Lee, John Richard

Publications

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selected publications

Evaluation of Immunocompetence and Biomarkers of Tolerance in Chimeric and Immunosuppression-free Kidney Allograft Recipients. Transplantation. 2023 Academic Article GET IT
Case Commentary: Unlocking the Potential of Bacteriophage to Prevent Recurrent Urinary Tract Infections after Kidney Transplantation. Antimicrobial agents and chemotherapy. 2023 Academic Article GET IT
KIBRA upregulation increases susceptibility to podocyte injury and glomerular disease progression. JCI insight. 2023 Academic Article GET IT
A Distinct Nasal Microbiota Signature in Peritoneal Dialysis Patients. medRxiv : the preprint server for health sciences. 2023 Article GET IT
Characteristics of natural immunity to SARS-CoV-2 over time in wait-listed dialysis patients and recent kidney transplant recipients. Nephrology, dialysis, transplantation : official publication of the European Dialysis and Transplant Association - European Renal Association. 2022 Letter GET IT
A metagenomic DNA sequencing assay that is robust against environmental DNA contamination. Nature communications. 2022 Academic Article GET IT
Times cited: 5
Detection of infiltrating fibroblasts by single-cell transcriptomics in human kidney allografts. PloS one. 2022 Academic Article GET IT
Times cited: 4
Serum MicroRNA Transcriptomics and Acute Rejection or Recurrent Hepatitis C Virus in Human Liver Allograft Recipients: A Pilot Study. Transplantation. 2022 Academic Article GET IT
Times cited: 6
A Community-Based Education Program for Overactive Bladder in a Predominantly Minority Older Female Population: A Pilot Study. Urologia internationalis. 2022 Academic Article GET IT
Times cited: 1
The gut, vaginal, and urine microbiome in overactive bladder: a systematic review. International urogynecology journal. 2022 Academic Article GET IT
Times cited: 3
Metagenomics combined with activity-based proteomics point to gut bacterial enzymes that reactivate mycophenolate. Gut microbes. 2022 Academic Article GET IT
Times cited: 4
Measurement Biases Distort Cell-Free DNA Fragmentation Profiles and Define the Sensitivity of Metagenomic Cell-Free DNA Sequencing Assays. Clinical chemistry. 2021 Academic Article GET IT
Times cited: 3
New insights into the microbiome in kidney transplantation. Current opinion in organ transplantation. 2021 Review GET IT
Times cited: 3
Deep significance clustering: a novel approach for identifying risk-stratified and predictive patient subgroups. Journal of the American Medical Informatics Association : JAMIA. 2021 Academic Article GET IT
Times cited: 3
A metagenomic DNA sequencing assay that is robust against environmental DNA contamination. bioRxiv : the preprint server for biology. 2021 Article GET IT
Peritoneal Effluent Cell-Free DNA Sequencing in Peritoneal Dialysis Patients With and Without Peritonitis. Kidney medicine. 2021 Academic Article GET IT
Times cited: 2
Kidney Allograft Function Is a Confounder of Urine Metabolite Profiles in Kidney Allograft Recipients. Metabolites. 2021 Academic Article GET IT
Times cited: 974
FOXP3 mRNA Profile Prognostic of Acute T Cell-mediated Rejection and Human Kidney Allograft Survival. Transplantation. 2021 Academic Article GET IT
Times cited: 7
Deep sequencing of DNA from urine of kidney allograft recipients to estimate donor/recipient-specific DNA fractions. PloS one. 2021 Academic Article GET IT
Gut microbiota profiles and fecal beta-glucuronidase activity in kidney transplant recipients with and without post-transplant diarrhea. Clinical transplantation. 2021 Academic Article GET IT
Times cited: 10
The Potential Role of the Gut Microbiota in Kidney Transplantation. Kidney360. 2021 Academic Article GET IT
Times cited: 53
Colonization with Gastrointestinal Pathogens Prior to Hematopoietic Cell Transplantation and Associated Clinical Implications. Transplantation and cellular therapy. 2021 Academic Article GET IT
Times cited: 2
Validation of a noninvasive prognostic signature for allograft failure following BK virus associated nephropathy. Clinical transplantation. 2021 Academic Article GET IT
Times cited: 2
Gut commensal microbiota and decreased risk for Enterobacteriaceae bacteriuria and urinary tract infection. Gut microbes. 2020 Academic Article GET IT
Times cited: 31
COVID-19 outcomes in patients waitlisted for kidney transplantation and kidney transplant recipients. American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons. 2020 Academic Article GET IT
Times cited: 56
Characteristics of Acute Kidney Injury in Hospitalized COVID-19 Patients in an Urban Academic Medical Center. Clinical journal of the American Society of Nephrology : CJASN. 2020 Letter GET IT
Times cited: 24
Blood Profiles of Gut Bacterial Tacrolimus Metabolite in Kidney Transplant Recipients. Transplantation direct. 2020 Academic Article GET IT
Times cited: 2
Kidney allograft recipients, immunosuppression, and coronavirus disease-2019: a report of consecutive cases from a New York City transplant center. Nephrology, dialysis, transplantation : official publication of the European Dialysis and Transplant Association - European Renal Association. 2020 Academic Article GET IT
Times cited: 60
Urinary cell transcriptomics and acute rejection in human kidney allografts. JCI insight. 2020 Academic Article GET IT
Times cited: 19
Separating the signal from the noise in metagenomic cell-free DNA sequencing. Microbiome. 2020 Academic Article GET IT
Times cited: 23
Avoiding infections in transplant recipients: does the gut microbiota have a key role?. Expert review of clinical immunology. 2020 Editorial Article GET IT
Gut uropathogen abundance is a risk factor for development of bacteriuria and urinary tract infection. Nature communications. 2019 Academic Article GET IT
Times cited: 92
Gastrointestinal pathogen colonization and the microbiome in asymptomatic kidney transplant recipients. Transplant infectious disease : an official journal of the Transplantation Society. 2019 Academic Article GET IT
Times cited: 10
Butyrate-producing gut bacteria and viral infections in kidney transplant recipients: A pilot study. Transplant infectious disease : an official journal of the Transplantation Society. 2019 Academic Article GET IT
Times cited: 28
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. 2019 Academic Article GET IT
Times cited: 38
Identification of Antibiotic Administration as a Potentially Novel Factor Associated With Tacrolimus Trough Variability in Kidney Transplant Recipients: A Preliminary Study. Transplantation direct. 2019 Academic Article GET IT
Times cited: 8
Landscape of innate immune system transcriptome and acute T cell-mediated rejection of human kidney allografts. JCI insight. 2019 Academic Article GET IT
Times cited: 22
Commensal Gut Bacteria Convert the Immunosuppressant Tacrolimus to Less Potent Metabolites. Drug metabolism and disposition: the biological fate of chemicals. 2018 Academic Article GET IT
Times cited: 66
Gut microbiota dysbiosis and diarrhea in kidney transplant recipients. American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons. 2018 Academic Article GET IT
Times cited: 51
Urinary cell-free DNA is a versatile analyte for monitoring infections of the urinary tract. Nature communications. 2018 Academic Article GET IT
Times cited: 100
Single nucleotide variant counts computed from RNA sequencing and cellular traffic into human kidney allografts. American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons. 2018 Academic Article GET IT
Times cited: 9
Urine biomarkers informative of human kidney allograft rejection and tolerance. Human immunology. 2018 Review GET IT
Times cited: 16
Kidney allograft failure in the steroid-free immunosuppression era: A matched case-control study. Clinical transplantation. 2017 Academic Article GET IT
Times cited: 9
Exome Sequencing and Prediction of Long-Term Kidney Allograft Function. PLoS computational biology. 2016 Academic Article GET IT
Times cited: 7131
Routine prophylaxis with proton pump inhibitors and post-transplant complications in kidney transplant recipients undergoing early corticosteroid withdrawal. Clinical transplantation. 2016 Academic Article GET IT
Times cited: 13
Development and validation of a prognostic index for allograft outcome in kidney recipients with transplant glomerulopathy. Kidney international. 2016 Academic Article GET IT
Times cited: 25
Epidemiology and outcomes of carbapenem-resistant Klebsiella pneumoniae bacteriuria in kidney transplant recipients. Transplant infectious disease : an official journal of the Transplantation Society. 2015 Academic Article GET IT
Times cited: 62
Urine Metabolite Profiles Predictive of Human Kidney Allograft Status. Journal of the American Society of Nephrology : JASN. 2015 Academic Article GET IT
Times cited: 49
Characteristics of Circulating Donor Human Leukocyte Antigen-specific Immunoglobulin G Antibodies Predictive of Acute Antibody-mediated Rejection and Kidney Allograft Failure. Transplantation. 2015 Academic Article GET IT
Times cited: 46
Gut microbiota and tacrolimus dosing in kidney transplantation. PloS one. 2015 Academic Article GET IT
Times cited: 119
Gut microbial community structure and complications after kidney transplantation: a pilot study. Transplantation. 2014 Academic Article GET IT
Times cited: 122
Circulating levels of 25-hydroxyvitamin D and acute cellular rejection in kidney allograft recipients. Transplantation. 2014 Academic Article GET IT
Times cited: 44
Allograft rejection and tubulointerstitial fibrosis in human kidney allografts: interrogation by urinary cell mRNA profiling. Transplantation reviews (Orlando, Fla.). 2014 Review GET IT
Times cited: 8
Urinary cell mRNA profiles and differential diagnosis of acute kidney graft dysfunction. Journal of the American Society of Nephrology : JASN. 2014 Academic Article GET IT
Times cited: 36
Urinary cell mRNA profiles predictive of human kidney allograft status. Immunological reviews. 2014 Review GET IT
Times cited: 35
Independent risk factors for urinary tract infection and for subsequent bacteremia or acute cellular rejection: a single-center report of 1166 kidney allograft recipients. Transplantation. 2013 Academic Article GET IT
Times cited: 109
Noninvasive prognostication of polyomavirus BK virus-associated nephropathy. Transplantation. 2013 Academic Article GET IT
Times cited: 21
HIV-infected kidney graft recipients managed with an early corticosteroid withdrawal protocol: clinical outcomes and messenger RNA profiles. Transplantation. 2013 Academic Article GET IT
Times cited: 11

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Research

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Funding awarded

Cell-Free DNA in Peritoneal Fluid as a Novel and Versatile Analyte for Monitoring Peritonitis awarded by National Institute of Allergy & Infectious Diseases Principal Investigator 2021 - 2024

Metagenomic profiling of urinary cell-free DNA to monitor urinary tract infection after kidney transplantation awarded by National Institute of General Medical Sciences Co-Investigator 2020 - 2025

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Background

education and training

M.S., Weill Cornell Graduate School of Medical Sciences 2016
M.D., Weill Cornell Medical College, Cornell University 2007
A.B., Harvard College 2003

Contact

full name

John Richard Lee

primary email

jrl2002@med.cornell.edu

webpage

Clinical Profile

VIVO Weill Cornell Medical College

John Richard Lee Associate Professor of Medicine

Publications

selected publications

Research

Funding awarded

Background

education and training

Contact

full name

primary email

webpage

Phone

Publications

selected publications

Research

Funding awarded

Background

education and training

Contact

full name

primary email

webpage