Pierre-Étienne Jacques

Prix et distinctions

• (2026) Bourse chercheur-boursier Senior - 269,932 $. Fonds de recherche du Québec - Santé (FRQS). (Distinction).
• (2022) Bourse chercheur-boursier Junior 2 - 309,891 $. Fonds de recherche du Québec - Santé (FRQS). (Distinction).
• (2018) Bourse chercheur-boursier Junior 1 - 277,526 $. Fonds de recherche du Québec - Santé (FRQS). (Distinction).
• (2009) Postdoctoral Fellowship - 57,000 $. CIHR supported IRCM Training Program in Cancer Research. (Distinction).
• (2004) Ph.D. Scholarship - 53,333 $. Fonds de recherche du Québec - Nature et technologies (FRQNT). (Distinction).

Financement

• Subvention. (Obtenu). Cochercheur. Systematic identification of synthetic interactions in bacteria towards the next-generation of antibiotics. Instituts de Recherche en Santé du Canada (IRSC). Project Grant. 841 500 $. (2023-2028)
• Bourse de recherche. (Obtenu). Chercheur principal. Development of bioinformatics platforms and tools to facilitate the analysis of epigenomics and genetics datasets. Fonds de recherche du Québec - Santé (FRQS). Chercheur-boursier Senior. 269 932 $. (2022-2026)
• Subvention. (Obtenu). Cochercheur. SecureData4Health. Fondation Canadienne pour l'Innovation (FCI). Innovation. 20 800 000 $. (2021-2026)
• Subvention. (Obtenu). Cochercheur. Deciphering the CTD code of RNA polymerase II in healthy and cancer cells. Fonds de recherche du Québec - Santé (FRQS). Programme bilatéral de recherche collaborative Québec – Fédération Wallonie-Bruxelles. 300 000 $. (2022-2025)
• Subvention. (Obtenu). Chercheur principal. Identification and integration of systems level microbial synthetic lethality interactions to enhance genome design. Conseil de Recherches en Sciences Naturelles et Génie du Canada (CRSNG). Subventions à la découverte. 180 000 $. (2020-2025)
• Subvention. (Obtenu). Cochercheur. Engineering of a probiotic bacterium for precise microbiome editing. Instituts de Recherche en Santé du Canada (IRSC). Project Grant. 814 725 $. (2019-2024)
• Subvention. (Obtenu). Cochercheur. Epithelial cell-specific role of SOCS1 in prevention of intestinal inflammation. Instituts de Recherche en Santé du Canada (IRSC). Project Grant. 787 950 $. (2019-2024)
• Subvention. (Obtenu). Cochercheur. Mutational signatures: predictors of the immunotherapy response in colorectal cancer. Institut de Recherche sur le Cancer de l’Université de Sherbrooke (IRCUS). Application génomique en oncologie. 25 000 $. (2023-2023)
• Subvention. (Obtenu). Cochercheur. Genetic instability of the haploid male germ cells. Instituts de Recherche en Santé du Canada (IRSC). Project Grant. 669 376 $. (2018-2023)
• (Obtenu). Chercheur principal. Advanced Research Computing Resource Allocation. Compute Canada. Resource Allocation Competition. 182 084 $. (2022-2023)
• Subvention. (Obtenu). Chercheur principal. Expansion of GenAP towards multiple single-cell modalities. CANARIE Inc (Ottawa, ON). Research Software Program. 250 000 $. (2020-2023)
• Bourse de recherche. (Terminé). Chercheur principal. Development of bioinformatics platforms and tools to facilitate the analysis of epigenomics and genetics datasets. Fonds de recherche du Québec - Santé (FRQS). Chercheur-boursier Junior 2. 309 891 $. (2018-2022)
• (Terminé). Chercheur principal. Advanced Research Computing Resource Allocation. Compute Canada. Resource Allocation Competition. 179 240 $. (2021-2022)
• Subvention. (Terminé). Cochercheur. Canadian Center for Computational Genomics (C3G). Génome Canada. Genomics Technology Platforms. 7 052 577 $. (2017-2022)
• Subvention. (Terminé). Candidat principal. Bourse de support à la publication. Centre de Recherche du Centre Hospitalier de l'Université de Sherbrooke Inc. (CRCHUS) (Sherbrooke, QC). Concours pour support à la publication. 2 000 $. (2021-2021)
• Subvention. (Terminé). Cochercheur. An integrative platform for metabolomics and systems biology. Génome Canada. Bioinformatics and Computational Biology (B/CB) Competition. 1 094 607 $. (2018-2021)
• (Terminé). Chercheur principal. Advanced Research Computing Resource Allocation. Compute Canada. Resource Allocation Competition. 142 629 $. (2020-2021)
• Subvention. (Terminé). Cochercheur. Defining a DNA Replication Stress Mutation Signature to personalize cancer treatments. Centre de Recherche du Centre Hospitalier de l'Université de Sherbrooke Inc. (CRCHUS) (Sherbrooke, QC). Programme d’aide de financement interne. 25 000 $. (2019-2021)
• Subvention. (Terminé). Chercheur principal. Generalization of GenAP toward the growing single-cell and metabolomic communities. CANARIE Inc (Ottawa, ON). Research Software Program. 224 627 $. (2018-2020)
• Subvention. (Terminé). Cochercheur. Plateforme intégrée pour l'ingénierie des génomes. Fonds de recherche du Québec - Nature et technologies (FRQNT). Équipe. 199 730 $. (2017-2020)
• Subvention. (Terminé). Cochercheur. Évaluation du potentiel d'une approche de thérapie épigénétique dans un contexte d'obésité nutritionnelle. Centre de Recherche du Centre Hospitalier de l'Université de Sherbrooke Inc. (CRCHUS) (Sherbrooke, QC). Programme projets structurants. 75 000 $. (2019-2020)
• Subvention. (Terminé). Cochercheur. CanDIG: Canadian Distributed cyber-Infrastructure for Genomics. Fondation Canadienne pour l'Innovation (FCI). Cyber-infrastruture. 4 900 000 $. (2016-2020)
• Subvention. (Terminé). Cochercheur. Engineering of a probiotic bacterium for precise microbiome editing. Instituts de Recherche en Santé du Canada (IRSC). Project Grant - Priority Announcement: Antimicrobial Resistance. 100 000 $. (2018-2019)
• Subvention. (Terminé). Cochercheur. Genetic instability of the haploid male germ cells. Instituts de Recherche en Santé du Canada (IRSC). Project Grant. 100 000 $. (2018-2019)

Publications

Articles de revue

• Champie A*, De Grandmaison A, Jeanneau S*, Grenier F, Jacques P-É, Rodrigue S. (2023). Enabling low-cost and robust essentiality studies with high-throughput transposon mutagenesis (HTTM). PloS one 18 (4), e0283990. (Article publié).
• Fafard-Couture É*, Jacques P-É@, Scott MS@. (2023). Motif conservation, stability, and host gene expression are the main drivers of snoRNA expression across vertebrates. Genome research (Article publié).
• Casimir L* , Zimmer S* , Racine-Brassard F* , Jacques P-É@, Maréchal A@. (2023). The mutational impact of Illudin S on human cells. DNA repair 122 103433. (Article publié).
• Légaré C , Desgagné V , Thibeault K , White F* , Clément AA , Poirier C , Luo ZC , Scott MS , Jacques PÉ , Perron P , Guérin R , Hivert MF , Bouchard L. (2022). First Trimester Plasma MicroRNA Levels Predict Risk of Developing Gestational Diabetes Mellitus. Frontiers in endocrinology 13 928508. (Article publié).
• Légaré C, Desgagné V, Poirier C, Thibeault K, White F*, Clément AA, Scott MS, Jacques PÉ, Perron P, Guérin R, Hivert MF, Bouchard L. (2022). First trimester plasma microRNAs levels predict Matsuda Index-estimated insulin sensitivity between 24th and 29th week of pregnancy. BMJ Open Diabetes Research & Care 10 (2), e002703. (Article publié).
• Légaré C, Clément AA, Desgagné V, Thibeault K, White F*, Guay SP, Arsenault BJ, Scott MS, Jacques PÉ, Perron P, Guérin R, Hivert MF, Bouchard L. (2022). Human plasma pregnancy-associated miRNAs and their temporal variation within the first trimester of pregnancy. Reproductive Biology and Endocrinology 20 (1), 14. (Article publié).
• Jeanneau S*, Jacques P-É@, Lafontaine DA@. (2022). Investigating the role of RNA structures in transcriptional pausing using in vitro assays and in silico analyses. RNA biology 19 (1), 916-927. (Article publié).
• Thibeault K, Légaré C, Desgagné V, White F*, Clément AA, Scott MS, Jacques P-É, Guérin R, Perron P, Hivert MF, Bouchard L. (2022). Maternal Body Mass Index Is Associated with Profile Variation in Circulating MicroRNAs at First Trimester of Pregnancy. Biomedicines 10 (7), 1726. (Article publié).
• Dursi JL, Bozoky Z, de Borja R, Li J, Bujold D, Lipski A, Rashid SF, Sethi A, Memon N, Naidoo D, Coral-Sasso F, Wong M, Quirion P-O, Lu Z, Agarwal S, Pavlov K, Ponomarev A, Husic M, Pace K, Palmer SL, Grover SA, Hakgor S, Siu LL, Malkin D, Virtanen C, Pugh TJ, Jacques P-É, Joly Y, Jones SJM, Bourque G, Brudno M. (2021). CanDIG: Federated network across Canada for multi-omic and health data discovery and analysis. Cell Genomics 1 (2), 100033. (Article publié).
• Groleau M* , White F* , Cardenas A , Perron P , Hivert MF , Bouchard L , Jacques PÉ @. (2021). Comparative epigenome-wide analysis highlights placenta-specific differentially methylated regions. Epigenomics 13 (5), 357-368. (Article publié).
• Lachance JC*, Matteau D*, Brodeur J, Lloyd CJ, Mih N, King ZA, Knight TF, Feist AM, Monk JM, Palsson BO, Jacques PÉ, Rodrigue S. (2021). Genome-scale metabolic modeling reveals key features of a minimal gene set. Molecular systems biology 17 (7), e10099. (Article publié).
• Smith-Peter E, Séguin DL, St-Pierre É, Sekulovic O, Jeanneau S*, Tremblay-Tétreault C, Lamontagne AM, Jacques PÉ, Lafontaine DA, Fortier LC. (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 18 699-710. (Article publié).
• Pang Z, Chong J, Zhou G, de Lima Morais DA*, Chang L, Barrette M*, Gauthier C*, Jacques PÉ, Li S, Xia J. (2021). MetaboAnalyst 5.0: narrowing the gap between raw spectra and functional insights. Nucleic Acids Research 49 W388-W396. (Article publié).
• Langlois JP , Millette G , Guay I , Dubé-Duquette A , Chamberland S , Jacques PÉ , Rodrigue S , Bouarab K , Marsault É , Malouin F. (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 11 805. (Article publié).
• Matteau D* , Lachance JC* , Grenier F , Gauthier S , Daubenspeck JM , Dybvig K , Garneau D , Knight TF , Jacques PÉ , Rodrigue S. (2020). Integrative characterization of the near-minimal bacterium Mesoplasma florum. Molecular systems biology 16 (12), e9844. (Article publié).
• Thuriot F , Gravel E , Buote C* , Doyon M , Lapointe E , Marcoux L , Larue S , Nadeau A , Chénier S , Waters PJ , Jacques PÉ , Gravel S , Lévesque S. (2020). Molecular diagnosis of muscular diseases in outpatient clinics: A Canadian perspective. Neurology Genetics 6 (2), e408. (Article publié).
• Yague-Sanz C , Vanrobaeys Y* , Fernandez R , Duval M , Larochelle M , Beaudoin J , Berro J , Labbé S , Jacques PÉ , Bachand F. (2020). Nutrient-dependent control of RNA polymerase II elongation rate regulates specific gene expression programs by alternative polyadenylation. Genes & development 34 (13-14), 883-897. (Article publié).
• Lachance JC*, Lloyd CJ, Monk JM, Yang L, Sastry AV, Seif Y, Palsson BO, Rodrigue S, Feist AM, King ZA @, Jacques PÉ @. (2019). BOFdat: Generating biomass objective functions for genome-scale metabolic models from experimental data. PLoS Computational Biology 15 (4), e1006971. (Article publié).
• Laperle J*, Hébert-Deschamps S*, Raby J*, Morais DAL*, Barrette M*, Bujold D, Bastin C*, Robert MA*, Harel M*, Nordell-Markovits A*, Veilleux A, Bourque G, Jacques PÉ @. (2019). The epiGenomic Efficient Correlator (epiGeEC) tool allows fast comparison of private datasets with thousands of public epigenomic datasets. Bioinformatics 35 (4), 674-676. (Article publié).
• Thuriot F , Buote C* , Gravel E , Chénier S , Désilets V , Maranda B , Waters PJ , Jacques PÉ , Lévesque S. (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 20 (9), 942-949. (Article publié).
• Larochelle M, Robert M-A*, Jacques PÉ @, Bachand F@. (2018). Common mechanism of transcription termination at coding and noncoding RNA genes in fission yeast. Nature Communication 9 (1), 4364. (Article publié).
• Bélanger S* , Marchand S , Jacques PÉ , Meyers B , Belzile F. (2018). Differential Expression Profiling of Microspores During the Early Stages of Isolated Microspore Culture Using the Responsive Barley Cultivar Gobernadora. G3 (Bethesda, Md.) 8 (5), 1603-1614. (Article publié).
• Lamontagne Boulet M , Isabelle C , Guay I , Brouillette E , Langlois JP , Jacques PÉ , Rodrigue S , Brzezinski R , Beauregard PB , Bouarab K , Boyapelly K , Boudreault PL , Marsault É , Malouin F. (2018). Staphylococcus aureusTomatidine, a lead antibiotic molecule that targets ATP synthase subunit C. Antimicrobial agents and chemotherapy 62 (6), e02197-1. (Article publié).
• Grégoire MC , Leduc F , Morin MH , Cavé T , Arguin M , Richter M , Jacques PÉ , Boissonneault G. (2018). The DNA double-strand "breakome" of mouse spermatids. Cellular and molecular life sciences 75 (15), 2859-2872. (Article publié).
• Lashgari A , Millau JF , Jacques PÉ , Gaudreau L. (2017). Global inhibition of transcription causes an increase in histone H2A.Z incorporation within gene bodies. Nucleic acids research 45 (22), 12715-12722. (Article publié).
• Meteignier LV , El Oirdi M , Cohen M , Barff T , Matteau D* , Lucier JF* , Rodrigue S , Jacques PÉ , Yoshioka K , Moffett P. (2017). Translatome analysis of an NB-LRR immune response identifies important contributors to plant immunity in Arabidopsis. Journal of experimental botany 68 (9), 2333-2344. (Article publié).
• Lévesque S , Auray-Blais C , Gravel E , Boutin M , Dempsey-Nunez L , Jacques PE , Chenier S , Larue S , Rioux MF , Al-Hertani W , Nadeau A , Mathieu J , Maranda B , Désilets V , Waters PJ , Keutzer J , Austin S , Kishnani P. (2016). Diagnosis of late-onset Pompe disease and other muscle disorders by next-generation sequencing. Orphanet journal of rare diseases 11 (1), 8. (Article publié).
• Bujold B, de Lima Morais DA, Gauthier C, Côté C, Caron M, Kwan T, Chen KC, Laperle J*, Nordell-Markovits A*, Pastinen T, Caron B, Veilleux A, Jacques PÉ, Bourque G. (2016). The IHEC Data Portal: a resource for discovering, analysing and sharing epigenomics data. Cell Systems S2405-4712 (16), 30362-3. (Article publié).
• Breeze CE, Paul DS, van Dongen J, Butcher LM, Ambrose JC, Barrett JE, Lowe R, Rakyan VK, Iotchkova V, Frontini M, Downes K, Ouwehand WH, Laperle J*, Jacques P-É, Bourque G, Bergmann A, Siebert R, Vellenga E, Saeed S, Matarese F, Martens JHA, Stunnenberg HG, Teschendorff AE, Herrero J, Birney E, Dunham I, Beck S. (2016). eFORGE: a tool for identifying cell type-specific signal in epigenomic data. Cell Reports 17 (8), 2137-2150. (Article publié).

Chapitres de livre

• Brunelle M*, S Rodrigue, Jacques PÉ, Gévry N. (2017). High-Resolution Genome-Wide Mapping of Nucleosome Positioning and Occupancy Level Using Paired-End Sequencing Technology. Leblanc BP, Rodrigue S. Methods in molecular biology - DNA-Protein Interactions - Principles and Protocols (1528, 229-243). États-Unis d'Amérique : Springer Protocols. (Article publié).
• Brunelle M*, Coulombe C*, Poitras C, Robert MA, Markovits AN*, Robert F, Jacques PÉ@. (2015). Aggregate and Heatmap Representations of Genome-Wide Localization Data Using VAP, a Versatile Aggregate Profiler. Leblanc BP, Rodrigue S. Methods in molecular biology - DNA-Protein Interactions - Principles and Protocols (Fourth, 1334, 273-98). États-Unis d'Amérique : Springer Protocols. (Article publié).

Articles de conférence

• Frosi G*, Raby J*, Jacques P-É@. (2022). Prediction of metadata from epigenomic data enabled validating/correcting/complementing IHEC EpiAtlas project and over 20,000 ChIP-Seq uniformly reprocessed public datasets. International Human Epigenome Consortium (IHEC) Annual Meeting. (Article publié).
• White F*, Groleau M*, Hivert MF, Bouchard L, Jacques P-É. (2021). Identification and application of circulating microRNA expression quantitative trait loci (eQTL) at the first trimester of pregnancy. ISMB/ECCB (Intelligent Systems for Molecular Biology & European Conference on Computational Biology). (Article publié).
• Raby J*, Laperle* J, Hébert-Deschamps S*, Jacques PÉ@. (2019). Epigenomic labeling prediction using machine learning on IHEC datasets. International Human Epigenome Consortium (IHEC) Annual Meeting. (Article publié).
• Lachance JC*, Lloyd CJ, Monk JM, Yang L, Sastry A, Seif Y, Palsson BO, Rodrigue S, Feist AM, King ZA@, Jacques P-É@. (2018). BOFdat: generating Biomass Objective Function for genome-scale metabolic models from experimental data. Research in Computational Molecular Biology (RECOMB) Comparative Genomics Annual Meeting. (Article publié).
• Laperle J*, Hébert-Deschamps S*, Jacques PÉ @. (2018). Epigenomic labeling prediction. International Human Epigenome Consortium (IHEC) Annual Meeting. (Article publié).
• Groleau M*, Bouchard L, Hivert MF@, Jacques P-É@. (2018). Genome-wide comparison of DNA methylation patterns between umbilical cord blood and placenta. Research in Computational Molecular Biology (RECOMB) Comparative Genomics Annual Meeting. (Article publié).
• Zimmer S*, Maréchal A@, Jacques P-É@. (2018). Mutational signatures of alternative DNA repair pathways in human cancer cells. Research in Computational Molecular Biology (RECOMB) Comparative Genomics Annual Meeting. (Article publié).
• White F*, Lévesque S@, Jacques P-É@. (2018). Outil bio-informatique de prédiction de l’ethnicité d’un individu à partir d’une liste de variants génétiques. Journée Phare, Congrés québécois en sciences de la santé. (Article publié).
• Bioteau A*, White F*, Jacques P-É@, Burrus V@. (2018). Study of conservation and diversity of mobile genomic islands in Vibrionaceae: detection, identification and classification. Research in Computational Molecular Biology (RECOMB) Comparative Genomics Annual Meeting. (Article publié).
• Nadeau JF*, Robert1 MA*, Jacques P-É. (2018). Using public data to conduct an epigenomic comparative study between species. Research in Computational Molecular Biology (RECOMB) Comparative Genomics Annual Meeting. (Article publié).
• Larochelle M, Robert M-A*, Hébert JN, Bachand F@, Jacques PÉ@. (2017). A universal mode of 3’ end processing and transcription termination for fission yeast RNA polymerase II-transcribed genes. RiboClub. (Article publié).
• Bélanger S*, Marchand S, Jacques P-É, Belzile F. (2016). Androgenic switch:changes in gene expression during early stages of androgenesis in thebarley microspore. Plant and Animal Genome Conference. (Article publié).
• Bujold D, Gauthier C, Busche S, Caron M, Nordell-Markovits A*, Morais D, Barrette M, Goerner-Potvin P, Kwan T, Pastinen T, Veilleux A, Jacques P-É, and Bourque G. (2016). Integrative Visualization and Distribution of Epigenomics Datasets with the IHEC Data Portal. International Human Epigenome Consortium (IHEC) Annual Meeting. (Article publié).
• Laperle J*, Robert M-A*, Bujold B, de Lima Morais DA, Barrette M, Bastin C*, Harel M*, Morin C*, Bourque G, Jacques P-É. (2016). Using the IHEC data through the Genomic Efficient Correlator (GeEC) tool. International Human Epigenome Consortium (IHEC) Annual Meeting. (Article publié).
• Laperle J*, Nordell-Markovits A*, Robert M-A*, Bujold B, de Lima Morais DA, Barrette M, Bourque G, Jacques P-É. (2015). Large-scale correlation of epigenomics data. Genome Informatics. (Article publié).
• Laperle J*, Nordell-Markovits A*, Robert M-A*, Bujold B, de Lima Morais DA, Barrette M, Bourque G, Jacques P-É. (2015). The Genomic Efficient Correlator (GeEC) tool. International Human Epigenome Consortium (IHEC) Annual Meeting. (Article publié).
• Buote C*, Thuriot F*, Edmont M, Gravel E, Trakadis Y, Theriault JF, Larochelle H, Maranda B, Chénier S, Jacques P-É and Lévesque S. (2014). PHENOVAR: a phenotype-driven approach to facilitate routine utilization of clinical exome sequencing for the diagnosis of polymalformative syndromes. Annual Meeting of the American Society of Human Genetics. (Article publié).
• Jacques P-É, 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, and Bourque G. (2014). The Genetics and Genomics Analysis Platform (GenAP). Biological Data Science. (Article publié).
• Brunelle M*, Nordell-Markovits A*, Rodrigue S, Lupien M, Jacques P-É, and Gévry N. (2014). The histone variant H2A.Z is an important regulator of enhancer activity. Histone variants meeting organized by European Molecular Biology Organization (EMBO). (Article publié).
• Coulombe C*, Poitras C, Nordell-Markovits A*, Brunelle M*, Lavoie M-A*, Robert F, Jacques P-É. (2014). The versatile aggregate profiler (VAP) for efficient genome-wide data representation and discovery. Big Data in Biology organized by Keystone Symposia. (Article publié).
• Brunelle M*, Nordell-Markovits A*, Lupien M, Rodrigue S, Jacques P-É, and Gévry N. (2013). A genome-wide study of the transcriptional and epigenetic functions of H2A.Z at distal ERa-enhancers. EMBO Conference Series, Chromatin and Epigenetics. (Article publié).
• Jacques P-É, Jeyakani J, Bourque G. (2012). Tissue-specific activation of transposons-derived sequences in normal and cancer cells. Epigenetics, Chromatin & Transcriptionorganized by Cold Spring Harbor Asia. (Article publié).
• Jacques P-É, Jeyakani J, Bourque G. (2011). Reactivation of genomic repeat subfamilies in cancer. Changing Landscape of the Cancer Genome organized by Keystone Symposia. (Article publié).
• many others!.