on de Bruijn graphs

Antoine Limasset , Jean-François Flot , Pierre Peterlongo
Article dans une revue hal-02407243v1

Standardized next-generation sequencing of immunoglobulin and T-cell receptor gene recombinations for MRD marker identification in acute lymphoblastic leukaemia; a EuroClonality-NGS validation study

Monika Brüggemann , Michaela Kotrova , Henrik Knecht , Jack Bartram , Myriam Boudjogrha et al.
Article dans une revue hal-02169053v1
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Norine: update of the nonribosomal peptide resource

Areski Flissi , Emma Ricart , Clémentine Campart , Mickael Chevalier , Yoann Dufresne et al.
Nucleic Acids Research, 2019, ⟨10.1093/nar/gkz1000⟩
Article dans une revue hal-02376009v1
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Complete Sequence, Multichromosomal Architecture and Transcriptome Analysis of the Solanum tuberosum Mitochondrial Genome

Jean-Stéphane Varré , Nunzio d'Agostino , Pascal Touzet , Sophie Gallina , Rachele Tamburino et al.
International Journal of Molecular Sciences, 2019, 20, ⟨10.3390/ijms20194788⟩
Article dans une revue hal-02298474v1

DiNAMO: highly sensitive DNA motif discovery in high-throughput sequencing data

Chadi Saad , Laurent Noé , Hugues Richard , Julie Leclerc , Marie-Pierre Buisine et al.
BMC Bioinformatics, 2018, 19 (1), ⟨10.1186/s12859-018-2215-1⟩
Article dans une revue hal-01881466v1

Dualities in Tree Representations

Rayan Chikhi , Alexander Schönhuth
2018
Pré-publication, Document de travail hal-01935566v1

Bipartite Graphs of Small Readability

Rayan Chikhi , Vladan Jovičić , Stefan Kratsch , Paul Medvedev , Martin Milanic et al.
COCOON 2018 - The 24th International Computing and Combinatorics Conference, Jul 2018, Qingdao, China
Communication dans un congrès hal-01935562v1

Bioinformatics tools for the discovery of new lipopeptides with biocontrol applications

Maude Pupin , Areski Flissi , Philippe Jacques , Valérie Leclère
European Journal of Plant Pathology, 2018, ⟨10.1007/s10658-018-1544-2⟩
Article dans une revue hal-01937890v1
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Practical dynamic de Bruijn graphs

Alan Kuhnle , Victoria G. Crawford , Christina Boucher , Rayan Chikhi , Travis Gagie et al.
Article dans une revue hal-01935559v1

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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Compression et indexation de séquences annotées

Tatiana Rocher
Bio-informatique [q-bio.QM]. Université de Lille, 2018. Français. ⟨NNT : ⟩
Thèse tel-01758361v1
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L codent, L créent: créations numériques artistiques pour démystifier l'informatique... au féminin! (descriptif d’atelier)

Philippe Marquet , Maude Pupin , Yann Secq
Didapro 7 – DidaSTIC. De 0 à 1 ou l’heure de l’informatique à l’école, Feb 2018, Lausanne, Suisse. pp.1-2
Communication dans un congrès hal-01753402v1