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VirHunter: a deep learning-based method for detection of novel viruses in plant sequencing data

Grigorii Sukhorukov , Macha Nikolski
PlantGen 2021, Jun 2021, Novosibirsk, Russia
Conference poster hal-03271424v1
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Approximation Hardness of the Cross-Species Conserved Active Modules Detection Problem

Thomas Hume , Hayssam Soueidan , Macha Nikolski , Guillaume Blin
41st International Conference on Current Trends in Theory and Practice of Computer Science (SOFSEM'15), Jan 2015, Pec pod Sněžkou, Czech Republic. pp. 242-253
Conference papers hal-01056406v1
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DypFISH: Dynamic Patterned FISH to Interrogate RNA and Protein Spatial and Temporal Subcellular Distribution

Anca Savulescu , Robyn Brackin , Emmanuel Bouilhol , Benjamin Dartigues , Jonathan H Warrell , et al.
Preprints, Working Papers, ... hal-02409081v1
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Genome-Wide Reconstitution of Chromatin Transactions: RSC Preferentially disrupts H2A.Z-Containing Nucleosomes

Aylin Cakiroglu , Cédric Clapier , Andreas H Ehrensberger , Elodie Darbo , Bradley R Cairns , et al.
Preprints, Working Papers, ... hal-01884309v1
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Microbiota Composition May Predict Anti-Tnf Alpha Response in Spondyloarthritis Patients: an Exploratory Study

Thomas Bazin , Katarzyna B Hooks , Thomas Barnetche , Marie-Elise Truchetet , Raphaël Enaud , et al.
Scientific Reports, 2018, 8 (1), pp.5446. ⟨10.1038/s41598-018-23571-4⟩
Journal articles hal-01760163v1
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YOC, A new strategy for pairwise alignment of collinear genomes

Raluca Uricaru , Célia Michotey , Hélène Chiapello , Eric Rivals
BMC Bioinformatics, 2015, 16 (1), pp.16:111. ⟨10.1186/s12859-015-0530-3⟩
Journal articles lirmm-01170968v1
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A community effort to create standards for evaluating tumor subclonal reconstruction

Adriana Salcedo , Maxime Tarabichi , Shadrielle Melijah G. Espiritu , Amit Deshwar , Matei David , et al.
Nature Biotechnology, 2020, 38 (1), pp.97-107. ⟨10.1038/s41587-019-0364-z⟩
Journal articles hal-02438695v1
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Genome Sequences of Two Tunisian Field Strains of Avian Mycoplasma, M. meleagridis and M. gallinarum

Elhem Yacoub , Pascal Sirand-Pugnet , Aurélien Barré , Alain Blanchard , Christophe Hubert , et al.
Genome Announcements, 2016, 4 (3), pp.e00558-16. ⟨10.1128/genomeA.00558-16⟩
Journal articles pasteur-02015202v1
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Towards an open grapevine information system

Anne-Françoise Adam-Blondon , Michael Alaux , Cyril Pommier , D Cantu , Z-M Cheng , et al.
Horticulture research, 2016, 3, pp.16056. ⟨10.1038/hortres.2016.56⟩
Journal articles hal-01404714v1
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Population genomics of apricots unravels domestication history and adaptive events

Alexis Groppi , Shuo Liu , A. Cornille , David Tricon , Quynh Trang Bui , et al.
Nature Communications, 2021, 12 (1), pp.3956. ⟨10.1038/s41467-021-24283-6⟩
Journal articles hal-03282504v1
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VirHunter: A Deep Learning-Based Method for Detection of Novel RNA Viruses in Plant Sequencing Data

Grigorii Sukhorukov , Maryam Khalili , Olivier Gascuel , Thierry Candresse , Armelle Marais , et al.
Frontiers in Bioinformatics, 2022, 2, pp.867111. ⟨10.3389/fbinf.2022.867111⟩
Journal articles hal-03671482v1
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Dysbiosis and Its Discontents

Katarzyna B Hooks , Maureen A O'Malley
mBio, 2017, 8 (5), pp. e01492-17. ⟨10.1128/mBio.01492-17⟩
Journal articles hal-01677295v1
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INEXTVIR: High throughput sequencing of the virome of agricultural crops and ecosystems across Europe

Kaoutar Daoud Hiri , Johan Rollin , Sukhorukov Grigorii , Macha Nikolski , Sébastien Massart , et al.
ESCS-ECCB 2020, Sep 2020, Barcelona, Spain
Conference poster hal-03271520v1
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Interrogating RNA and protein spatial subcellular distribution in smFISH data with DypFISH

Anca Savulescu , Robyn Brackin , Emmanuel Bouilhol , Benjamin Dartigues , Jonathan Warrell , et al.
Cell Reports Methods, 2021, 1 (5), pp.100068. ⟨10.1016/j.crmeth.2021.100068⟩
Journal articles hal-03349483v1
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Composting-Like Conditions Are More Efficient for Enrichment and Diversity of Organisms Containing Cellulase-Encoding Genes than Submerged Cultures

Senta Heiss-Blanquet , Francoise M Fayolle-Guichard , Vincent M Lombard , Agnès M Hébert , Pedro M Coutinho , et al.
PLoS ONE, 2016, 11 (12), pp.497 - 497. ⟨10.1371/journal.pone.0167216⟩
Journal articles hal-01455050v1
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FluoSim: simulator of single molecule dynamics for fluorescence live-cell and super-resolution imaging of membrane proteins

Matthieu Lagardère , Ingrid Chamma , Emmanuel Bouilhol , Macha Nikolski , Olivier Thoumine
Scientific Reports, 2020, 10, ⟨10.1038/s41598-020-75814-y⟩
Journal articles hal-03010357v1
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The invasive proteome of glioblastoma revealed by laser-capture microdissection

Thomas Daubon , Joris Guyon , Anne-Aurélie Raymond , Benjamin Dartigues , Justine Rudewicz , et al.
Neuro-Oncology Advances, 2019, 1 (1), pp.1-12. ⟨10.1093/noajnl/vdz029⟩
Journal articles hal-02347439v1
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Intestinal Inflammation in Children with Cystic Fibrosis Is Associated with Crohn’s-Like Microbiota Disturbances

Raphaël Enaud , Katarzyna B Hooks , Aurélien Barré , Thomas Barnetche , Christophe Hubert , et al.
Journal of Clinical Medicine, 2019, 8 (5), pp.645. ⟨10.3390/jcm8050645⟩
Journal articles hal-02126914v1
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Transgenerational endocrine disruptor effects of cadmium in zebrafish and contribution of standing epigenetic variation to adaptation

Fabien Pierron , Guillemine Daffe , Flore Daramy , Débora Heroin , Aurélien Barré , et al.
Journal of Hazardous Materials, 2023, 455, pp.131579. ⟨10.1016/j.jhazmat.2023.131579⟩
Journal articles hal-04093643v1
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TGFβ promotes low IL10-producing ILC2 with profibrotic ability involved in skin fibrosis in systemic sclerosis

Paôline Laurent , Benoit Allard , Pauline Manicki , Valérie Jolivel , Emeline Levionnois , et al.
Annals of the Rheumatic Diseases, 2021, pp.annrheumdis-2020-219748. ⟨10.1136/annrheumdis-2020-219748⟩
Journal articles hal-03386391v1
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Proposal for a European Public Health Research Infrastructure for Sharing of health and Medical administrative data (PHRIMA).

Anita Burgun , Dina V Oksen , Wolfgang Kuchinke , Hans-Ulrich Prokosch , Thomas Ganslandt , et al.
Studies in Health Technology and Informatics, 2015, 216, pp.1005. ⟨10.3233/978-1-61499-564-7-1005⟩
Journal articles hal-01232643v1
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Genetic and epigenetic interplay allows rapid transgenerational adaptation to metal pollution in zebrafish

Fabien Pierron , Débora Heroin , Guillemine Daffe , Flore Daramy , Aurélien Barré , et al.
Environmental Epigenetics, 2022, 8 (1), ⟨10.1093/eep/dvac022⟩
Journal articles hal-04065814v1
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Pacific Biosciences Sequencing and IMGT/HighV-QUEST Analysis of Full-Length Single Chain Fragment Variable from an In Vivo Selected Phage-Display Combinatorial Library

Audrey Hémadou , Véronique Giudicelli , Melissa Laird Smith , Marie-Paule Lefranc , Patrice Duroux , et al.
Frontiers in Immunology, 2017, 8, ⟨10.3389/fimmu.2017.01796⟩
Journal articles hal-01677196v1
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Colib’read on galaxy: a tools suite dedicated to biological information extraction from raw NGS reads

Yvan Le Bras , Olivier Collin , Cyril Monjeaud , Vincent Lacroix , Eric Rivals , et al.
GigaScience, 2016, 5 (1), ⟨10.1186/s13742-015-0105-2⟩
Journal articles hal-01280238v1
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Novel analytical methods to interpret large sequencing data from small sample sizes

Florence Lichou , Sébastien Orazio , Stéphanie Dulucq , Gabriel Etienne , Michel Longy , et al.
Human Genomics, 2019, 13 (1), ⟨10.1186/s40246-019-0235-1⟩
Journal articles hal-02359853v1
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Reference-free compression of high throughput sequencing data with a probabilistic de Bruijn graph

Gaëtan Benoit , Claire Lemaitre , Dominique Lavenier , Erwan Drezen , Thibault Dayris , et al.
BMC Bioinformatics, 2015, 16 (1), ⟨10.1186/s12859-015-0709-7⟩
Journal articles hal-01214682v1
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Looking for mutations in PacBio cancer data: an alignment-free method

Justine Rudewicz , Hayssam Soueidan , Raluca Uricaru , Richard Iggo , Jonas Bergh , et al.
JOBIM 2015, Jul 2015, Clermont-Ferrand, France
Conference poster hal-01254846v1
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Early Medieval Muslim Graves in France: First Archaeological, Anthropological and Palaeogenomic Evidence

Yves Gleize , Fanny Mendisco , Marie-Hélène Pemonge , Christophe Hubert , Alexis Groppi , et al.
Journal articles hal-01673021v1
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DeepSpot: a deep neural network for RNA spot enhancement in smFISH microscopy images

Emmanuel Bouilhol , Anca Flavia Savulescu , Edgar Lefevre , Benjamin Dartigues , Robyn Brackin , et al.
Biological Imaging, 2022, pp.1-18. ⟨10.1017/S2633903X22000034⟩
Journal articles hal-03659677v1
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COordination of Standards in MetabOlomicS (COSMOS): facilitating integrated metabolomics data access

Reza M. Salek , Steffen Neumann , Daniel Schober , Jan Hummel , Kenny Billiau , et al.
Metabolomics, 2015, 11 (6), pp.Journal no. 11306. ⟨10.1007/s11306-015-0810-y⟩
Journal articles hal-01165673v1