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Publications

  • Adkar-Purushothama CR, Chettimada A, Murali TS, Muthusamy A, Bouarab K, Perreault JP. (2026). Non-Chemical Control of Fungal Pathogens in Crops: A One-Health Perspective on Strategies, Mechanisms, and Future Directions. Frontiers in Plant Science (Accepted).

  • Turcotte MA, Crespo LDJ, Perreault JP (2026). Are Traditional mutant controls sufficient to identify true RNA G-quadruplex binding proteins? Biochimie, 241:11-15. DOI: 10.1016/j.biochi.2025.10.018. 

  • Perreault JP, Pelchat M, Adkar-Purushothama CR (2025). Chapter 31, Viroids and related RNA Species. Eds: Acheson N, and Richardson C. In: Fundamental molecular virology, 3rd edition, Publisher, Wiley. page 420-430. ISBN: 978-1-119-88588-7.

  • Naoi T, Zhang Z, Adkar-Purushothama CR, Perreault JP & Sano T (2025). Resistance and tolerance to viroid infection: status and prospects. J Gen Plant Pathol, DOI: 10.1007/s10327-025-01264-x

  • Lejault P, Bolduc F, Turcotte MA & Perreault JP (2025). G-quadruplexes in the proximity 3′-UTR enhances alternative polyadenylation of Neogenin 1. iScience, 28(12) 113952.  DOI: 10.1016/j.isci.2025.113952
  • Turcotte MA & Perreault JP (2025). RNA G-Quadruplex Reprogramming with Guanine-Rich Antisense Oligonucleotides Inhibits Monoamine Oxidase B’s Translation. ACS Bio & Med Chem Au, 5(3) 403-414. DOI: 10.1021/acsbiomedchemau.5c00004. 

  • Adkar-Purushothama CR, Lejault P, Turcotte MA & Perreault JP (2024). Viroids : infectious non coding RNAs. Virologie (Montrouge, France). 28: 199-215. DOI: 10.1684/vir.2024.1051.

  • Turcotte, MA & Perreault JP (2024). Pathogenic SNPs Affect Both RNA and DNA G-Quadruplexes’ Responses to Ligands. ACS chemical biology, 19. DOI: 10.1021/acschembio.4c00104.

     

  • Vannutelli A, Ouangraoua A & Perreault JP (2023). Toward a Better Understanding of G4 Evolution in the 3 Living Kingdoms. Evolutionary Bioinformatics, 19:1-13. DOI: 10.1177/11769343231212075.
  • Adkar-Purushothama CR,  Sano T & Perreault JP (2023). Hop Latent Viroid: A Hidden Threat to the Cannabis Industry. Viruses, 15(3):681. DOI: 10.3390/v15030681.
  • Turcotte  MA,  Bolduc F, Vannutelli A, Mitteaux J, Monchaud D & Perreault JP (2023). Development of a highly optimized procedure for the discovery of RNA G-quadruplexes by combining several strategies. Biochimie, 214:24-32. DOI: 10.1016/j.biochi.2023.07.014.
  • Lejault P, Prudent L, Terrier MP & Perreault JP (2023). Small molecule chaperones facilitate the folding of long-non coding RNA. Biochimie, 214:83-90. DOI: 10.1101/2023.04.04.535601.
  • Lejault P, Terrier MP, Vannutelli A, Bolduc F, Brand C, Bisaillon M & Perreault JP (2023). G-quadruplexes as a structural modulator of Intron retention upon viral infection. bioRxiv, DOI: 10.1101/2023.04.12.536615

  • Perreault JP, Bolduc F & Adkar-Purushothama CR (2023). Chapter 3, Structure of viroids. Eds: Adkar-Purushothama CR, Sano T, Perreault JP, Sreenivasa MY, Di Serio F & Daròs JA. In: Fundamentals of Viroid Biology, page 45-61. Publisher: Elsevier. DOI: 10.1016/B978-0-323-99688-4.00012-2.

  • Adkar-Purushothama CR, Di Serio F, Perreault JP & Sano T (2023). Chapter 11, Viroid Pathogenesis. Eds: Adkar-Purushothama CR, Sano T, Perreault JP, Sreenivasa MY, Di Serio F & Daròs JA. In:Fundamentals of Viroid Biology, page 203-223. Publisher: Elsevier. DOI: 10.1016/B978-0-323-99688-4.00026-2.

  • Adkar-Purushothama CR, Perreault JP & Sano T (2023). Chapter 15, Viroid-induced RNA silencing and its secondary effect on the host transcriptome. Eds: Adkar-Purushothama CR, Sano T, Perreault JP, Sreenivasa MY, Di Serio F & Daròs JA. In:Fundamentals of Viroid Biology, page 275-295. Publisher: Elsevier. DOI:10.1016/B978-0-323-99688-4.00022-5.

  • Katsarou K, Adkar-Purushothama CR, Tassios E, Samotaki M, Andronis C, Lison P, Nikolau C, Perreault JP & Kalantidis K (2022). Revisiting non-coding nature of viroids. Cells, 11:265. DOI: 10.3390/cells11020265.

  • Vannutelli A,  Perreault JP & Ouangraoua A (2022). G-quadruplex occurrence and conservation: more than just a question of guanine-cytosine content. Nucleic Acids Res. Genomics and Bioinformatic, 4(1):lqac010. DOI: 10.1093/nargab/lqac010.

  • Boudreault S, Durand M, Martineau CA, Perreault JP, Lemay G &  Bisaillon M (2022). Reovirus µ2 protein modulates host cell alternative splicing by reducing protein level of U5 snRNP core components. Nucleic Acids Res, 50(9):5263-5281. DOI: 10.1093/nar/gkac272

  • Vannutelli A, Schell L, Perreault JP & Ouangraoua A (2022). GAIA: G-quadruplexes in alive creature database. Nucleic Acids Res, 51(D1):D135–D140. DOI: 10.1093/nar/gkac657.

     

  • Adkar-Purushothama CR, Iyer P, Sano T & Perreault JP (2021). sRNA Profiler: A User-Focused Interface for Small RNA Mapping and Profiling. Cells, 10(7):1771. DOI: 10.3390/cells10071771.
  • Xu D, Adkar-Purushothama CR, Pierre L,  Perreault JP & Fall M (2021). First Report of Grapevine Yellow Speckle Viroid 1 Infecting Grapevine ( Vitis vinifera ) in Canada. Plant Dis, 105. DOI: 10.1094/PDIS-04-21-0863-PDN.
  • Turcotte MA, Garant JM, Cossette-Roberge H &  Perreault JP (2021). Guanine Nucleotide-Binding Protein-Like 1 (GNL1) binds RNA G-quadruplex structures in genes associated with Parkinson’s disease. RNA Biol, 18(9):1339-1353. DOI: 10.1080/15476286.2020.1847866

  • Adkar-Purushothama CR & Perreault JP (2020). Impact of Nucleic Acid Sequencing on Viroid Biology. International Journal of Molecular Sciences, 21(15):5532. DOI: 10.3390/ijms21155532.
  • Adkar-Purushothama CR, Bolduc F,  Bru P & Perreault JP (2020). Insights Into Potato Spindle Tuber Viroid Quasi-Species From Infection to Disease. Frontiers in Microbiology, 11. 1235. DOI: 10.3389/fmicb.2020.01235.
  • Bolduc F, Turcotte MA & Perreault JP (2020). The Small Nuclear Ribonucleoprotein Polypeptide A (SNRPA) binds to the G-quadruplex of the BAG-1 5′UTR. Biochimie, 176:122-127. DOI: 10.1016/j.biochi.2020.06.013.
  • Adkar-Purushothama CR & Perreault JP (2020). Current overview on viroid-host interactions. Wiley interdisciplinary Reviews (WIRE) – RNA, 11(2):e1570.  DOI: 10.1002/wrna.1570.
  • Vannutelli A, Belhamiti S, Garant JM, Ouangraoua A & Perreault JP (2020). Where are G-quadruplexes located in the human transcriptome. Nucleic Acid Res. - Genomics and Bioinformatics, 2(2):lqaa035. DOI: 10.1093/nargab/lqaa035.
  • Rouleau S, Jodoin R, Garant JM &  Perreault JP (2020). RNA Quadruplexes as key motifs of the transcriptomes. Advances in Biochemical Engineering/Biotechnology, 170:1-20. DOI: 10.1007/10_2017_8.

 

  • Adkar-Purushothama CR & Perreault JP (2019). Suppression of RNA-Dependent RNA Polymerase 6 Favors the Accumulation of Potato Spindle Tuber Viroid in Nicotiana Benthamiana. Viruses, 11(4):345. DOI: 10.3390/v11040345.
  • Boudreault S, Saavedra Armero VE, Scott MS, Perreault JP & Bisaillon M (2019). The Epstein-Barr virus EBNA1 protein modulates the alternative splicing of cellular genes. Virology Journal, 16(1):29. DOI: 10.1186/s12985-019-1137-5.
  • Martenon Brodeur C, Thibault P, Durand M, Perreault JP & Bisaillon M (2019). Dissecting the expression landscape of cytochrome P450 in hepatocellular carcinoma: towards novel molecular biomarkers. Genes and Cancer, 10(3-4):97-108. DOI: 10.18632/genesandcancer.190.
  • Cottilli P, Belda-Palazon B, Adkar-Puroshuthama CR, Perreault JP, Schieiff E, Rodrigo I, Ferrando A & Lison P (2019). Citrus exocortis viroid causes ribosomal stress in tomato plants. Nucleic Acids Res, 47(16):8649-8661. DOI: 10.1093/nar/gkz679.
  • Jodoin R, Carrier J, Rivard N, Bisaillon M & Perreault JP (2019). G-quadruplex located in the 5’UTR of the Bag-1 mRNA affects both its cap-dependent and cap-independent translation through global secondary structure maintenance. Nucleic Acids Res, 47(19):10247-10266. DOI: 10.1093/nar/gkz777.

  • Jodoin R & Perreault JP (2018). G-quadruplexes formation in the 5’UTRs of mRNAs associated with colorectal cancer pathways. PloS One, 13(12):e0208363. DOI: 10.1371/journal.pone.0208363.
  • Adkar-Purushothama CR, Sano T & Perreault JP (2018). Viroid derived small RNA induces early flowering in tomato plants by RNA silencing. Molecular Plant Pathology, 19(11):2446-2458. DOI: 10.1111/mpp.12721.
  • Garant JM, Perreault JP & Scott MS (2018). G4RNA screener web server: User focused interface for RNA G-quadruplex prediction. Biochimie, 151:115-118. DOI: 10.1016/j.biochi.2018.06.002.
  • Adkar-Purushothama CR & Perreault JP (2018).Alterations of the viroid regions that interact with the host defense genes attenuate viroid infection in host plant. RNA Biology, 15(7):955-966. DOI: 10.1080/15476286.2018.1462653.
  • Rouleau S, Garant JM, Bolduc F, Bisaillon M & Perreault JP (2018). G-quaduplexes influence pri-microRNA processing. RNA Biology, 15(2):198-206. DOI: 10.1080/15476286.2017.1405211.

 

  • Rouleau S, Garant JM, Bolduc F, Bisaillon M & Perreault JP (2017). G-Quadruplexes influence pri-microRNA processing. RNA Biology,15(2):198-206. DOI: 10.1080/15476286.2017.1405211.
  • Adkar-Purushothama CR, Bru P & Perreault JP (2017). 3′ RNA Ligase Mediated Rapid Amplification of cDNA ends for validating viroid induced cleavage at the 3′ extremity of the host mRNA. Journal of Virological Methods, 250:29-33. DOI: 10.1016/j.jviromet.2017.09.023.
  • Adkar-Purushothama CR, Iyer P & Perreault JP (2017). Potato spindle tuber viroid infection triggers degradation of chloride channel protein CLC-b-like and Ribosomal protein S3a-like mRNAs in tomato plants. Scientific Reports, 7:8341. DOI: 10.1038/s41598-017-08823-z.
  • Giguère T & Perreault JP (2017). Classification of the Pospiviroidae based on their structural hallmarks. PloS One, 12(8):e0182536. DOI: 10.1371/journal.pone.0182536.
  • Garant JM, Perreault JP& Scott MS (2017). Motif independent identification of potential RNA G-quadruplexes by G4RNA screener. Bioinformatics, 33(22):3532–3537. DOI: 10.1093/bioinformatics/btx498.
  • Glouzon JPS, Perreault JP & Wang S (2017). Structurexplor: A platform for the exploration of structural features of RNA secondary structures. Bioinformatics, 33(19):3117–3120. DOI: 10.1093/bioinformatics/btx323.  
  • Glouzon JPS, Perreault JP & Wang S (2017). The super-n-motifs model: a novel alignment-free approach for representing and comparing RNA secondary structures. Bioinformatics, 33(8):1169-1178.DOI: 10.1093/bioinformatics/btw773.
  • Steger G, Maurel MC, Riesner D & Perreault JP (2017). Chapter 6, Viroid Structure. In: Viroid and Satellites. Eds: Hadidi A, Flores R, Randles JW & Palukaitis P.
  • Amero V, Tremblay MP, Allaire A, Boudreault S, Matenon C, Duval C, Durand M, Lapointe E, Thibault P, Tremblay-Létourneau M, Perreault JP, Scott MS & Bisaillon M (2017). Transcriptome-wide analysis of alternative RNA splicing events in Epstein-Barr virus-associated gastric carcinomas. PLoS One, 12(5):e0176880.  DOI: 10.1371/journal.pone.0176880.
  • Rouleau S, Glouzon JPS, Brumwell A & Perreault JP (2017). 3’UTR G-quadruplexes regulate miRNA binding. RNA, 23(8):1172-1179. DOI: 10.1261/rna.060962.117.

  • Boudreault S, Martenon-Brodeur C, Caron M, Garant JM, Tremblay MP, Armero VE, Durand M, Lapointe E, Thibault P, Tremblay-Létourneau M, Perreault JP, Scott MS, Lemay G & Bisaillon M (2016). Global profiling of the cellular alternative RNA splicing landscape during virus-host interactions. PLoS One, 11(9):e0161914. doi: 10.1371/journal.pone.0161914.

  • Bolduc F, Garant JM, Allard F & Perreault JP (2016). Irregular G-quadruplexes found in the untranslated regions of human mRNAs influence transition. J Biol Chem, 291(41):21751-21760. DOI: 10.1074/jbc.M116.744839.

  • Song J, Perreault JP, Topisirovic I & Richard S (2016). RNA G-quadruplexes and their potential regulatory roles in translation. Translation (Austin), 4(2):e1244031. DOI: 10.1080/21690731.2016.1244031.

  • Tremblay MP, Amero V, Allaire A, Boudreault S, Matenon C, Durand M, Lapointe E, Thibault P, Tremblay-Létourneau M, Perreault JP, Scott MS & Bisaillon M (2016). Global profiling of alternative RNA splicing events provides insights info molecular differences between various types of hepatocellular carcinoma. BMC Genomics, 17(1):683. DOI: 10.1186/s12864-016-3029-z.
  • Steger G & Perreault JP (2016). Structure and associated biological functions of viroid. Advances in Virus Research, 94:141-72. DOI: 10.1016/bs.aivir.2015.11.002.

  • Rouleau S, Beaudoin JD, Bisaillon M & Perreault JP (2015). Small antisense oligonucleotides against G-quadrulexes: specific mRNA translational switches. Nucleic Acids Res, 43(1):595-606. DOI: 10.1093/nar/gku1311.

  • Garant JM, Luce MJ, Scott MS & Perreault JP (2015). G4RNA: an RNA G-quadruplex database. Database (Oxford), 2015:bav059. DOI: 10.1093/database/bav059.
  • Thandapani P, Gandin V, Rouleau S, Garant JM, Boisvert FM, Perreault JP, Topisirovic I & Richard S (2015). Aven recognition of G-quadruplex regulates the translation of mixed lineage leukemia proteins. eLife, 4:e06234. DOI: 10.7554/eLife.06234.
  • Adkar-Puroshothama CR, Perreault JP & Sano T (2015). Analysis of small RNA production patterns among the two potatoes spindle tuber viroid variants in tomato plants. Genomics Data, 6:65-6. DOI: 10.1016/j.gdata.2015.08.008.
  • Adkar-Puroshothama CR, Brosseau C, Giguère T, Sano T, Moffett P & Perreault JP (2015). Small RNA derived from the virulence modulating region of the potato spindle tuber viroid silences callose synthase genes of tomato plants. Plant Cell, 27(8):2178-94. DOI: 10.1105/tpc.15.00523.

  • Brosseau JP, Lucier JF, Lamarche AA, Shkreta L, Gendron D, Lapointe E, Thibault P, Paquet E, Perreault JP, Abou Elela S & Chabot B (2014). Redirecting splicing with bifunctional oligonucleotides. Nucleic Acids Res, 42(6):e40. DOI: 10.1093/nar/gkt1287.
  • Beaudoin JD, Jodoin R & Perreault JP (2014). New scoring system to identify RNA G-quadruplex folding. Nucleic Acids Res, 42(2):1209-23. DOI: 10.1093/nar/gkt904.
  • Scarborough RJ, Lévesque MV, Perreault JP & Gatignol A (2014). Design and evaluation of clinically relevant SOFA-HDV ribozymes targeting HIV RNA. Methods Molecular Biology, 1103:31-43. DOI: 10.1007/978-1-62703-730-3_3.
  • Giguère T, Adkar-Puroshothama CR & Perreault JP (2014). Comprehensive secondary structure elucidation of four genera of family Pospiviroidae. PLoS One, 9(6):e98655. DOI: 10.1371/journal.pone.0098655.
  • Jodoin R, Bauer L, Garant JM, Lavoie M & Perreault JP (2014). The folding of 5’UTR human G-quadruplexes possessing a long central loop. RNA, 20(7):1129-41. DOI: 10.1261/rna.044578.114.
  • Giguère T, Adkar-Puroshothama CR, Bolduc F & Perreault JP (2014). Elucidation of the structures of all members of the Avsunviroidae family. Molecular Plant Pathology, 15(8):767-79. DOI: 10.1111/mpp.12130.
  • Glouzon JPS, Bolduc F, Wang S, Najmanovich RJ & Perreault JP (2014). Deep sequencing of the peach latentmosaic viroid revcals new aspects of population heterogeneity. PLoS One, 9(1):e87297. DOI: 10.1371/journal.pone.0087297.
  • Scarborough RJ, Lévesque MV, Boudrias-Dalle E, Chute IC, Daniels AM, Ouellette RJ, Perreault JP & Gatignol A (2014). A conserved target site in HIV-I Gag RNA is accessible to inhibition by both on HDV ribozyme and a short hairpin RNA. Molecular Therapy Nucleic Acids, 3(7):e178. DOI: 10.1038/mtna.2014.31.
  • Ouellet J, Ananvoranich S & Perreault JP (2014). Structural Analysis of Ribozymes. Encyclopedia of Analytical Chemistry. Edited by John Wiley & Sons Ltd. DOI: 10.1002/9780470027318.a1427.pub2

  • Beaudoin JD & Perreault JP (2013). Exploring mRNA 3’UTR G-quadruplexes: evidence of roles in both alternative polyadenylation and mRNA shortening. Nucleic Acids Res, 41(11):5898–5911. DOI: 10.1093/nar/gkt265.
  • Beaudoin JD, Jodoin R & Perreault JP (2013). New scoring system to identify RNA G-quadruplex folding. Nucleic Acids Res, 42(2):1209-23. DOI: 10.1093/nar/gkt904.
  • Beaudoin JD, Jodoin R & Perreault JP (2013). In-line probing of RNA G-quadruplexes. Methods, 64(1):79-87. DOI: 10.1016/j.ymeth.2013.02.017.
  • Brosseau JP, Lucier JF, Nwilati H, Thibault P, Garneau D, Gendron D, Durand M, Couture S, Lapointe E, Prinos P, Klinck R, Perreault JP, Chabot B & Abou-Elela S (2013). Tumor microenvironment-associated modifications of alternative splicing. RNA, 20(2):189-201. DOI: 10.1261/rna.042168.113.

  • Xu W, Bolduc F, Hong N & Perreault JP (2012). The use of a combination of computer-assisted structure prediction and SHAPE probing to elucidate the secondary structures of five viroids. Molecular Plant Pathology, 13(7):666-676. DOI: 10.1111/j.1364-3703.2011.00776.x.
  • Aissa MB, April MC, Bergeron LJr, Perreault JP & Lévesque G (2012). Silencing of amyloid precursor protein expression using a new engineered delta ribozyme. Int J Alzheimer Disease, 2012:947147. DOI: 10.1155/2012/947147
  • Lévesque MV & Perreault JP (2012). Target induced SOFA-HDV ribozymes. Methods Molecular Biology,848:369-384. DOI: 10.1007/978-1-61779-545-9_23.
  • Lévesque D, Reymond C & Perreault JP (2012). Characterization of the trans Watson-Crick GU base pair located in the catalytic core of the antigenomic HDV ribozyme. PLoS One, 7(6):e40309. DOI: 10.1371/journal.pone.0040309
  • Prinos P, Klinck R, Verables JP, Perreault JP, Wellinger RJ, Abou Elela S & Chabot B (2012). L’épissage alternative: un générateur de diversité fonctionnelle dans les cancers – Alternative splicers as a generator of functional diversity in cancer. Medicine Sciences Amerique1:4
  • Perreault JP, Lavoie L & Sullivan M (2012). La recherche en santé dans le réseau universitaire de Sherbrooke. Medicine Sciences Amerique1:4
  • Rouleau SG, Jodoin R, Bisaillon M & Perreault JP (2012). Programming a highly structured ribozyme into complex allostery using RNA oligonucleotides. ACS Chemical Biology 7(11):1802-1806. DOI: 10.1021/cb300319m.

  • Dubé A, Sikora D, Pelchat M & Perreault JP (2011). Chapter 31, Viroids and related RNA species. In: Fundamental molecular virology. Ed: N. Achelson, 2nd edition (John Wiley & Sons). Page: 378-386.
  • Lainé S, Searborough RJ, Lévesque D, Didierlaurent ML, Soye KJ, Mougel M, Perreault JP & Gatignol A (2011). Inhibition of HIV-1 expression and virion production by SOFA-HDV ribozymes against Tat and Rev mRNA sequences. Retrovirology, 6(Suppl 2):P47. Doi: 10.1186/1742-4690-6-S2-P47.
  • Dubé A, Bolduc F, Bisaillon M & Perreault JP (2011). Mapping studies of the Peach latent mosaïc viroid reveal novel structutal features. Mol Plant Pathol, 12(7):688-701. DOI: 10.1111/j.1364-3703.2010.00703.x.
  • D’Anjou F, Routhier S, Perreault JP, Latil A, Bonnel D, Fournier I, Salzet M & Day R (2011). Molecular validation of PACE4 as target in prostate cancer. Translational Oncology, 4(3):157-172. DOI: 10.1593/tlo.10295.
  • Lévesque MV, Rouleau SG & Perreault JP (2011). Selection of the most potent specific on/off adaptor-hepatitis delta virus ribozymes for use in gene targeting. Nucleic Acid Therapeutics, 21(4):241-252. DOI: 10.1089/nat.2011.0301
  • Prinos P, Garneau D, Lucier JF, Gendron D, Couture S, Boivin M, Brosseau JP, Lapointe E, Thibault P, Durand M, Tremblay K, Gervais-Bird J, Nwilati H, Klinck R, Chabot B, Perreault JP, Wellinger RJ & Abou Elela S (2011). Alternative splicing of SYK regulates mitosis and cell survival. Nature Structural Molecular Biology, 18(6):1673-1679. DOI: 10.1038/nsmb.2040.
  • Motard J, Rouvel R, Paun A, Von Messling V, Bisaillon M & Perreault JP (2011). A novel ribozyme-based prophylaxis inhibits influenza A virus replication and protects from severe disease. PLoS ONE,6(11):e2732. DOI: 10.1371/journal.pone.0027327.

  • Dubé A, Baumstark T, Bisaillon M & Perreault JP (2010). The RNA strands of the plus and minus polarities of Peach latent mosaic viroid fold into different structures. RNA, 16(3):463-473. DOI: 10.1261/rna.1826710.
  • Brosseau JP, Lucier JF, Lapointe E, Durand M, Gendron D, Gervais-Bird J, Tremblay K, Perreault JP & Abou Elela S (2010). High-throughput quantification of splicing isoforms. RNA, 16(2):442-449. DOI: 10.1261/rna.1877010.
  • Bolduc F, Hoareau C, St-Pierre P & Perreault JP (2010). In-depth sequencing of the siRNAs associated with peach latent mosaic infection. BMC Mol Biol,11:16. DOI: 10.1186/1471-2199-11-16.
  • Levésque MV, Levésque D, Brière FP & Perreault JP (2010). Investigating a new generation of ribozymes in order to target HCV. PLoS One,5(3):e9627. DOI: 10.1371/journal.pone.0009627.
  • Beaudoin JD & Perreault JP (2010). 5’UTR G-quadruplex structures acting as translational repressors. Nucleic Acids Res, 38(20):7022-7036. DOI: 10.1093/nar/gkq557.
  • Soulière MF, Perreault JP & Bisaillon M (2010). Insights into the molecular determinants involved in cap recognition by the vaccinia virus D10 decapping enzyme. Nucleic Acids Res,38(21):7599-7610. DOI: 10.1093/nar/gkq62
  • Bergeron LJr, Perreault JP & Abou Elela S (2010). Short RNA duplexe guide sequence dependent cleavage by human dicer. RNA, 16(12):2464-2473. DOI: 10.1261/rna.2346510.
  • Reymond C, Lévesque D, Bisaillon M & Perreault JP (2010). Developping three-dimensional models of the HDV ribozyme’s putative folding intermediates. Structure, 18(12):1608–1616. DOI: 10.1016/j.str.2010.09.024.

  • Reymond C, Bisaillon M & Perreault JP (2009). Monitoring of an RNA multistep folding pathway by isothermal titration calorimetry. Biophysical J, 96(1):132-140. DOI: 10.1016/j.bpj.2008.09.033.
  • St-Pierre P, Fekih Hassen I, Thompson D & Perreault JP (2009). Characterization of the siRNAs associated with peach latent mosaic viroid infection. Virology, 383(2):178-182. DOI: 10.1016/j.virol.2008.11.008.
  • Soulière MF, Perreault JP & Bisaillon M (2009). Characterization of the vaccinia virus D10 decapping enzyme provides evicence for a two-metal ion mechanism. Biochem J, 420(1):27-35. DOI: 10.1042/BJ20082296.
  • Reymond C, Beaudoin JD & Perreault JP (2009). Modulating RNA structure and catalysis: lessons from small cleaving ribozymes. Cellular Molecular Life Sciences, 66(24):3937-3950. DOI: 10.1007/s00018-009-0124-1.
  • Dubé A, Bisaillon M & Perreault JP (2009). Identification of proteins from prunus persica that interact with peach latent mosaic viroid. J Virology, 83(23): 12057-12067. DOI: 10.1128/JVI.01151-09.

  • Soulière MF, Perreault JP and Bisaillon M (2008). Magnesium-binding studies reveal fundamental differences between closely related RNA triphosphatases. Nucleic Acids Res, 36(2):451-461. DOI: 10.1093/nar/gkm1067.
  • Soulière MF, Perreault JP & Bisaillon M (2008). Kinetic and thermodynamic characterization of the RNA guanylyltransferase reaction. Biochemistry, 47(12):3863-3874. DOI: 10.1021/bi702054a.
  • Beaudoin JD & Perreault JP (2008). Potassium ions modulate a G-quadruplex-ribozyme’s activity. RNA,14(6):1018-1025. DOI: 10.1261/rna.963908.
  • Robichaud GA, Perreault JP & Ouellet RJ (2008). Development of an isoform-specific gene suppression system: The study of the human Pax-5B transcriptional element. Nucleic Acids Res, 36(14):4609-4620. DOI: 10.1093/nar/gkn432.
  • Motard J, Bolduc F, Thompson D & Perreault JP (2008). The peach latent mosaic viroid replication initiation site is located at a universal position that appears to be defined by a conserved sequence. Virology, 373(2):362-375. DOI: 10.1016/j.virol.2007.12.010.

  • Hassen IF, Massart S, J. Motard, Roussel S, Parisi O, Kummert J, Fakhfakh H, Massakchi M, Perreault JP & Jijakli MH (2007). Molecular feature of new peach latent mosaic viroid variants suggest that recombination may have contributed to the evolution of this infectious RNA. Virology 360(1):50-57. DOI: 10.1016/j.virol.2006.10.021.
  • Levesque D, Beaudoin JD, Roy S & Perreault JP (2007). In vitro selection and characterization of RNA aptamers binding thyroxine hormone. Biochemical J, 403(1):129-138. DOI: 10.1042/BJ20061216.
  • Reymond C, Ouellet J, Bisaillon M & Perreault JP (2007). Examination of the folding pathway of the antigenomic hepatitis delta virus ribozyme reveals key interactions of the L3 loop. RNA, 13(1):44-54. DOI: 10.1261/rna.263407.
  • Lucier JF, Perreault J, Noël JF, Boire G & Perreault JP (2007). RT Analyzer: a web application for finding new retrotransposons and detecting L1 retrotransposition signatures.  Nucleic Acids Res, 35(Web Server issue):W269-274. DOI: 10.1093/nar/gkm313
  • Asif-Ullah M, Lévesque M, Robichaud G & Perreault JP (2007). Development of ribozyme-based gene-inactivations; the example of the hepatitis delta virus ribozyme. Curr Gene Ther, 7(3):205-216. DOI: 10.2174/156652307780859008.
  • Perreault J, Perreault JP & Boire G (2007). Ro associated Y RNAs in metazoans: evolution and diversification. Molecular Biology Evolution, 24(8):1678-1689. DOI: 10.1093/molbev/msm084.
  • Lévesque D, Brière FP & Perreault JP (2007) A modern mode of activation for nucleic acid and enzymes. PLoS One, 2(7):e673. DOI: 10.1371/journal.pone.0000673.
  • Nehdi A, Perreault J, Beaudoin JD & Perreault JP (2007). A novel structural rearrangement of hepatitis delta virus antigenomic ribozyme. Nucleic Acids Res, 35(20):6820-6831. DOI: 10.1093/nar/gkm674. 

  • Fiola K, Perreault JP & Cousineau B (2006). Gene targeting in the gram-positive bacterium Lactococcus lactis using different delta ribozymes. Applied Envir Micro, 72(1):869-879. DOI: 10.1128/AEM.72.1.869-879.2006.
  • Pelchat M & Perreault JP (2006). Chapter, Viroids and Related RNA Species. In: Fundamental Molecular Virology. Eds: Achelson N (John Wiley & Sons). page: 315-322.
  • Nehdi A & Perreault JP (2006). Unbiased in vitro selection reveals the unique character of the self-cleaving antigenomic HDV RNA sequence. Nucleic Acids Res, 34(2):584-592. DOI: 10.1093/nar/gkj463.
  • Lucier JF, Bergeron LJr, F. Brière, R. Ouellette, Abou Elela S & Perreault JP (2006). RiboSubstrates: a web application addressing the cleavage specificities of ribozymes in designated genomes. BMC Bioinformatics,7:480. DOI: 10.1186/1471-2105-7-480.
  • Elleuch A, Djilani Khouaja F, Hamdi I, Bsais N, Perreault JP, Marrakchi M and Fakhfakh H (2006). Sequence analysis of three citrus viroids infecting a single Tunisian citrus tree (Citrus reticulate, Clementine). Genetics and Molecular Biology, 29(4):705-710. DOI: 10.1590/S1415-47572006000400020.

  • Elleuch A, Marrakchi M, Fakhfakh H, Lévesque D, Perreault JP & Bessais N (2005). Interaction between Citrus Cachexia virus and closely related sequence variants may impair expression of cachexia symptoms. Acta Hort, 657: 401-405. DOI: 10.17660/ActaHortic.2004.657.64.
  • Bergeron LJ & Perreault JP (2005). Target-dependent on/off switch increases ribozyme fidelity. Nucleic Acids Res, 33(4): 1240-1248. DOI: 10.1093/nar/gki278.
  • Landry P & Perreault JP (2005) Identification of a peach latent mosaic viroid hairpin able to act as a Dicer-like substrate. J Virology, 79(10): 6540-6543. DOI: 10.1128/JVI.79.10.6540-6543.2005.
  • Perreault J, Noël JF, Brière F, Cousineau B, Lucier JF, Perreault JP and Boire G (2005). Retropseudogenes derived from the human Ro/SS-A autoantigen-associated hY RNAs. Nucleic Acids Res, 33(6): 2032-2041. DOI: 10.1093/nar/gki504.
  • Bergeron LJr, Reymond C & Perreault JP (2005). Functional characterization of the SOFA delta ribozyme. RNA, 11(12):1858-1868. DOI: 10.1261/rna.2112705.

  • D’Anjou F, Bergeron LJ, Larbi NB, Fournier I, Salzet M, Perreault JP* & Day R (2004). Silencing of SPC2 expression using an engineered delta ribozyme in the mouse BTC-3 endocrine cell line. J Biol Chem, 279(14):14232-14239. DOI: 10.1074/jbc.M310632200.
  • Landry P & Perreault JP (2004). The role of viroids in gene silencing: the model case of peach latent mosaic viroid. Canadian J Plant Pathol, 26:31-38. DOI: 10.1080/07060660409507109
  • Ouellet J & Perreault JP (2004). Cross-linking experiments reveal the presence of novel structural features between a hepatitis delta virus ribozyme and its substrate. RNA, 10(7):1059-1075. DOI: 10.1261/rna.7230604.
  • Pelchat M & Perreault JP (2004). Binding site of Escherichia coli RNA polymerase to an RNA promoter. Biochem Biophys Res Comm, 319(2): 626-642. DOI: 10.1016/j.bbrc.2004.05.044.

  • Côté F, De La Penya M, Flores R & Perreault JP (2003). Chapter, Ribozyme reactions of viroids. In: Viroid. Eds: Hadidi A (CSIRO) page: 350-356.
  • Pelchat M, Rocheleau L, Perreault J & Perreault JP (2003). Sub-viral RNA: A database of the smallest known auto-replicable RNA species. Nucleic Acids Res, 31(1):444-445. DOI: 10.1093/nar/gkg026.
  • Deschênes P, Ouellet J, Perreault J & Perreault JP (2003). Formation of the P1.1 pseudoknot is critical for both the cleavage activity and substrate specificity of an antigenomic trans-acting hepatitis deltaribozyme. Nucleic Acids Res, 31(8):2087-2096. DOI: 10.1093/nar/gkg307.
  • Elleuch A, Marrakchi M, Perreault JP & Fakhfakh H (2003). First report of australian grapevine viroid from the Mediterranean region. J Plant Pathology, 85(1):53-57.
  • Bergeron LJ, Ouellet J & Perreault JP (2003). Ribozyme-based gene-inactivation systems require a fine comprehension of their substrate specificities: The case of the delta ribozyme. Curr Med Chem,10(23):2589-2597. DOI: 10.2174/0929867033456486.
  • Bussière F, Le Dû S, Girard M, Héroux M, Perreault JP & Matton DP (2003). Development of an efficient cis-trans-cis ribozyme cassette to inactivate plant genes. Plant Biotechnol J, 1(6):423-435. DOI: 10.1046/j.1467-7652.2003.00039.x.
  • Elleuch A, Marrakchi M, D. Lévesque M, N. Bessais, Perreault JP & Fakhfakh H (2003). Molecular variability of citrus exocortis viroid in a single naturally infected citrus tree. Plant ProtectSci, 39(4):139-145. DOI: 10.17221/3833-PPS.

  • Lévesque D, Choufani S & Perreault JP (2002). Delta Ribozyme benefits from a good stability in vitro that becomes outstanding in vivo. RNA, 8(4):464-477. DOI: 10.1017/s1355838202020289.
  • Pelchat M, C. Grenier & Perreault JP (2002). Characterization of the DNA-dependent RNA polymerase from Escherichia coli. Biochemistry, 41(20): 6561-6571. DOI: 10.1021/bi025595k.
  • Fiola K & Perreault JP (2002). Kinetic and binding analysis of the catalytic involvement of ribose moieties of a trans-acting delta ribozyme. J Biol Chem, 277(29): 26508-26516. DOI: 10.1074/jbc.M203468200
  • Elleuch A, Fakhfakh H, Pelchat M, Landry P, Marrakchi M & Perreault JP (2002). Sequencing of Australian grapevine viroid and yellow speckle viroid isolated from a Tunisian grapevine without passage in an indicator plant. Eur J Plant Pathology, 108:815-820. DOI: 10.1023/A:1020855405948.
  • Bergeron LJ & Perreault JP (2002). Development and comparison of procedures for the selection of deltaribozyme cleavage sites within the hepatitis B virus. Nucleic Acids Res, 30(21):4682-4691. DOI: 10.1093/nar/gkf598.

  • Côté F, Lévesque D & Perreault JP (2001). Natural 2', 5'-phosphodiester bonds found at the ligation sites of peach latent mosaic viroid. J Virology, 75(1):19-25. DOI: 10.1128/JVI.75.1.19-25.2001.
  • Ananvoranich S, Fiola K, Ouellet J, Deschênes P & Perreault JP (2001). Kinetic analysis of a bimolecular hepatitis delta ribozyme. Methods Enzymol, 341:553-556. DOI: 10.1016/s0076-6879(01)41176-1
  • Pelchat M, Côté F, & Perreault JP (2001). Study of the polymerization step of the rolling circle replication of the peach latent mosaic viroid. Advances Virology, 146(9):1753-1763. DOI: 10.1007/s007050170061.

  • Poisson V, Ménard DB, Frost E & Perreault JP (2000). A Canadian isolate of hepatitis delta virus. Can J Gastro, 14:Suppl B:36B-40B. DOI: 10.1155/2000/397947.
  • Deschênes P, Lafontaine DA, Charland S & Perreault JP (2000). Nucleotides –1 to –4 of hepatitis deltaribozyme substrate increase the specificity of ribozyme cleavage. Antisense and Nucleic Acid Drug Development, 10(1):53-61. DOI: 10.1089/oli.1.2000.10.53.
  • Ananvoranich S & Perreault JP (2000). Chapter, Structural Analysis of Ribozymes. In: Encyclopedia of Analytical Chemistry. Ed. Meyers RA, John Wiley & Sons, page: 5273-5285.
  • Pelchat M, Deschênes P & Perreault JP (2000). The database of the smallest known auto-replicable RNA species: viroids and viroid-like RNAs. Nucleic Acids Res, 28(1):179-180. DOI: 10.1093/nar/28.1.179.
  • Bussière F, Ouellet J, Côté F, Lévesque D & Perreault JP (2000). Mapping in solution shows the peach latent mosaic viroid to possess a new pseudoknot in a complex, branched secondary structure. J Virology, 74(6):2647-2654. DOI: 10.1128/jvi.74.6.2647-2654.2000.
  • Ananvoranich S & Perreault JP (2000). The kinetic and magnesium requirements for the folding of antigenomic delta ribozymes. Biochem Biophys Res Comm, 270(2):600-607. DOI: 10.1006/bbrc.2000.2465.
  • Pelchat M, Lévesque D, Ouellet J, Laurendeau S, Lévesque S, Lehoux J, Thompson DA, Eastwell KC,Skrzeczkowski LJ & Perreault JP (2000). Sequencing of peach latent mosaic viroid variants from nine peach North American cultivars shows that this RNA folds into a complex secondary structure. Virology, 271(1):37-45. DOI: 10.1006/viro.2000.0288.

  • Roy G, Ananvoranich S & Perreault JP (1999). Delta ribozyme has the ability to cleave in trans mRNA. Nucleic Acids Res, 27(4):942-948. DOI: 10.1093/nar/27.4.942.
  • Ananvoranich S, Lafontaine DA, & Perreault JP (1999). Mutational analysis of the antigenomic trans-acting delta ribozyme: The alterations of the middle nucleotides located on the P1 stem. Nucleic Acids Res, 27(6):1473-1479. DOI: 10.1093/nar/27.6.1473.
  • Lafontaine DA, Deschênes P, Bussière F, V. Poisson & Perreault JP (1999). The viroid and viroid-like database. Nucleic Acids Res, 27(1):186-187. DOI: 10.1093/nar/27.1.186.
  • Bussière F, Lehoux J, Thompson DA, Skrzeczkowski LJ & Perreault JP (1999). Subcellular localization and rolling circle replication of peach latent mosaic viroid: Hallmarks of group A viroids. J Virology,73(8):6353-6360. DOI: 10.1128/JVI.73.8.6353-6360.1999.
  • Le Dû S, Deschênes P, Ananvoranich S & Perreault JP (1999). Review of the substrate specificity for delta ribozyme cleavage. Nucleic Acids Symposium Series, 41:24-26
  • Lafontaine DA, Ananvoranich S, Mercure S, & Perreault JP (1999). Presence of coordinated metal in a trans-acting antigenomic delta ribozyme. Nucleic Acid Res, 27(15):3236-3243. DOI: 10.1093/nar/27.15.3236.

  • Lafontaine DA, Mercure S & Perreault JP (1998). Identification of a Crohn's disease specific transcript with potential as a diagnostic marker. Gut, 42(6):878-882. DOI: 10.1136/gut.42.6.878.
  • Ananvoranich S & Perreault JP (1998). Substrate specificity of delta ribozyme cleavage. J Biol Chem, 273(21):13182-13188. DOI: 10.1074/jbc.273.21.13182.
  • Mercure S, Lafontaine DA, Ananvoranich S & Perreault JP (1998). Kinetic analysis of delta ribozyme cleavage. Biochemistry, 37(48):16975-16982. DOI: 10.1021/bi9809775.

  • Lafontaine DA, Mercure S & Perreault JP (1997). Update of the viroid and viroid-like sequence database: Addition of a hepatitis delta virus (vHDV) RNA section. Nucleic Acids Res, 25(1):123-125. DOI: 10.1093/nar/25.1.123
  • Mercure S, Lafontaine DA,G. Roy & Perreault JP (1997). Le motif autocatalytique d'ARN du virus delta de l'hépatite humaine. Médecine/Science, 13:662-669
  • Côté F, & Perreault JP (1997). Peach latent mosaic viroid is locked by a 2',5'-phosphodiester bond produced by in vitro self-ligation. J Mol Biol, 273(3):533-543. DOI: 10.1006/jmbi.1997.1355.
  • Poisson V, Mercure S, Lafontaine DA & Perreault JP (1997). Development of a bimolecular delta ribozyme. Nucleic Acids Symposium Series, 36:83-85.
  • Roy G, Ananvoranich S & Perreault JP (1997). Design of ribozymes to selectively cleave the human hepatitis delta virus mRNA. Nucleic Acids Symposium Series, 36:893-895.
  • Lafontaine DA, Mercure S, Poisson V & Perreault JP (1998). The viroid and viroid-like RNA database. Nucleic Acids Res, 26(1):190-191. DOI: 10.1093/nar/26.1.190.
  • Roy G, Beaudry D, Beuvon P & Perreault JP (1997). Characterization of stable RNAs from the resected intestinal tissues of individuals with either Crohn's disease or ulcerative colitis. Biochem Cell Biol,75(6):789-794. DOI: 10.1139/o97-065.

  • Bussière F, Lafontaine DA & Perreault JP (1996). Compilation and analysis of viroid and viroid-like RNA sequences. Nucleic Acids Res, 24(10):1793-1798. DOI: 10.1093/nar/24.10.1793.

  • Beaudry D, Bussière F, Lareau F, Lessard C & Perreault JP (1995). The RNA of both polarities of the peach latent mosaic viroid self-cleave in vitro solely by single hammerhead structure. Nucleic Acids Res, 23(5):745-52. DOI: 10.1093/nar/23.5.745.
  • Lafontaine DA, Marquis P, Beaudry D & Perreault JP (1995). Intra- and intermolecular nonenzymatic ligations occur within transcripts derived from the peach latent mosaic viroid. Virology, 12(2):705-709. DOI: 10.1006/viro.1995.1528.
  • Bussière F & Perreault JP (1995). On the road to a DNA-protein World. RNA, 1(5):451-452.
  • Beaudry D & Perreault JP (1995). An efficient strategy for the synthesis of circular RNA molecules. Nucleic Acids Res, 23(15):3064-3066. DOI: 10.1093/nar/23.15.3064.
  • Bussière F, Lafontaine DA, Côté F, Beaudry D & Perreault JP (1995).  Evidence for a model ancestral viroid. Nucleic Acids Symposium Series 33:143-144.
  • Perreault JP (1995) Rôle possible des viroïdes dans la maladie de Crohn. Recherche en Santé, 9:20-21.

  • Perreault JP & Altman S (1993). The pathway of activation by magnesium ions of substrates for RNase P from Escherichia coli. J Mol Biol, 230(3):750-6. DOI: 10.1006/jmbi.1993.1197.

  • Perreault JP & Altman S (1992). The important 2'-hydroxyl groups in small model substrates for M1 RNA, the catalytic RNA subunit of RNase P from Escherichia coli. J Mol Biol, 226(2):399-409. DOI: 10.1016/0022-2836(92)90955-j.

  • Perreault JP & Altman S (1991). “Ribonuclease P: a true enzyme in vitro”. Médecine/Science, 7:847-850.
  • Perreault JP, Labuda D, Usman N, Yang JH & Cedergren RJ (1991). The relationship between 2'-hydroxyls and magnesium binding in the hammerhead RNA domain: A model for ribozyme catalysis. Biochemistry, 30(16):4020-5. DOI: 10.1021/bi00230a029.

  • Yang JH, Perreault JP, Labuda D, N Usman & Cedergren RJ (1990). Mixed DNA/RNA polymers are cleaved by the hammerhead ribozyme. Biochemistry, 29(51):11156-60. DOI: 10.1021/bi00503a002.
  • Bratty J, Wu TF, Nicoghosian K, Ogilvie JJ, Perreault JP & Cedergren RJ (1990). Characterization of a chemically synthesized RNA having the sequence of the yeast initiator tRNA (Met). FEBS Letters,269(1):60-4. DOI: 10.1016/0014-5793(90)81118-8.
  • Perreault JP, Wu TF, Ogilvie KK & Cedergren RJ(1990). Mixed deoxyribo- and ribo-oligonucleotides with catalytic activity. Nature, 344(6266):565-567. DOI: 10.1038/344565a0.

  • Wu T, Ogilvie KK, Perreault JP & Cedergren RJ (1989). Convenient procedure for the preparation of specific mixed DNA-RNA polymers. J Am Chem Soc, 111(22):8531-8533. DOI: 10.1021/ja00204a043.
  • Perreault JP, Pon RT, Jiang M, Usman N, Pika J, Ogilvie KK & Cedergren RJ (1989). The synthesis and functional evaluation of RNA and DNA polymers having the sequence of Escherichia Coli tRNA (fMet). Eur J Biochem, 186(1-2):87-93. DOI: 10.1111/j.1432-1033.1989.tb15181.x.