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Spencer J Fox

@foxandtheflu.bsky.social
782 followers 378 following 192 posts

Assistant prof at NAU in disease modeling, and data science. Posts are my own opinions

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Spencer J Fox @foxandtheflu.bsky.social · 11/08/2026
We’re officially in Chennai to lead a workshop on forecasting and the MicroHub tool with the CDC and ICMR! 35 attendees from 5 countries 🤯
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Spencer J Fox @foxandtheflu.bsky.social · 09/08/2026
Flying to Chennai to give our third forecasting workshop on the MicroHub tool we have been developing, and I am feeling grateful for all of the hard work my students + post-docs have put into our forecast efforts the past few years! Also grateful for free wifi on the plane 😱
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Spencer J Fox @foxandtheflu.bsky.social · 24/07/2026
Finishing up the SISMID course on simulation-based inference of epidemiological models with instructions on how to run Bayesian, metapopulation, and phylodynamic models in pomp. Check out all of the lectures and exercises here: rubbislam.quarto.pub/episim/
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Spencer J Fox @foxandtheflu.bsky.social · 23/07/2026
Our group traveled to Santiago with PAHO and the CDC to carry out a training on forecasting and our MicroHub tool, so that the MoH can run their own forecasts. PAHO just published a nice article about the visit if you're interested in the international work we're doing! www.paho.org/en/news/26-6...
paho.org
Chile implements respiratory virus forecasting with support from PAHO, CDC, and Northern Arizona University
Santiago, Chile, June 26, 2026 (PAHO) – Technical teams from the Chilean Ministry of Health, the Pan American Health Organization (PAHO/WHO), the U.S. Centers for Disease Control and Prevention (CDC),...
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Spencer J Fox @foxandtheflu.bsky.social · 23/07/2026
2nd day of our simulation-baesd inference for epidemiological models course at SISMID! Qianying, teaching particle filtering approaches to estimate likelihoods in the pomp R package now! I always learn something new watching her teach this stuff 😅
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Spencer J Fox @foxandtheflu.bsky.social · 22/07/2026
Really interesting talk at CSTE from Matt Doxey at google talking about using AI agents for public health modeling!
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Spencer J Fox @foxandtheflu.bsky.social · 21/07/2026
Excited to be back in Atlanta for both the CSTE Forecasting workshop and SISMID! Hope to see some of y’all there
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Joshua Weitz @joshuasweitz.bsky.social · 22/04/2026
Today, our #SCIMaP team released an impact analysis of the White House proposed FY 2027 NIH and NSF budgets. Bottom-line: if enacted, cuts to science and medical research would lead to $35B in economic losses and 150,000 lost jobs in communities all across the US. scienceimpacts.org 🧵
Landing page for scienceimpacts.org
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Dr Roz Eggo @rozeggo.bsky.social · 12/04/2026
Great speakers at this symposium - 22 April 2026 at LSHTM. Join online or in person (email if in person) to hear great talks at the cutting edge of Inequalities in infectious disease dynamics. www.lshtm.ac.uk/newsevents/e...
lshtm.ac.uk
Inequalities in infectious disease dynamics symposium | LSHTM
Join us for the Social Inequalities in Infectious Disease Dynamics Symposium at the London School of Hygiene & Tropical Medicine (LSHTM). The day features a full programme of presentations and invited
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Spencer J Fox @foxandtheflu.bsky.social · 01/04/2026
I need this to be real, so I can get around NAUs rules against spending funds on coffee machines/accessories
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Spencer J Fox @foxandtheflu.bsky.social · 31/03/2026
I have been playing with Codex and Claude extensively for about 6 months now, and while they are clearly impressive, I don't see them replacing software engineers in the near future and I don't understand how people can trust their work without knowing how to code
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Sam Abbott @seabbs.bsky.social · 25/03/2026
I really like this idea of multiple baselines with different contexts. some relationship to this basket of baselines idea I was chatting about a while ago community.epinowcast.org/t/a-basket-o...
community.epinowcast.org
A basket of baselines
Been thinking about the overlap between baseline models (Manuel Stapper is working on this), the method of analogs (stuff @nickreich and co are going on about), and model output evaluation (i.e. @kat...
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Spencer J Fox @foxandtheflu.bsky.social · 24/03/2026
🚨 New preprint from our lab! How much does the design of “simple” baseline models matter for forecast hubs? We show that small design choices in baseline models can substantially change model performance, and thus the relative rankings of the other models www.medrxiv.org/content/10.6...
medrxiv.org
Basic Baseline model design choices can substantially influence performance in collaborative forecast hubs
Over the past decade, outbreak forecasting has become an increasingly used tool to assist public health decision-making during epidemics. Collaborative forecast hubs, where multiple teams submit predi...
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Spencer J Fox @foxandtheflu.bsky.social · 26/02/2026
Attending the @gs-idd.bsky.social launch seminar. Couldn't be more excited to see this effort take shape and can't wait to see how it helps push the infectious disease dynamics community forward! Thank you to all of the founding members and organizers 🙏
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Elizabeth Jacobs, PhD @elizabethjacobs.bsky.social · 24/02/2026
Republicans in Arizona want voters to get rid of childhood vaccine requirements for school entry. They are planning to add a ballot proposition for November’s election in the hopes of ending the requirements, which they are framing as an issue of “medical freedom”. This would be catastrophic.
azcentral.com
Arizona voters could decide future of government vaccine mandates
The Arizona Legislature is considering whether to refer a proposed constitutional amendment to the 2026 statewide general election ballot.
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Cevian Labs @cevianlabs.io · 24/02/2026
Today we’re excited to announce a new product: COI Pond is a tool for faculty and grant staff that converts an academic CV into a draft NSF Collaborators and Other Affiliations (COA) Form. COA forms are tedious work, and COI Pond makes it a snap. Try it for free, here cevianlabs.io/coipond/start/ /1
Screenshot of the COI Pond webpage: 

Upload your academic CV and generate a draft NSF Collaborators and Other Affiliations (COA) Form to submit with your NSF grant proposals.

COI Pond parses your CV to extract:
Coauthors of articles published, in the last 48 months
Collaborators on funded projects, in last 48 months
Past PhD advisees & your own PhD advisor(s)
Editorial roles, in last 24 months
After extraction, you can edit the draft COA form before downloading a final version (in xslx format) that you can submit to NSF.

COI Pond is a free tool* from Cevian Labs.
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Dan Larremore @danlarremore.bsky.social · 24/02/2026
You know that annoying NSF form "List every coauthor/co-PI from the last 4y" ? At @cevianlabs.io we built a free tool that drafts the COI form from your PDF CV in minutes. Check it out 👇
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Spencer J Fox @foxandtheflu.bsky.social · 23/02/2026
Who is this for? If you don't know the material from the class, how can you review the outputs? If you have it auto-submit why are you even paying for the class? companion.ai/einstein
companion.ai
Einstein - AI Homework Agent
Einstein logs into Canvas and does your homework automatically. He has his own computer — he can watch lectures, read essays, write papers, and participate in discussions.
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Adam Kucharski @adamjkucharski.bsky.social · 23/02/2026
Interested in learning outbreak analytics and modelling, with a focus on real-life case studies and tools actively used in responses? Apply for the popular @lshtm.bsky.social R shortcourse, led by @jwlambert.bsky.social & @andreevallecam.bsky.social More: www.lshtm.ac.uk/study/course...
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Spencer J Fox @foxandtheflu.bsky.social · 19/02/2026
If anyone is interested in writing an NSF PRFB applications on the intersection of AI, disease forecasting, and understanding drivers of transmission (or related topics), please reach out! I think it would be a great fit with the work happening in our lab: www.nsf.gov/bio/updates/...
nsf.gov
Supporting exciting biological sciences ideas and impacts on AI and biotechnology
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Spencer J Fox @foxandtheflu.bsky.social · 18/02/2026
We have to protect our public lands at all costs! This is a great summary of the current plans to infringe on Grand Staircase Escalante National Monument, a truly ecologically important, beautiful, and culturally significant region of Southern Utah. writersontherange.org/a-utah-monum...
writersontherange.org
A Utah monument comes under attack—again - Writers On The Range
Utah Republican Congresswoman Celeste Maloy is irritated. Her most recent attack on Grand Staircase-Escalante National Monument spurred wide and deep...
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Sam Abbott @seabbs.bsky.social · 17/02/2026
Really cool that @kaitejohnson9.bsky.social is giving a keynote at the next Stan conference!
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Holly Bik @hollybik.bsky.social · 16/02/2026
We are hiring at UGA! We’re looking for a full professor & director of the Skidaway Institute of Oceanography (based right on the coast in Savannah, GA). Please pass on the job ad to anyone in your networks who may be interested: www.ugajobsearch.com/postings/468...
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Dr Roz Eggo @rozeggo.bsky.social · 04/02/2026
Excited for the sixth instalment of our meeting on infectious disease dynamics!
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Daniel Bolnick @danielbolnick.bsky.social · 30/01/2026
If you are a student whose NSF GRFP application was returned without review for vague 'eligibility' reasons: 1) Let your department chair & Graduate School know. Encourage them to contact NSF & congress 2) Write to your congressional reps. 3) Write to grfp@nsf.gov to request re-consideration;
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Guppy Stott @guppy-stott.bsky.social · 30/01/2026
Howdy y'all! I'm planning to graduate in May. If you are in need of a postdoc with knowledge of phylogenetics, graph databases, and Nextflow pipelines (or know of someone who is), please send them my way!
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Dr Roz Eggo @rozeggo.bsky.social · 26/01/2026
IDDconf 2026 - July 7-9 in Ambleside, UK. A new summer date & a new ticketing system! Plus, 2 exciting workshops this year! See IDDconf.org for more info Tickets will go on sale on 2nd Feb. To be notified when, sign up at: tinyurl.com/IDDconf2026
iddconf.org
IDDconf 2026
A Conference on Infectious Disease Dynamics. IDDconf is the second instalment of a new meeting series focussing on innovative research in infectious disease dynamics.
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Santa Fe Institute @sfiscience.bsky.social · 27/01/2026
Final week to apply for SFI’s 2026 immersive, summer programs in complexity science: Apply by Feb 4, 2026 CSSS and GWCSS : www.santafe.edu/engage/learn... Journalism Fellowship: santafe.edu/journalism-f...
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Mallory Harris, PhD @malar0ne.bsky.social · 27/01/2026
In a new preprint, we combine modeling with school-level vaccine data to contextualize the risk of 'breakthrough infections' and impacts on the ongoing US measles outbreak. #idsky #episky www.medrxiv.org/content/10.6...
medrxiv.org
Interpreting Breakthrough Infections Given Assortative Mixing of Partially Vaccinated Populations
Declining vaccine coverage across the United States has increased the risk of outbreaks of vaccine-preventable diseases. Even when vaccines have low primary failure rates, conventional epidemic theory...
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Nicola Low @nicolamlow.bsky.social · 25/01/2026
🧪 💉 Bill Foege is an absolute #PublicHealth legend And furious to the end about the destruction of US public health “Kennedy’s words can be as lethal as the smallpox virus,” he wrote… “I had no idea I would be this angry at the age of 89.” Ht @boghuma.bsky.social www.nytimes.com/2026/01/24/u...
nytimes.com
William H. Foege, Key Figure in the Eradication of Smallpox, Dies at 89
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Nathan Lo @nathanlo.bsky.social · 22/01/2026
Our latest study in @jama.com on trends in county-level vaccine exemptions, demonstrating geographic pockets of high vaccine exemptions and high susceptibility to vaccine-preventable diseases. Great collab with @nbcnews.com colleagues and our Stanford team. jamanetwork.com/journals/jam...
jamanetwork.com
Trends in County-Level Childhood Vaccination Exemptions in the US
This study examines US county-level trends in nonmedical and medical exemptions to childhood vaccination requirements.
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Vittoria Colizza @vcolizza.bsky.social · 21/01/2026
*New paper in Nature Health* Why did the 2022 mpox outbreak in Paris decline so abruptly? rdcu.be/eZ24H
rdcu.be
Role of behaviour change in controlling the 2022 Paris mpox outbreak
Nature Health - Behaviour changes, rather than vaccination or postinfection immunity, best explained the sudden decline of mpox cases among men who have sex with men during an outbreak in the Paris...
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Simon Cauchemez @scauchemez.bsky.social · 19/01/2026
Dont miss the ESPIDAM summer program in June 2026 in Stockholm, covering many key concepts for ID modelling: stochastic models, AI for ID control, nowcasting and forecasting, phylodynamics, data analysis, network models, within-host models, health economics www.statistics.su.se/english/divi...
statistics.su.se
ESPIDAM, the European Summer Program in Infectious Disease Analysis and Modelling - Stockholms universitet
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Spencer J Fox @foxandtheflu.bsky.social · 16/01/2026
Here's something I hadn't heard about the planned then cancelled then re-planned unethical Hep B trials: Bill Ackman is funding half the cost, who knew! www.rollingstone.com/politics/pol...
rollingstone.com
HHS Gave a $1.6 Million Grant to a Controversial Vaccine Study. These Emails Show How That Happened
Two Danish researchers faced accusations of “questionable research practices” as RFK Jr.’s top appointees made their study a “funding priority.”
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Spencer J Fox @foxandtheflu.bsky.social · 16/01/2026
Nice to see the new NIAID vision laid out in a paywalled journal article. Since NIH funds contributed to it I am looking forward to reading the open access version soon... www.nature.com/articles/s41...
nature.com
The new vision from the National Institute of Allergy and Infectious Diseases (NIAID) - Nature Medicine
Preparing for tomorrow’s threats by enhancing our ability to help patients today.
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Kristian G. Andersen @kgandersen.bsky.social · 15/01/2026
A few updates on the deeply unethical study to probe "non-specific" effects of the birth dose HepB vaccine in Guinea-Bissau by Danish investigators. 1️⃣ The study was canceled as per AfricaCDC - HHS disputes this. 2️⃣ Full protocol was leaked and it's bad. Quick 🧵 www.theguardian.com/us-news/2026...
theguardian.com
Controversial US study on hepatitis B vaccines in Africa is cancelled
$1.6m project drew outrage over ethical questions about withholding vaccines proven to prevent disease
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Spencer J Fox @foxandtheflu.bsky.social · 14/01/2026
This is some great forensics. Good reminder that it is extremely difficult to know how many people are infected at any given moment in the absence of serology data.
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Santa Fe Institute @sfiscience.bsky.social · 14/01/2026
Advance your research and expand your network at SFI's 2026 CSSS program with lectures, application-focused seminars, and team projects. Participants gain experience in transdisciplinary collaboration and explore real-world questions through complexity science. Apply by Feb 4, 2026 santafe.edu/csss
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Spencer J Fox @foxandtheflu.bsky.social · 13/01/2026
First day of my forecasting class at NAU. This is the first course I fully prepped (mostly) from scratch and I tried to have fun with it. ✅ Students are making flu forecasts. ✅ There’s a class leaderboard and competition. ✅ Plaque to commemorate annual winners.
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Nathan Grubaugh @nathangrubaugh.bsky.social · 12/01/2026
Check out our new print that combines dense sequencing and phylodynamics to uncover a bunch of 😎 things about an understudied virus. - Doesn't evolve for 10 months a year ✅ - Uses some mossies for maintenance, others for spread ✅ - Established in Northeast for ~300 years ✅
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Spencer J Fox @foxandtheflu.bsky.social · 06/01/2026
We are still accepting applications for the postdoctoral scholar position here at NAU in my lab (with remote optional). Please reach out if you have any questions or would like more information: careers.nau.edu/jobs/postdoc...
careers.nau.edu
Postdoctoral Scholar - Flagstaff, Arizona, United States
Special Information This position is an on-site position which requires the incumbent to complete their work primarily at an NAU site, campus, or facility with or without accommodation. Opportunities...
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Sebastian Funk @sbfnk.bsky.social · 17/12/2025
Two more fully funded PhDs in real-time infectious disease modelling & forecasting — developing methods for operational use by @ukhsa.bsky.social and others in outbreak response. UK home students, starting April or September 2026. www.lshtm.ac.uk/study/fees-a...
lshtm.ac.uk
PhD Studentships in Health Analytics and Modelling | LSHTM
The London School of Hygiene & Tropical Medicine (LSHTM), Imperial College London and the UK Health Security Agency (UKHSA) are pleased to invite applications for two PhD studentships in real-time
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Dr Roz Eggo @rozeggo.bsky.social · 16/12/2025
Symposium & workshop on inequalities in infectious disease dynamics at LSHTM in April 2026. We aim to will bring together leading researchers and practitioners to share ideas, discuss recent advances, and reflect on future directions. Details & application: iddconf.org/lshtm-sympos... Closing 21 Jan
iddconf.org
Social Inequalities in Infectious Disease Dynamics: a Symposium and Workshop
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Spencer J Fox @foxandtheflu.bsky.social · 11/12/2025
I'm glad someone did the work to lay this concept out so nicely! Predicting the size of an influenza season is not as easy as seeing a new variant and extrapolating trends. This may be a bad flu season, but it's way too soon to tell! christinapagel.substack.com/p/is-it-real...
christinapagel.substack.com
Is it really a super flu year?
We're in the middle of a serious flu wave, but we just can't tell yet how bad it's going to be. Week-on-week comparisons are being used in a misleading way!
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Claus Wilke @clauswilke.com · 11/12/2025
Become a colleague in my department! Applications close in four days, December 15.
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Stuart McDaniel @stuartmcdaniel.bsky.social · 10/12/2025
UF Biology is searching for an Asst Prof in Evolution, Ecology of Infectious Disease - spread the word! @ufresearch.bsky.social @ufgeog.bsky.social @sse-evolution.bsky.social explore.jobs.ufl.edu/en-us/job/53...
explore.jobs.ufl.edu
University of Florida - Details - Assistant Professor in Ecology and Evolution of Infectious Disease
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Spencer J Fox @foxandtheflu.bsky.social · 10/12/2025
Most of the Fox lab got to experience ~7000ft of elevation change going from #Epidemics10 in San Diego to Flagstaff, AZ for a writing retreat. Here we are on our celebratory visit to the Grand Canyon afterwards!
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Spencer J Fox @foxandtheflu.bsky.social · 10/12/2025
Considering going to the International Symposium on Forecasting (isf.forecasters.org/overview/abo...) in Montreal this summer - has anyone been before or have recommendations of whether it's useful/informative for disease forecasters?
isf.forecasters.org
About the ISF - International Symposium on Forecasting
The International Symposium on Forecasting, presented by the International Institute of Forecasters (IIF), is the premier international event for professional
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Juliana Taube @julianataube.bsky.social · 08/12/2025
The MIDAS Trainee Executive Committee is recruiting new members for 2026! 🤓 This is a great opportunity for grad students & postdocs in infectious disease modeling to gain experience organizing events & connect with peers. Applications are due by 9am ET on 1/1/2026, link in flyer & alt text.
Advertisement to apply to join the MIDAS Trainee Executive Committee for 2026. Recruiting grad students or post docs doing infectious disease modeling research that are motivated to strengthen the trainee community. Responsibilities of committee members include organizing trainee events, representing trainee perspectives to the broader MIDAS network, and fostering trainee connections.

Applications are due by 9am ET Jan 1, 2026 at: https://forms.gle/16ZuG5oTBFwpnR4W8
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Joshua Weitz @joshuasweitz.bsky.social · 03/12/2025
Precisely so, I look forward to convening a Wed AM panel on "Confronting Covid's Wake." We will explore the link between COVID responses, anti-science, and misinformation… and how & why to support evidence-based inquiry to confront disease threats. virtual.oxfordabstracts.com/event/public...
virtual.oxfordabstracts.com
OA Virtual conferences
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