Publications

Also on Google Scholar and ORCID. * co-first author; † corresponding author.

Research articles: first or co-first author

  • Ormancey M*, Tremblay BJM*, Cheng Y*, et al. (2026). Autumn–winter progression triggers distinct transcriptional programs in Arabidopsis thaliana. Genome Biology. doi:10.1186/s13059-026-04289-3 · Code
  • Tremblay BJM†, Adeel SA, Saechao M, et al. (2026). Methylthioadenosine-driven rewiring of sulfur assimilation lowers the methyl index and fertility in Arabidopsis. Journal of Experimental Botany 77, 6209–6223. doi:10.1093/jxb/erag135 · Code
  • Tremblay BJM, Santini CP, Cheng Y, et al. (2024). Interplay between coding and non-coding regulation drives the Arabidopsis seed-to-seedling transition. Nature Communications 15, 1724. doi:10.1038/s41467-024-46082-5 · Code
  • Tremblay BJM, Lobb B, Doxey AC (2021). PhyloCorrelate: inferring bacterial gene-gene functional associations through large-scale phylogenetic profiling. Bioinformatics 37, 17–22. doi:10.1093/bioinformatics/btaa1105 · Code · Web app code
  • Mansfield MJ*, Tremblay BJM*, Zeng J, et al. (2020). Phylogenomics of 8,839 Clostridioides difficile genomes reveals recombination-driven evolution and diversification of toxin A and B. PLOS Pathogens 16, e1009181. doi:10.1371/journal.ppat.1009181 · DiffBase · Analysis code
  • Banerjee A*, Doxey AC*, Tremblay BJM*, Mansfield MJ*, et al. (2020). Predicting the recombination potential of severe acute respiratory syndrome coronavirus 2 and Middle East respiratory syndrome coronavirus. Journal of General Virology 101, 1251–1260. doi:10.1099/jgv.0.001491

Preprints

  • Cameron ES, Tremblay BJM, Yahr R, et al. (2026). Transposable element diversification and the evolution of Peltigerales lichen symbionts. bioRxiv. doi:10.64898/2026.02.14.705750

Software papers

Research articles: co-author

  • Cheng Y, Tremblay BJM, Balanzá V, et al. (2025). The transcriptional regulator VAL1 promotes Arabidopsis flowering by repressing the organ boundary genes BOP1 and BOP2. Plant Physiology 198, kiaf160. doi:10.1093/plphys/kiaf160
  • Hodgins HP, …, Tremblay BJM, et al. (2023). Ancient Clostridium DNA and variants of tetanus neurotoxins associated with human archaeological remains. Nature Communications 14, 5475. doi:10.1038/s41467-023-41174-0 · Code · msaviz
  • Tian S, …, Tremblay BJM, et al. (2022). Identification of TFPI as a receptor reveals recombination-driven receptor switching in Clostridioides difficile toxin B variants. Nature Communications 13, 6786. doi:10.1038/s41467-022-33964-9 · Code
  • Wentz TG, Tremblay BJM, Bradshaw M, et al. (2022). Endogenous CRISPR-Cas systems in group I Clostridium botulinum and Clostridium sporogenes do not directly target the botulinum neurotoxin gene cluster. Frontiers in Microbiology 12, 787726. doi:10.3389/fmicb.2021.787726
  • Lobb B, Tremblay BJM, Moreno-Hagelsieb G, Doxey AC (2021). PathFams: statistical detection of pathogen-associated protein domains. BMC Genomics 22, 663. doi:10.1186/s12864-021-07982-8
  • Cameron ES, Schmidt PJ, Tremblay BJM, et al. (2021). Enhancing diversity analysis by repeatedly rarefying next generation sequencing data describing microbial communities. Scientific Reports 11, 22302. doi:10.1038/s41598-021-01636-1 · mirlyn
  • Banerjee A, …, Tremblay BJM, et al. (2021). Experimental and natural evidence of SARS-CoV-2-infection-induced activation of type I interferon responses. iScience 24, 102477. doi:10.1016/j.isci.2021.102477
  • Fantauzzi MF, Aguiar JA, Tremblay BJM, et al. (2020). Expression of endocannabinoid system components in human airway epithelial cells: impact of sex and chronic respiratory disease status. ERJ Open Research 6, 00128-2020. doi:10.1183/23120541.00128-2020
  • Cao Q, Aguiar JA, Tremblay BJM, et al. (2020). ABCF1 regulates dsDNA-induced immune responses in human airway epithelial cells. Frontiers in Cellular and Infection Microbiology 10, 487. doi:10.3389/fcimb.2020.00487
  • Aguiar JA, Tremblay BJM, Mansfield MJ, et al. (2020). Gene expression and in situ protein profiling of candidate SARS-CoV-2 receptors in human airway epithelial cells and lung tissue. European Respiratory Journal 56, 2001123. doi:10.1183/13993003.01123-2020
  • Lobb B, Tremblay BJM, Moreno-Hagelsieb G, Doxey AC (2020). An assessment of genome annotation coverage across the bacterial tree of life. Microbial Genomics 6, e000341. doi:10.1099/mgen.0.000341

Reviews and book chapters

  • Tremblay BJM, Qüesta JI (2026). Identification of accessible transcription factor binding sites during the seed-to-seedling transition. Methods in Molecular Biology 2985, 51–62. doi:10.1007/978-1-0716-4972-5_4
  • Tremblay BJM, Qüesta JI (2025). Non-coding and epigenetic mechanisms in the regulation of seed germination in Arabidopsis thaliana. Journal of Experimental Botany 76, 2455–2467. doi:10.1093/jxb/eraf051
  • Tremblay BJM, Qüesta JI (2023). Mechanisms of epigenetic regulation of transcription by lncRNAs in plants. IUBMB Life 75, 427–439. doi:10.1002/iub.2681

Features in Plant Physiology

  • Tremblay BJM (2026). A link to the past: the Bangia genome connects an ancient body plan to modern stress biology. Plant Physiology kiag830. doi:10.1093/plphys/kiag830
  • Tremblay BJM (2026). Two genes, one switch: a bidirectional promoter strategy for inducible plant immunity. Plant Physiology 201, kiag243. doi:10.1093/plphys/kiag243
  • Tremblay BJM (2026). Position matters: light repatterns m6A to tune anthocyanin accumulation in roses. Plant Physiology 200, kiag125. doi:10.1093/plphys/kiag125