Nos publications

Les publications listées ci-dessous présentent des exemples d’applications qui ont été réalisées par ViroScan3D.

Type de publication :

CD1d-restricted peripheral T cell lymphoma in mice and humans.

Bachy E, Urb M, Chandra S, Robinot R, Bricard G, de Bernard S, Traverse-Glehen A, Gazzo S, Blond O, Khurana A, Baseggio L, Heavican T, Ffrench M, Crispatzu G, Mondière P, Schrader A, Taillardet M, Thaunat O, Martin N, Dalle S, Le Garff-Tavernier M, Salles G, Lachuer J, Hermine. Exp. Med. 2016. 213(5):841.

Transcriptome.

Sequencing the genome of Indian Flying Fox, natural reservoir of Nipah virus, using hybrid assembly and conservative secondary scaffolding.

Fouret J., Brunet F.G., Binet M., Aurine N., Enchéry F., Croze S., Guinier M., Goumaidi A., Preininger D., Volff J.N., Bailly-Bechet M., Lachuer J., Horvat B., Legras-Lachuer C., Frontier in Microbiology, 2020 (in press)

Genome de-novo, DNASeq Illumina-MinION, bat genome, NIV.

Human Respiratory Syncytial Virus-induced immune signature of infection revealed by transcriptome analysis of clinical pediatric nasopharyngeal swab samples.

Nicolas De Lamballerie C., Pizzorno A. Dubois J., Padey B., Julien T., Traversier A., Carbonneau J., Orcel E., Lina B., Roche M., Textoris J. Boivin G., Legras-Lachuer C., Terrier O., and M. Rosa-Calatrava., J. Inf. Dis. 2020 (in press).

Transcriptome, Drug repositioning, Illumina, respiratory virus.

Uncovering the Translational Regulatory Activity of the Tumor Suppressor BRCA1.

Berthel E, Vincent A, Eberst L, Torres AG, Dacheux E, Rey C, Marcel V, Paraqindes H, Lachuer J, Catez F, Pouplana LR, Treilleux I, Diaz JJ, Venezia ND. Cells. 2020 Apr 10;9(4). pii: E941. doi: 10.3390/cells9040941. PMID: 32290274

Transcriptome, polysomes profiling, transcriptome, Affymetrix microarrays, cancer.

A polyphenotypic malignant paediatric brain tumour presenting a MN1-PATZ1 fusion, no epigenetic similarities with CNS High-Grade Neuroepithelial Tumour with MN1 Alteration (CNS HGNET-MN1) and related to PATZ1-fused sarcomas.

Burel-Vandenbos F, Pierron G, Thomas C, Reynaud S, Gregoire V, Duhil De Benaze G, Croze S, Chivoret N, Honavar M, Figarella-Branger D, Maurage CA, Pedeutour F, Hasselblatt M, Godfraind C. Neuropathol Appl Neurobiol. 2020 May 12. doi: 10.1111/nan.12626. [Epub ahead of print] PMID: 32397004

DNA methylation, Beadarray 850K, FFPE, cancer.

How consistent is RAD-seq divergence with DNA-barcode based clustering in insects?

Cariou M, Henri H, Martinez S, Duret L, Charlat S. How consistent is RAD-seq divergence with DNA-barcode based clustering in insects? Mol Ecol Resour. 2020 Apr 27. doi: 10.1111/1755 0998.13178. [Epub ahead of print] PMID: 32340081

Metagenomes, Microbiome, Viromes, Fungiomes, RAD-seq

 

Effects of dietary arginine supplementation in pregnant mares on maternal metabolism, placental structure and function and foal growth.

Robles M, Couturier-Tarrade A, Derisoud E, Geeverding A, Dubois C, Dahirel M, Aioun J, Prezelin A, Calvez J, Richard C, Wimel L, Chavatte-Palmer P. Sci Rep. 2019 Apr 23;9(1):6461. doi: 10.1038/s41598-019-42941-0. PMID:31015538

Transcriptome, RNA extraction, RT-qPCR, transcriptome, equine

Effects of first-generation in utero exposure to diesel engine exhaust on second-generation placental function, fatty acid profiles and foetal metabolism in rabbits: preliminary results.

Rousseau-Ralliard D, Valentino SA, Aubrière MC, Dahirel M, Lallemand MS, Archilla C, Jouneau L, Fournier N, Richard C, Aioun J, Vitorino Carvalho A, Jérôme L, Slama R, Duranthon V, Cassee FR, Chavatte-Palmer P, Couturier-Tarrade A. Sci Rep. 2019 Jul 4;9(1):9710. doi: 10.1038/s41598-019-46130-x. PMID: 31273257

Transcriptome, RNA extraction, RT-qPCR, transcriptome, equine

 

A Similar Secretome Disturbance as a Hallmark of Non-pathogenic Botrytis cinerea ATMT-Mutants?

De Vallée A, Bally P, Bruel C, Chandat L, Choquer M, Dieryckx C, Dupuy JW, Kaiser S, Latorse MP, Loisel E, Mey G, Morgant G, Rascle C, Schumacher J, Simon A, Souibgui E, Viaud M, Villalba F, Poussereau N. Front Microbiol. 2019 Dec 6;10:2829. doi: 10.3389/fmicb.2019.02829. eCollection 2019. PMID: 31866989.

Transcriptome, RNA-seq, fungi, infectious disease, plants

Inflammatory skin is associated with changes in the skin microbiota composition on the back of severe acne patients.

Dagnelie MA, Montassier E, Khammari A, Mounier C, Corvec S, Dréno B. Exp Dermatol. 2019 Aug;28(8):961-967. doi: 10.1111/exd.13988. Epub 2019 Jul 3. PMID: 31173650.

Metagenomes, Microbiome, Viromes, Fungiomes, RNA 16S, skin, human

Caractérisation génomique de l’ADN extracellulaire du RET (Root Extracellular Trap) et analyses transcriptomiques et protéomiques des cellules bordantes.

Chambard Marie, Lysa N’guessan, Carole Plasson, Gaëlle Durambur, Marie-Christine Kiefer Meyer, Benjamin Lefranc, Jérôme Leprince, Azeddine Driouich, Maïté Vicré, Marie-Laure Follet-Gueye, et al. 2019 HAL Id: hal-02276917

Transcriptome, mRNA-seq, plants.

Emerging mechanisms of antimicrobial resistance in bacteria and fungi: advances in the era of genomics.

Sekyere JO, Asante J. Emerging mechanisms of antimicrobial resistance in bacteria and fungi: advances in the
era of genomics. Future Microbiol. 2018 Feb;13:241-262. doi: 10.2217/fmb-2017-0172. Epub 2018 Jan 10. Review. PMID:29319341

Metagenomes, Microbiomes, Viromes, Fungiomes, Genomics, Microbiology

Genomic analysis of reduced susceptibility to tigecycline in Enterococcus faecium.

Cattoir V, Isnard C, Cosquer T, Odhiambo A, Bucquet F, Guérin F, Giard JC
Antimicrob Agents Chemother. 2015 Jan;59(1):239-44. doi: 10.1128/AAC.04174-14. Epub 2014
Oct 27. PMID: 25348531

Genotyping, WGS, bacteria

TWIST microdeletion identified by array CGH in a patient presenting Saethre-Chotzen phenotype and a complex rearrangement involving chromosomes 2 and 7.

Schluth-Bolard C., M. Till, A. Labalme, C. Rey , E. Banquart, A. Fautrelle, T. Martin-Denavit, M. Le Lorc’h, S. P. Romana, V. Lazar , P. Edery, D. Sanlaville Eur J Med Genet. 2008 Mar-Apr;51(2):156-64. Epub 2007 Dec 24.

Genotypage, NGS Illumina

High Pathogenicity of Nipah Virus from Pteropus lylei Fruit Bats, Cambodia.
Gaudino M, Aurine N, Dumont C, Fouret J, Ferren M, Mathieu C, Reynard O, Volchkov VE, Legras-Lachuer C, Georges-Courbot MC, Horvat B..Emerg Infect Dis.
2020 Jan;26(1):104-113. doi: 10.3201/eid2601.191284.

Genome virus, NGS, Nipah virus, NGS Illumina

 

Vaccines inducing immunity to Lassa virus glycoprotein and nucleoprotein protect macaques after a single shot.
Mateo M, Reynard S, Carnec X, Journeaux A, Baillet N, Schaeffer J, Picard C, Legras-Lachuer C, Allan R, Perthame E, Hillion KH, Pietrosemoli N, Dillies MA, Barrot L, Vallve A, Barron S, Fellmann L, Gaillard JC, Armengaud J, Carbonnelle C, Raoul H, Tangy F, Baize S.Sci Transl Med.
2019 Oct 2;11(512). pii: eaaw3163. doi: 10.1126/scitranslmed.aaw3163.

Transcriptome, mRNA-seq, virology, vaccine, Lassa virus, simian

Characterization of cellular transcriptomic signatures induced by different respiratory viruses in human reconstituted airway epithelia.
Nicolas de Lamballerie C, Pizzorno A, Dubois J, Julien T, Padey B, Bouveret M, Traversier A, Legras-Lachuer C, Lina B, Boivin G, Terrier O, Rosa-Calatrava
M.Sci Rep. 2019 Aug 7;9(1):11493. doi: 10.1038/s41598-019-48013-7.

 

Repurposing of Drugs as Novel Influenza Inhibitors From Clinical Gene Expression Infection Signatures.
Pizzorno A, Terrier O, Nicolas de Lamballerie C, Julien T, Padey B, Traversier A, Roche M, Hamelin ME, Rhéaume C, Croze S, Escuret V, Poissy J, Lina B, Legras-Lachuer C, Textoris J, Boivin G, Rosa-Calatrava M. Front Immunol.
2019 Jan 29;10:60. doi: 10.3389/fimmu.2019.00060. eCollection 2019.

Transcriptome, microarrays Affymetrix, RNAseq, virology, drug repositioning, Influenza

Environmental Variations in Mycobacterium ulcerans Transcriptome: Absence of Mycolactone Expression in Suboptimal Environments.
Sanhueza D, Guégan JF, Jordan H, Chevillon C.Toxins (Basel).
2019 Mar 4;11(3). pii: E146. doi: 10.3390/toxins11030146.

Transcriptome, RNA-seq, low-amount samples, bacteria, mycobacterium ulcerans

Investigation of potential pathogenicity of Willaertia magna by investigating the transfer of bacteria pathogenicity genes into its genome.
Hasni I1,2, Chelkha N1, Baptiste E1, Mameri MR2, Lachuer J3,4,5, Plasson F2, Colson P1, La Scola B6 Investigation of potential pathogenicity of Willaertia magna by investigating the transfer of bacteria pathogenicity genes into its genome Sci Rep.
2019 Dec 4;9(1):18318. doi: 10.1038/s41598-019-54580-6.

Genome de novo, trancriptome de novo, NGS Illumina