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A new fingerprint to predict nonribosomal peptides activity.

Ammar Hasan Abdo , Ségolène Caboche , Valérie Leclère , Philippe Jacques , Maude Pupin
Journal of Computer-Aided Molecular Design, 2012, 26 (10), pp.1187-94. ⟨10.1007/s10822-012-9608-4⟩
Article dans une revue hal-00750002v1

Turbo prediction: a new approach for bioactivity prediction

Ammar Abdo , Maude Pupin
Journal of Computer-Aided Molecular Design, 2022, 36 (1), pp.77-85. ⟨10.1007/s10822-021-00440-3⟩
Article dans une revue hal-03833232v1
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Prediction of New Bioactive Molecules using a Bayesian Belief Network

Ammar Abdo , Valérie Leclère , Philippe Jacques , Naomie Salim , Maude Pupin
Journal of Chemical Information and Modeling, 2014, 54 (1), pp.30-36. ⟨10.1021/ci4004909⟩
Article dans une revue hal-01090611v1

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

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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Toward Optimal Fingerprint Indexing for Large Scale Genomics

Clément Agret , Bastien Cazaux , Antoine Limasset
WABI 2022 - 22nd International Workshop on Algorithms in Bioinformatics, Sep 2022, Postdam, Germany. pp.25:1-25:15, ⟨10.4230/LIPIcs.WABI.2022.25⟩
Communication dans un congrès hal-04121819v1

RedOak: a reference-free and alignment-free structure for indexing a collection of similar genomes

Clément Agret , Annie Chateau , Gaetan Droc , Gautier Sarah , Manuel Ruiz , et al.
Journal of Open Source Software, 2022, 7 (80), pp.4363. ⟨10.21105/joss.04363⟩
Article dans une revue lirmm-03920648v1

NIQKI

Clément Agret , Bastien Cazaux , Antoine Limasset
Logiciel lirmm-04121986v1
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SARS-CoV-2 Through the Lens of Computational Biology: How bioinformatics is playing a key role in the study of the virus and its origins

Samuel Alizon , Frédéric Cazals , Stéphane Guindon , Claire Lemaitre , Tristan Mary-Huard , et al.
[Research Report] CNRS. 2021, pp.1-35
Rapport hal-03170023v1
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BRASERO: A resource for benchmarking RNA secondary structure comparison algorithms

Julien Allali , Cédric Saule , Cedric Chauve , Yves d'Aubenton-Carafa , Alain Denise , et al.
Advances in Bioinformatics, 2012, 2012, pp.1-5. ⟨10.1155/2012/893048⟩
Article dans une revue hal-00647725v1

Proteomic characterisation of leech microglia extracellular vesicles (EVs): comparison between differential ultracentrifugation and Optiprep™ density gradient isolation

T Arab , A Raffo-Romero , C van Camp , Q Lemaire , F Le Marrec-Croq , et al.
Journal of Extracellular Vesicles, 2019, 8 (1), pp.1603048. ⟨10.1080/20013078.2019.1603048⟩
Article dans une revue inserm-02941660v1
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Genetic basis for virulence differences of various Cryptosporidium parvum carcinogenic isolates

Christophe Audebert , Franck Bonardi , Ségolène Caboche , Karine Guyot , Hélène Touzet , et al.
Scientific Reports, 2020, 10 (1), pp.7316. ⟨10.1038/s41598-020-64370-0⟩
Article dans une revue inserm-02873228v1
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DE-kupl: exhaustive capture of biological variation in RNA-seq data through k-mer decomposition

Jérôme Audoux , Nicolas Philippe , Rayan Chikhi , Mikael Salson , Mélina Gallopin , et al.
Genome Biology, 2017, 18 (1), pp.1-15. ⟨10.1186/s13059-017-1372-2⟩
Article dans une revue hal-01728770v1
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SimBA: A methodology and tools for evaluating the performance of RNA-Seq bioinformatic pipelines

Jérôme Audoux , Mikaël Salson , Christophe Grosset , Sacha Beaumeunier , Jean-Marc Holder , et al.
BMC Bioinformatics, 2017, 18 (1), pp.428. ⟨10.1186/s12859-017-1831-5⟩
Article dans une revue inserm-02437931v1
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Tn-phyto: essential genomes of nine bacterial phytopathogens

Julie Baltenneck , Ben Moussa , Loïc Couderc , Areski Flissi , Jacques Pédron , et al.
4. International Ewinia workshop (IEW), Jul 2022, Assise, Italy
Poster de conférence hal-03721522v1
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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

biomanycores.org: 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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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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Mitochondrial genes support a common origin of rodent malaria parasites and Plasmodium falciparum's relatives infecting great apes

Samuel Blanquart , Olivier Gascuel
BMC Evolutionary Biology, 2011, 11 (1), pp.70. ⟨10.1186/1471-2148-11-70⟩
Article dans une revue hal-00784426v1
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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

Porechop_ABI: discovering unknown adapters in Oxford Nanopore Technology sequencing reads for downstream trimming

Quentin Bonenfant , Laurent Noé , Hélène Touzet
Bioinformatics Advances, 2023, ⟨10.1093/bioadv/vbac085⟩
Article dans une revue hal-03932719v1

Traitement des données - introduction

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

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

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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Mise en place d'une plate-forme logicielle pour l'analyse des peptides non-ribosomiaux

Ségolène Caboche
Bio-informatique [q-bio.QM]. Université des Sciences et Technologie de Lille - Lille I, 2009. Français. ⟨NNT : ⟩
Thèse tel-00823447v1
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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
Journal of Bacteriology, 2010, 192 (19), pp.5143-50. ⟨10.1128/JB.00315-10⟩
Article dans une revue hal-00641488v1
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Structural pattern matching of nonribosomal peptides.

Ségolène Caboche , Maude Pupin , Valérie Leclère , Philippe Jacques , Gregory Kucherov
BMC Structural Biology, 2009, 9 (15), ⟨10.1186/1472-6807-9-15⟩
Article dans une revue hal-00641486v1
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NORINE: a database of nonribosomal peptides.

Ségolène Caboche , Maude Pupin , Valérie Leclère , Arnaud Fontaine , Philippe Jacques , et al.
Nucleic Acids Research, 2008, Database issue, 36 (Database issue), pp.D326-31. ⟨10.1093/nar/gkm792⟩
Article dans une revue inria-00281012v1
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Prediction of Monomer Isomery in Florine: A Workflow Dedicated to Nonribosomal Peptide Discovery

Thibault Caradec , Maude Pupin , Aurélien Vanvlassenbroeck , Marie-Dominique Devignes , Malika Smaïl-Tabbone , et al.
PLoS ONE, 2014, 9 (1), pp.e85667. ⟨10.1371/journal.pone.0085667⟩
Article dans une revue hal-01090619v1

From Sequences to Graphs: Discrete Methods and Structures for Bioinformatics

Annie Chateau , Mikaël Salson
Ouvrages hal-03920813v1