Sean L. Wu, PhD

 

PhD in Epidemiology & Computational Biology (Designated Emphasis)
University of California, Berkeley
slwu89 (at) berkeley (dot) edu
(he/him)

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  Table of Contents
  1. Research Interests
  2. Introduction
  3. Publications
  4. Personal Projects
  5. Rogues' Gallery
  6. Miscellany


Research Interests

Major Interests:

Minor Interests:


Introduction

I attended the University of California (UC), Irvine from 2008 to 2013 where I studied International Studies & Statistics. I received my MPH in Epidemiology & Biostatistics in 2016, and my PhD in Epidemiology with a designated emphasis in Computational Biology in 2020, both under John M. Marshall at UC Berkeley.

My main research interest is the process of going from a whiteboard description of a complex system to a verifiable simulation program. This process tends to proceed from observation about a real system to a conceptual model, usually expressed with some kind of graphical formalism, which is often a unique minimal representation of that system (such that anything simpler isn't that system). The conceptual model may then be turned into a mathematical model, which respects all the assumptions and simplifications made at the conceptual stage. From there, often times scientific code must be written to simulate solutions of the mathematical model. I am interested in developing methods and software to help scientists better navigate this process while respecting the complexity of the processes under study.

I have been involved in various research projects, including a research internship at Microsoft Research where I worked on detailed stochastic models of mosquito ecology under Simon D.W. Frost. I have also been at the Malaria Elimination Initiative at UC San Francisco, and spent a summer in Sichuan Province, China studying possible genetic biomarkers of susceptibility to schistosomiasis infection at the Berkeley Schistosomiasis Group, under Robert C. Spear. During the first year of my PhD I attended the Complex Systems Summer School (2017) at the Santa Fe Institute and found it life changing.

My middle name is Lawrence. My Chinese name is 吳瑞華 (wú ruì huá). My father is Cantonese Chinese from Hong Kong and my mother is Scandinavian & Oglala Sioux from San Diego, California and am proud of my mixed heritage. I grew up in and around San Diego, California. Before coming to Berkeley I worked as a computer hardware repairperson for a cardiology group, office assistant at UC Irvine, waiter at a Taiwanese beef noodle soup restaurant, clinical care assistant at a large hospital, and medical assistant at a pediatric office. My favorite TV show is Battlestar Galactica. I like to read books; some recent favorites are the Area X trilogy by Jeff VanderMeer and the Three Body Problem by Liu Cixin. I have recently been playing a lot of Disco Elysium. My favorite philosopher is the criminally underrated Plotinus.

In addition to English I speak fluent Mandarin Chinese. I am trying to learn Cantonese and Taiwanese.

Languages I can speak to computers are R (native), C++ (fluent), C (conversational), and Julia (conversational).


Publications

Journal Articles

  1. Measuring the accuracy of gridded human population density surfaces: A case study in Bioko Island, Equatorial Guinea.
    Fries B, Guerra CA, García GA, Wu SL, Smith JM, Oyono JN, Donfack OT, Nfumu JO, Smith DL, Dolgert AJ.
    PLoS one. 2021 Sep 1;16(8):e0248646.
  2. Quantifying malaria acquired during travel and its role in malaria elimination on Bioko Island.
    Citron DT, Guerra CA, Garcia GA, Wu SL, Battle KE, Gibson HS, Smith DL.
    Malaria Journal. 2021 Aug 31: 20,359.
  3. MGDrivE 2: A simulation framework for gene drive systems incorporating seasonality and epidemiological dynamics.
    Wu SL, Bennett JB, Sánchez HC, Dolgert AJ, León TM, Marshall JM.
    PLoS computational biology. 2021 May 21;17(5):e1009030.
  4. Comparing metapopulation dynamics of infectious diseases under different models of human movement.
    Citron DT, Smith DL, Wu SL, Sánchez HC, Dolgert AJ, Henry JM, Guerra CA.
    PNAS May 4, 2021 118 (18) e2007488118.
  5. School closures reduced social mixing of children during COVID-19 with implications for transmission risk and school reopening policies.
    Head JR, Andrejko K, Cheng Q, Collender PA, Phillips S, Boser A, Heaney AK, Hoover CM, Wu SL, Northrup GR, Click K, Harrison R, Lewnard JA, Remais JV.
    J. R. Soc. Interface 18: 20200970.
  6. New genotype invasion of dengue virus serotype 1 drove massive outbreak in Guangzhou, China.
    Ma MM, Wu SL, He ZJ, Yuan LH, Bai ZJ, Marshall JM, Lu JH, Yang ZC, Jing QL.
    Parasites & Vectors 14.1 (2021): 1-12.
  7. Pregnancy does not modify the risk of MS in genetically susceptible women.
    Adams CJ, Wu SL, Shao XR, Bradshaw PT, Gonzales E, Smith JB, Xiang AH, Bellesis KH, Chinn T, Bos SD, Wendel-Haga MW, Olsson T, Kockum I, Langer-Gould AM, Schaefer C, Alfredsson L, Barcellos LF.
    Neurol Neuroimmunol Neuroinflamm Nov 2020, 7 (6).
  8. Substantial underestimation of SARS-CoV-2 infection in the United States.
    Wu SL, Mertens A, Crider YS, Nguyen A, Pokpongkiat NN, Djajadi S, Seth A, Hsiang MS, Colford JM, Reingold A, Arnold BF, Hubbard A, Benjamin-Chung J.
    Nature Communications. 11, 4507 (2020).
  9. Vector bionomics and vectorial capacity as emergent properties of mosquito behaviors and ecology.
    Wu SL, Sánchez HC, Henry JM, Citron DT, Zhang Q, Compton K, Liang B, Verma A, Cummings DA, Le Menach A, Scott TW, Wilson AL, Lindsay SW, Moyes CL, Hancock PA, Russell TL, Burkot TR, Marshall JM, Kiware S, Reiner RC, Smith DL.
    PLoS computational biology. 2020 Apr 22;16(4):e1007446.
  10. Modeling confinement and reversibility of threshold-dependent gene drive systems in spatially-explicit Aedes aegypti populations.
    Sánchez HC, Bennett JB, Wu SL, Rašić G, Akbari OS, Marshall JM.
    BMC biology. 2020 Dec;18:1-4.
  11. MGDrivE: A modular simulation framework for the spread of gene drives through spatially explicit mosquito populations.
    Sánchez HC, Wu SL, Bennett JB, Marshall JM.
    Methods in Ecology and Evolution. 2020 Feb;11(2):229-39.
  12. An example of augmenting regional sensitivity analysis using machine learning software.
    Spear RC, Cheng Q, Wu SL.
    Water Resources Research. 2020 Apr;56(4):e2019WR026379.
  13. Transforming insect population control with precision guided sterile males with demonstration in flies.
    Kandul NP, Liu J, Sánchez HC, Wu SL, Marshall JM, Akbari OS.
    Nature communications. 2019 Jan 8;10(1):1-2.
  14. Mathematical models of human mobility of relevance to malaria transmission in Africa.
    Marshall JM, Wu SL, Sánchez HC, Kiware SS, Ndhlovu M, Ouédraogo AL, Touré MB, Sturrock HJ, Ghani AC, Ferguson NM.
    Scientific reports. 2018 May 16;8(1):1-2.
  15. Attacking the mosquito on multiple fronts: Insights from the Vector Control Optimization Model (VCOM) for malaria elimination.
    Kiware S, Chitnis N, Tatarsky A, Wu SL, Sánchez HC, Gosling R, Smith DL, Marshall JM.
    PLoS one. 2017 Dec 1;12(12):e0187680.

Preprints

  1. Eliminating Aedes aegypti from its southern margin in Australia: insights from genomic data and simulation modeling.
    Rašić G, Filipović I, Wu SL, León TM, Bennett JB, Sánchez HC, Marshall JM, Trewin B.
    bioRxiv. 2021 Aug 22.
  2. (Under review at Journal of Open Source Software) individual: An R package for individual based epidemiological models.
    Charles GD, Wu SL.
    JOSS. 2021 Jul 25.
  3. Principled simulation of agent-based models in epidemiology.
    Wu SL, Dolgert AJ, Lewnard JA, Marshall JM, Smith DL.
    bioRxiv. 2020 Dec 21.
  4. Effects of Spatial Heterogeneity on Transmission Potential in Vectorial-Contact Networks: A Comparison of Three Aedes aegypti Control Strategies.
    Sánchez HC, Marshall JM, Wu SL, Vallejo EE.
    bioRxiv. 2017 Oct 28.

Software

  1. individual: Framework for Specifying and Simulating Individual Based Models
    R package available on CRAN and GitHub
    Charles G, Wu SL, Winskill P (2021).
  2. MGDrivE2: Mosquito Gene Drive Explorer 2
    R package available on CRAN
    Wu SL, Bennett JB, Sánchez HC, León TM, Dolgert AJ, Marshall JM (2020).
  3. MGDrivE: Mosquito Gene Drive Explorer
    R package available on CRAN
    Sánchez HC, Bennett JB, Wu SL, Marshall JM (2019).

Miscellaneous

  1. Organic Urban Boundaries and Clusters - Analyzing Singapore as an Example.
    Zhou Y, Park D, Wu SL.
    Sante Fe Institute Complex Systems Summer School 2017 Proceedings
  2. Quantifying and comparing 'memory' in biological, ecological, physical, and socio-economic systems
    Jurgens A, Kraay A, Weissman J, Dong J, Pangallo M, Wu SL, Stopnitzky S, Zhan SH, Gurevich Y, Liu Y
    Sante Fe Institute Complex Systems Summer School 2017 Proceedings

Personal Projects

Inspiration for collecting these notes and scraps is largely from Cosma Shalizi's excellent and voluminous collection of notebooks on everything under the sun.

Notebooks, to keep things around I want to remember in the future. These are personal and thus have strange allusions, (not funny) humor, and misspellings. There may even be errors.

Writing too disorganized to even be called notes.


Rogues' Gallery

Friends, Mentors, Acquaintances

People with Interesting Web Pages, and other internet oddities

Other


Miscellany

This website benefitted substantially from Dave Raggett's guides to HTML.

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