June 02, 2025
Alexandre Pellan Cheng
Professeur
Department
Département de génie des systèmes
Degrees
B.Eng. (Polytechnique Montréal), PhD (Cornell University)
Office
A-3752
Research axe
- Health Technologies
Research areas
- Artificial intelligence
- Diagnostic devices
- Bioinformatics
- Computational biology
- DNA sequencing
Publications
- A. P. Cheng, P. Burnham, M. P. Cheng, K. Chen, D. Dadhania, W. Gu, J. R. Lee, J. S. Lenz, F. M. Marty, J. L. Orejas, E. Silverman, M. Suthanthiran, K. M. Timblin, J. Ritz, I. De Vlaminck. 2020 « Cell-free DNA tissues-of-origin profiling to monitor infectious and immune-related disease ». Affiche présentée lors de la conférence : American Society of Human Genetics Annual Meeting (Online, Oct. 27-30, 2020)
- Alexandre P. Cheng. 2020 « A cell-free DNA metagenomic sequencing assay to simultaneously profile infection and tissue damage ». Affiche présentée lors de la conférence : Biology of Genomes (Virtual, May 05-08, 2020)
- Alexandre Pellan Cheng, Adam J. Widman, Anushri Arora, Itai Rusinek, Aaron Sossin, Srinivas Rajagopalan, Nicholas Midler, William F. Hooper, Rebecca M. Murray, Daniel Halmos, Theophile Langanay, Hoyin Chu, Giorgio Inghirami, Catherine Potenski, Soren Germer, Melissa Marton, Dina Manaa, Adrienne Helland, Rob Furatero, Jaime McClintock, Lara Winterkorn, Zoe Steinsnyder, Yohyoh Wang, Asrar I. Alimohamed, Murtaza S. Malbari, Ashish Saxena, Margaret K. Callahan, Dennie T. Frederick, Lavinia Spain, Michael Sigouros, Jyothi Manohar, Abigail King, David Wilkes, John Otilano, Olivier Elemento, Juan Miguel Mosquera, Ariel Jaimovich, Doron Lipson, Samra Turajlic, Michael C. Zody, Nasser K. Altorki, Jedd D. Wolchok, Michael A. Postow, Nicolas Robine, Bishoy M. Faltas, Genevieve Boland, Dan A. Landau. 2025 « Error-corrected flow-based sequencing at whole-genome scale and its application to circulating cell-free DNA profiling ». Nature Methods
- Liz-Audrey Kounatse Djomnang, Carol Li, Omary Mzava, Alexandre Pellan Cheng, Adrienne Chang, Joan Sesing Lenz, Manikkam Suthanthiran, John R. Lee, Darshana M. Dadhania, Iwijn De Vlaminck. 2024 « A quantitative comparison of urine centrifugation and filtration for the isolation and analysis of urinary nucleic acid biomarkers ». Scientific Reports vol. 14 , nº 1
- Adam J. Widman, Minita Shah, Amanda Frydendahl, Daniel Halmos, Cole C. Khamnei, Nadia Øgaard, Srinivas Rajagopalan, Anushri Arora, Aditya Deshpande, William F. Hooper, Jean Quentin, Jake Bass, Mingxuan Zhang, Theophile Langanay, Laura Andersen, Zoe Steinsnyder, Will Liao, Mads Heilskov Rasmussen, Tenna Vesterman Henriksen, Sarah Østrup Jensen, Jesper Nors, Christina Therkildsen, Jesus Sotelo, Ryan Brand, Joshua S. Schiffman, Ronak H. Shah, Alexandre Pellan Cheng, Colleen Maher, Lavinia Spain, Kate Krause, Dennie T. Frederick, Wendie den Brok, Caroline Lohrisch, Tamara Shenkier, Christine Simmons, Diego Villa, Andrew J. Mungall, Richard Moore, Elena Zaikova, Viviana Cerda, Esther Kong, Daniel Lai, Murtaza S. Malbari, Melissa Marton, Dina Manaa, Lara Winterkorn, Karen Gelmon, Margaret K. Callahan, Genevieve Boland, Catherine Potenski, Jedd D. Wolchok, Ashish Saxena, Samra Turajlic, Marcin Imielinski, Michael F. Berger, Sam Aparicio, Nasser K. Altorki, Michael A. Postow, Nicolas Robine, Claus Lindbjerg Andersen, Dan A. Landau. 2024 « Ultrasensitive plasma-based monitoring of tumor burden using machine-learning-guided signal enrichment ». Nature Medicine vol. 30 , nº 6. p. 1655-1666
- Conor J. Loy, Alicia Sotomayor-Gonzalez, Venice Servellita, Jenny Nguyen, Joan Lenz, Sanchita Bhattacharya, Meagan E. Williams, Alexandre P. Cheng, Andrew Bliss, Prachi Saldhi, Noah Brazer, Jessica Streithorst, William Suslovic, Charlotte J. Hsieh, Burak Bahar, Nathan Wood, Abiodun Foresythe, Amelia Gliwa, Kushmita Bhakta, Maria A. Perez, Laila Hussaini, Evan J. Anderson, Ann Chahroudi, Meghan Delaney, Atul J. Butte, Roberta L. DeBiasi, Christina A. Rostad, Iwijn De Vlaminck, Charles Y. Chiu. 2023 « Nucleic acid biomarkers of immune response and cell and tissue damage in children with COVID-19 and MIS-C ». Cell Reports Medicine vol. 4 , nº 6
- Philip Burnham, Fanny Chen, Alexandre P. Cheng, Vesh Srivatana, Lisa T. Zhang, Emmanuel Edusei, Shady Albakry, Brittany Botticelli, Xunxi Guo, Amanda Renaghan, Jeffrey Silberzweig, Darshana M. Dadhania, Joan S. Lenz, Michael Heyang, Iliyan D. Iliev, Joshua A. Hayden, Lars F. Westblade, Iwijn De Vlaminck, John R. Lee. 2022 « Peritoneal effluent cell-free DNA sequencing in peritoneal dialysis patients with and without peritonitis ». Kidney Medicine vol. 4 , nº 1
- Ramya Chandrasekaran, Colleen Mathieu, Rishi Sheth, Alexandre P. Cheng, David Fong, Robert McCormack, Hani El-Gabalawy, Suman Alishetty, Mikell Paige, Caroline D. Hoemann. 2022 « UDP-glucose dehydrogenase (UGDH) activity is suppressed by peroxide and promoted by PDGF in fibroblast-like synoviocytes: Evidence of a redox control mechanism ». PLoS ONE vol. 17 , nº 9
- Adrienne Chang, Omary Mzava, Joan S. Lenz, Alexandre P. Cheng, Philip Burnham, S. Timothy Motley, Crissa Bennett, John T. Connelly, Darshana M. Dadhania, Manikkam Suthanthiran, John R. Lee, Amy Steadman, Iwijn De Vlaminck. 2022 « Measurement biases distort cell-free DNA fragmentation profiles and define the sensitivity of metagenomic cell-free DNA sequencing assays ». Clinical Chemistry vol. 68 , nº 1. p. 163-171
- Omary Mzava, Alexandre Pellan Cheng, Adrienne Chang, Sami Smalling, Liz-Audrey Kounatse Djomnang, Joan Sesing Lenz, Randy Longman, Amy Steadman, Luis G. Gómez-Escobar, Edward J. Schenck, Mirella Salvatore, Michael J. Satlin, Manikkam Suthanthiran, John R. Lee, Christopher E. Mason, Darshana Dadhania, Iwijn De Vlaminck. 2022 « A metagenomic DNA sequencing assay that is robust against environmental DNA contamination ». Nature Communications vol. 13 , nº 1
- Alexandre Pellan Cheng, Matthew Pellan Cheng, Conor James Loy, Joan Sesing Lenz, Kaiwen Chen, Sami Smalling, Philip Burnham, Kaitlyn Marie Timblin, José Luis Orejas, Emily Silverman, Paz Polak, Francisco M. Marty, Jerome Ritz, Iwijn De Vlaminck. 2022 « Cell-free DNA profiling informs all major complications of hematopoietic cell transplantation ». Proceedings of the National Academy of Sciences of the United States of America vol. 119 , nº 4
- Alexandre P. Cheng, Dan A. Landau. 2021 « Lightning does strike twice: Leveraging phased variants to enhance minimal residual disease detection ». Med vol. 2 , nº 10. p. 1114-1116
- Alexandre Pellan Cheng, Matthew Pellan Cheng, Wei Gu, Joan Sesing Lenz, Elaine Hsu, Erwin Schurr, Guillaume Bourque, Mathieu Bourgey, Jerome Ritz, Francisco M. Marty, Charles Y. Chiu, Donald C. Vinh, Iwijn De Vlaminck. 2021 « Cell-free DNA tissues of origin by methylation profiling reveals significant cell, tissue, and organ-specific injury related to COVID-19 severity ». Med vol. 2 , nº 4. p. 411-422.e415
- Philip Burnham, Nardhy Gomez-Lopez, Michael Heyang, Alexandre Pellan Cheng, Joan Sesing Lenz, Darshana M. Dadhania, John Richard Lee, Manikkam Suthanthiran, Roberto Romero, Iwijn De Vlaminck. 2020 « Separating the signal from the noise in metagenomic cell-free DNA sequencing ». Microbiome vol. 8 , nº 1
- Matthew P. Cheng, Robyn S. Lee, Alexandre P. Cheng, Samuel De L’étoile-Morel, Koray Demir, Cedric P. Yansouni, Patrick Harris, Emily G. McDonald, Todd C. Lee. 2019 « Beta-lactam/beta-lactamase inhibitor therapy for potential ampC-producing organisms: A systematic review and meta-analysis ». Open Forum Infectious Diseases vol. 6 , nº 7
- Alexandre Pellan Cheng, Philip Burnham, John Richard Lee, Matthew Pellan Cheng, Manikkam Suthanthiran, Darshana M. Dadhania, Iwijn De Vlaminck. 2019 « A cell-free DNA metagenomic sequencing assay that integrates the host injury response to infection ». Proceedings of the National Academy of Sciences of the United States of America vol. 116 , nº 37. p. 18738-18744
- Matthew P. Cheng, Alexandre P. Cheng, Todd C. Lee. 2018 « The reply ». American Journal of Medicine vol. 131 , nº 4
- Samuel De L’Étoile-Morel, Matthew P. Cheng, Alexander P. Cheng, Emily G. McDonald, Todd C. Lee. 2018 « Piperacillin-tazobactam use in esbl escherichia coli bacteremia: Should reporting be revised? ». Journal of the Association of Medical Microbiology and Infectious Disease Canada vol. 3 , nº 1. p. 24-29
- Alexandre Pellan Cheng, Philip Burnham, Iwijn De Vlaminck. 2018 « Biopsy-free screening for glioma ». EMBO molecular medicine vol. 10 , nº 12
- David Fong, Pascal Grégoire-Gélinas, Alexandre P. Cheng, Tal Mezheritsky, Marc Lavertu, Sachiko Sato, Caroline D. Hoemann. 2017 « Lysosomal rupture induced by structurally distinct chitosans either promotes a type 1 IFN response or activates the inflammasome in macrophages ». Biomaterials vol. 129. p. 127-138
- Guillaume Butler-Laporte, Matthew P. Cheng, Alexandre P. Cheng, Emily G. McDonald, Todd C. Lee. 2016 « Using MRSA screening tests to predict methicillin resistance in Staphylococcus aureus bacteremia ». Antimicrobial Agents and Chemotherapy vol. 60 , nº 12. p. 7444-7448
- Matthew P. Cheng, Pierre René, Alexandre P. Cheng, Todd C. Lee. 2016 « Back to the future: Penicillin-susceptible staphylococcus aureus ». American Journal of Medicine vol. 129 , nº 12. p. 1331-1333
- Iwijn De Vlaminck, John Richard Lee, Philip Smith Burnham, Alexandre Pellan Cheng, Manikkam Suthanthiran, Darshana Dadhania. 2023-09-20 « Methods of detecting cell-free DNA in biological samples ». Brevet américain US 11,781,188.
- Alexandre Pellan Cheng. 2024 « WGS for sensitive ctDNA cancer monitoring ». Communication lors de la conférence : 13th CNAPS International Symposium on Circulating Nucleic Acids in Plasma and Serum (Graz, Austria, Mar. 04-06, 2024)
- A. P. Cheng, P. Burnham, D. Dadhania, J. R. Lee, M. Suthanthiran, I. De Vlaminck. 2018 « Distinguishing infection from infectious disease using methylation marks comprised within cell-free DNA ». Communication lors de la conférence : American Society of Human Genetics Annual Meeting (San Diego, CA, USA, Oct. 16-20, 2018)
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