Jonathan Z. Li

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All published works

Action	Title	Year	Authors
+	Modeling suggests SARS-CoV-2 rebound after nirmatrelvir-ritonavir treatment is driven by target cell preservation coupled with incomplete viral clearance	2025	Tin Phan Ruy M. Ribeiro Gregory E. Edelstein Julie Boucau Rockib Uddin Caitlin Marino May Y. Liew Mamadou Ciré Barry Manish C. Choudhary Dessie Tien
+ PDF Chat	Modeling the emergence of viral resistance for SARS-CoV-2 during treatment with an anti-spike monoclonal antibody	2024	Tin Phan Carolin Zitzmann Kara W. Chew Davey M. Smith Eric S. Daar David A. Wohl Joseph J. Eron Judith S. Currier Michael D. Hughes Manish C. Choudhary
+	Modeling the emergence of viral resistance for SARS-CoV-2 during treatment with an anti-spike monoclonal antibody	2023	Tin Phan Carolin Zitzmann Kara W. Chew Davey M. Smith Eric S. Daar David A. Wohl Joseph J. Eron Judith S. Currier Michael D. Hughes Manish C. Choudhary
+ PDF Chat	Variant-Specific Viral Kinetics in Acute COVID-19	2023	Ruy M. Ribeiro Manish C. Choudhary Rinki Deo Mark J. Giganti Carlee Moser Justin Ritz Alexander L. Greninger James Regan James P. Flynn David A. Wohl
+ PDF Chat	Statistical Challenges when Analyzing SARS-CoV-2 RNA Measurements Below the Assay Limit of Quantification in COVID-19 Clinical Trials	2023	Carlee Moser Kara W. Chew Mark J. Giganti Jonathan Z. Li Evgenia Aga Justin Ritz Alexander L. Greninger Arzhang Cyrus Javan Rachel Bender Ignacio Eric S. Daar
+ PDF Chat	Symptom and Viral Rebound in Untreated SARS-CoV-2 Infection	2023	Rinki Deo Manish C. Choudhary Carlee Moser Justin Ritz Eric S. Daar David A. Wohl Alexander L. Greninger Joseph J. Eron Judith S. Currier Michael D. Hughes
+ PDF Chat	Viral and Symptom Rebound in Untreated COVID-19 Infection	2022	Rinki Deo Manish C. Choudhary Carlee Moser Justin Ritz Eric S. Daar David A. Wohl Alexander L. Greninger Joseph J. Eron Judith S. Currier Michael D. Hughes
+	Uncovering hidden sources of SARS‐CoV‐2 viral evolution: A call to action	2022	Manish C. Choudhary Jonathan Z. Li
+ PDF Chat	Determining the Incidence of Asymptomatic SARS-CoV-2 Among Early Recipients of COVID-19 Vaccines (DISCOVER-COVID-19): A Prospective Cohort Study of Healthcare Workers Before, During and After Vaccination	2021	Crystal M. North Amy K. Barczak Robert H. Goldstein Brian C. Healy Dianne M. Finkelstein Delaney D Ding Andy Kim Julie Boucau Bennett Shaw Rebecca F. Gilbert
+ PDF Chat	Viral Load Kinetics of Severe Acute Respiratory Syndrome Coronavirus 2 in Hospitalized Individuals With Coronavirus Disease 2019	2021	James Regan James P. Flynn Alexandra Rosenthal Hannah Jordan Yijia Li Rida Chishti Françoise Giguel Heather Corry Kendyll Coxen Jesse Fajnzylber
+	Uncovering Ways That Emerging Severe Acute Respiratory Syndrome Coronavirus 2 Lineages May Increase Transmissibility	2021	Jacob E. Lemieux Jonathan Z. Li
+ PDF Chat	SARS-CoV-2 viral load is associated with increased disease severity and mortality	2020	Jesse Fajnzylber James Regan Kendyll Coxen Heather Corry Colline Wong Alexandra Rosenthal Daniel Worrall Françoise Giguel Alicja Piechocka‐Trocha Caroline Atyeo

Common Coauthors

Coauthor	Papers Together
Manish C. Choudhary	9
Michael D. Hughes	6
David A. Wohl	6
Judith S. Currier	6
Eric S. Daar	6
Kara W. Chew	6
Davey M. Smith	6
Alan S. Perelson	5
Ruy M. Ribeiro	5
Joseph J. Eron	5
Julie Boucau	4
James Regan	4
Justin Ritz	4
Carlee Moser	4
Alexander L. Greninger	4
Rinki Deo	4
Tin Phan	3
Yijia Li	3
James P. Flynn	3
Jacob E. Lemieux	3
Lindsey R. Baden	3
Chenyang Jiang	2
Heather Corry	2
Patrick Allen	2
Falisha A. Porto	2
Mark J. Siedner	2
Jordan Marchewka	2
Christian Nambu	2
Pilar García–Broncano	2
Elise Gettings	2
Christianne Sharr	2
Amanda Griffin	2
Sarah Luthern	2
Vlasta LaValle	2
Kendyll Coxen	2
Kelsey Finn	2
Ruian Ke	2
Kathleen Selleck	2
Meg Healy	2
Hannah Jordan	2
Keith T. Flaherty	2
Siobhan Boyce	2
Alexandra Reissis	2
Kimberly Smith Sheppard	2
Evan C. Lam	2
Hannah Ticheli	2
Nikolaus Jilg	2
Chantal Kayitesi	2
Claire O’Callaghan	2
Alexandra Rosenthal	2

Commonly Cited References

Action	Title	Year	Authors	# of times referenced
+ PDF Chat	Temporal dynamics in viral shedding and transmissibility of COVID-19	2020	Xi He Eric H. Y. Lau Peng Wu Xilong Deng Jian Wang Xinxin Hao Yiu Chung Lau Jessica Y. Wong Yujuan Guan Xinghua Tan	4
+	In vivo kinetics of SARS-CoV-2 infection and its relationship with a person’s infectiousness	2021	Ruian Ke Carolin Zitzmann David D. Ho Ruy M. Ribeiro Alan S. Perelson	4
+	Mechanistic Modeling of SARS‐CoV‐2 and Other Infectious Diseases and the Effects of Therapeutics	2021	Alan S. Perelson Ruian Ke	4
+	Modeling the viral dynamics of SARS-CoV-2 infection	2020	Sunpeng Wang Yang Pan Quanyi Wang Hongyu Miao Ashley N. Brown Libin Rong	3
+ PDF Chat	How robust are estimates of key parameters in standard viral dynamic models?	2024	Carolin Zitzmann Ruian Ke Ruy M. Ribeiro Alan S. Perelson	3
+ PDF Chat	An explanation for SARS-CoV-2 rebound after Paxlovid treatment	2023	Alan S. Perelson Ruy M. Ribeiro Tin Phan	3
+	A quantitative model used to compare within-host SARS-CoV-2, MERS-CoV, and SARS-CoV dynamics provides insights into the pathogenesis and treatment of SARS-CoV-2	2021	Kwang Su Kim Keisuke Ejima Shoya Iwanami Yasuhisa Fujita Hirofumi Ohashi Yoshiki Koizumi Yusuke Asai Shinji Nakaoka Koichi Watashi Kazuyuki Aihara	3
+ PDF Chat	Identifiability of parameters in mathematical models of SARS-CoV-2 infections in humans	2022	Stanca M. Ciupe Necibe Tuncer	3
+ PDF Chat	Daily longitudinal sampling of SARS-CoV-2 infection reveals substantial heterogeneity in infectiousness	2022	Ruian Ke Pamela P. Martinez Rebecca L. Smith Laura Gibson Agha Zeeshan Mirza Madison Conte Nicholas Gallagher Chun Huai Luo Junko Jarrett Ruifeng Zhou	3
+ PDF Chat	SARS-CoV-2 viral load is associated with increased disease severity and mortality	2020	Jesse Fajnzylber James Regan Kendyll Coxen Heather Corry Colline Wong Alexandra Rosenthal Daniel Worrall Françoise Giguel Alicja Piechocka‐Trocha Caroline Atyeo	3
+	In-host Mathematical Modelling of COVID-19 in Humans	2020	Esteban A. Hernández-Vargas Jorge X. Velasco‐Hernández	3
+	The within-host viral kinetics of SARS-CoV-2	2020	Chentong Li Jinhu Xu Jiawei Liu Yicang Zhou	2
+	Multimodel Inference	2004	Kenneth P. Burnham David R. Anderson	2
+	Emergence of Drug Resistance during an Influenza Epidemic: Insights from a Mathematical Model	1998	Nikolaos I. Stilianakis Alan S. Perelson Frederick G. Hayden	2
+ PDF Chat	Incubation Period and Other Epidemiological Characteristics of 2019 Novel Coronavirus Infections with Right Truncation: A Statistical Analysis of Publicly Available Case Data	2020	Natalie M. Linton T. Kobayashi Yichi Yang Katsuma Hayashi Andrei R. Akhmetzhanov Sung-mok Jung Baoyin Yuan Ryo Kinoshita Hiroshi Nishiura	2
+ PDF Chat	The Incubation Period of Coronavirus Disease 2019 (COVID-19) From Publicly Reported Confirmed Cases: Estimation and Application	2020	Stephen A. Lauer Kyra H. Grantz Qifang Bi Forrest K. Jones Qulu Zheng Hannah R. Meredith Andrew S. Azman Nicholas G Reich Justin Lessler	2
+	SARS-CoV-2 (COVID-19) by the numbers	2020	Yinon M. Bar-On Avi I. Flamholz Rob Phillips Ron Milo	2
+	Mathematical modeling of interaction between innate and adaptive immune responses in COVID‐19 and implications for viral pathogenesis	2020	Sean Quan Du Weiming Yuan	2
+ PDF Chat	Timing of Antiviral Treatment Initiation is Critical to Reduce SARS‐CoV‐2 Viral Load	2020	Antônio Gonçalves Julie Bertrand Ruian Ke Emmanuelle Comets Xavier de Lamballerie Denis Malvy Andrés Pizzorno Olivier Terrier Manuel Rosa‐Calatrava France Mentré	2
+	Dynamics of SARS-CoV-2 infection model with two modes of transmission and immune response	2020	Khalid Hattaf Noura Yousfi	2
+ PDF Chat	A Model for SARS-CoV-2 Infection with Treatment	2020	Amar Nath Chatterjee Fahad Al Basir	2
+	Modeling SARS-CoV-2 viral kinetics and association with mortality in hospitalized patients from the French COVID cohort	2021	Nadège Néant Guillaume Lingas Quentin Le Hingrat Jade Ghosn Ilka Engelmann Quentin Lepiller Alexandre Gaymard Virginie Ferré Cédric Hartard Jean‐Christophe Plantier	2
+	SARS-CoV-2 viral dynamics in non-human primates	2021	António Gonçalves Pauline Maisonnasse Flora Donati Mélanie Albert Sylvie Behillil Vanessa Contreras Thibaut Naninck Romain Marlin Caroline Solas Andrés Pizzorno	2
+	Comparing antiviral strategies against COVID-19 via multiscale within-host modelling	2021	Farzad Fatehi Richard J. Bingham Eric C. Dykeman Peter G. Stockley Reidun Twarock	2
+ PDF Chat	Modeling within-host and aerosol dynamics of SARS-CoV-2: The relationship with infectiousness	2022	Nora Heitzman-Breen Stanca M. Ciupe	2
+	Quantifying the impact of immune history and variant on SARS-CoV-2 viral kinetics and infection rebound: A retrospective cohort study	2022	James A. Hay Stephen M Kissler Joseph R. Fauver Christina Mack Caroline G. Tai Radhika M Samant Sarah Connolly Deverick J. Anderson Gaurav Khullar Matthew MacKay	2
+	Effect of cellular regeneration and viral transmission mode on viral spread	2022	Asher Haun Baylor G. Fain Hana M. Dobrovolny	2
+	Using statistics and mathematical modelling to understand infectious disease outbreaks: COVID-19 as an example	2020	Christopher E. Overton Helena B. Stage Shazaad S.Y. Ahmad Jacob Curran-Sebastian Paul Dark Rajenki Das Elizabeth Fearon Timothy Felton Martyn Fyles Nick Gent	1
+ PDF Chat	Estimated transmissibility and impact of SARS-CoV-2 lineage B.1.1.7 in England	2020	Nicholas G. Davies Sam Abbott Rosanna C. Barnard Christopher Jarvis Adam J. Kucharski James D. Munday Carl A. B. Pearson Timothy Russell Damien C. Tully Alex Washburne	1
+ PDF Chat	SARS-CoV-2 Transmission From People Without COVID-19 Symptoms	2021	Michael A. Johansson Talía M. Quandelacy Sarah Kada Pragati Prasad Molly Steele John T. Brooks Rachel B. Slayton Matthew Biggerstaff Jay C. Butler	1
+ PDF Chat	Estimating clinical severity of COVID-19 from the transmission dynamics in Wuhan, China	2020	Joseph T. Wu Kathy Leung Mary Bushman Nishant Kishore René Niehus Pablo M. De Salazar Benjamin J. Cowling Marc Lipsitch GM Leung	1
+ PDF Chat	Heterogeneous SARS-CoV-2 kinetics due to variable timing and intensity of immune responses	2024	Katherine Owens Shadisadat Esmaeili Joshua T. Schiffer	1
+	Viral load and contact heterogeneity predict SARS-CoV-2 transmission and super-spreading events	2021	Ashish Goyal Daniel B. Reeves E. Fabián Cardozo-Ojeda Joshua T. Schiffer Bryan T. Mayer	1
+	Success of prophylactic antiviral therapy for SARS-CoV-2: Predicted critical efficacies and impact of different drug-specific mechanisms of action	2021	Peter Czuppon Florence Débarre António Gonçalves Olivier Tenaillon Alan S. Perelson Jérémie Guedj François Blanquart	1
+ PDF Chat	Sharing a household with children and risk of COVID-19: a study of over 300 000 adults living in healthcare worker households in Scotland	2021	Rachael Wood Emma C. Thomson Robert M. Galbraith Ciara Gribben David Caldwell Jennifer L. Bishop Martin Reid Anoop Shah Kate Templeton David Goldberg	1
+	Mixed Effects Models with Censored Data with Application to HIV RNA Levels	1999	James P. Hughes	1
+	SARS-CoV-2 Infection after Vaccination in Health Care Workers in California	2021	Jocelyn Keehner Lucy E. Horton Michael A. Pfeffer Chris Longhurst Robert T. Schooley Judith S. Currier Shira R. Abeles Francesca J. Torriani	1
+ PDF Chat	Causes and Consequences of Spatial Within-Host Viral Spread	2018	Molly E. Gallagher Christopher B. Brooke Ruian Ke Katia Koelle	1
+ PDF Chat	Viral Load Kinetics of Severe Acute Respiratory Syndrome Coronavirus 2 in Hospitalized Individuals With Coronavirus Disease 2019	2021	James Regan James P. Flynn Alexandra Rosenthal Hannah Jordan Yijia Li Rida Chishti Françoise Giguel Heather Corry Kendyll Coxen Jesse Fajnzylber	1
+ PDF Chat	Prevalence of Asymptomatic SARS-CoV-2 Infection	2020	Daniel P. Oran Eric J. Topol	1
+ PDF Chat	Immune‐viral dynamics modeling for SARS‐CoV‐2 drug development	2021	Youfang Cao Wei Gao Luzelena Caro Julie A. Stone	1
+	A retrospective cohort study of Paxlovid efficacy depending on treatment time in hospitalized COVID-19 patients	2024	Zhanwei Du Lin Wang Yuan Bai Liu Yun-hu Eric H. Y. Lau Alison P. Galvani Robert M. Krug Benjamin J. Cowling Lauren Ancel Meyers	1
+	A Modified Poisson Regression Approach to Prospective Studies with Binary Data	2004	Guangyong Zou	1
+ PDF Chat	SARS-CoV-2 prolonged infection during advanced HIV disease evolves extensive immune escape	2022	Sandile Cele Farina Karim Gila Lustig James Emmanuel San Tandile Hermanus Houriiyah Tegally Jumari Snyman Thandeka Moyo-Gwete Eduan Wilkinson Mallory Bernstein	1
+ PDF Chat	Duration of Infectious Virus Shedding by SARS-CoV-2 Omicron Variant–Infected Vaccinees	2022	Kenichiro Takahashi Masahiro Ishikane Mugen Ujiie Noriko Iwamoto Nobumasa Okumura Testsuro Sato Maki Nagashima Ataru Moriya Michiyo Suzuki Masayuki Hojo	1
+	Analysis and design issues for studies using censored biomarker measurements with an example of viral load measurements in HIV clinical trials	2000	Michael D. Hughes	1
+	Viral Dynamics of SARS-CoV-2 Variants in Vaccinated and Unvaccinated Persons	2021	Stephen M. Kissler Joseph R Fauver Christina Mack Caroline G. Tai Mallery I. Breban Anne E. Watkins Radhika M Samant Deverick J. Anderson Jessica Metti Gaurav Khullar	1
+ PDF Chat	Modeling recapitulates the heterogeneous outcomes of SARS-CoV-2 infection and quantifies the differences in the innate immune and CD8 T-cell responses between patients experiencing mild and severe symptoms	2022	Budhaditya Chatterjee Harshbir Singh Sandhu Narendra M. Dixit	1
+ PDF Chat	Modeling the emergence of viral resistance for SARS-CoV-2 during treatment with an anti-spike monoclonal antibody	2024	Tin Phan Carolin Zitzmann Kara W. Chew Davey M. Smith Eric S. Daar David A. Wohl Joseph J. Eron Judith S. Currier Michael D. Hughes Manish C. Choudhary	1
+	Epidemiologic Evaluation of Measurement Data in the Presence of Detection Limits	2004	Jay H. Lubin Joanne S. Colt David Camann Scott Davis James R. Cerhan Richard K. Severson Leslie Bernstein Patricia Hartge	1