Pierre-Étienne Jacques

Publications

Articles

• Pierre-Étienne Jacques, Antoine Champie; Amélie De Grandmaison; Simon Jeanneau; Frédéric Grenier; Sébastien Rodrigue. (2023). Enabling Low-Cost and Robust Essentiality Studies with High-Throughput Transposon Mutagenesis (HTTM). PloS One, 18(4). DOI
• Pierre-Étienne Jacques, Étienne Fafard-Couture; Michelle S. Scott. (2023). Motif Conservation, Stability, and Host Gene Expression are the Main Drivers of SnoRNA Expression Across Vertebrates. Genome Research, Vol. 33, Issue 4. DOI
• Pierre-Étienne Jacques, Lisa Casimir; Samuel Zimmer; Félix Racine-Brassard; Alexandre Maréchal. (2023). The Mutational Impact of Illudin S on Human Cells. DNA Repair, Vol. 122. DOI
• Pierre-Étienne Jacques, Cécilia Légaré; Véronique Desgagné; Kathrine Thibeault; Frédérique White, Andrée-Anne Clément; Cédrick Poirier, Zhong Cheng Luo; Michelle S. Scott; Patrice Perron, Renée Guérin; Marie-France Hivert; Luigi Bouchard. (2022). First Trimester Plasma MicroRNA Levels Predict Risk of Developing Gestational Diabetes Mellitus. Frontiers in Endocrinology, Vol. 13. DOI
• Pierre-Étienne Jacques, Cécilia Légaré; Véronique Desgagné; Cédrik Poirier; Kathrine Thibeault , Frédérique White; Andrée-Anne Clément; Marie-France Hivert; Luigi Bouchard. (2022). First Trimester Plasma MicroRNAs Levels Predict Matsuda Index-Estimated Insulin Sensitivity Between 24th and 29th Week of Pregnancy. BMJ Open Diabetes Research & Care, Vol. 10, Issue 2. DOI
• Pierre-Étienne Jacques, Cécilia Légaré; Andrée-Anne Clément; Véronique Desgagné; Kathrine Thibeault; Frédérique White, Simon-Pierre Guay; Benoît J. Arsenault; Michelle S. Scott; Patrice Perron, Renée Guérin; Marie-France Hivert; Luigi Bouchard. (2022). Human Plasma Pregnancy-Associated miRNAs and Their Temporal Variation Within the First Trimester of Pregnancy. Reproductive Biology and Endocrinology, Vol. 20, Issue 1. DOI
• Pierre-Étienne Jacques, Simon Jeanneau; Daniel A. Lafontaine. (2022). Investigating the Role of RNA Structures in Transcriptional Pausing Using In Vitro Assays and In Silico Analyses. RNA Biology, Volume 19, Issue 1. DOI
• Pierre-Étienne Jacques, Karine Thibeault; Cécilia Légaré; Véronique Desgagné; Frédérique White; Andrée-Anne Clément, Michelle S. Scott; Renée Guérin; Patrice Perron; Marie-France Hivert; Luigi Bouchard. (2022). Maternal Body Mass Index is Associated with Profile Variation in Circulating MicroRNAs at First Trimester of Pregnancy. Biomedicines, Vol. 10, Issue 7. DOI
• Pierre-Étienne Jacques, L. Jonathan Dursi; Zoltan Bozoky; Richard de Borja; Haoyuan Li; David Bujold, Adam Lipski; Shaik Farhan Rashid; Amanjeev Sethi; Neelam Memon, Dashaylan Naidoo; Felipe Coral-Sasso; Matthew Wong; P-O Quirion; Zhibin Lu, Samarth Agarwal; Yuriy Pavlov; Andrew Ponomarev; Mia Husic; Krista Pace, Samantha Palmer; Michael Brudno. (2021). CanDIG: Federated Network Across Canada for Multi-Omic and Health Data Discovery and Analysis. Cell Genomics, Volume 1, Issue 2. DOI
• Pierre-Étienne Jacques, Marika Groleau; Frédérique White; Andres Cardenas; Patrice Perron, Marie-France Hivert; Luigi Bouchard. (2021). Comparative Epigenome-Wide Analysis Highlights Placenta-Specific Differentially Methylated Regions. Epigenomics, Vol. 13, Issue 5. DOI
• Pierre-Étienne Jacques, Jean-Christophe Lachance; Dominick Matteau; Joëlle Brodeur; Colton J. Lloyd; Nathan Mih, Zachary A. King; Thomas F. Knight; Adam M. Feist; Jonathan M. Monk; Bernhard O. Palsson, Sébastien Rodrigue. (2021). Genome-Scale Metabolic Modeling Reveals Key Features of a Minimal Gene Set. Molecular Systems Biology, Vol. 17. DOI
• Pierre-Étienne Jacques, Erich Smith-Peter; David Lalonde Séguin; Émilie St-Pierre; Ognjen Sekulovic; Simon Jeanneau, Cédrick Tremblay-Tétreault; Anne-Marie Lamontagne; Daniel A. Lafontaine; Louis-Charles Fortier. (2021). Inactivation of the Riboswitch-Controlled GMP Synthase GuaA in Clostridioides Difficile is Associated With Severe Growth Defects and Poor Infectivity in a Mouse Model of Infection. RNA Biology, Vol. 18, Issue Suppl. 2. DOI
• Pierre-Étienne Jacques, Zhiqiang Pang; Jasmine Chong; Guangyan Zhou; David Anderson de Lima Morais; Le Chang, Michel Barrette; Carol Gauthier; Shuzhao Li; Jianguo Xia. (2021). MetaboAnalyst 5.0: Narrowing the Gap Between Raw Spectra and Functional Insights. Nucleic Acids Research, Vol. 49, Issue W1. DOI
• Pierre-Étienne Jacques, Jean-Philippe Langlois; Guillaume Millette; Isabelle Guay; Alexis Dubé-Duquette, Suzanne Chamberland; Sébastien Rodrigue; Kamal Bouarab; Éric Marsault; François Malouin. (2020). Bactericidal Activity of the Bacterial ATP Synthase Inhibitor Tomatidine and the Combination of Tomatidine and Aminoglycoside Against Persistent and Virulent Forms of Staphylococcus Aureus. Frontiers in Microbiology, Vol. 11. DOI
• Pierre-Étienne Jacques, Dominick Matteau; Jean-Christophe Lachance; Frédéric Grenier; Samuel Gauthier, James M. Daubenspeck; Kevin Dybvig; Daniel Garneau; Thomas F. Knight; Sébastien Rodrigue. (2020). Integrative Characterization of the Near-Minimal Bacterium Mesoplasma Florum. Molecular Systems Biology, Vol. 16, Issue 12. DOI
• Pierre-Étienne Jacques, Fanny Thuriot; Elaine Gravel; Caroline Buote; Marianne Doyon; Elvy Lapointe; Lydia Marcoux, Sandrine Larue; Amélie Nadeau; Sébastien Chénier; Paula J. Waters; Serge Gravel; Sébastien Lévesque. (2020). Molecular Diagnosis of Muscular Diseases in Outpatient Clinics: A Canadian Perspective. Neurology Genetics, Vol. 6, Issue 2. DOI
• Pierre-Étienne Jacques, Carlo Yague-Sanz; Yann Vanrobaeys; Ronan Fernandez; Maxime Duval; Marc Larochelle, Jude Beaudoin; Julien Berro; Simon Labbé; François Bachand. (2020). Nutrient-Dependent Control of RNA Polymerase II Elongation Rate Regulates Specific Gene Expression Programs by Alternative Polyadenylation. Genes & Development, Vol. 34, Issues 13-14. DOI
• Pierre-Étienne Jacques, Jean-Christophe Lachance; Colton J. Lloyd; Jonathan M. Monk; Laurence Yang; Anand V. Sastry, Yara Seif; Bernhard O. Palsson; Sébastien Rodrigue; Adam M. Feist; Zachary A. King. (2019). BOFdat: Generating Biomass Objective Functions for Genome-Scale Metabolic Models From Experimental Data. PLoS Computational Biology, 15(4). DOI
• Pierre-Étienne Jacques, Jonathan Laperle; Simon Hébert-Deschamps; Joanny Raby; David A. de Lima Morais, Michel Barrette; David Bujold; Charlotte Bastin; Marc-Antoine Robert; Jean-François Nadeau, Marie Harel; Alexei Nordell-Markovits; Alain Veilleux; Guillaume Bourque. (2019). The EpiGenomic Efficient Correlator (epiGeEC) Tool Allows Fast Comparison of Private Datasets With Thousands of Public Epigenomic Datasets. Bioinformatics, Vol. 35, Issue 4. DOI
• Pierre-Étienne Jacques, Fanny Thuriot; Caroline Buote; Elaine Gravel; Sébastien Chénier; Valérie Désilets, Bruno Maranda; Paula J. Waters; Sébastien Lévesque. (2018). Clinical Validity of Phenotype-Driven Analysis Software PhenoVar as a Diagnostic Aid for Clinical Geneticists in the Interpretation of Whole-Exome Sequencing Data. Genetics in Medicine, Vol. 20, Issue 9. DOI
• Pierre-Étienne Jacques, Marc Larochelle; Marc-Antoine Robert; Jean-Nicolas Hébert; Xiaochuan Liu; Dominique Matteau, Sébastien Rodrigue; Bin Tian; François Bachand. (2018). Common Mechanism of Transcription Termination at Coding and Noncoding RNA Genes in Fission Yeast. Nature Communication, Vol. 9, Issue 1. DOI
• Pierre-Étienne Jacques, Sébastien Bélanger; Suzanne Marchand; Blake Meyers; François Belzile. (2018). Differential Expression Profiling of Microspores During the Early Stages of Isolated Microspore Culture Using the Responsive Barley Cultivar Gobernadora. G3 : Genes, Genomes, Genetics, Vol. 8, Issue 5. DOI
• Pierre-Étienne Jacques, Marie-Chantal Grégoire; Frédéric Leduc; Martin H. Morin; Tiphanie Cavé; Mélina Arguin, Martin Richter; Guylain Boissonneault. (2018). The DNA Double-Strand "Breakome" of Mouse Spermatids. Cellular and Molecular Life Sciences, 75(15). DOI
• Pierre-Étienne Jacques, Maxime Lamontagne Boulet; Charles Isabelle; Isabelle Guay; Eric Brouillette; Jean-Philippe Langlois, Sébastien Rodrigue; Ryszard Brzezinski; Pascale B. Beauregard; Kamal Bouarab, Kumaraswamy Boyapelly; Pierre-Luc Boudreault; Éric Marsault; François Malouin. (2018). Tomatidine is a Lead Antibiotic Molecule that Targets Staphylococcus Aureus ATP Synthase Subunit C. Antimicrobial Agents and Chemotherapy, 62(6). DOI
• Pierre-Étienne Jacques, Anahita Lashgari; Jean-François Millau; Luc Gaudreau. (2017). Global Inhibition of Transcription Causes an Increase in Histone H2A.Z Incorporation Within Gene Bodies. Nucleic Acids Research, 45(22). DOI
• Pierre-Étienne Jacques, Louis-Valentin Meteignier; Mohamed el Oirdi; Mathias Cohen; Teura Barff; Dominik Matteau, Jean-François Lucier; Sébastien Rodrigue; Keiko Yoshioka; Peter Moffet. (2017). Translatome Analysis of An NB-LRR Immune Response Identifies Important Contributors to Plant Immunity in Arabidopsis. Journal of Experimental Botany, 68(9). DOI
• Pierre-Étienne Jacques, Sébastien Lévesque; Christiane Auray-Blais; Elaine Gravel; Michel Boutin; Laura Dempsey-Nunez, Sébastien Chenier; Sandrine Larue; Marie-France Rioux; Walla Al-Hertani; Amélie Nadeau, Jean Mathieu; Bruno Maranda; Valérie Désilets; Paula J. Waters, Joan Keutzer; Stephanie Austin; Priya Kishnani. (2016). Diagnosis of Late-Onset Pompe Disease and Other Muscle Disorders by Next-Generation Sequencing. Orphanet Journal of Rare Diseases, 11(1).
• Pierre-Étienne Jacques, David Bujold; David Anderson de Lima Morais; Carol Gauthier, Catherine Côté; Maxime Caron; Tony Kwan; Kuang Chung Chen, Jonathan Laperle; Alexei Nordell Markovits; Tomi Pastinen, Bryan Caron; Alain Veilleux; Guillaume Bourque. (2016). The International Human Epigenome Consortium Data Portal. Cell Systems, Vol. 3, Issue 5. DOI
• Pierre-Étienne Jacques, Charles E. Breeze; Dirk S. Paul; Jenny van Dongen; Lee M. Butcher; John C. Ambrose, James E. Barrett; Robert Lowe; Vardhman K. Rakyan; Valentina Lotchkova; Mattia Frontini, Kates Downes; Willem H. Ouwehand; Jonathan Laperle; Guillaume Bourque; Anke K. Bergman, Reiner Siebert; Edo Vellenga; Sadia Saeed; Filomena Matarese; Joost H.A. Martens, Hendrik G. Stunnenberg; Andrew E. Teschendorff; Javier Herrero; Ewan Birney, Ian Dunham; Stephan Beck. (2016). eFORGE: A Tool for Identifying Cell Type-Specific Signal in Epigenomic Data. Cell Reports, 17(8). DOI

Chapitres de livre

• Pierre-Étienne Jacques, Mylène Brunelle; Sébastien Rodrigue; Nicolas Gévry, Springer Protocols (Editor). (2017). High-Resolution Genome-Wide Mapping of Nucleosome Positioning and Occupancy Level Using Paired-End Sequencing Technology. Methods in Molecular Biology, Vol. 1528. DOI
• Pierre-Étienne Jacques, Mylène Brunelle; Charles Coulombe; Christian Poitras; Marc-Antoine Robert, Alexei Nordell Markovits; François Robert, Springer Protocols (Editor). (2015). Aggregate and Heatmap Representations of Genome-Wide Localization Data Using VAP, a Versatile Aggregate Profiler. Methods in Molecular Biology, Vol. 1334. DOI

Articles de conférence

• Pierre-Étienne Jacques, Frosi G.; Raby J. (2022). Prediction of Metadata from Epigenomic Data Enabled Validating/Correcting/Complementing IHEC EpiAtlas Project and Over 20,000 ChIP-Seq Uniformly Reprocessed Public Datasets. Proceedings of the International Human Epigenome Consortium (IHEC) Annual Meeting.
• Pierre-Étienne Jacques, White F.; Groleau M.; Hivert M.F.; Bouchard L. (2021). Identification and Application of Circulating MicroRNA Expression Quantitative Trait Loci (eQTL) at the First Trimester of Pregnancy. Proceeding of the Intelligent Systems for Molecular Biology & European Conference on Computational Biology (ISMB/ECCB).
• Pierre-Étienne Jacques, Raby J.; Laperle J.; Hébert-Deschamps S. (2019). Epigenomic Labeling Prediction Using Machine Learning on IHEC Datasets. Proceedings of the International Human Epigenome Consortium (IHEC) Annual Meeting.
• Pierre-Étienne Jacques, Groleau M.; Bouchard L.; Hivert M.F. (2018). Genome-Wide Comparison of DNA Methylation Patterns Between Umbilical Cord Blood and Placenta. Proceedings of the Research in Computational Molecular Biology (RECOMB) Annual Meeting.
• Pierre-Étienne Jacques, Zimmer S.; Maréchal A. (2018). Mutational Signatures of Alternative DNA Repair Pathways in Human Cancer Cells. Proceedings of the Research in Computational Molecular Biology (RECOMB) Annual Meeting.
• Pierre-Étienne Jacques, White F.; Lévesque S. (2018). Outil bio-informatique de prédiction de l'ethnicité d'un individu à partir d'une liste de variants génétiques. Journée Phare : Congrès québécois en sciences de la santé.
• Pierre-Étienne Jacques, Bioteau A.; White F.; Burrus V. (2018). Study of Conservation and Diversity of Mobile Genomic Islands in Vibrionaceae: Detection, Identification and Classification. Proceedings of the Research in Computational Molecular Biology (RECOMB) Annual Meeting.
• Pierre-Étienne Jacques, Nadeau J.F.;Robert M.A. (2018). Using Public Data to Conduct an Epigenomic Comparative Study Between Species. Proceedings of the Research in Computational Molecular Biology (RECOMB) Annual Meeting.
• Pierre-Étienne Jacques, Larochelle M.;Robert M-A.; Hébert J.N.; Bachand F. (2017). A Universal Mode of 3' End Processing and Transcription Termination for Fission Yeast RNA Polymerase II-Transcribed Genes. Proceedings of the 18th Annual RiboClub Meeting.
• Pierre-Étienne Jacques, Bélanger S.; Marchand S.; Belzile F. (2016). Androgenic Switch: Changes in Gene Expression During Early Stages of Androgenesis in the Barley Microspore. Proceedings of the Plant and Animal Genome (PAG) Conference.
• Pierre-Étienne Jacques, Bujold D.; Gauthier C.; Busche S.; Caron M.; Nordell-Markovits A.; Morais D.; Barrette M., Goerner-Potvin P.; Kwan T.; Pastinen T.; Veilleux A.; Bourque G. (2016). Integrative Visualization and Distribution of Epigenomics Datasets with the IHEC Data Portal. Proceedings of the International Human Epigenome Consortium (IHEC) Annual Meeting.
• Pierre-Étienne Jacques, Laperle J.; Robert M-A.; Bujold B.; de Lima Morais D.A.;Barrette M., Bastin C.; Harel M.; Morin C.; Bourque G. (2016). Using the IHEC Data Through the Genomic Efficient Correlator (GeEC) Tool. Proceedings of the International Human Epigenome Consortium (IHEC) Annual Meeting.
• Pierre-Étienne Jacques, Laperle J.; Nordell-Markovits A.; Robert M-A.; Bujold B.; de Lima Morais D.A., Barrette M.; Bourque G. (2015). Large-Scale Correlation of Epigenomics Data. Proceedings of the Genome Informatics Meeting.
• Pierre-Étienne Jacques, Laperle J.; Nordell-Markovits A.; Robert M-A,; Bujold B.; de Lima Morais D.A., Barrette M.; Bourque G. (2015). The Genomic Efficient Correlator (GeEC) Tool. Proceedings of the International Human Epigenome Consortium (IHEC) Annual Meeting.
• Pierre-Étienne Jacques, Buote C.; Thuriot F.; Edmont M. Gravel E. Trakadis Y., Theriault J.F.; Larochelle H.; Maranda B.; Chénier S.; Lévesque S. (2014). PHENOVAR: A Phenotype-Driven Approach to Facilitate Routine Utilization of Clinical Exome Sequencing for the Diagnosis of Polymalformative Syndromes. Proceedings of the American Society of Human Genetics Annual Meeting.
• Pierre-Étienne Jacques, Gauthier C.; Bujold D.; Morais D.; Barrette M.; Nordell-Markovits A.; Létourneau L.; Lévesque M., Fillon J.; Chen K-C.; Lucier J-F.; Veilleux A.; Bourque G. (2014). The Genetics and Genomics Analysis Platform (GenAP). Proceedings of the Biological Data Science Conference.
• Pierre-Étienne Jacques, Brunelle M.; Nordell-Markovits A.; Rodrigue S.; Lupien M.; Gévry N. (2014). The Histone Variant H2A.Z is an Important Regulator of Enhancer Activity. Proceedings of the Histone Variants Meeting, Organized by the European Molecular Biology Organization (EMBO).
• Pierre-Étienne Jacques, Coulombe C.; Poitras C.; Nordell-Markovits A.; Brunelle M.; Lavoie M-A.; Robert F. (2014). The Versatile Aggregate Profiler (VAP) for Efficient Genome-Wide Data Representation and Discovery. Proceedings of the Big Data in Biology Symposium, Organized by the Keystone Symposia.
• Pierre-Étienne Jacques, Brunelle M.; Nordell-Markovits A.; Lupien M.; Rodrigue S.; Gévry N. (2013). A Genome-Wide Study of the Transcriptional and Epigenetic Functions of H2A.Z at Distal ERa-Enhancers. Proceedings of the Chromatin and Epigenetics EMBO Conference Series.
• Pierre-Étienne Jacques, Jeyakani J.; Bourque G. (2012). Tissue-Specific Activation of Transposons-Derived Sequences in Normal and Cancer Cells. Proceedings of the Epigenetics, Chromatin & Transcription Conference, Organized by Cold Spring Harbor Asia.
• Pierre-Étienne Jacques, Jeyakani J.; Bourque G. (2011). Reactivation of Genomic Repeat Subfamilies in Cancer. Proceedings of the Changing Landscape of the Cancer Genome Conference, Organized by Keystone Symposia.

Autres contributions

Cours enseignés ou supervisés à l'UdeS

• BFT403 - Outils bio-informatiques. (2026). (3CR).
• BFT703 - Outils bio-informatiques. (2026). (3CR).
• BFT711 - Initiation à la programmation et utilisation de calcul informatique de pointe. (2025-2026). (3CR).
• OMP700 - Projet de spécialité en sciences omiques appliquées. (2026). (9CR).
• OMP701 - Projet expérimental I en sciences omiques appliquées. (2025-2026). (3CR).
• OMP702 - Projet expérimental II en sciences omiques appliquées. (2025-2026). (3CR).
• OMP704 - Sujets spéciaux en sciences omiques appliquées. (2025-2026). (3CR).
• OMX700 - Technologies de séquençage à haut débit pour les sciences omiques appliquées. (2025-2026). (3CR).
• OMX701 - Méthodes transcriptomiques. (2026). (3CR).
• OMX702 - Approches épigénomiques - protéines. (2026). (3CR).
• OMX703 - Approches métagénomiques. (2026). (3CR).
• OMX704 - Méthodes protéomiques. (2026). (3CR).
• OMX760 - Initiation à la mutagénèse par insertion de transposons. (2026). (3CR).
• BFT708 - Introduction aux méthodes et aux données génomiques. (2023-2025). (1CR).
• BFT710 - Introduction à la bio-informatique génomique. (2024-2025). (2CR).
• BFT402 - Outils bio-informatiques. (2023-2024). (2CR).
• BFT702 - Outils bio-informatiques. (2023-2024). (2CR).