Dr. Sen Pei is an Assistant Professor in the Department of Environmental Health Sciences at Mailman School of Public Health, Columbia University. With a background in applied mathematics, network science, and complex systems, he studies environmental, social, and ecological determinants of infectious disease, aiming to better understand, predict, and prepare for recurrent and emerging outbreaks. Using a variety of data sources, he develops mathematical models and computational tools to advance surveillance, forecasting, and control of seasonal and emerging infectious agents. His recent studies focus on respiratory viruses and antimicrobial-resistant pathogens in healthcare systems.
He/him/his
United States
National Institutes of Health, National Institute of General Medical Sciences
People: Sen Pei
2025 – 2029 Continue Reading Early detection and inference for emerging infectious agents in data-sparse settings
National Institutes of Health, National Institute of Allergy and Infectious Diseases
People: Sen Pei
2023 – 2026 Continue Reading Inference of heterogeneous transmission of antimicrobial resistant pathogens in health care settings
National Science Foundation, Mathematical and Physical Sciences (MPS)
People: Sen Pei
2022 – 2026 Continue Reading RAISE: IHBEM: Human Behavior Driven Mathematical Modeling and Forecasting of Respiratory Disease Transmission in Urban Settings
National Institutes of Health, National Center for Emerging and Zoonotic Infectious Diseases
People: Jeffrey Shaman, Sen Pei
2020 – 2025 Continue Reading RFA-CK20-003: Analysis and Simulation of Bacterial Infections and Resource Strain in Hospitals during the COVID-19 Pandemic
Qin Y, Du H, Pei S. (2026). Learning shared forecast-error structure to improve ensemble forecasts of seasonal respiratory outbreaks. medRxiv : the preprint server for health sciences
Achangwa C, Cho S, Ko Y, Kim BI, Ali ST, Pei S, Ryu S. (2026). Incubation Period of Pertussis During a School-based Outbreak, South Korea, 2024. The Journal of infectious diseases
Guo P, Loh WY, Maung K, Dickens BL, Pei S, Choo ELW, Tan KB, Abishgenadan J, Ma P, Lim JT. (2026). Ascertaining cause-specific emergency department demand using forecast combinations. BMC emergency medicine
Wang P, Wang X, Zhang W, Wang Y, Pei S, Xu XK, Yang W. (2026). Rural-to-urban migrant worker mobility shaped measles epidemics in China. PLoS computational biology, 22(4)
Zhang R, Deng R, Liu S, Yao Q, Shaman J, Grenfell BT, Viboud C, Pei S. (2026). Reconstructing the early spatial spread of pandemic respiratory viruses in the United States. Proceedings of the National Academy of Sciences of the United States of America, 123(2)
Zhang R, Tai J, Yao Q, Yang W, Ruggeri K, Shaman J, Pei S. (2025). Behavior-driven forecasts of neighborhood-level COVID-19 spread in New York City. PLoS computational biology, 21(4)
Jiang X, Li H, Ren H, Liu M, Zhou D, Lin S, Liu Z, Yuan J, Xie N, Cohen AA, Pei S, Zhou J. (2026). The Disrupted Bidirectional Regulation and Coupling of Resting-State Blood Pressure and Heartbeat in Hypertension. Aging cell, 25(1)
Cascante Vega J, Yaari R, Robin T, Wen L, Zucker J, Uhlemann AC, Pei S, Shaman J. (2025). Estimating nosocomial transmission of micro-organisms in hospital settings using patient records and culture data. Epidemics, (50)
Pei S, Seeram D, Blumberg S, Shopsin B, Uhlemann AC, Shaman J. (2025). Inferring asymptomatic carriers of antimicrobial-resistant organisms in hospitals using genomic, microbiological and patient mobility data. Nature communications, 16(1)
Cohen AA, Picard M, Beard JR, Belsky DW, Herbstman J, Kuryla CL, Liu M, Makarem N, Malinsky D, Pei S, Wei Y, Fried LP. (2025). Intrinsic health as a foundation for a science of health. Science advances, 11(25)
Cheng Z, Ruktanonchai NW, Wesolowski A, Pei S, Wang J, Cockings S, Tatem AJ, Lai S. (2025). Social, mobility and contact networks in shaping health behaviours and infectious disease dynamics: a scoping review. Infectious diseases of poverty, 14(1)
Yao Q, Lynch VD, Liu M, Wu X, Parks RM, Pei S. (2025). Adaptive mobility responses during Hurricanes Helene and Milton in 2024. medRxiv : the preprint server for health sciences
Cai X, Wang X, Ni H, Zhou J, Liang Y, Yao Y, Fang X, Dai T, Wang L, Fang L, Chen Y, Wu Y, Wu B, Zhang W, Zhang R, Pei S, Liu X, Hao Y, Guo P. (2025). Epidemiological characteristics and transmission dynamics of epidemic Japanese encephalitis in China: a modelling study. The Journal of infection
Yao Q, Zhang R, Britton T, Pei S. (2025). Inferring pathogen superspreading potential using early spatial spread patterns. medRxiv : the preprint server for health sciences
Shaman J, Kandula S, Pei S, Galanti M, Olfson M, Gould M, Keyes K. (2024). Quantifying suicide contagion at population scale. Science advances, 10(31)
Mathis SM, Webber AE, León TM, Murray EL, Sun M, White LA, Brooks LC, Green A, Hu AJ, Rosenfeld R, Shemetov D, Tibshirani RJ, McDonald DJ, Kandula S, Pei S, Yaari R, Yamana TK, Shaman J, Agarwal P, Balusu S, Gururajan G, Kamarthi H, Prakash BA, Raman R, Zhao Z, Rodríguez A, Meiyappan A, Omar S, Baccam P, Gurung HL, Suchoski BT, Stage SA, Ajelli M, Kummer AG, Litvinova M, Ventura PC, Wadsworth S, Niemi J, Carcelen E, Hill AL, Loo SL, McKee CD, Sato K, Smith C, Truelove S, Jung SM, Lemaitre JC, Lessler J, McAndrew T, Ye W, Bosse N, Hlavacek WS, Lin YT, Mallela A, Gibson GC, Chen Y, Lamm SM, Lee J, Posner RG, Perofsky AC, Viboud C, Clemente L, Lu F, Meyer AG, Santillana M, Chinazzi M, Davis JT, Mu K, Pastore Y Piontti A, Vespignani A, Xiong X, Ben-Nun M, Riley P, Turtle J, Hulme-Lowe C, Jessa S, Nagraj VP, Turner SD, Williams D, Basu A, Drake JM, Fox SJ, Suez E, Cojocaru MG, Thommes EW, Cramer EY, Gerding A, Stark A, Ray EL, Reich NG, Shandross L, Wattanachit N, Wang Y, Zorn MW, Aawar MA, Srivastava A, Meyers LA, Adiga A, Hurt B, Kaur G, Lewis BL, Marathe M, Venkatramanan S, Butler P, Farabow A, Ramakrishnan N, Muralidhar N, Reed C, Biggerstaff M, Borchering RK. (2024). Title evaluation of FluSight influenza forecasting in the 2021-22 and 2022-23 seasons with a new target laboratory-confirmed influenza hospitalizations. Nature communications, 15(1)
Robin TT, Cascante-Vega J, Shaman J, Pei S. (2024). System identifiability in a time-evolving agent-based model. PloS one, 19(1)
Ni H, Cai X, Ren J, Dai T, Zhou J, Lin J, Wang L, Wang L, Pei S, Yao Y, Xu T, Xiao L, Liu Q, Liu X, Guo P. (2024). Epidemiological characteristics and transmission dynamics of dengue fever in China. Nature communications, 15(1)
He K, Foerster S, Vora NM, Blaney K, Keeley C, Hendricks L, Varma JK, Long T, Shaman J, Pei S. (2024). Evaluating completion rates of COVID-19 contact tracing surveys in New York City. BMC public health, 24(1)
Yamana TK, Rajagopal S, Hall DC Jr., Moustafa AM, Feder A, Ahmed A, Bianco C, Harris R, Coffin S, Campbell AE, Pei S, Mell JC, Planet PJ, Shaman J. (2024). A two-variant model of SARS-COV-2 transmission: estimating the characteristics of a newly emerging strain. BMC infectious diseases, 24(1)
Lopez VK, Cramer EY, Pagano R, Drake JM, O'Dea EB, Adee M, Ayer T, Chhatwal J, Dalgic OO, Ladd MA, Linas BP, Mueller PP, Xiao J, Bracher J, Castro Rivadeneira AJ, Gerding A, Gneiting T, Huang Y, Jayawardena D, Kanji AH, Le K, Mühlemann A, Niemi J, Ray EL, Stark A, Wang Y, Wattanachit N, Zorn MW, Pei S, Shaman J, Yamana TK, Tarasewicz SR, Wilson DJ, Baccam S, Gurung H, Stage S, Suchoski B, Gao L, Gu Z, Kim M, Li X, Wang G, Wang L, Wang Y, Yu S, Gardner L, Jindal S, Marshall M, Nixon K, Dent J, Hill AL, Kaminsky J, Lee EC, Lemaitre JC, Lessler J, Smith CP, Truelove S, Kinsey M, Mullany LC, Rainwater-Lovett K, Shin L, Tallaksen K, Wilson S, Karlen D, Castro L, Fairchild G, Michaud I, Osthus D, Bian J, Cao W, Gao Z, Lavista Ferres J, Li C, Liu TY, Xie X, Zhang S, Zheng S, Chinazzi M, Davis JT, Mu K, Pastore Y Piontti A, Vespignani A, Xiong X, Walraven R, Chen J, Gu Q, Wang L, Xu P, Zhang W, Zou D, Gibson GC, Sheldon D, Srivastava A, Adiga A, Hurt B, Kaur G, Lewis B, Marathe M, Peddireddy AS, Porebski P, Venkatramanan S, Wang L, Prasad PV, Walker JW, Webber AE, Slayton RB, Biggerstaff M, Reich NG, Johansson MA. (2024). Challenges of COVID-19 Case Forecasting in the US, 2020-2021. PLoS computational biology, 20(5)
Zhong L, Lopez D, Pei S, Gao J. (2024). Healthcare system resilience and adaptability to pandemic disruptions in the United States. Nature medicine
Zhang L, Zhang Z, Pei S, Gao Q, Chen W. (2024). Quantifying the presymptomatic transmission of COVID-19 in the USA. Mathematical biosciences and engineering : MBE, 21(1)
Hajlasz M, Pei S. (2024). Predictability of human mobility during the COVID-19 pandemic in the United States. PNAS nexus, 3(8)
Zhang R, Qu X, Zhang Q, Xu X, Pei S. (2024). Influence maximization based on threshold models in hypergraphs. Chaos (Woodbury, N.Y.), 34(2)
Boldea O, Alipoor A, Pei S, Shaman J, Rozhnova G. (2024). Age-specific transmission dynamics of SARS-CoV-2 during the first 2 years of the pandemic. PNAS nexus, 3(2)
Zhang R, Tai J, Pei S. (2023). Ensemble inference of unobserved infections in networks using partial observations. PLoS computational biology, 19(8)
Zeng Q, Yu X, Ni H, Xiao L, Xu T, Wu H, Chen Y, Deng H, Zhang Y, Pei S, Xiao J, Guo P. (2023). Dengue transmission dynamics prediction by combining metapopulation networks and Kalman filter algorithm. PLoS neglected tropical diseases, 17(6)
Cascante-Vega J, Galanti M, Schley K, Pei S, Shaman J. (2023). Inference of transmission dynamics and retrospective forecast of invasive meningococcal disease. PLoS computational biology, 19(10)
Du Z, Zhang X, Wang L, Yao S, Bai Y, Tan Q, Xu X, Pei S, Xiao J, Tsang TK, Liao Q, Lau EHY, Wu P, Gao C, Cowling BJ. (2023). Characterizing Human Collective Behaviors During COVID-19 - Hong Kong SAR, China, 2020. China CDC weekly, 5(4)
Yamana TK, Galanti M, Pei S, Di Fusco M, Angulo FJ, Moran MM, Khan F, Swerdlow DL, Shaman J. (2023). The impact of COVID-19 vaccination in the US: Averted burden of SARS-COV-2-related cases, hospitalizations and deaths. PloS one, 18(4)
Howerton E, Contamin L, Mullany LC, Qin M, Reich NG, Bents S, Borchering RK, Jung SM, Loo SL, Smith CP, Levander J, Kerr J, Espino J, van Panhuis WG, Hochheiser H, Galanti M, Yamana T, Pei S, Shaman J, Rainwater-Lovett K, Kinsey M, Tallaksen K, Wilson S, Shin L, Lemaitre JC, Kaminsky J, Hulse JD, Lee EC, McKee CD, Hill A, Karlen D, Chinazzi M, Davis JT, Mu K, Xiong X, Pastore Y Piontti A, Vespignani A, Rosenstrom ET, Ivy JS, Mayorga ME, Swann JL, España G, Cavany S, Moore S, Perkins A, Hladish T, Pillai A, Ben Toh K, Longini I Jr., Chen S, Paul R, Janies D, Thill JC, Bouchnita A, Bi K, Lachmann M, Fox SJ, Meyers LA, Srivastava A, Porebski P, Venkatramanan S, Adiga A, Lewis B, Klahn B, Outten J, Hurt B, Chen J, Mortveit H, Wilson A, Marathe M, Hoops S, Bhattacharya P, Machi D, Cadwell BL, Healy JM, Slayton RB, Johansson MA, Biggerstaff M, Truelove S, Runge MC, Shea K, Viboud C, Lessler J. (2023). Evaluation of the US COVID-19 Scenario Modeling Hub for informing pandemic response under uncertainty. Nature communications, 14(1)
Mathis SM, Webber AE, León TM, Murray EL, Sun M, White LA, Brooks LC, Green A, Hu AJ, McDonald DJ, Rosenfeld R, Shemetov D, Tibshirani RJ, Kandula S, Pei S, Shaman J, Yaari R, Yamana TK, Agarwal P, Balusu S, Gururajan G, Kamarthi H, Prakash BA, Raman R, Rodríguez A, Zhao Z, Meiyappan A, Omar S, Baccam P, Gurung HL, Stage SA, Suchoski BT, Ajelli M, Kummer AG, Litvinova M, Ventura PC, Wadsworth S, Niemi J, Carcelen E, Hill AL, Jung SM, Lemaitre JC, Lessler J, Loo SL, McKee CD, Sato K, Smith C, Truelove S, McAndrew T, Ye W, Bosse N, Hlavacek WS, Lin YT, Mallela A, Chen Y, Lamm SM, Lee J, Posner RG, Perofsky AC, Viboud C, Clemente L, Lu F, Meyer AG, Santillana M, Chinazzi M, Davis JT, Mu K, Piontti APY, Vespignani A, Xiong X, Ben-Nun M, Riley P, Turtle J, Hulme-Lowe C, Jessa S, Nagraj VP, Turner SD, Williams D, Basu A, Drake JM, Fox SJ, Gibson GC, Suez E, Thommes EW, Cojocaru MG, Cramer EY, Gerding A, Stark A, Ray EL, Reich NG, Shandross L, Wattanachit N, Wang Y, Zorn MW, Al Aawar M, Srivastava A, Meyers LA, Adiga A, Hurt B, Kaur G, Lewis BL, Marathe M, Venkatramanan S, Butler P, Farabow A, Muralidhar N, Ramakrishnan N, Reed C, Biggerstaff M, Borchering RK. (2023). Evaluation of FluSight influenza forecasting in the 2021-22 and 2022-23 seasons with a new target laboratory-confirmed influenza hospitalizations. medRxiv : the preprint server for health sciences
Sun HC, Pei S, Wang L, Sun YY, Xu XK. (2023). The Impact of Spring Festival Travel on Epidemic Spreading in China. Viruses, 15(7)
Ryu S, Han C, Ali ST, Achangwa C, Yang B, Pei S. (2023). Association of public health and social measures on the hand-foot-mouth epidemic in South Korea. Journal of infection and public health, 16(6)
Luo W, Liu Q, Zhou Y, Ran Y, Liu Z, Hou W, Pei S, Lai S. (2023). Spatiotemporal variations of "triple-demic" outbreaks of respiratory infections in the United States in the post-COVID-19 era. BMC public health, 23(1)
Ryu S, Han C, Ali ST, Achangwa C, Yang B, Pei S. (2023). Corrigendum to "Association of public health and social measures on the hand-foot-mouth epidemic in South Korea" [J Infect Public Health 16 (2023) 859-64]. Journal of infection and public health
Prasad PV, Steele MK, Reed C, Meyers LA, Du Z, Pasco R, Alfaro-Murillo JA, Lewis B, Venkatramanan S, Schlitt J, Chen J, Orr M, Wilson ML, Eubank S, Wang L, Chinazzi M, Pastore Y Piontti A, Davis JT, Halloran ME, Longini I, Vespignani A, Pei S, Galanti M, Kandula S, Shaman J, Haw DJ, Arinaminpathy N, Biggerstaff M. (2023). Multimodeling approach to evaluating the efficacy of layering pharmaceutical and nonpharmaceutical interventions for influenza pandemics. Proceedings of the National Academy of Sciences of the United States of America, 120(28)
Howerton E, Contamin L, Mullany LC, Qin M, Reich NG, Bents S, Borchering RK, Jung SM, Loo SL, Smith CP, Levander J, Kerr J, Espino J, van Panhuis WG, Hochheiser H, Galanti M, Yamana T, Pei S, Shaman J, Rainwater-Lovett K, Kinsey M, Tallaksen K, Wilson S, Shin L, Lemaitre JC, Kaminsky J, Hulse JD, Lee EC, McKee C, Hill A, Karlen D, Chinazzi M, Davis JT, Mu K, Xiong X, Piontti APY, Vespignani A, Rosenstrom ET, Ivy JS, Mayorga ME, Swann JL, Espana G, Cavany S, Moore S, Perkins A, Hladish T, Pillai A, Toh KB, Longini I Jr., Chen S, Paul R, Janies D, Thill JC, Bouchnita A, Bi K, Lachmann M, Fox S, Meyers LA, , Srivastava A, Porebski P, Venkatramanan S, Adiga A, Lewis B, Klahn B, Outten J, Hurt B, Chen J, Mortveit H, Wilson A, Marathe M, Hoops S, Bhattacharya P, Machi D, Cadwell BL, Healy JM, Slayton RB, Johansson MA, Biggerstaff M, Truelove S, Runge MC, Shea K, Viboud C, Lessler J. (2023). Informing pandemic response in the face of uncertainty. An evaluation of the U.S. COVID-19 Scenario Modeling Hub. medRxiv : the preprint server for health sciences
Dai K, Foerster S, Vora NM, Blaney K, Keeley C, Hendricks L, Varma JK, Long T, Shaman J, Pei S. (2023). Community transmission of SARS-CoV-2 during the Delta wave in New York City. BMC infectious diseases, 23(1)
Schneider T, Dunbar ORA, Wu J, Böttcher L, Burov D, Garbuno-Inigo A, Wagner GL, Pei S, Daraio C, Ferrari R, Shaman J. (2022). Epidemic management and control through risk-dependent individual contact interventions. PLoS computational biology, 18(6)
Zhang B, Huang W, Pei S, Zeng J, Shen W, Wang D, Wang G, Chen T, Yang L, Cheng P, Wang D, Shu Y, Du X. (2022). Mechanisms for the circulation of influenza A(H3N2) in China: A spatiotemporal modelling study. PLoS pathogens, 18(12)
Borchering RK, Mullany LC, Howerton E, Chinazzi M, Smith CP, Qin M, Reich NG, Contamin L, Levander J, Kerr J, Espino J, Hochheiser H, Lovett K, Kinsey M, Tallaksen K, Wilson S, Shin L, Lemaitre JC, Hulse JD, Kaminsky J, Lee EC, Hill AL, Davis JT, Mu K, Xiong X, Pastore Y Piontti A, Vespignani A, Srivastava A, Porebski P, Venkatramanan S, Adiga A, Lewis B, Klahn B, Outten J, Hurt B, Chen J, Mortveit H, Wilson A, Marathe M, Hoops S, Bhattacharya P, Machi D, Chen S, Paul R, Janies D, Thill JC, Galanti M, Yamana T, Pei S, Shaman J, España G, Cavany S, Moore S, Perkins A, Healy JM, Slayton RB, Johansson MA, Biggerstaff M, Shea K, Truelove SA, Runge MC, Viboud C, Lessler J. (2023). Impact of SARS-CoV-2 vaccination of children ages 5-11 years on COVID-19 disease burden and resilience to new variants in the United States, November 2021-March 2022: A multi-model study. Lancet regional health. Americas, (17)
Zhang R, Wang Y, Lv Z, Pei S. (2022). Evaluating the impact of stay-at-home and quarantine measures on COVID-19 spread. BMC infectious diseases, 22(1)
Chen Y, Liu T, Yu X, Zeng Q, Cai Z, Wu H, Zhang Q, Xiao J, Ma W, Pei S, Guo P. (2022). An ensemble forecast system for tracking dynamics of dengue outbreaks and its validation in China. PLoS computational biology, 18(6)
Du Z, Wang L, Shan S, Lam D, Tsang TK, Xiao J, Gao H, Yang B, Ali ST, Pei S, Fung IC, Lau EHY, Liao Q, Wu P, Meyers LA, Leung GM, Cowling BJ. (2022). Pandemic fatigue impedes mitigation of COVID-19 in Hong Kong. Proceedings of the National Academy of Sciences of the United States of America, 119(48)
Huang B, Huang Z, Chen C, Lin J, Tam T, Hong Y, Pei S. (2022). Social vulnerability amplifies the disparate impact of mobility on COVID-19 transmissibility across the United States. Humanities & social sciences communications, 9(1)
Truelove S, Smith CP, Qin M, Mullany LC, Borchering RK, Lessler J, Shea K, Howerton E, Contamin L, Levander J, Kerr J, Hochheiser H, Kinsey M, Tallaksen K, Wilson S, Shin L, Rainwater-Lovett K, Lemairtre JC, Dent J, Kaminsky J, Lee EC, Perez-Saez J, Hill A, Karlen D, Chinazzi M, Davis JT, Mu K, Xiong X, Pastore Y Piontti A, Vespignani A, Srivastava A, Porebski P, Venkatramanan S, Adiga A, Lewis B, Klahn B, Outten J, Orr M, Harrison G, Hurt B, Chen J, Vullikanti A, Marathe M, Hoops S, Bhattacharya P, Machi D, Chen S, Paul R, Janies D, Thill JC, Galanti M, Yamana TK, Pei S, Shaman JL, Healy JM, Slayton RB, Biggerstaff M, Johansson MA, Runge MC, Viboud C. (2022). Projected resurgence of COVID-19 in the United States in July-December 2021 resulting from the increased transmissibility of the Delta variant and faltering vaccination. eLife, (11)
Zhang C, Zhang X, Bai Y, Lau EHY, Pei S. (2022). The Structural Identifiability of a Humidity-Driven Epidemiological Model of Influenza Transmission. Viruses, 14(12)
Cramer EY, Ray EL, Lopez VK, Bracher J, Brennen A, Castro Rivadeneira AJ, Gerding A, Gneiting T, House KH, Huang Y, Jayawardena D, Kanji AH, Khandelwal A, Le K, Mühlemann A, Niemi J, Shah A, Stark A, Wang Y, Wattanachit N, Zorn MW, Gu Y, Jain S, Bannur N, Deva A, Kulkarni M, Merugu S, Raval A, Shingi S, Tiwari A, White J, Abernethy NF, Woody S, Dahan M, Fox S, Gaither K, Lachmann M, Meyers LA, Scott JG, Tec M, Srivastava A, George GE, Cegan JC, Dettwiller ID, England WP, Farthing MW, Hunter RH, Lafferty B, Linkov I, Mayo ML, Parno MD, Rowland MA, Trump BD, Zhang-James Y, Chen S, Faraone SV, Hess J, Morley CP, Salekin A, Wang D, Corsetti SM, Baer TM, Eisenberg MC, Falb K, Huang Y, Martin ET, McCauley E, Myers RL, Schwarz T, Sheldon D, Gibson GC, Yu R, Gao L, Ma Y, Wu D, Yan X, Jin X, Wang YX, Chen Y, Guo L, Zhao Y, Gu Q, Chen J, Wang L, Xu P, Zhang W, Zou D, Biegel H, Lega J, McConnell S, Nagraj VP, Guertin SL, Hulme-Lowe C, Turner SD, Shi Y, Ban X, Walraven R, Hong QJ, Kong S, van de Walle A, Turtle JA, Ben-Nun M, Riley S, Riley P, Koyluoglu U, DesRoches D, Forli P, Hamory B, Kyriakides C, Leis H, Milliken J, Moloney M, Morgan J, Nirgudkar N, Ozcan G, Piwonka N, Ravi M, Schrader C, Shakhnovich E, Siegel D, Spatz R, Stiefeling C, Wilkinson B, Wong A, Cavany S, España G, Moore S, Oidtman R, Perkins A, Kraus D, Kraus A, Gao Z, Bian J, Cao W, Lavista Ferres J, Li C, Liu TY, Xie X, Zhang S, Zheng S, Vespignani A, Chinazzi M, Davis JT, Mu K, Pastore Y Piontti A, Xiong X, Zheng A, Baek J, Farias V, Georgescu A, Levi R, Sinha D, Wilde J, Perakis G, Bennouna MA, Nze-Ndong D, Singhvi D, Spantidakis I, Thayaparan L, Tsiourvas A, Sarker A, Jadbabaie A, Shah D, Della Penna N, Celi LA, Sundar S, Wolfinger R, Osthus D, Castro L, Fairchild G, Michaud I, Karlen D, Kinsey M, Mullany LC, Rainwater-Lovett K, Shin L, Tallaksen K, Wilson S, Lee EC, Dent J, Grantz KH, Hill AL, Kaminsky J, Kaminsky K, Keegan LT, Lauer SA, Lemaitre JC, Lessler J, Meredith HR, Perez-Saez J, Shah S, Smith CP, Truelove SA, Wills J, Marshall M, Gardner L, Nixon K, Burant JC, Wang L, Gao L, Gu Z, Kim M, Li X, Wang G, Wang Y, Yu S, Reiner RC, Barber R, Gakidou E, Hay SI, Lim S, Murray C, Pigott D, Gurung HL, Baccam P, Stage SA, Suchoski BT, Prakash BA, Adhikari B, Cui J, Rodríguez A, Tabassum A, Xie J, Keskinocak P, Asplund J, Baxter A, Oruc BE, Serban N, Arik SO, Dusenberry M, Epshteyn A, Kanal E, Le LT, Li CL, Pfister T, Sava D, Sinha R, Tsai T, Yoder N, Yoon J, Zhang L, Abbott S, Bosse NI, Funk S, Hellewell J, Meakin SR, Sherratt K, Zhou M, Kalantari R, Yamana TK, Pei S, Shaman J, Li ML, Bertsimas D, Skali Lami O, Soni S, Tazi Bouardi H, Ayer T, Adee M, Chhatwal J, Dalgic OO, Ladd MA, Linas BP, Mueller P, Xiao J, Wang Y, Wang Q, Xie S, Zeng D, Green A, Bien J, Brooks L, Hu AJ, Jahja M, McDonald D, Narasimhan B, Politsch C, Rajanala S, Rumack A, Simon N, Tibshirani RJ, Tibshirani R, Ventura V, Wasserman L, O'Dea EB, Drake JM, Pagano R, Tran QT, Ho LST, Huynh H, Walker JW, Slayton RB, Johansson MA, Biggerstaff M, Reich NG. (2022). Evaluation of individual and ensemble probabilistic forecasts of COVID-19 mortality in the United States. Proceedings of the National Academy of Sciences of the United States of America, 119(15)
Du Z, Wang C, Liu C, Bai Y, Pei S, Adam DC, Wang L, Wu P, Lau EHY, Cowling BJ. (2022). Systematic review and meta-analyses of superspreading of SARS-CoV-2 infections. Transboundary and emerging diseases
Galanti M, Pei S, Yamana TK, Angulo FJ, Charos A, Swerdlow DL, Shaman J. (2021). Social distancing remains key during vaccinations. Science (New York, N.Y.), 371(6528)
Pei S, Yamana TK, Kandula S, Galanti M, Shaman J. (2021). Burden and characteristics of COVID-19 in the United States during 2020. Nature
Gimbrone C, Rutherford C, Kandula S, Martínez-Alés G, Shaman J, Olfson M, Gould MS, Pei S, Galanti M, Keyes KM. (2021). Associations between COVID-19 mobility restrictions and economic, mental health, and suicide-related concerns in the US using cellular phone GPS and Google search volume data. PloS one, 16(12)
Qi Y, Shaman J, Pei S. (2021). Quantifying the impact of COVID-19 non-pharmaceutical interventions on influenza transmission in the United States. The Journal of infectious diseases
Pei S, Yamana TK, Kandula S, Galanti M, Shaman J. (2021). Publisher Correction: Burden and characteristics of COVID-19 in the United States during 2020. Nature
Zebrowski A, Rundle A, Pei S, Yaman T, Yang W, Carr BG, Sims S, Doorley R, Schluger N, Quinn JW, Shaman J, Branas CC. (2021). A Spatiotemporal Tool to Project Hospital Critical Care Capacity and Mortality From COVID-19 in US Counties. American journal of public health
Ma Y, Pei S, Shaman J, Dubrow R, Chen K. (2021). Role of meteorological factors in the transmission of SARS-CoV-2 in the United States. Nature communications, 12(1)
Pei S, Teng X, Lewis P, Shaman J. (2021). Optimizing respiratory virus surveillance networks using uncertainty propagation. Nature communications, 12(1)
Pei S, Liljeros F, Shaman J. (2021). Identifying asymptomatic spreaders of antimicrobial-resistant pathogens in hospital settings. Proceedings of the National Academy of Sciences of the United States of America, 118(37)
Xu XK, Wang L, Pei S. (2021). Multiscale mobility explains differential associations between the gross domestic product and COVID-19 transmission in Chinese cities. Journal of travel medicine
Pei S, Wang J, Morone F, Makse HA. (2020). Influencer identification in dynamical complex systems. Journal of complex networks, 8(2)
Kramer SC, Pei S, Shaman J. (2020). Forecasting influenza in Europe using a metapopulation model incorporating cross-border commuting and air travel. PLoS computational biology, 16(10)
Zhou B, Pei S, Muchnik L, Meng X, Xu X, Sela A, Havlin S, Stanley HE. (2020). Realistic modelling of information spread using peer-to-peer diffusion patterns. Nature human behaviour
Pei S, Shaman J. (2020). Aggregating forecasts of multiple respiratory pathogens supports more accurate forecasting of influenza-like illness. PLoS computational biology, 16(10)
Li R, Pei S, Chen B, Song Y, Zhang T, Yang W, Shaman J. (2020). Substantial undocumented infection facilitates the rapid dissemination of novel coronavirus (COVID-19). medRxiv : the preprint server for health sciences
Li R, Pei S, Chen B, Song Y, Zhang T, Yang W, Shaman J. (2020). Substantial undocumented infection facilitates the rapid dissemination of novel coronavirus (SARS-CoV2). Science (New York, N.Y.)
Ma Y, Pei S, Shaman J, Dubrow R, Chen K. (2020). Role of air temperature and humidity in the transmission of SARS-CoV-2 in the United States. medRxiv : the preprint server for health sciences
Pei S, Kandula S, Shaman J. (2020). Differential effects of intervention timing on COVID-19 spread in the United States. Science advances, 6(49)
Bomfim R, Pei S, Shaman J, Yamana T, Makse HA, Andrade JS Jr., Lima Neto AS, Furtado V. (2020). Predicting dengue outbreaks at neighbourhood level using human mobility in urban areas. Journal of the Royal Society, Interface, 17(171)
Pei S, Dahl KA, Yamana TK, Licker R, Shaman J. (2020). Compound Risks of Hurricane Evacuation Amid the COVID-19 Pandemic in the United States. GeoHealth, 4(12)
Pei S, Cane MA, Shaman J. (2019). Predictability in process-based ensemble forecast of influenza. PLoS computational biology, 15(2)
Kandula S, Pei S, Shaman J. (2019). Improved forecasts of influenza-associated hospitalization rates with Google Search Trends. Journal of the Royal Society, Interface, 16(155)
Sy KTL, Shaman J, Kandula S, Pei S, Gould M, Keyes KM. (2019). Spatiotemporal clustering of suicides in the US from 1999 to 2016: a spatial epidemiological approach. Social psychiatry and psychiatric epidemiology, 54(12)
Wang J, Zhang R, Wei W, Pei S, Zheng Z. (2018). On the stability of multilayer Boolean networks under targeted immunization. Chaos (Woodbury, N.Y.), 29(1)
Pei S, Morone F, Liljeros F, Makse H, Shaman JL. (2018). Inference and control of the nosocomial transmission of methicillin-resistant Staphylococcus aureus. Elife, (7)
Fu C, Dong Z, Shen J, Yang Z, Liao Y, Hu W, Pei S, Shaman J. (2018). Rotavirus Gastroenteritis Infection Among Children Vaccinated and Unvaccinated With Rotavirus Vaccine in Southern China: A Population-Based Assessment. JAMA network open, 1(4)
Pei S, Teng X, Shaman J, Morone F, Makse HA. (2017). Efficient collective influence maximization in cascading processes with first-order transitions. Scientific reports, (7)
Fu C, Shen J, Lu L, Li Y, Cao Y, Wang M, Pei S, Yang Z, Guo Q, Shaman J. (2017). Pre-vaccination evolution of antibodies among infants 0, 3 and 6months of age: A longitudinal analysis of measles, enterovirus 71 and coxsackievirus 16. Vaccine, 35(31)
Pei S, Shaman J. (2017). Counteracting structural errors in ensemble forecast of influenza outbreaks. Nature communications, 8(1)
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