Search Results - "Tremblay, Benjamin J. M."

Interplay between coding and non-coding regulation drives the Arabidopsis seed-to-seedling transition by Tremblay, Benjamin J. M., Santini, Cristina P., Cheng, Yajiao, Zhang, Xue, Rosa, Stefanie, Qüesta, Julia I.

“…Translation of seed stored mRNAs is essential to trigger germination. However, when RNAPII re-engages RNA synthesis during the seed-to-seedling transition has…”
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Ancient Clostridium DNA and variants of tetanus neurotoxins associated with human archaeological remains by Hodgins, Harold P., Chen, Pengsheng, Lobb, Briallen, Wei, Xin, Tremblay, Benjamin J. M., Mansfield, Michael J., Lee, Victoria C. Y., Lee, Pyung-Gang, Coffin, Jeffrey, Duggan, Ana T., Dolphin, Alexis E., Renaud, Gabriel, Dong, Min, Doxey, Andrew C.

“…The analysis of microbial genomes from human archaeological samples offers a historic snapshot of ancient pathogens and provides insights into the origins of…”
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Enhancing diversity analysis by repeatedly rarefying next generation sequencing data describing microbial communities by Cameron, Ellen S., Schmidt, Philip J., Tremblay, Benjamin J.-M., Emelko, Monica B., Müller, Kirsten M.

“…Amplicon sequencing has revolutionized our ability to study DNA collected from environmental samples by providing a rapid and sensitive technique for microbial…”
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Gene expression and in situ protein profiling of candidate SARS-CoV-2 receptors in human airway epithelial cells and lung tissue by Aguiar, Jennifer A, Tremblay, Benjamin J-M, Mansfield, Michael J, Woody, Owen, Lobb, Briallen, Banerjee, Arinjay, Chandiramohan, Abiram, Tiessen, Nicholas, Cao, Quynh, Dvorkin-Gheva, Anna, Revill, Spencer, Miller, Matthew S, Carlsten, Christopher, Organ, Louise, Joseph, Chitra, John, Alison, Hanson, Paul, Austin, Richard C, McManus, Bruce M, Jenkins, Gisli, Mossman, Karen, Ask, Kjetil, Doxey, Andrew C, Hirota, Jeremy A

“…In December 2019, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged, causing the coronavirus disease 2019 (COVID-19) pandemic. SARS-CoV, the…”
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PhyloCorrelate: inferring bacterial gene–gene functional associations through large-scale phylogenetic profiling by Tremblay, Benjamin J -M, Lobb, Briallen, Doxey, Andrew C

“…Abstract Motivation Statistical detection of co-occurring genes across genomes, known as ‘phylogenetic profiling’, is a powerful bioinformatic technique for…”
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Mechanisms of epigenetic regulation of transcription by lncRNAs in plants by Tremblay, Benjamin J.M., Qüesta, Julia I.

“…Long noncoding RNAs (lncRNAs) are an ubiquitous feature of eukaryotic genomes and in recent decades have been shown to be highly abundant and varied. Many…”
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Predicting the recombination potential of severe acute respiratory syndrome coronavirus 2 and Middle East respiratory syndrome coronavirus by Banerjee, Arinjay, Doxey, Andrew C, Tremblay, Benjamin J-M, Mansfield, Michael J, Subudhi, Sonu, Hirota, Jeremy A, Miller, Matthew S, McArthur, Andrew G, Mubareka, Samira, Mossman, Karen

“…Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) recently emerged to cause widespread infections in humans. SARS-CoV-2 infections have been…”
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Endogenous CRISPR-Cas Systems in Group I Clostridium botulinum and Clostridium sporogenes Do Not Directly Target the Botulinum Neurotoxin Gene Cluster by Wentz, Travis G, Tremblay, Benjamin J M, Bradshaw, Marite, Doxey, Andrew C, Sharma, Shashi K, Sauer, John-Demian, Pellett, Sabine

“…Most strains of proteolytic group I (G1 ) and some strains of possess genes encoding botulinum neurotoxin (BoNT), a potent neuroparalytic agent. Within G1 ,…”
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Experimental and natural evidence of SARS-CoV-2-infection-induced activation of type I interferon responses by Banerjee, Arinjay, El-Sayes, Nader, Budylowski, Patrick, Jacob, Rajesh Abraham, Richard, Daniel, Maan, Hassaan, Aguiar, Jennifer A., Demian, Wael L., Baid, Kaushal, D'Agostino, Michael R., Ang, Jann Catherine, Murdza, Tetyana, Tremblay, Benjamin J.-M., Afkhami, Sam, Karimzadeh, Mehran, Irving, Aaron T., Yip, Lily, Ostrowski, Mario, Hirota, Jeremy A., Kozak, Robert, Capellini, Terence D., Miller, Matthew S., Wang, Bo, Mubareka, Samira, McGeer, Allison J., McArthur, Andrew G., Doxey, Andrew C., Mossman, Karen

“…Type I interferons (IFNs) are our first line of defense against virus infection. Recent studies have suggested the ability of SARS-CoV-2 proteins to inhibit…”
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ABCF1 Regulates dsDNA-induced Immune Responses in Human Airway Epithelial Cells by Cao, Quynh T, Aguiar, Jennifer A, Tremblay, Benjamin J-M, Abbas, Nadin, Tiessen, Nicholas, Revill, Spencer, Makhdami, Nima, Ayoub, Anmar, Cox, Gerard, Ask, Kjetil, Doxey, Andrew C, Hirota, Jeremy A

“…The airway epithelium represents a critical component of the human lung that helps orchestrate defenses against respiratory tract viral infections, which are…”
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Expression of endocannabinoid system components in human airway epithelial cells: impact of sex and chronic respiratory disease status by Fantauzzi, Matthew F, Aguiar, Jennifer A, Tremblay, Benjamin J-M, Mansfield, Michael J, Yanagihara, Toyoshi, Chandiramohan, Abiram, Revill, Spencer, Ryu, Min Hyung, Carlsten, Chris, Ask, Kjetil, Stämpfli, Martin, Doxey, Andrew C, Hirota, Jeremy A

“…Cannabis smoking is the dominant route of delivery, with the airway epithelium functioning as the site of first contact. The endocannabinoid system is…”
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Phylogenomics of 8,839 Clostridioides difficile genomes reveals recombination-driven evolution and diversification of toxin A and B by Mansfield, Michael J, Tremblay, Benjamin J-M, Zeng, Ji, Wei, Xin, Hodgins, Harold, Worley, Jay, Bry, Lynn, Dong, Min, Doxey, Andrew C

“…Clostridioides difficile is the major worldwide cause of antibiotic-associated gastrointestinal infection. A pathogenicity locus (PaLoc) encoding one or two…”
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Quaqc: Efficient and quick ATAC-seq quality control and filtering by Tremblay, Benjamin J M, Qüesta, Julia I

“…quaqc allows for ATAC-seq-specific quality control and read filtering of NGS data with minimal processing time and extremely low memory overhead. An efficient…”
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