Publications from the lab

Find all of our publications on pubmed

2025

  • Genome-wide profiling of RNA 2’- O-methylation in neurons and identification of orphan snoRNA targets.
    Ye, Xuan; Zhu, Yinzhou; Alshawi, Sarah A.; Elliot, Brittany A.; Holley, Christopher L.; Beaudoin, Jean-Denis; Graveley, Brenton R.; Carmichael, Gordon G.# bioRxiv. 2025. doi:10.64898/2025.12.17.694928.

  • The differential mechanisms of eIF4A1-mediated translational activation instructed by distinct RNA features.
    Schmidt, Tobias; Turnbull, Andrew P.; Gupta, Amit; Waldron, Joseph A.; Pollock, Katie; Munro, June; Nepravishta, Ridvan; Herviou, Pauline; Dabrowska, Adrianna; Hodge, Kelly; Voelker, Allyson M.; Pang, Leon; Pasquali, Camila; Kanellos, Georgios; Zanivan, Sara; Sansom, Owen J.; Beaudoin, Jean-Denis; Bushell, Martin# bioRxiv. 2025. doi:10.1101/2025.03.24.644895.

  • An engineered glutamic acid tRNA for efficient suppression of pathogenic nonsense mutations.
    Specht, Caitlin*; Tapia, Alejandro*; Penrod, Sarah; Soriano, Gabriela A.; Awawdeh, Aya; Alshawi, Sarah A.; White, Cody A.; Beaudoin, Jean-Denis; Doud, Emma H.; Vargas-Rodriguez, Oscar; Huang, Yunjie; Tharp, Jeffery M.# Nucleic Acids Res. 2025. PMID: 40539513.

2024

  • NaP-TRAP, a novel massively parallel reporter assay to quantify translation control.
    Strayer, Ethan C.; Krishna, Srikar; Lee, Haejeong; Vejnar, Charles; Neuenkirchen, Nils; Gupta, Amit; Beaudoin, Jean-Denis#; Giraldez, Antonio J.# Nat Commun. 2024. PMID: 39738051.

  • Efficient suppression of premature termination codons with alanine by engineered chimeric pyrrolysine tRNAs.
    Awawdeh, Aya; Tapia, Alejandro; Alshawi, Sarah A.; Dawodu, Olabode; Gaier, Sarah A.; Specht, Caitlin; Beaudoin, Jean-Denis; Tharp, Jeffrey M.#; Vargas-Rodriguez, Oscar# Nucleic Acids Res. 2024. PMID: 39558163.

2023

  • Nano3P-seq: transcriptome-wide analysis of gene expression and tail dynamics using end-capture nanopore cDNA sequencing.
    Begik, Oguzhan; Diensthuber, Gregor; Liu, Huanle; Delgado-Tejedor, Anna; Kontur, Cassandra; Niazi, Adnan Muhammad; Valen, Eivind; Giraldez, Antonio J.; Beaudoin, Jean-Denis; Mattick, John S.; Novoa, Eva Maria Nature Methods. 2023. PMID: 36536091.

# 2021
  • Extreme conservation encodes the structural dynamics and function of 5’ UTRs.
    Gupta, Amit; Beaudoin, Jean-Denis Nature Genetics. 2021. PMID: 33888910.

2020

  • A Functional Non-coding RNA Is Produced from xbp-1 mRNA.
    Liu, Xiao; Beaudoin, Jean-Denis; Davison, Carrie Ann; Kosmaczewski, Sara G.; Meyer, Benjamin I.; Giraldez, Antonio J.; Hammarlund, Marc Neuron. 2020. PMID: 32640191.

2019

  • Genome wide analysis of 3’ UTR sequence elements and proteins regulating mRNA stability during maternal-to-zygotic transition in zebrafish.
    Vejnar, Charles E.; Abdel Messih, Mario; Takacs, Carter M.; Yartseva, Valeria; Oikonomou, Panos; Christiano, Romain; Stoeckius, Marlon; Lau, Stephanie; Lee, Miler T.; Beaudoin, Jean-Denis; Musaev, Damir; Darwich-Codore, Hiba; Walther, Tobias C.; Tavazoie, Saeed; Cifuentes, Daniel; Giraldez, Antonio J. Genome research. 2019. PMID: 31227602.

  • Brd4 and P300 Confer Transcriptional Competency during Zygotic Genome Activation.
    Chan, Shun Hang; Tang, Yin; Miao, Liyun; Darwich-Codore, Hiba; Vejnar, Charles E.; Beaudoin, Jean-Denis; Musaev, Damir; Fernandez, Juan P.; Benitez, Maria D. J.; Bazzini, Ariel A.; Moreno-Mateos, Miguel A.; Giraldez, Antonio J. Developmental cell. 2019. PMID: 31211993.

2018

  • Analyses of mRNA structure dynamics identify embryonic gene regulatory programs.
    Beaudoin, Jean-Denis; Novoa, Eva Maria; Vejnar, Charles E.; Yartseva, Valeria; Takacs, Carter M.; Kellis, Manolis; Giraldez, Antonio J. Nature structural & molecular biology. 2018. PMID: 30061596.

2015

  • CRISPRscan: designing highly efficient sgRNAs for CRISPR-Cas9 targeting in vivo.
    Moreno-Mateos, Miguel A.; Vejnar, Charles E.; Beaudoin, Jean-Denis; Fernandez, Juan P.; Mis, Emily K.; Khokha, Mustafa K.; Giraldez, Antonio J. Nature methods. 2015. PMID: 26322839.

  • Small antisense oligonucleotides against G-quadruplexes: specific mRNA translational switches.
    Rouleau, Samuel G.; Beaudoin, Jean-Denis; Bisaillon, Martin; Perreault, Jean-Pierre Nucleic acids research. 2015. PMID: 25510493.

2014

  • New scoring system to identify RNA G-quadruplex folding.
    Beaudoin, Jean-Denis; Jodoin, Rachel; Perreault, Jean-Pierre Nucleic acids research. 2014. PMID: 24121682.

2013

  • Exploring mRNA 3’-UTR G-quadruplexes: evidence of roles in both alternative polyadenylation and mRNA shortening.
    Beaudoin, Jean-Denis; Perreault, Jean-Pierre Nucleic acids research. 2013. PMID: 23609544.

  • In-line probing of RNA G-quadruplexes.
    Beaudoin, Jean-Denis; Jodoin, Rachel; Perreault, Jean-Pierre Methods (San Diego, Calif.). 2013. PMID: 23500045.

2010 and earlier

  • 5’-UTR G-quadruplex structures acting as translational repressors.
    Beaudoin, Jean-Denis; Perreault, Jean-Pierre Nucleic acids research. 2010. PMID: 20571090.

  • Modulating RNA structure and catalysis: lessons from small cleaving ribozymes.
    Reymond, Cedric; Beaudoin, Jean-Denis; Perreault, Jean-Pierre Cellular and molecular life sciences : CMLS. 2009. PMID: 19718544.

  • Potassium ions modulate a G-quadruplex-ribozyme’s activity.
    Beaudoin, Jean-Denis; Perreault, Jean-Pierre RNA (New York, N.Y.). 2008. PMID: 18456841.

  • A novel structural rearrangement of hepatitis delta virus antigenomic ribozyme.
    Nehdi, Atef; Perreault, Jonathan; Beaudoin, Jean-Denis; Perreault, Jean-Pierre Nucleic acids research. 2007. PMID: 17933779.

  • In vitro selection and characterization of RNA aptamers binding thyroxine hormone.
    Levesque, Dominique; Beaudoin, Jean-Denis; Roy, Sebastien; Perreault, Jean-Pierre The Biochemical journal. 2007. PMID: 17163839.