Jonathan E. Pekar

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All published works

Action	Title	Year	Authors
+ PDF Chat	Random-Effects Substitution Models for Phylogenetics via Scalable Gradient Approximations	2024	Andrew F. Magee Andrew J. Holbrook Jonathan E. Pekar Itzue W. Caviedes-Solis F. A. Matsen Guy Baele Joel O. Wertheim Ji Xiang Philippe Lemey Marc A. Suchard
+	Random-effects substitution models for phylogenetics via scalable gradient approximations	2023	Andrew F. Magee Andrew J. Holbrook Jonathan E. Pekar Itzue W. Caviedes-Solis Fredrick A. Matsen Guy Baele Joel O. Wertheim Ji Xiang Philippe Lemey Marc A. Suchard
+ PDF Chat	The Huanan Seafood Wholesale Market in Wuhan was the early epicenter of the COVID-19 pandemic	2022	Michael Worobey Joshua I. Levy Lorena M. Malpica Serrano Alexander Crits‐Christoph Jonathan E. Pekar Stephen A. Goldstein Angela L. Rasmussen Moritz U. G. Kraemer Chris Newman Marion Koopmans
+ PDF Chat	The molecular epidemiology of multiple zoonotic origins of SARS-CoV-2	2022	Jonathan E. Pekar Andrew F. Magee Edyth Parker Niema Moshiri Katherine Izhikevich Jennifer L. Havens Karthik Gangavarapu Lorena M. Malpica Serrano Alexander Crits‐Christoph Nathaniel L. Matteson
+	Timing the SARS-CoV-2 index case in Hubei province	2021	Jonathan E. Pekar Michael Worobey Niema Moshiri Konrad Scheffler Joel O. Wertheim
+	Timing the SARS-CoV-2 Index Case in Hubei Province	2020	Jonathan E. Pekar Michael Worobey Niema Moshiri Konrad Scheffler Joel O. Wertheim
+ PDF Chat	The emergence of SARS-CoV-2 in Europe and North America	2020	Michael Worobey Jonathan E. Pekar Brendan B. Larsen Martha I. Nelson Verity Hill Jeffrey B. Joy Andrew Rambaut Marc A. Suchard Joel O. Wertheim Philippe Lemey
+	The emergence of SARS-CoV-2 in Europe and the US	2020	Michael Worobey Jonathan E. Pekar Brendan B. Larsen Martha I. Nelson Verity Hill Jeffrey B. Joy Andrew Rambaut Marc A. Suchard Joel O. Wertheim Philippe Lemey

Common Coauthors

Coauthor	Papers Together
Joel O. Wertheim	8
Michael Worobey	6
Marc A. Suchard	6
Philippe Lemey	5
Andrew Rambaut	4
Niema Moshiri	3
Andrew F. Magee	3
Joshua I. Levy	2
Brendan B. Larsen	2
Itzue W. Caviedes-Solis	2
Andrew J. Holbrook	2
Verity Hill	2
Edward C. Holmes	2
Kristian G. Andersen	2
Jeffrey B. Joy	2
Ji Xiang	2
Alexander Crits‐Christoph	2
Robert F. Garry	2
Guy Baele	2
Martha I. Nelson	2
Konrad Scheffler	2
Lorena M. Malpica Serrano	2
Mohd Noor Mat Isa	1
Jungmin Lee	1
Man‐Seong Park	1
Marion Koopmans	1
Jade Wang	1
Fredrick A. Matsen	1
Yusuf Muhammad Noor	1
Angela L. Rasmussen	1
Stephen A. Goldstein	1
Katherine Ching Zi Yan	1
Raymond Tzer Pin Lin	1
Chris Newman	1
Edyth Parker	1
Jennifer L. Havens	1
Moritz U. G. Kraemer	1
Heedo Park	1
Tetyana I. Vasylyeva	1
Mark Zeller	1
Karthik Gangavarapu	1
Nathaniel L. Matteson	1
Scott Hughes	1
Katherine Izhikevich	1
David L. Robertson	1
F. A. Matsen	1

Commonly Cited References

Action	Title	Year	Authors	# of times referenced
+ PDF Chat	Social Contacts and Mixing Patterns Relevant to the Spread of Infectious Diseases	2008	Joël Mossong Niel Hens Mark Jit Philippe Beutels Kari Auranen Rafael Mikolajczyk Marco Massari Stefania Salmaso Gianpaolo Scalia Tomba Jacco Wallinga	5
+	Early Transmission Dynamics in Wuhan, China, of Novel Coronavirus–Infected Pneumonia	2020	Qun Li Xuhua Guan Peng Wu Xiaoye Wang Lei Zhou Yeqing Tong Ruiqi Ren Kathy Leung Eric H. Y. Lau Jessica Y. Wong	4
+	Timing the SARS-CoV-2 index case in Hubei province	2021	Jonathan E. Pekar Michael Worobey Niema Moshiri Konrad Scheffler Joel O. Wertheim	4
+ PDF Chat	Reconstruction of the full transmission dynamics of COVID-19 in Wuhan	2020	Xingjie Hao Shanshan Cheng Degang Wu Tangchun Wu Xihong Lin Chaolong Wang	3
+ PDF Chat	The emergence of SARS-CoV-2 in Europe and North America	2020	Michael Worobey Jonathan E. Pekar Brendan B. Larsen Martha I. Nelson Verity Hill Jeffrey B. Joy Andrew Rambaut Marc A. Suchard Joel O. Wertheim Philippe Lemey	3
+ PDF Chat	Assessing Uncertainty in the Rooting of the SARS-CoV-2 Phylogeny	2020	Lenore Pipes Hongru Wang John P. Huelsenbeck Rasmus Nielsen	3
+ PDF Chat	Emergence of Scaling in Random Networks	1999	Albert‐László Barabási Réka Albert	3
+ PDF Chat	GEMFsim: A stochastic simulator for the generalized epidemic modeling framework	2017	Faryad Darabi Sahneh Aram Vajdi Heman Shakeri Futing Fan Caterina Scoglio	3
+ PDF Chat	Unifying Viral Genetics and Human Transportation Data to Predict the Global Transmission Dynamics of Human Influenza H3N2	2014	Philippe Lemey Andrew Rambaut Trevor Bedford Nuno R. Faria Filip Bielejec Guy Baele Colin A. Russell Derek J. Smith Oliver G. Pybus Dirk Brockmann	3
+ PDF Chat	Establishment and lineage dynamics of the SARS-CoV-2 epidemic in the UK	2021	Louis du Plessis John T. McCrone Alexander E. Zarebski Verity Hill Christopher Ruis Bernardo Gutiérrez Jayna Raghwani Jordan Ashworth Rachel Colquhoun Thomas R. Connor	2
+	Household transmission of SARS-CoV-2 and risk factors for susceptibility and infectivity in Wuhan: a retrospective observational study	2021	Fang Li Yuan-Yuan Li Ming-Jin Liu Li-Qun Fang Natalie E. Dean Gary Wong Xiao-Bing Yang Ira M. Longini M. Elizabeth Halloran Huai-Ji Wang	2
+ PDF Chat	Introductions and early spread of SARS-CoV-2 in the New York City area	2020	Ana S. González-Reiche Matthew M. Hernandez Mitchell J. Sullivan Brianne Ciferri Hala Alshammary Ajay Obla Shelcie Fabre Giulio Kleiner José Polanco Zenab Khan	2
+ PDF Chat	GISAID: Global initiative on sharing all influenza data – from vision to reality	2017	Yuelong Shu John W. McCauley	2
+ PDF Chat	Epidemiology and transmission dynamics of COVID-19 in two Indian states	2020	Ramanan Laxminarayan Brian Wahl ShankarReddy Dudala Kathiresan Gopal Chandra Mohan B S. Neelima K. S. Jawahar Reddy Jayachandran Radhakrishnan Joseph A. Lewnard	2
+	Estimating the overdispersion in COVID-19 transmission using outbreak sizes outside China	2020	Akira Endo Sam Abbott Adam J. Kucharski Sebastian Funk	2
+	The origins of SARS-CoV-2: A critical review	2021	Edward C. Holmes Stephen A. Goldstein Angela L. Rasmussen David L. Robertson Alexander Crits‐Christoph Joel O. Wertheim Simon J. Anthony William Barclay Maciej F. Boni Peter C. Doherty	2
+ PDF Chat	Dissecting the early COVID-19 cases in Wuhan	2021	Michael Worobey	2
+	Transmission of 2019-nCoV Infection from an Asymptomatic Contact in Germany	2020	Camilla Rothe Mirjam Schunk Peter Sothmann Gisela Bretzel Guenter Froeschl Claudia Wallrauch Thorbjörn Zimmer Verena Thiel Christian Jänke Wolfgang Guggemos	2
+ PDF Chat	Temporal signal and the phylodynamic threshold of SARS-CoV-2	2020	Sebastián Duchêne Leo Featherstone Melina Haritopoulou-Sinanidou Andrew Rambaut Philippe Lemey Guy Baele	2
+	Estimating the overdispersion in COVID-19 transmission using outbreak sizes outside China	2020	Akira Endo Sam Abbott Adam J. Kucharski Sebastian Funk	2
+ PDF Chat	The Huanan Seafood Wholesale Market in Wuhan was the early epicenter of the COVID-19 pandemic	2022	Michael Worobey Joshua I. Levy Lorena M. Malpica Serrano Alexander Crits‐Christoph Jonathan E. Pekar Stephen A. Goldstein Angela L. Rasmussen Moritz U. G. Kraemer Chris Newman Marion Koopmans	2
+ PDF Chat	Serosurvey for SARS-CoV-2 among blood donors in Wuhan, China from September to December 2019	2022	Le Chang Lei Zhao Yan Xiao Tingting Xu Lan Chen Yan Cai Xiaojing Dong Conghui Wang Xia Xiao Lili Ren	2
+ PDF Chat	Clustering and superspreading potential of SARS-CoV-2 infections in Hong Kong	2020	Dillon C. Adam Peng Wu Jessica Y. Wong Eric H. Y. Lau Tim K. Tsang Simon Cauchemez GM Leung Benjamin J. Cowling	2
+ PDF Chat	Reconstruction of Transmission Pairs for Novel Coronavirus Disease 2019 (COVID-19) in Mainland China: Estimation of Superspreading Events, Serial Interval, and Hazard of Infection	2020	Xiao-Ke Xu Xiao Fan Liu Ye Wu Sheikh Taslim Ali Zhanwei Du Paolo Bosetti Eric H. Y. Lau Benjamin J. Cowling Lin Wang	2
+	Sequencing identifies multiple early introductions of SARS-CoV-2 to the New York City Region	2020	Matthew T. Maurano Sitharam Ramaswami Paul Zappile Dacia Dimartino Ludovic Boytard André M. Ribeiro-dos-Santos Nicholas A. Vulpescu Gael Westby Guomiao Shen Xiaojun Feng	2
+ PDF Chat	Sequencing identifies multiple early introductions of SARS-CoV-2 to the New York City region	2020	Matthew T. Maurano Sitharam Ramaswami Paul Zappile Dacia Dimartino Ludovic Boytard André M. Ribeiro-dos-Santos Nicholas A. Vulpescu Gael Westby Guomiao Shen Xiaojun Feng	2
+ PDF Chat	Epidemiology and transmission of COVID-19 in 391 cases and 1286 of their close contacts in Shenzhen, China: a retrospective cohort study	2020	Qifang Bi Yongsheng Wu Shujiang Mei Chenfei Ye Xuan Zou Zhen Zhang Xiaojian Liu Lan Wei Shaun Truelove Tong Zhang	2
+ PDF Chat	Coast-to-Coast Spread of SARS-CoV-2 during the Early Epidemic in the United States	2020	Joseph R. Fauver Mary E. Petrone Emma B. Hodcroft Kayoko Shioda Hanna Y. Ehrlich Alexander Watts Chantal B. F. Vogels Anderson F. Brito Tara Alpert Anthony Muyombwe	2
+	Early Detection of Covid-19 through a Citywide Pandemic Surveillance Platform	2020	Helen Y. Chu Janet A. Englund Lea M. Starita Michael Famulare Elisabeth Brandstetter Deborah A. Nickerson Mark J. Rieder Amanda Adler Karine Lacombe Ashley E. Kim	2
+ PDF Chat	Investigation of a COVID-19 outbreak in Germany resulting from a single travel-associated primary case: a case series	2020	Merle M. Böhmer Udo Buchholz Victor M. Corman Martin Hoch Katharina Katz Durdica Marosevic Stefanie Böhm Tom Woudenberg Nikolaus Ackermann Regina Konrad	2
+ PDF Chat	Inferring Heterogeneous Evolutionary Processes Through Time: from Sequence Substitution to Phylogeography	2014	Filip Bielejec Philippe Lemey Guy Baele Andrew Rambaut Marc A. Suchard	2
+ PDF Chat	Evidence for Limited Early Spread of COVID-19 Within the United States, January–February 2020	2020	Michelle Jorden Sarah L. Rudman Elsa Villarino Stacey Hoferka Megan T. Patel Kelley Bemis Cristal R. Simmons Megan Jespersen Jenna Iberg Johnson Elizabeth Mytty	2
+ PDF Chat	The Epidemiological Characteristics of an Outbreak of 2019 Novel Coronavirus Diseases (COVID-19) — China, 2020	2020	China CDC Weekly	1
+ PDF Chat	Exploring Urban Spatial Features of COVID-19 Transmission in Wuhan Based on Social Media Data	2020	Zhenghong Peng Ru Wang Lingbo Liu Hao Wu	1
+	Seroconversion of a city: Longitudinal monitoring of SARS-CoV-2 seroprevalence in New York City	2020	Daniel Stadlbauer Jessica Tan Kaijun Jiang Matthew M. Hernandez Shelcie Fabre Fatima Amanat Su Hui Catherine Teo Guha Asthagiri Arunkumar Meagan McMahon Jeffrey S. Jhang	1
+	Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus	2020	Bette Korber Will Fischer S. Gnanakaran Hyejin Yoon James Theiler W. P. Abfalterer Nicolas Hengartner Elena E. Giorgi Tanmoy Bhattacharya Brian Foley	1
+	The challenges of modeling and forecasting the spread of COVID-19	2020	Andrea L. Bertozzi Elisa Marques Franco George Mohler Martin B. Short Daniel Sledge	1
+ PDF Chat	Relaxed Random Walks at Scale	2020	Alexander A. Fisher Xiang Ji Zhenyu Zhang Philippe Lemey Marc A. Suchard	1
+	Influenza versus COVID-19 cases among influenza-like illness patients in travelers from Wuhan to Hong Kong in January 2020	2020	Jun Tao Huizhi Gao Shuying Zhu Lin Yang Daihai He	1
+ PDF Chat	Epidemiological characteristics and the entire evolution of coronavirus disease 2019 in Wuhan, China	2020	Dongming Wang Jing Cai Tingming Shi Yang Xiao Xiaobin Feng Meng Yang Wenzhen Li Wei Liu Linling Yu Zi Ye	1
+ PDF Chat	Disease burden and clinical severity of the first pandemic wave of COVID-19 in Wuhan, China	2020	Juan Yang Xinhua Chen Xiaowei Deng Zhiyuan Chen Hui Gong Yan Han Qianhui Wu Huilin Shi Shengjie Lai Marco Ajelli	1
+ PDF Chat	Age-specific mortality and immunity patterns of SARS-CoV-2	2020	Megan O’Driscoll Gabriel Ribeiro dos Santos Lin Wang Derek A. T. Cummings Andrew S. Azman Juliette Paireau Arnaud Fontanet Simon Cauchemez Henrik Salje	1
+ PDF Chat	SARS-CoV-2 (COVID-19) superspreader events	2020	Dasha Majra Jayme D. Benson Jennifer M. Pitts Justin Stebbing	1
+	Timing the SARS-CoV-2 Index Case in Hubei Province	2020	Jonathan E. Pekar Michael Worobey Niema Moshiri Konrad Scheffler Joel O. Wertheim	1
+	Transmission of SARS-CoV-2 Lineage B.1.1.7 in England: Insights from linking epidemiological and genetic data	2021	Erik Volz Swapnil Mishra Meera Chand Jeffrey C. Barrett Robert Johnson Lily Geidelberg Wes Hinsley Daniel J. Laydon Gavin Dabrera Áine O’Toole	1
+ PDF Chat	The epidemiological characteristics of deaths with COVID-19 in the early stage of epidemic in Wuhan, China	2020	Jianjun Bai Fang Shi Jinhong Cao Haoyu Wen Fang Wang Sumaira Mubarik Xiaoxue Liu Yong Yu Jianbo Ding Chuanhua Yu	1
+ PDF Chat	Antibody seroprevalence in the epicenter Wuhan, Hubei, and six selected provinces after containment of the first epidemic wave of COVID-19 in China	2021	Zhongjie Li Xuhua Guan Naiying Mao Huiming Luo Ying Qin Na He Zhen Zhu Jianxing Yu Yu Li Jianhua Liu	1
+	Estimating the reproductive number R0 of SARS-CoV-2 in the United States and eight European countries and implications for vaccination	2021	Ruian Ke Ethan Romero-Severson Steven Sanche Nicolas Hengartner	1
+ PDF Chat	Seroprevalence and humoral immune durability of anti-SARS-CoV-2 antibodies in Wuhan, China: a longitudinal, population-level, cross-sectional study	2021	Zhenyu He Lili Ren Juntao Yang Li Guo Shuo Feng Chao Ma Xia Wang Zhiwei Leng Xunliang Tong Wang Zhou	1
+	Speed and strength of an epidemic intervention	2021	Jonathan Dushoff Sang Woo Park	1