Spencer J Fox
@foxandtheflu.bsky.social
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Assistant prof at NAU in disease modeling, and data science. Posts are my own opinions
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Spencer J Fox
Joshua Weitz
27 days ago
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
🧵
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Spencer J Fox
Dr Roz Eggo
about 1 month ago
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...
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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
https://www.lshtm.ac.uk/newsevents/events/inequalities-infectious-disease-dynamics-symposium
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I need this to be real, so I can get around NAUs rules against spending funds on coffee machines/accessories
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about 2 months ago
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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
about 2 months ago
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Spencer J Fox
Sam Abbott
about 2 months ago
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...
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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...
https://community.epinowcast.org/t/a-basket-of-baselines/325
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🚨 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...
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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...
https://www.medrxiv.org/content/10.64898/2026.03.18.26348748v1
about 2 months ago
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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 🙏
3 months ago
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Spencer J Fox
Elizabeth Jacobs, PhD
3 months ago
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.
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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.
https://www.azcentral.com/story/news/politics/elections/2026/02/24/vaccine-mandates-on-arizona-ballot/88743995007/?gnt-cfr=1&gca-cat=p&gca-uir=true&gca-epti=undefined&gca-ft=0&gca-ds=sophi
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Cevian Labs
3 months ago
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/
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Spencer J Fox
Dan Larremore
3 months ago
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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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
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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.
https://companion.ai/einstein
3 months ago
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Spencer J Fox
Adam Kucharski
3 months ago
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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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/...
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Supporting exciting biological sciences ideas and impacts on AI and biotechnology
https://www.nsf.gov/bio/updates/supporting-exciting-biological-sciences-ideas-impacts-ai
3 months ago
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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...
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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...
https://writersontherange.org/a-utah-monument-comes-under-attack-again/
3 months ago
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Spencer J Fox
Sam Abbott
3 months ago
Really cool that
@kaitejohnson9.bsky.social
is giving a keynote at the next Stan conference!
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Spencer J Fox
Holly Bik
3 months ago
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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Spencer J Fox
Dr Roz Eggo
3 months ago
Excited for the sixth instalment of our meeting on infectious disease dynamics!
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Spencer J Fox
Daniel Bolnick
4 months ago
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
[email protected]
to request re-consideration;
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Guppy Stott
4 months ago
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
4 months ago
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
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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.
https://IDDconf.org
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Spencer J Fox
Santa Fe Institute
4 months ago
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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Spencer J Fox
Mallory Harris, PhD
4 months ago
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...
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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...
https://www.medrxiv.org/content/10.64898/2026.01.22.26344544v1
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Spencer J Fox
Nicola Low
4 months ago
🧪 💉 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...
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William H. Foege, Key Figure in the Eradication of Smallpox, Dies at 89
https://www.nytimes.com/2026/01/24/us/william-h-foege-dead.html
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Spencer J Fox
Nathan Lo
4 months ago
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...
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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.
https://jamanetwork.com/journals/jama/fullarticle/2843870
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Spencer J Fox
Vittoria Colizza
4 months ago
*New paper in Nature Health* Why did the 2022 mpox outbreak in Paris decline so abruptly?
rdcu.be/eZ24H
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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...
https://rdcu.be/eZ24H
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Spencer J Fox
Simon Cauchemez
4 months ago
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...
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ESPIDAM, the European Summer Program in Infectious Disease Analysis and Modelling - Stockholms universitet
https://www.statistics.su.se/english/divisions/department-of-mathematics/research/conferences-and-seminars/espidam-the-european-summer-program-in-infectious-disease-analysis-and-modelling
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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...
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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.”
https://www.rollingstone.com/politics/politics-news/danish-vaccine-study-emails-hhs-rfk-jr-1235498456/
4 months ago
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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...
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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.
https://www.nature.com/articles/s41591-025-04160-1
4 months ago
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Spencer J Fox
Kristian G. Andersen
4 months ago
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...
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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
https://www.theguardian.com/us-news/2026/jan/15/hepatitis-b-vaccines-study-africa-cancel?CMP=Share_AndroidApp_Other
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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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4 months ago
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Spencer J Fox
Santa Fe Institute
4 months ago
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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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.
4 months ago
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Spencer J Fox
Nathan Grubaugh
4 months ago
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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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...
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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...
https://careers.nau.edu/jobs/postdoctoral-scholar-flagstaff-arizona-united-states-8493df28-5f4e-4dfb-bf94-03b16478fcd0?lApplicationSubSourceID=
4 months ago
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Spencer J Fox
Sebastian Funk
5 months ago
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...
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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
https://www.lshtm.ac.uk/study/fees-and-funding/funding-scholarships/phd-studentships-health-analytics-and-modelling
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Spencer J Fox
Dr Roz Eggo
5 months ago
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
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Social Inequalities in Infectious Disease Dynamics: a Symposium and Workshop
https://iddconf.org/lshtm-symposium/
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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...
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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!
https://christinapagel.substack.com/p/is-it-really-a-super-flu-year?r=g27c2&utm_medium=ios&triedRedirect=true
5 months ago
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Claus Wilke
5 months ago
Become a colleague in my department! Applications close in four days, December 15.
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Stuart McDaniel
5 months ago
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...
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University of Florida - Details - Assistant Professor in Ecology and Evolution of Infectious Disease
https://explore.jobs.ufl.edu/en-us/job/537810/assistant-professor-in-ecology-and-evolution-of-infectious-disease
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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!
5 months ago
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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?
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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
https://isf.forecasters.org/overview/about/
5 months ago
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Spencer J Fox
Juliana Taube
5 months ago
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.
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Joshua Weitz
6 months ago
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...
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OA Virtual conferences
https://virtual.oxfordabstracts.com/event/public/73356/program?session=185769&program&date=%222025-12-3%22
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Spencer J Fox
Southern Utah Wilderness Alliance
6 months ago
Federal government and Utah leaders are having a meeting this week to discuss co-management of national parks in Utah, setting a dangerous precedent for national parks across the nation. Read more:
www.thetravel.com/us-governmen...
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U.S. Government Eyes Utah National Parks For “Dangerous” Plan That Could Spread To Parks Across The Country
The alleged meeting fears the public and environmentalists it might involve the Mighty Five.
https://www.thetravel.com/us-government-eyes-utah-national-parks-for-dangerous-plan-that-could-spread-to-parks-across-the-country/
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John M. Drake
6 months ago
A challenge in epidemic forecasting is that ML models overfit while mechanistic models miss changing transmission conditions. Our new JR Soc Interface paper tests whether physics-informed neural networks—which embed an epidemiological ODE system inside a neural net—can address this.
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ID folks, come find me at the poster session tonight (2.041) or dm me if you’re looking for a postdoctoral position and want to hear more about our work/group.
#Epidemics10
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6 months ago
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Vittoria Colizza
6 months ago
Brilliant and inspiring talk by Shweta Bansal
@bansallab.bsky.social
at
#Epidemics10
on contact patterns at the interface of data, modelling and public health — and even across species!
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Melody Schreiber
6 months ago
Good news! The Ebola outbreak in DRC has been contained
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@bansallab.bsky.social
gives a tour de force of behavioral models and theory as a keynote at
#epidemics10
. How COVID-19 and animal behavior have helped improve our understanding of human behaviors and disease dynamics
6 months ago
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Alessandro Vespignani
6 months ago
We’ve just released Epistorm-Mix, a new open dataset on how people in the U.S. mix across ages and settings in the post-COVID era. 📊 Contact-level data + contact matrices Built for epidemic modeling & forecasting Fully open data & code 🔗
www.epistorm.org/data/epistor...
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Epistorm-Mix: Mapping Social Contact Patterns in the Post-Pandemic United States
Epistorm-Mix provides individual-level contact data and contacts patterns characterization relevant for the spread of respiratory infectious diseases within the US population.
https://www.epistorm.org/data/epistorm-mix
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