Sen Pei @senpei.bsky.social · 01/10/2026Welcome to join the Columbia Mailman Seminar Series on Infectious Disease Modeling, featuring Prof. Mauricio Santillana from Northeastern University & Harvard on 10/7 Wed at 12 pm ET! This is a hybrid event with both in-person and Zoom options, open to the public. Please register using the QR code! 121
Reposted by Sen PeiCMMID @cmmid-lshtm.bsky.social · 01/09/2026🏛️ We’re kicking off the first seminar of the new academic year with @senpei.bsky.social He will discuss how to use mathematical models to uncover hidden disease transmission, improve forecasting, surveillance, risk assessment, and outbreak control Details 🔽 www.lshtm.ac.uk/newsevents/e... 053
Sen Pei @senpei.bsky.social · 03/08/2026🌪️ We’re launching the Hurricane Mobility Tracker, an interactive dashboard showing how population movement changes before, during, and after hurricanes, using cellphone-derived foot-traffic data. Check it out and share with anyone who may be interested! 🔗 hurricane-mobility.fly.dev 030
Sen Pei @senpei.bsky.social · 30/07/2026I’m delighted to be an invited speaker at the ARCANE Workshop on Modeling Antimicrobial Resistance, October 19-21, 2026 in Paris. The call for abstracts is now open! Submit your abstract here: arcane.sciencesconf.org Thanks to the organizers. Look forward to seeing many colleagues in Paris! 051
Sen Pei @senpei.bsky.social · 23/06/2026Congratulations to Dr. Han Yong Wunrow on successfully defending his PhD in Applied Math at Columbia APAM! Han Yong is the first PhD student I co-supervised. His research advances data-driven ID modeling using data assimilation and AI. Excited for his next chapter at Google! 041
Sen Pei @senpei.bsky.social · 09/06/2026Congratulations to Fintan Mooney, our brilliant doctoral student at Columbia EHS, for passing his qualification exam today! Fin is passionate about research on extreme weathers and population health. We look forward to his impactful works in this space! 020
Sen Pei @senpei.bsky.social · 01/06/2026That is why conferences should not be overlapped. It’s a tough decision! 😅 010
Sen Pei @senpei.bsky.social · 01/06/2026Great weather in Boston. Excited to be at NetSci Conference 2026 this week! Our group has two presentations - welcome to stop by and chat. Looking forward to the fantastic science near the Charles River! 110
Sen Pei @senpei.bsky.social · 31/05/2026👇 Great opportunity to work with Prof. Alan Cohen @cusciofhealth.bsky.social and me to develop novel metrics of biological health at the whole-organism level. Please reach out if you are interested! 000
Sen Pei @senpei.bsky.social · 15/05/2026Important work from @dalarsen.bsky.social on wastewater surveillance! Genetic variability in wastewater is a better indicator of community transmission. A great reminder that existing surveillance data often contain far more information than we currently extract. www.science.org/doi/10.1126/...science.orgGenetic variability of SARS-CoV-2 in wastewater and associations with community transmissionSequencing genetic material from community wastewater facilitates the study of virus diversity. Diversity can be estimated using the variation in nucleotides and number of variants identified, increas... 061
Sen Pei @senpei.bsky.social · 27/04/2026Welcome to join Columbia Mailman seminar series on infectious disease modeling featuring Prof. Jessica Metcalf @jessmetcalf.bsky.social from Princeton University on 5/5 Tue at 12 pm ET! Open to the public over Zoom. For information and registration: events.columbia.edu/cal/event/ev... 161
Sen Pei @senpei.bsky.social · 13/04/2026Welcome to join Columbia Mailman seminar series on infectious disease modeling featuring Prof. Pejman Rohani from the University of Georgia on 4/21 Tue at 2 pm ET! Open to the public over Zoom. For information and registration: events.columbia.edu/cal/event/ev... 122
Sen Pei @senpei.bsky.social · 31/03/2026Welcome to join Columbia Mailman seminar series on infectious disease modeling featuring Prof. Jeff Imai-Eaton @jeff-imai-eaton.bsky.social from Harvard @hsph.harvard.edu on 4/7 Tue at 12 pm ET! Open to the public over Zoom. For information and registration: events.columbia.edu/cal/event/ev... 131
Sen Pei @senpei.bsky.social · 25/03/2026Really enjoyed presenting at the Columbia Global Research Stabilization Fund Spring Showcase today. RSF’s support last year was critical in keeping our epidemic forecasting work moving. Inspired by the breadth of research and looking forward to what comes next! 000
Reposted by Sen PeiVittoria Colizza @vcolizza.bsky.social · 19/03/2026Join ESPIDAM 2026 — the European Summer Program in Infectious Disease Analysis & Modelling! A unique training opportunity for early-career researchers in epidemic modelling 🦠📊 ⏳ Early bird deadline: March 31 www.su.se/english/divi... 077
Reposted by Sen PeiThe Ferrari Lab @theferrarilab.bsky.social · 19/03/2026Come work with me at Penn State on the dynamics of pathogen elimination. We're hiring up to two positions to support our work on measles/rubella and foot and mouth disease elimination @ciddpsu.bsky.socialpsu.wd1.myworkdayjobs.comPostdoctoral Scholar - Ferrari labAPPLICATION INSTRUCTIONS: CURRENT PENN STATE EMPLOYEE (faculty, staff, technical service, or student), please login to Workday to complete the internal application process. Please do not apply here, a... 01114
Sen Pei @senpei.bsky.social · 18/03/2026It was a great pleasure to host a visit by @theferrarilab.bsky.social ! Super interesting talk and tons of impactful works on measles and rubella. 020
Sen Pei @senpei.bsky.social · 13/03/2026Honored to be elected as a Steering Committee Member of the MIDAS network @midas-network.bsky.social Grateful to give back to a community that has shaped my career, and looking forward to supporting early-career investigators and strengthening engagement with international scholars. 050
Reposted by Sen PeiVittoria Colizza @vcolizza.bsky.social · 10/03/2026Two postdoc positions open at SUMOC (Sorbonne Université | INSERM), Paris, within the EPIcx lab. 🦠 Network epidemiology of healthcare-associated infections (ARCANE) 🧠 Coupled behavior–disease modeling (PREVIX) 2-y positions | Start June 2026 #epidemiology #networks #matrices 1913
Sen Pei @senpei.bsky.social · 09/03/2026Welcome to join Columbia Mailman seminar series on infectious disease modeling featuring Prof. Matthew Ferrari @theferrarilab.bsky.social from Penn State on 3/17 Tue at 12 pm EST! Open to the public over Zoom. For more information and registration: events.columbia.edu/cal/event/ev... 131
Sen Pei @senpei.bsky.social · 03/02/2026Welcome to join Columbia Mailman seminar series on infectious disease modeling featuring Prof. Virginia Pitzer from Yale on 2/10 Tue at 12 pm EST! Open to the public over Zoom. For more information and registration: events.columbia.edu/cal/event/ev... 131
Sen Pei @senpei.bsky.social · 28/01/2026Presymptomatic transmission is a key determinant of the controllability of respiratory viruses. This nice study used household data to quantify presymptomatic transmission of influenza and Omicron. Important findings with implications for modeling and control. www.nature.com/articles/s44...nature.comFrequent presymptomatic household transmission of influenza A but not influenza B virus - Nature HealthBased on two waves of data collection from 748 households in Hong Kong, this analysis sheds light on the number of transmission events that occurred before manifestation of symptoms in influenza A and... 030
Reposted by Sen PeiSimon Cauchemez @scauchemez.bsky.social · 19/01/2026Dont 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.seESPIDAM, the European Summer Program in Infectious Disease Analysis and Modelling - Stockholms universitet 1118
Sen Pei @senpei.bsky.social · 06/01/2026Here is the link to the paper: doi.org/10.1073/pnas...doi.orgPNASProceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans... 020
Sen Pei @senpei.bsky.social · 06/01/2026Takeaway: Pandemic respiratory viruses spread fast and stochastically, often before we can clearly detect them. Preparedness needs to plan for uncertainty, and surveillance must be broad, not just focused on a few major hubs. Grateful to an amazing group of collaborators across institutions! 110
Sen Pei @senpei.bsky.social · 06/01/2026We also ran simulations for future pandemics. Results suggest that wastewater surveillance limited to a few major hubs isn’t enough - broader coverage is needed to meaningfully slow early geographic spread. 120
Sen Pei @senpei.bsky.social · 06/01/2026Main finding: both pandemics spread to most US metro areas within weeks, leaving a very narrow window for early detection and containment. The two viruses followed different transmission routes, but shared key spread hubs. 100
Sen Pei @senpei.bsky.social · 06/01/2026Key question: How fast did the last two pandemics spread in the US? Did they follow the same spatial transmission routes? Using high-resolution disease data and human mobility, we built an ensemble inference framework that explicitly accounts for stochasticity and superspreading in early outbreaks. 100
Sen Pei @senpei.bsky.social · 06/01/2026Excited to share a new study published in PNAS! @pnas.org We reconstructed the early, cryptic spatial spread of 2009 H1N1 influenza and SARS-CoV-2 across US metropolitan areas. Link👉https://www.pnas.org/doi/10.1073/pnas.2518051123 #PandemicPreparedness #InfectiousDisease #HumanMobility 1225
Sen Pei @senpei.bsky.social · 31/12/20252025 was a challenging year for many of us. As the year comes to a close, let's pause to recognize and celebrate every accomplishment and milestone, big or small. Each step forward matters. As we head into 2026, let’s keep climbing with aspiration, resilience, and strength! 020
Sen Pei @senpei.bsky.social · 18/12/2025This approach helps address common issues like filter divergence and underestimation of uncertainty in data assimilation. More importantly, we can reconstruct epidemic curves with time-varying Rt using forward simulations, which are essential for running counterfactual analyses. 000
Sen Pei @senpei.bsky.social · 18/12/2025Our results show that ensemble filter/smoother methods with adaptive inflation give more accurate and robust Rt estimates, especially around sudden changes in transmission dynamics. 100
Sen Pei @senpei.bsky.social · 18/12/2025Accurately estimating Rt and its uncertainty is central to understanding infectious disease dynamics and informing public health decisions. We systematically evaluated multiple data assimilation methods for estimating Rt using both synthetic epidemic simulations and real COVID-19 case data. 100
Sen Pei @senpei.bsky.social · 18/12/2025Glad to share our latest study, led by Han Yong Wunrow @hwunrow.bsky.social, on estimating time-varying reproduction numbers (Rt) using data assimilation methods, now published in the Journal of the Royal Society Interface! Link: royalsocietypublishing.org/rsif/article... 1104
Sen Pei @senpei.bsky.social · 11/12/2025I am teaching Introduction to Network Science for a third year at Columbia Mailman! @cupublichealth.bsky.social Very grateful to have positive evaluations from students with diverse backgrounds. Welcome to join this small-size, engaged course if you are interested in networks and systems thinking! 050
Sen Pei @senpei.bsky.social · 10/12/2025Very interesting study on respiratory virus transmission in schools! "Prolonged exposure in shared, poorly ventilated spaces, which potentially includes several infectious sources, drives respiratory virus transmission more than close contact." www.nature.com/articles/s41...nature.comThe relative contribution of close-proximity contacts, shared classroom exposure and indoor air quality to respiratory virus transmission in schools - Nature CommunicationsThe relative importance of close-proximity interactions, shared space and air quality to the transmission of respiratory viruses is not well understood. Here, the authors investigate this question by ... 052
Sen Pei @senpei.bsky.social · 08/12/2025Welcome to join Columbia Mailman @cupublichealth.bsky.social seminar series on infectious disease modeling featuring Prof. Mark Jit @markjit.bsky.social from NYU on 12/16 Tue at 12 pm EST! Open to the public over Zoom. For more information and registration: 👉 events.columbia.edu/cal/event/ev... 161
Sen Pei @senpei.bsky.social · 30/11/2025Grateful to @natcomms.nature.com for featuring our AMRO inference study as one of the Editors’ Highlights in #PublicHealth: www.nature.com/collections/...nature.comPublic healthOur recent highlights in the field of public health, including epidemiological studies investigating the social, environmental, genetic, and behavioural ... 040
Sen Pei @senpei.bsky.social · 29/11/2025Sunny and warm in San Diego. Preparing for #EPIDEMICS10 next week! 020
Sen Pei @senpei.bsky.social · 19/11/2025Read a story from Mailman on this study: www.publichealth.columbia.edu/news/scienti... end/publichealth.columbia.eduScientists Use Computer Model to Improve Hospitals’ Ability to Limit Spread of Drug-Resistant InfectionsA new analytical tool can improve a hospital’s ability to limit the spread of antibiotic-resistant infections compared to traditional methods like contact tracing. 000
Sen Pei @senpei.bsky.social · 19/11/2025Huge thanks to my collaborators and co-authors for their incredible work on this project! Code and examples are available here 👉 github.com/SenPei-CU/AM... 6/ 100
Sen Pei @senpei.bsky.social · 19/11/2025We found that even limited sequence data can meaningfully improve carrier inference when integrated with other data. By linking patient mobility, genomics, EHR, and culture data, we move closer to spotting the silent spreaders of AMROs in hospitals and intervening more strategically. 5/ 100
Sen Pei @senpei.bsky.social · 19/11/2025The inference framework was validated using both simulated outbreaks and real-world data on carbapenem-resistant Klebsiella pneumoniae in a large hospital. Inference with multiple data streams can better identify carriers and inform more effective target interventions. 4/ 100
Sen Pei @senpei.bsky.social · 19/11/2025We then built an inference framework that combines patient movement, clinical cultures, whole-genome sequencing, and risk factors in electronic health records to estimate who is likely colonized. 3/ 110
Sen Pei @senpei.bsky.social · 19/11/2025Asymptomatic carriers drive silent transmission of AMROs in hospitals, but they’re hard to detect due to sparse observations. We developed an agent-based model informed by real-world time-varying contact networks in hospitals to simulate AMRO transmission and community importation. 2/ 110
Sen Pei @senpei.bsky.social · 19/11/2025Sharing our new study on identifying asymptomatic carriers of antimicrobial-resistant organisms (AMROs) in hospitals, out in @natcomms.nature.com. We combine patient mobility, clinical cultures, EHR, and genomics to identify hidden AMRO carriers. #AMR #HAI #HospitalEpi Link 👉 rdcu.be/eQKKF 1/ 172
Sen Pei @senpei.bsky.social · 14/11/2025A super interesting study on how ants alter their nest networks to prevent epidemics! Network topology metrics were used to measure the effect on disease transmission. www.science.org/doi/full/10.... 081
Sen Pei @senpei.bsky.social · 12/11/2025Excellent work on the ecology and spread of H5N1 in North America 👉 060