Publications by authors named "Alexandre P Cheng"

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Large-scale single-cell phylogenetic mapping of clonal evolution in the human aging esophagus.
Tamara Prieto, Dennis J Yuan, John Zinno, Clayton Hughes, Nicholas Midler, Alexandre Pellan Cheng

bioRxiv· October 2025

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Paired plus-minus sequencing is an ultra-high throughput and accurate method for dual strand sequencing of DNA molecules.
Alexandre Pellan Cheng, Itai Rusinek, Aaron Sossin, Adam J Widman, Eti Meiri

bioRxiv· August 2025

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Error-corrected flow-based sequencing at whole-genome scale and its application to circulating cell-free DNA profiling.
Alexandre Pellan Cheng, Adam J Widman, Anushri Arora, Itai Rusinek, Aaron Sossin

Nat Methods· May 2025

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Ultrasensitive plasma-based monitoring of tumor burden using machine-learning-guided signal enrichment.
Adam J Widman, Minita Shah, Amanda Frydendahl, Daniel Halmos, Cole C Khamnei, Alexandre Pellan Cheng

Nat Med· June 2024

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A quantitative comparison of urine centrifugation and filtration for the isolation and analysis of urinary nucleic acid biomarkers.
Liz-Audrey Kounatse Djomnang, Carol Li, Omary Mzava, Alexandre Pellan Cheng, Adrienne Chang

Sci Rep· May 2024

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Nucleic acid biomarkers of immune response and cell and tissue damage in children with COVID-19 and MIS-C.
Conor J Loy, Alicia Sotomayor-Gonzalez, Venice Servellita, Jenny Nguyen, Joan Lenz, Alexandre P Cheng

Cell Rep Med· June 2023

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UDP-glucose dehydrogenase (UGDH) activity is suppressed by peroxide and promoted by PDGF in fibroblast-like synoviocytes: Evidence of a redox control mechanism.
Ramya Chandrasekaran, Colleen Mathieu, Rishi Sheth, Alexandre P Cheng, David Fong

PLoS One· September 2022

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A metagenomic DNA sequencing assay that is robust against environmental DNA contamination.
Omary Mzava, Alexandre Pellan Cheng, Adrienne Chang, Sami Smalling, Liz-Audrey Kounatse Djomnang

Nat Commun· July 2022

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Cell-free DNA profiling informs all major complications of hematopoietic cell transplantation.
Alexandre Pellan Cheng, Matthew Pellan Cheng, Conor James Loy, Joan Sesing Lenz, Kaiwen Chen

Proc Natl Acad Sci U S A· January 2022

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Peritoneal Effluent Cell-Free DNA Sequencing in Peritoneal Dialysis Patients With and Without Peritonitis.
Philip Burnham, Fanny Chen, Alexandre P Cheng, Vesh Srivatana, Lisa T Zhang

Kidney Med· January 2022

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Measurement Biases Distort Cell-Free DNA Fragmentation Profiles and Define the Sensitivity of Metagenomic Cell-Free DNA Sequencing Assays.
Adrienne Chang, Omary Mzava, Joan S Lenz, Alexandre P Cheng, Philip Burnham

Clin Chem· December 2021

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A metagenomic DNA sequencing assay that is robust against environmental DNA contamination.
Omary Mzava, Alexandre Pellan Cheng, Adrienne Chang, Sami Smalling, Liz-Audrey Djomnang Kounatse

bioRxiv· November 2021

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Lightning does strike twice: leveraging phased variants to enhance minimal residual disease detection.
Alexandre P Cheng, Dan A Landau

Med· October 2021

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Cell-free DNA tissues of origin by methylation profiling reveals significant cell, tissue, and organ-specific injury related to COVID-19 severity.
Alexandre Pellan Cheng, Matthew Pellan Cheng, Wei Gu, Joan Sesing Lenz, Elaine Hsu

Med· April 2021

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Cell-Free DNA in Blood Reveals Significant Cell, Tissue and Organ Specific injury and Predicts COVID-19 Severity.
Alexandre Pellan Cheng, Matthew Pellan Cheng, Wei Gu, Joan Sesing Lenz, Elaine Hsu

medRxiv· July 2020

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Separating the signal from the noise in metagenomic cell-free DNA sequencing.
Philip Burnham, Nardhy Gomez-Lopez, Michael Heyang, Alexandre Pellan Cheng, Joan Sesing Lenz

Microbiome· February 2020

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A cell-free DNA metagenomic sequencing assay that integrates the host injury response to infection.
Alexandre Pellan Cheng, Philip Burnham, John Richard Lee, Matthew Pellan Cheng, Manikkam Suthanthiran

Proc Natl Acad Sci U S A· September 2019

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Beta-Lactam/Beta-Lactamase Inhibitor Therapy for Potential AmpC-Producing Organisms: A Systematic Review and Meta-Analysis.
Matthew P Cheng, Robyn S Lee, Alexandre P Cheng, Samuel De L'étoile-Morel, Koray Demir

Open Forum Infect Dis· July 2019

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Biopsy-free screening for glioma.
Alexandre Pellan Cheng, Philip Burnham, Iwijn De Vlaminck

EMBO Mol Med· December 2018

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The Reply.
Matthew P Cheng, Alexandre P Cheng, Todd C Lee

Am J Med· April 2018

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Lysosomal rupture induced by structurally distinct chitosans either promotes a type 1 IFN response or activates the inflammasome in macrophages.
David Fong, Pascal Grégoire-Gélinas, Alexandre P Cheng, Tal Mezheritsky, Marc Lavertu

Biomaterials· June 2017

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Back to the Future: Penicillin-Susceptible Staphylococcus aureus.
Matthew P Cheng, Pierre René, Alexandre P Cheng, Todd C Lee

Am J Med· December 2016

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Using MRSA Screening Tests To Predict Methicillin Resistance in Staphylococcus aureus Bacteremia.
Guillaume Butler-Laporte, Matthew P Cheng, Alexandre P Cheng, Emily G McDonald, Todd C Lee

Antimicrob Agents Chemother· December 2016

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