Redmond Smyth

41
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Publications

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Demultiplexing and barcode-specific adaptive sampling for nanopore direct RNA sequencing

Wiep van der Toorn , Patrick Bohn , Wang Liu-Wei , Marco Olguin-Nava , Anne-Sophie Gribling-Burrer et al.
Nature Communications, 2025, 16 (1), pp.3742. ⟨10.1038/s41467-025-59102-9⟩
Article dans une revue hal-05221440 v1
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Selectively expressed RNA molecules as a versatile tool for functionalized cell targeting

Frederik Rastfeld , Marco Hoffmann , Sylvie Krüger , Patrick Bohn , Anne-Sophie Gribling-Burrer et al.
Nature Communications, 2025, 16 (1), pp.420. ⟨10.1038/s41467-024-55547-6⟩
Article dans une revue hal-05362432 v1
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Giant RNA genomes: Roles of host, translation elongation, genome architecture, and proteome in nidoviruses

Benjamin W Neuman , Alexandria Smart , Orian Gilmer , Redmond Smyth , Josef Vaas et al.
Proceedings of the National Academy of Sciences of the United States of America, 2025, 122 (7), ⟨10.1073/pnas.2413675122⟩
Article dans une revue hal-05362414 v1
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The translational landscape of HIV-1 infected cells reveals key gene regulatory principles

Anuja Kibe , Stefan Buck , Anne-Sophie Gribling-Burrer , Orian Gilmer , Patrick Bohn et al.
Nature Structural and Molecular Biology, 2025, 32 (5), pp.841-852. ⟨10.1038/s41594-024-01468-3⟩
Article dans une revue hal-05362403 v1
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Visualizing the transcription and replication of influenza A viral RNAs in cells by multiple direct RNA padlock probing and <i>in situ</i> sequencing (mudRapp-seq)

Shazeb Ahmad , Jianhui Li , Joél Schaust , Anne-Sophie Gribling-Burrer , Nina Geiger et al.
Nucleic Acids Research, 2025, 53 (11), ⟨10.1093/nar/gkaf461⟩
Article dans une revue hal-05224563 v1

Isoform-specific RNA structure determination using Nano-DMS-MaP

Anne-Sophie Gribling-Burrer , Patrick Bohn , Redmond Smyth
Nature Protocols, 2024, 19 (6), pp.1835-1865. ⟨10.1038/s41596-024-00959-3⟩
Article dans une revue hal-05362521 v1

Sequencing accuracy and systematic errors of nanopore direct RNA sequencing

Wang Liu-Wei , Wiep van der Toorn , Patrick Bohn , Martin Hölzer , Redmond Smyth et al.
BMC Genomics, 2024, 25 (1), pp.528. ⟨10.1186/s12864-024-10440-w⟩
Article dans une revue hal-05363230 v1
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NEAT1 promotes genome stability via m<sup>6</sup>A methylation-dependent regulation of CHD4

Victoria Mamontova , Barbara Trifault , Anne-Sophie Gribling-Burrer , Patrick Bohn , Lea Boten et al.
Genes and Development, 2024, 38, pp.915-930. ⟨10.1101/gad.351913.124⟩
Article dans une revue hal-05362438 v1
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The conserved noncoding RNA ModT coordinates growth and virulence in Clostridioides difficile

Tina Lenče , Johannes Sulzer , Kilian Andress , Anne-Sophie Gribling-Burrer , Vanessa Lamm-Schmidt et al.
PLoS Biology, 2024, 22 (12), pp.e3002948. ⟨10.1371/journal.pbio.3002948⟩
Article dans une revue hal-05362436 v1
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Recruitment of multi-segment genomic RNAs by Bluetongue virus requires a preformed RNA network

Po-Yu Sung , Jody E Phelan , Dongsheng Luo , Raghavendran Kulasegaran-Shylini , Patrick Bohn et al.
Nucleic Acids Research, 2024, 52 (14), pp.8500-8514. ⟨10.1093/nar/gkae404⟩
Article dans une revue hal-05362448 v1

Cis -mediated interactions of the SARS-CoV-2 frameshift RNA alter its conformations and affect function

Lukas Pekarek , Matthias Zimmer , Anne-Sophie Gribling-Burrer , Stefan Buck , Redmond Smyth et al.
Nucleic Acids Research, 2023, 51 (2), pp.728-743. ⟨10.1093/nar/gkac1184⟩
Article dans une revue hal-05362501 v1

Nano-DMS-MaP allows isoform-specific RNA structure determination

Patrick Bohn , Anne-Sophie Gribling-Burrer , Uddhav Ambi , Redmond Smyth
Nature Methods, 2023, 20 (6), pp.849-859. ⟨10.1038/s41592-023-01862-7⟩
Article dans une revue hal-05362507 v1

Advanced fluorescence microscopy in respiratory virus cell biology

Enyu Xie , Shazeb Ahmad , Redmond P Smyth , Christian Sieben
Advances in Virus Research, 2023, Advances in Virus Research, 116, pp.123-172. ⟨10.1016/bs.aivir.2023.05.002⟩
Article dans une revue hal-05362701 v1
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Sequential disruption of SPLASH-identified vRNA–vRNA interactions challenges their role in influenza A virus genome packaging

Celia Jakob , Gabriel L Lovate , Daniel Desirò , Lara Gießler , Redmond P Smyth et al.
Nucleic Acids Research, In press, ⟨10.1093/nar/gkad442⟩
Article dans une revue hal-04110802 v1

SND1 binds SARS-CoV-2 negative-sense RNA and promotes viral RNA synthesis through NSP9

Nora Schmidt , Sabina Ganskih , Yuanjie Wei , Alexander Gabel , Sebastian Zielinski et al.
Cell, 2023, 186 (22), pp.4834-4850.e23. ⟨10.1016/j.cell.2023.09.002⟩
Article dans une revue hal-05362516 v1

Short- and long-range interactions in the HIV-1 5′ UTR regulate genome dimerization and packaging

Liqing Ye , Anne-Sophie Gribling-Burrer , Patrick Bohn , Anuja Kibe , Charlene Börtlein et al.
Nature Structural and Molecular Biology, 2022, 29 (4), pp.306-319. ⟨10.1038/s41594-022-00746-2⟩
Article dans une revue hal-05362491 v1

The short isoform of the host antiviral protein ZAP acts as an inhibitor of SARS-CoV-2 programmed ribosomal frameshifting

Matthias Zimmer , Anuja Kibe , Ulfert Rand , Lukas Pekarek , Liqing Ye et al.
Nature Communications, 2021, 12 (1), pp.7193. ⟨10.1038/s41467-021-27431-0⟩
Article dans une revue hal-05362486 v1
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RNA Structures and Their Role in Selective Genome Packaging

Liqing Ye , Uddhav Ambi , Marco Olguin-Nava , Anne-Sophie Gribling-Burrer , Shazeb Ahmad et al.
Viruses, 2021, 13 (9), pp.1788. ⟨10.3390/v13091788⟩
Article dans une revue hal-05363203 v1
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RNA Structure—A Neglected Puppet Master for the Evolution of Virus and Host Immunity

Redmond P Smyth , Matteo Negroni , Andrew Lever , Johnson Mak , Julia Kenyon
Frontiers in Immunology, 2018, 9, pp.2097. ⟨10.3389/fimmu.2018.02097⟩
Article dans une revue (article de synthèse) hal-02118729 v1
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Structural and Functional Motifs in Influenza Virus RNAs

Damien Ferhadian , Maud Contrant , Anne Printz-Schweigert , Redmond P Smyth , Jean-Christophe Paillart et al.
Frontiers in Microbiology, 2018, 9, pp.559. ⟨10.3389/fmicb.2018.00559⟩
Article dans une revue (article de synthèse) hal-02118745 v1
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In cell mutational interference mapping experiment (in cell MIME) identifies the 5′ polyadenylation signal as a dual regulator of HIV-1 genomic RNA production and packaging

Redmond P Smyth , Maureen R Smith , Anne-Caroline Jousset , Laurence Despons , Géraldine Laumond et al.
Nucleic Acids Research, 2018, 46 (9), pp.e57-e57. ⟨10.1093/nar/gky152⟩
Article dans une revue hal-02141231 v1
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A step forward understanding HIV-1 diversity

Redmond P Smyth , Matteo Negroni
Retrovirology, 2016, 13 (1), ⟨10.1186/s12977-016-0259-8⟩
Article dans une revue hal-02294753 v1
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The life-cycle of the HIV-1 Gag-RNA complex

Élodie Mailler , Serena Bernacchi , Roland Marquet , Jean-Christophe Paillart , Valerie Vivet Boudou et al.
Viruses, 2016, 8 (9), ⟨10.3390/v8090248⟩
Article dans une revue hal-05255386 v1

HIV-1 Pr55 Gag binds genomic and spliced RNAs with different affinity and stoichiometry

Serena Bernacchi , Ekram Abd El-Wahab , Noé Dubois , Marcel Hijnen , Redmond P Smyth et al.
RNA Biology, 2016, 14 (1), pp.90-103. ⟨10.1080/15476286.2016.1256533⟩
Article dans une revue hal-02171331 v1

MIMEAnTo: profiling functional RNA in mutational interference mapping experiments

Maureen R Smith , Redmond P Smyth , Roland Marquet , Max von Kleist
Bioinformatics, 2016, 32 (21), pp.3369-3370. ⟨10.1093/bioinformatics/btw479⟩
Article dans une revue hal-02294750 v1
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HIV-1 Mutation and Recombination Rates Are Different in Macrophages and T-cells

Deborah Cromer , Timothy Schlub , Redmond P Smyth , Andrew Grimm , Abha Chopra et al.
Viruses, 2016, 8 (4), pp.118. ⟨10.3390/v8040118⟩
Article dans une revue hal-02294111 v1

Mutational interference mapping experiment (MIME) for studying RNA structure and function.

Redmond P Smyth , Laurence Despons , Gong Huili , Serena Bernacchi , Marcel Hijnen et al.
Nature Methods, 2015, 12 (9), pp.866-872. ⟨10.1038/nmeth.3490⟩
Article dans une revue hal-05259396 v1

Properties of HIV-1 associated cholesterol in addition to raft formation are important for virus infection

David Hawkes , Kate Jones , Redmond P Smyth , Cândida Pereira , Robert Bittman et al.
Virus Research, 2015, 210, pp.18-21. ⟨10.1016/j.virusres.2015.06.023⟩
Article dans une revue istex hal-05362211 v1
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Evaluation of anti-HIV-1 mutagenic nucleoside analogues.

Valérie Vivet-Boudou , Catherine Isel , Yazan El Safadi , Redmond P Smyth , Géraldine Laumond et al.
Journal of Biological Chemistry, 2015, 290 (1), pp.371-383. ⟨10.1074/jbc.M114.616383⟩
Article dans une revue hal-05258403 v1

15-20% of HIV substitution mutations are associated with recombination.

Timothy Schlub , Andrew Grimm , Redmond P Smyth , Deborah Cromer , Abha Chopra et al.
Journal of Virology, 2014, 88 (7), pp.3837-3849. ⟨10.1128/JVI.03136-13⟩
Article dans une revue hal-05259225 v1

Specific recognition of the HIV-1 genomic RNA by the Gag precursor.

Ekram Abd El-Wahab , Redmond P Smyth , Élodie Mailler , Serena Bernacchi , Valerie Vivet Boudou et al.
Nature Communications, 2014, 5 (1), pp.4304. ⟨10.1038/ncomms5304⟩
Article dans une revue hal-05260015 v1

Identifying recombination hotspots in the HIV-1 genome

Redmond Smyth , T Schlub , A Grimm , C Waugh , P Ellenberg et al.
Journal of Virology, 2014, 88 (5), pp.2891-2902. ⟨10.1128/JVI.03014-13⟩
Article dans une revue hal-05259627 v1

Intracellular Dynamics of HIV Infection

Janka Petravic , Paula Ellenberg , Ming-Liang Chan , Geza Paukovics , Redmond P Smyth et al.
Journal of Virology, 2014, 88 (2), pp.1113-1124. ⟨10.1128/JVI.02038-13⟩
Article dans une revue hal-05362139 v1

Improved quantification of HIV-1-infected CD4+ T cells using an optimised method of intracellular HIV-1 gag p24 antigen detection

Hongbing Yang , Elisabeth Yorke , Gemma Hancock , Genevieve Clutton , Nellia Sande et al.
Journal of immunological methods, 2013, 391 (1-2), pp.174-178. ⟨10.1016/j.jim.2013.03.001⟩
Article dans une revue istex hal-05258663 v1

A functional sequence-specific interaction between influenza A virus genomic RNA segments

Cyrille Gavazzi , Matthieu Yver , Catherine Isel , Redmond P Smyth , Manuel Rosa-Calatrava et al.
Proceedings of the National Academy of Sciences of the United States of America, 2013, 110 (41), pp.16604-16609. ⟨10.1073/pnas.1314419110⟩
Article dans une revue hal-05258420 v1

The origin of genetic diversity in HIV-1

Redmond Smyth , Miles Davenport , Johnson Mak
Virus Research, 2012, 169 (2), pp.415-429. ⟨10.1016/j.virusres.2012.06.015⟩
Article dans une revue istex hal-04306411 v1

Early Events of HIV-1 Infection: Can Signaling be the Next Therapeutic Target?

Kate Jones , Redmond Smyth , Cândida Pereira , Paul Cameron , Sharon Lewin et al.
Journal of Neuroimmune Pharmacology, 2011, 6 (2), pp.269-283. ⟨10.1007/s11481-011-9268-5⟩
Article dans une revue istex hal-05362980 v1
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8-Modified-2'-Deoxyadenosine Analogues Induce Delayed Polymerization Arrest during HIV-1 Reverse Transcription

Valérie Vivet-Boudou , Catherine Isel , Marwan Sleiman , Redmond Smyth , Nouha Ben Gaied et al.
PLoS ONE, 2011, 6 (11), ⟨10.1371/journal.pone.0027456⟩
Article dans une revue hal-05254494 v1

Accurately Measuring Recombination between Closely Related HIV-1 Genomes

Timothy Schlub , Redmond Smyth , Andrew Grimm , Johnson Mak , Miles Davenport
PLoS Computational Biology, 2010, 6 (4), pp.e1000766. ⟨10.1371/journal.pcbi.1000766⟩
Article dans une revue hal-05362681 v1

Reducing chimera formation during PCR amplification to ensure accurate genotyping

Redmond P Smyth , T.E. Schlub , A. Grimm , V. Venturi , A. Chopra et al.
Gene, 2010, 469 (1-2), pp.45-51. ⟨10.1016/j.gene.2010.08.009⟩
Article dans une revue istex hal-05362452 v1

The A-rich RNA sequences of HIV-1 pol are important for the synthesis of viral cDNA.

Cameron P Keating , Melissa K Hill , David J Hawkes , Redmond P Smyth , Catherine Isel et al.
Nucleic Acids Research, 2009, 37 (3), pp.945-56. ⟨10.1093/nar/gkn1015⟩
Article dans une revue hal-00372893 v1