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1.

Accurate expression quantification from nanopore direct RNA sequencing with NanoCount.

Gleeson, Josie; Leger, Adrien; Prawer, Yair D J; Lane, Tracy A; Harrison, Paul J; Haerty, Wilfried; Clark, Michael B.

Nucleic Acids Res ; 50(4): e19, 2022 02 28.

Article in English | MEDLINE | ID: mdl-34850115

2.

Nanopore ReCappable sequencing maps SARS-CoV-2 5' capping sites and provides new insights into the structure of sgRNAs.

Ugolini, Camilla; Mulroney, Logan; Leger, Adrien; Castelli, Matteo; Criscuolo, Elena; Williamson, Maia Kavanagh; Davidson, Andrew D; Almuqrin, Abdulaziz; Giambruno, Roberto; Jain, Miten; Frigè, Gianmaria; Olsen, Hugh; Tzertzinis, George; Schildkraut, Ira; Wulf, Madalee G; Corrêa, Ivan R; Ettwiller, Laurence; Clementi, Nicola; Clementi, Massimo; Mancini, Nicasio; Birney, Ewan; Akeson, Mark; Nicassio, Francesco; Matthews, David A; Leonardi, Tommaso.

Nucleic Acids Res ; 50(6): 3475-3489, 2022 04 08.

Article in English | MEDLINE | ID: mdl-35244721

3.

Chemical and photochemical error rates in light-directed synthesis of complex DNA libraries.

Lietard, Jory; Leger, Adrien; Erlich, Yaniv; Sadowski, Norah; Timp, Winston; Somoza, Mark M.

Nucleic Acids Res ; 49(12): 6687-6701, 2021 07 09.

Article in English | MEDLINE | ID: mdl-34157124

4.

pycoMeth: a toolbox for differential methylation testing from Nanopore methylation calls.

Snajder, Rene; Leger, Adrien; Stegle, Oliver; Bonder, Marc Jan.

Genome Biol ; 24(1): 83, 2023 04 20.

Article in English | MEDLINE | ID: mdl-37081487

5.

Natural genetic variation quantitatively regulates heart rate and dimension.

Gierten, Jakob; Welz, Bettina; Fitzgerald, Tomas; Thumberger, Thomas; Hummel, Oliver; Leger, Adrien; Weber, Philipp; Hassel, David; Hübner, Norbert; Birney, Ewan; Wittbrodt, Joachim.

bioRxiv ; 2023 Nov 02.

Article in English | MEDLINE | ID: mdl-37693611

6.

Long-read sequencing of diagnosis and post-therapy medulloblastoma reveals complex rearrangement patterns and epigenetic signatures.

Rausch, Tobias; Snajder, Rene; Leger, Adrien; Simovic, Milena; Giurgiu, Madalina; Villacorta, Laura; Henssen, Anton G; Fröhling, Stefan; Stegle, Oliver; Birney, Ewan; Bonder, Marc Jan; Ernst, Aurelie; Korbel, Jan O.

Cell Genom ; 3(4): 100281, 2023 Apr 12.

Article in English | MEDLINE | ID: mdl-37082141

7.

The Medaka Inbred Kiyosu-Karlsruhe (MIKK) panel.

Fitzgerald, Tomas; Brettell, Ian; Leger, Adrien; Wolf, Nadeshda; Kusminski, Natalja; Monahan, Jack; Barton, Carl; Herder, Cathrin; Aadepu, Narendar; Gierten, Jakob; Becker, Clara; Hammouda, Omar T; Hasel, Eva; Lischik, Colin; Lust, Katharina; Sokolova, Natalia; Suzuki, Risa; Tsingos, Erika; Tavhelidse, Tinatini; Thumberger, Thomas; Watson, Philip; Welz, Bettina; Khouja, Nadia; Naruse, Kiyoshi; Birney, Ewan; Wittbrodt, Joachim; Loosli, Felix.

Genome Biol ; 23(1): 59, 2022 02 21.

Article in English | MEDLINE | ID: mdl-35189950

8.

Genomic variations and epigenomic landscape of the Medaka Inbred Kiyosu-Karlsruhe (MIKK) panel.

Leger, Adrien; Brettell, Ian; Monahan, Jack; Barton, Carl; Wolf, Nadeshda; Kusminski, Natalja; Herder, Cathrin; Aadepu, Narendar; Becker, Clara; Gierten, Jakob; Hammouda, Omar T; Hasel, Eva; Lischik, Colin; Lust, Katharina; Sokolova, Natalia; Suzuki, Risa; Tavhelidse, Tinatini; Thumberger, Thomas; Tsingos, Erika; Watson, Philip; Welz, Bettina; Naruse, Kiyoshi; Loosli, Felix; Wittbrodt, Joachim; Birney, Ewan; Fitzgerald, Tomas.

Genome Biol ; 23(1): 58, 2022 02 21.

Article in English | MEDLINE | ID: mdl-35189951

9.

Nanopore RNA Sequencing Analysis.

Leonardi, Tommaso; Leger, Adrien.

Methods Mol Biol ; 2284: 569-578, 2021.

Article in English | MEDLINE | ID: mdl-33835464

10.

AAV8 locoregional delivery induces long-term expression of an immunogenic transgene in macaques despite persisting local inflammation.

Gernoux, Gwladys; Guilbaud, Mickaël; Devaux, Marie; Journou, Malo; Pichard, Virginie; Jaulin, Nicolas; Léger, Adrien; Le Duff, Johanne; Deschamps, Jack-Yves; Le Guiner, Caroline; Moullier, Philippe; Cherel, Yan; Adjali, Oumeya.

Mol Ther Methods Clin Dev ; 20: 660-674, 2021 Mar 12.

Article in English | MEDLINE | ID: mdl-33718516

11.

RNA modifications detection by comparative Nanopore direct RNA sequencing.

Leger, Adrien; Amaral, Paulo P; Pandolfini, Luca; Capitanchik, Charlotte; Capraro, Federica; Miano, Valentina; Migliori, Valentina; Toolan-Kerr, Patrick; Sideri, Theodora; Enright, Anton J; Tzelepis, Konstantinos; van Werven, Folkert J; Luscombe, Nicholas M; Barbieri, Isaia; Ule, Jernej; Fitzgerald, Tomas; Birney, Ewan; Leonardi, Tommaso; Kouzarides, Tony.

Nat Commun ; 12(1): 7198, 2021 12 10.

Article in English | MEDLINE | ID: mdl-34893601

12.

Single-Stranded DNA Virus Sequencing (SSV-Seq) for Characterization of Residual DNA and AAV Vector Genomes.

Lecomte, Emilie; Leger, Adrien; Penaud-Budloo, Magalie; Ayuso, Eduard.

Methods Mol Biol ; 1950: 85-106, 2019.

Article in English | MEDLINE | ID: mdl-30783969

13.

Genetics instability of wtAAV2 genome and AAV promoter activities in the Baculovirus/Sf9 cells system.

Savy, Adrien; Kaikkonen, Minna U; Léger, Adrien; Dickx, Yohann; Galibert, Lionel; Merten, Otto-Wilhelm.

PLoS One ; 13(7): e0199866, 2018.

Article in English | MEDLINE | ID: mdl-29975713

14.

RNA-Seq Analysis of an Antisense Sequence Optimized for Exon Skipping in Duchenne Patients Reveals No Off-Target Effect.

Domenger, Claire; Allais, Marine; François, Virginie; Léger, Adrien; Lecomte, Emilie; Montus, Marie; Servais, Laurent; Voit, Thomas; Moullier, Philippe; Audic, Yann; Le Guiner, Caroline.

Mol Ther Nucleic Acids ; 10: 277-291, 2018 Mar 02.

Article in English | MEDLINE | ID: mdl-29499940

15.

Accurate Identification and Quantification of DNA Species by Next-Generation Sequencing in Adeno-Associated Viral Vectors Produced in Insect Cells.

Penaud-Budloo, Magalie; Lecomte, Emilie; Guy-Duché, Aurélien; Saleun, Sylvie; Roulet, Alain; Lopez-Roques, Céline; Tournaire, Benoît; Cogné, Benjamin; Léger, Adrien; Blouin, Véronique; Lindenbaum, Pierre; Moullier, Philippe; Ayuso, Eduard.

Hum Gene Ther Methods ; 28(3): 148-162, 2017 06.

Article in English | MEDLINE | ID: mdl-28463571

16.

Identification of miRNAs Involved in Reprogramming Acinar Cells into Insulin Producing Cells.

Teichenne, Joan; Morró, Meritxell; Casellas, Alba; Jimenez, Veronica; Tellez, Noelia; Leger, Adrien; Bosch, Fatima; Ayuso, Eduard.

PLoS One ; 10(12): e0145116, 2015.

Article in English | MEDLINE | ID: mdl-26690959

17.

Advanced Characterization of DNA Molecules in rAAV Vector Preparations by Single-stranded Virus Next-generation Sequencing.

Lecomte, Emilie; Tournaire, Benoît; Cogné, Benjamin; Dupont, Jean-Baptiste; Lindenbaum, Pierre; Martin-Fontaine, Mélanie; Broucque, Frédéric; Robin, Cécile; Hebben, Matthias; Merten, Otto-Wilhelm; Blouin, Véronique; François, Achille; Redon, Richard; Moullier, Philippe; Léger, Adrien.

Mol Ther Nucleic Acids ; 4: e260, 2015 Oct 27.

Article in English | MEDLINE | ID: mdl-26506038

18.

Short-lived recombinant adeno-associated virus transgene expression in dystrophic muscle is associated with oxidative damage to transgene mRNA.

Dupont, Jean-Baptiste; Tournaire, Benoit; Georger, Christophe; Marolleau, Béatrice; Jeanson-Leh, Laurence; Ledevin, Mireille; Lindenbaum, Pierre; Lecomte, Emilie; Cogné, Benjamin; Dubreil, Laurence; Larcher, Thibaut; Gjata, Bernard; Van Wittenberghe, Laetitia; Le Guiner, Caroline; Penaud-Budloo, Magalie; Snyder, Richard O; Moullier, Philippe; Léger, Adrien.

Mol Ther Methods Clin Dev ; 2: 15010, 2015.

Article in English | MEDLINE | ID: mdl-26029721

19.

Adeno-associated viral vector-mediated transgene expression is independent of DNA methylation in primate liver and skeletal muscle.

Léger, Adrien; Le Guiner, Caroline; Nickerson, Michael L; McGee Im, Kate; Ferry, Nicolas; Moullier, Philippe; Snyder, Richard O; Penaud-Budloo, Magalie.

PLoS One ; 6(6): e20881, 2011.

Article in English | MEDLINE | ID: mdl-21687632

20.

NGS library preparation may generate artifactual integration sites of AAV vectors.

Cogné, Benjamin; Snyder, Richard; Lindenbaum, Pierre; Dupont, Jean-Baptiste; Redon, Richard; Moullier, Philippe; Leger, Adrien.

Nat Med ; 20(6): 577-8, 2014 Jun.

Article in English | MEDLINE | ID: mdl-24901560

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