Jun CaiDepartment of Earth System ScienceTsinghua University

Room S1016, Meng Minwei BuildingTsinghua University

Beijing 100084, ChinaH +(86) 157 1100 7525

B cai-j12@mails.tsinghua.edu.cnÍ blog.tonytsai.name

caijun

Education2012.09–present Ph.D. (expected October 2019), Department of Earth System Science, Ts-

inghua University, Beijing, China.Major Ecology Supervisor Prof. Bing Xu

Research Interest Influenza Transmission Dynamics, Infectious Disease Epi-demiology, Infectious Disease Ecology, Environmental Health

2008.09–2012.06 B.S., School of Resource and Environmental Science, Wuhan University,Wuhan, China.

Major Geographic Information SystemThesis Spatio-temporal Characteristics of Influenza

A(H1N1)pdm09 during Early Phase in Mainland ChinaAdvisors Prof. Huanfeng Shen and Prof. Bing Xu

Work Experiences2016.05–2016.11 Visiting Predoctoral Fellow, Division of International Epidemiology and Popu-

lation Studies (DIEPS), Fogarty International Center (FIC), National Institutesof Health (NIH), Bethesda, MD, USA.Co-funded by Tsinghua Scholarship for Overseas Graduate Studies and SupplementalPre-doc Fellowship from the NIH Visiting ProgramFocus on modeling spatial-temporal transmission of influenza A(H1N1)pdm09 in main-land China supervised by Dr. Cecile Viboud.

2015.05–2015.08 Google Summer of Code 2015 participant with R, Beijing, China.Optimize disk usage for animint package by saving common data in every tsv into acommon tsv mentored by Dr. Toby Dylan Hocking.

2014.09–2015.06 Intern, Big Data Lab at Baidu, Inc, Beijing, China.Utilize Baidu search querys and Baidu Map position data to improve influenza forecast-ing accuracy of Baidu Disease Trend supervised by Dr. Zhiyong Shen.

2012.09–Current Research Assistant, Department of Earth System Science, Tsinghua Univer-sity, Beijing, China.

Participation in Projects and Workshops{ Projects

863 Program Spatio-temporal Transmission of Influenza and Early Warning System underGlobal Change

973 Program Impacts of Climate Change on Human Health and Adaptation Mechanisms

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{ WorkshopsNov 2016 Multinational Influenza Seasonal Mortality Study (MISMS) Workshop, FIC of

NIH, Bethesda, MD, USA.Sep 2016 Summer School of Computational Biology for Infectious Diseases in the epi-

demics forecasting specialty, USTH, CAMPUS FRANCE, La France au Viet-nam, IRD, cnrs, FIC of NIH, GREASE, CDC, Institut Pasteur InternationalNetwork, FONDATION MERIEUX, wellcome trust, WHO, Hanoi, Vietnam.

Oct 2015 MISMS Workshop, FIC and NCBI of NIH, APCMV 2015 and National TaiwanUniversity, Taipei, China.

Nov 2013 EMBO Practical Course-Bioinformatics and Statistics for Large-scale Data, BGI,Shenzhen, China.

Jun 2013 1st CPGIS Health-GIS Workshop on Applications of GIS in Public Health,CPGIS, Beijing, China.

Publications Google Scholar Citations: 169, h-index: 7, i10-index: 7{ Journal

Influenza — Infectious Diseases[1] Xu, B.; Cai, J.; He, D.; Chowell, G. & Xu, B. (2019). Mechanistic Modelling of Multiple

Waves in an Influenza Epidemic or Pandemic. Journal of Theoretical Biology. [UnderReview]

[2] Li, Y.; Cazelles, B.; Yang, G.; Laine, M.; Huang, Z.; Cai, J.; Tan, H.; Stenseth, N. &Tian, H. (2019). Intrinsic and extrinsic drivers of transmission dynamics of the hemor-rhagic fever with renal syndrome caused by the Seoul virus. PLOS Neglected TropicalDiseases. [Submitted]

[3] Zhang, B.; Deng, X.; Yang, Y.; Cai, J.; Liu, T.; Lin, H.; He, H.; Rutherford, S.; Hu, Y.;Zhu, G.; Xiao, J.; Xie, S.; Du, X. & Ma, W. (2019). Assessment of the impact of mete-orological factors on pathogen transmission and reporting in a mechanistic transmissionmodel: the population case of mumps. PLOS Computational Biology. [Under Review]

[4] Cai, J.; Zhang, X.; Xu, B.; Chan, K. K. Y.; Chowell, G.; Tian, H. & Xu, B. (2019). Amaximum curvature method for estimating epidemic onset of seasonal influenza in Japan.BMC Infectious Diseases. doi:10.1186/s12879-019-3777-x.

[5] Kamvar, Z. N.; Cai, J.; Pulliam, J. R.; Schumacher, J. & Jombart, T. (2019). Epidemiccurves made easy using the R package incidence [version 1; peer review: 1 approved, 1approved with reservations]. F1000Research, 8:139. doi:10.12688/f1000research.18002.1.

[6] Cai, J.; Xu, B.; Chan, K. K. Y.; Zhang, X.; Zhang, B.; Chen, Z. & Xu, B. (2019).Roles of Different Transport Modes in the Spatial Spread of the 2009 Influenza A(H1N1)Pandemic in Mainland China. International Journal of Environmental Research and PublicHealth, 16(2), 222. doi:10.3390/ijerph16020222.

[7] Tian, H.; Yu, P.; Cazelles, B.; Xu, L.; Tan, H.; Yang, J.; Huang, S.; Xu, B.; Cai, J.; Ma,C.; Wei, J.; Li, S.; Qu, J.; Laine, M.; Wang, J.; Tong, S.; Stenseth, N. & Xu, B. (2017).Interannual cycles of Hantaan virus outbreaks at the human–animal interface in CentralChina are controlled by temperature and rainfall. Proceedings of the National Academyof Sciences, 201701777. doi:10.1073/pnas.1701777114.

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[8] Li, R.; Bai, Y.; Heaney, A.; Kandula, S.; Cai, J.; Zhao, X.; Xu, B. & Shaman, J. (2017).Inference and forecast of H7N9 influenza in China, 2013 to 2015. Eurosurveillance,22(7):pii=30462. doi:10.2807/1560-7917.ES.2017.22.7.30462.

[9] Zhao, X.; Cai, J.; Feng, D.; Feng, Y. & Xu, B. (2016). Meteorological Influence on the2009 Influenza A (H1N1) Pandemic in Mainland China. Environmental Earth Sciences,75(10), 1-9. doi:10.1007/s12665-016-5275-4.

[10]Jiang, Z.; Bai, J.; Cai, J.; Li, R.; Jin, Z. & Xu, B. (2012). Characterization of theGlobal Spatio-temporal Transmission of the 2009 Pandemic H1N1 Influenza. Journal ofGeo-Information Science, 14, 794-799. doi:10.3724/SP.J.1047.2012.00794. [In Chinese]

Non-communicable Diseases[11]Feng, Y.*; Cai, J.*; Tong, X.; Chen, R.; Zhu, Y.; Xu, B. & Mo, X. (2018). Non-

inheritable risk factors during pregnancy for congenital heart defects in offspring: amatched case-control study. International Journal of Cardiology, 264, 45-52. doi:10.1016/j.ijcard.2018.04.003.

Statistics and Visualizations[12]Sievert, C.; VanderPlas, S.; Cai, J.; Ferris, K.; Khan, F. U. F. & Hocking, T. D. (2018).

Extending ggplot2 for linked and dynamic web graphics. Journal of Computational andGraphical Statistics, 1-10. doi:10.1080/10618600.2018.1513367.

Air Quality — Remote Sensing[13]Chen, Z.; Chen, D.; Zhao, C.; Kwan, M.; Cai, J.; Zhuang, Y.; Zhao, B.; Wang, X.;

Chen, B.; Yang, J.; Li, R.; He, B.; Gao, B.; Wang, K. & Xu, B. (2019). Influence ofmeteorological conditions on PM2.5 concentrations in China: a review of methodologyand mechanism. Environment International. [Submitted]

[14]Chen, Z.; Chen, D.; Li, R.; Cai, J.; Zhuang, Y.; Gao, B.; Yang, L. & Li, M. (2019).Understanding the causal influence of major meteorological factors on ground ozoneconcentrations across China. Environmental Science & Technology. [Submitted]

[15]Chen, Z.; Chen, D.; Xie, X.; Cai, J.; Zhuang, Y.; Cheng, N.; He, B. & Gao, B. (2019).Spatial self-aggregation effects and national division of city-level PM2.5 concentrations inChina based on spatio-temporal clustering. Journal of Cleaner Production, 207, 875-881.doi:10.1016/j.jclepro.2018.10.080.

[16]Zhuang, Y.; Chen, D.; Li, R.; Chen, Z.; Cai, J.; He, B.; Gao, B.; Cheng, N. & Huang,Y. (2018). Understanding the Influence of Crop Residue Burning on PM2.5 and PM10Concentrations in China from 2013 to 2017 Using MODIS Data. International Journalof Environmental Research and Public Health, 15(7), 1504. doi:10.3390/ijerph15071504.

[17]Chen, Z.; Xie, X.; Cai, J.; Chen, D.; Gao, B.; He, B.; Cheng, N. & Xu, B. (2018).Understanding meteorological influences on PM2.5 concentrations across China: a tem-poral and spatial perspective. Atmospheric Chemistry and Physics, 18(8), 5343-5358.doi:10.5194/acp-18-5343-2018.

[18]Chen, Z.; Chen, D.; Zhuang, Y.; Cai, J.; Zhao, N.; He, B.; Gao, B. & Xu, B. (2017).Examining the Influence of Crop Residue Burning on Local PM2.5 Concentrations in

*Co-first authors

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Heilongjiang Province Using Ground Observation and Remote Sensing Data. RemoteSensing, 9(10), 971. doi:10.3390/rs91009714.

[19]Lv, B.; Cai, J.; Xu, B. & Bai, Y. (2017). Understanding the Rising Phase of thePM2.5 Concentration Evolution in Large China Cities. Scientific Reports, 7, 46456.doi:10.1038/srep46456.

[20]Chen, Z.*; Cai, J.*; Gao, B.; Xu, B.; Dai, S.; He, B. & Xie, X. (2017). Detecting thecausality influence of individual meteorological factors on local PM2.5 concentration inthe Jing-Jin-Ji region. Scientific Reports, 7, 40735. doi:10.1038/srep40735.

[21]Lv, B.; Hu, Y.; Chang H.; Russell A.; Cai, J.; Xu, B. & Bai, Y. (2017). Daily estimationof ground-level PM2.5 concentrations at 4 km resolution over Beijing-Tianjin-Hebei byfusing MODIS and ground observations. Science of The Total Environment, 580, 235-244. doi:10.1016/j.scitotenv.2016.12.049.

[22]Chen, Z.; Xu, B.; Cai, J. & Gao, B. (2016). Understanding tempo-patterns and charac-teristics of air quality in the city of Beijing: a local and regional perspective. AtmosphericEnvironment, 127, 303-315. doi:10.1016/j.atmosenv.2015.12.011.

[23]Zhang, Y.; Lu, H.; Shen, S. & Cai, J. (2015). Comment on ”Do aerosols impact groundobservation of total cloud cover over the North China Plain?”. Global and PlanetaryChange, 133, 120-124. doi:10.1016/j.gloplacha.2015.08.008.

[24]Lu, H.; Zhang, Y. & Cai, J. (2015). Consistency and differences between remotely sensedand surface observed total cloud cover over China. International Journal of RemoteSensing, 36, 4160-4176. doi:10.1080/01431161.2015.1072651.

[25]Chen, L.; Jin, Z.; Michishita, R.; Cai, J.; Yue, T.; Chen, B. & Xu, B. (2014). Dynamicmonitoring of wetland cover changes using time-series remote sensing imagery. EcologicalInformatics, 24, 17-26. doi:10.1016/j.ecoinf.2014.06.007.

{ Conference[1] Cai, J. (2018, May). Non-inheritable risk factors during pregnancy for congenital heart

defects in offspring: a matched case-control study. The 11th China R Conference (Bei-jing). [Slides]

[2] Cai, J. (2017, May). R Epidemics Consortium and Using Its Packages to Analyze In-fluenza Data. The 10th China R Conference (Beijing). [Slides]

[3] Cai, J. & Xu, B. Air and Railway Travels Accelerated Spatial Spread of 2009 PandemicInfluenza A(H1N1) in mainland China [abstract]. International Conference on EmergingInfectious Diseases 2015 poster and oral presentation abstracts. Emerg Infect Dis. 2015Sep. http://wwwnc.cdc.gov/eid/article/21/9/nn-2109. doi:10.3201/eid2109.NN2109. [Poster]

[4] Zhang, Y.; Lu, H. & Cai, J. (2014, November). Towards the comparison of satelliteand ground based cloud amount over China. In SPIE Asia Pacific Remote Sensing (pp.92590A-92590A-8). International Society for Optics and Photonics. doi:10.1117/12.2068979.

[5] Zhang, Y.; Lu, H. & Cai, J. (2014, July). Estimating regional amount of low cloudsover North China plain from multi-source remote sensing data. In Geoscience and Re-mote Sensing Symposium (IGARSS), 2014 IEEE International (pp. 4131-4134). IEEE.doi:10.1109/IGARSS.2014.6947396.

{ Book

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[1] Paul Murrell. R Graphics, 2nd Edition. 2011. Hu, S., Zhang, Y., & Cai, J., translated.R 绘图系统. 2016. Posts & Telecom Press. Beijing, China.

Teaching ExperiencesTeaching Assistant

Fall 2015 Data Analysis in Ecology, Prof. Jun Yang, Department of Earth SystemScience, Tsinghua University, Graduate-level.This course introduced students to R programming and data analysis principles andmethods used in ecology.Prepared laboratory materials, instructed laboratory section, graded homework

Professional ServicesReviewer for

PLOS Neglected Tropical Diseases, PLOS Computational Biology, BMC Infectious Diseases

SN Applied Sciences

Member ofR Epidemics Consortium

SkillsProgramming Languages

R Data Analysis, Statistical and Dynamic Modeling, Data Visualization. Authorof geoChina and humidity packages, contributor of animint, AnomalyDetection,corrplot, incidence, ncf and rEDM packages.

Python Automated Data Collection and Batch for ArcGIS Tools. Deveoped PFDProject.

IDL Remote Sensing Image Processing and Application Development for ENVI. De-veloped LCF Project.

MATLAB Mathematical Modeling.Miscellaneous National Computer Rank Examination for Grade 4 Database Engineer.

Software ArcGIS, ENVI OS macOS, Windows, Linux

Awards2012.06 Outstanding Graduate of Wuhan University2010.09 National Second Prize in China Undergraduate Mathematical Contest in Mod-

eling of Higher Education Press Cup (with Zhu, Z. & Wang, Sh.)2008.10 Outstanding Volunteer of 6th Network Originality Competition (NOC) Final

CoursesSchool

{ Applied Statistics{ Introduction to High Performance Computing

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{ Quantitative Environmental Remote SensingMOOC*

{ Computing for Data Analysis, Johns Hopkins University on Coursera{ Probability, National Taiwan University on Coursera{ Statistical Learning, Stanford Open Edx{ 6.00.1x: Introduction to Computer Programming Using Python, edX MITx{ 6.00.2x: Introduction to Computational Thinking and Data Science, edX

MITx

*All are earned certificates with grades > 94.

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