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Samuel Scarpino

Director of AI + Life Sciences and Professor of the Practice, Northeastern University.

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(2019) Rohani P & Scarpino SV. The integrative biology of Pertussis: epidemiology, immunology & evolution. Oxford University Press.

Professional Publications

(In press) Wastewater surveillance facilitates climate-change resilient pathogen monitoring (with A Diamond MB, Yee E, Bhinge M). Science Translational Medicine.

(In press) The unintended consequences of inconsistent closure policies and mobility restrictions during epidemics (with Althouse BM, Wallace B, Case B, Allard A, Berdhal A, White ER, and Hebert-Dufresne L). BMC Global and Public Health.

(In press) Characterizing collective physical distancing in the U.S. during the first nine months of the COVID-19 pandemic (with Klein B, LaRock T, McCabe S, Torres L, Friedland L, Privitera F, Lake B, Kraemer MUG, Brownstein JS, Lazer D, Eliassi-Rad T, Vespignani A, and Chinazzi M). PLoS Digital Health.

(2023) The COVID-19 pandemic amplified long-standing racial disparities in the United States criminal legal system (with Klein B, Ogbunugafor CB, Schafer BJ, Bhadricha Z, Kori P, Sheldon J, Kaza N, Wang EA, Eliassi-Rad T, and Hinton E). Nature.

(2023) Wastewater monitoring can anchor global disease surveillance systems (with Keshaviah A, Diamond MB, Wade MJ, and the Global Wastewater Action Group). The Lancet Global Health.

(2023) Forecasting hospital-level COVID-19 admissions using real-time mobility data (with Zenteno AC, Joseph D, Zahedi M, Hu M, Copenhaver M, Kraemer MUG, Chinazzi M, Klompas M, Vespignani A, and Salmasian H). Nature Communications Medicine.

(2023) The role of directionality, heterogeneity and correlations in epidemic risk and spread. (with Allard A, Moore C, Althouse BM, Hebert-Dufresne L). SIAM Review.

(2023) The ensemble of gene regulatory networks at mutation-selection balance (with Yang CH). Roy. Soc. Interface.

(2022) Effective resistance for pandemics: Mobility network sparsification for high-fidelity epidemic simulation (with Mercier AM and Moore C). PLoS Computational Biology.

(2022) Higher education responses to COVID-19 in the United States: Evidence for the impacts of university policy (with Klein B, Generous N, Chinazzi M, Bhadricha Z, Gunashekar R, Kori P, Li B, McCabe S, Green J, Lazer D, Marsicano CR, and Vespignani A). PLoS Digital Health.

(2022) A family of fitness landscapes modeled through gene regulatory networks. (with Yang CH). Entropy.

(2022) Exploring noise, degeneracy, and determinism in biological networks with the einet package. (with Klein B, Swain A, Byrum T, Fagan W). Methods in Ecology and Evolution.

(2022) Higher-order interactions in biology: the case of epistasis. In: Battiston F & Petri G (ed.), Higher-order systems. (with Ogbunugafor CB). Higher-order systems. Understanding Complex Systems Series: Springer.

(2022) Development and validation of manually modified and supervised machine learning (ML) clinical assessment algorithms for malaria in Nigerian children. (with McLaughlin M, Pellé KG, Giwa A, Mount-Finette E, Haidar N, Adamu F, Adeyoju T, Ravi N, Thompson A, Heath B, Dittrich S, and Finette B). Frontiers in Artificial Intelligence.

(2021) Spatio-temporal invasion dynamics of SARS-CoV-2 lineage B.1.1.7 emergence. (with Kraemer MUG, Hill V, Ruis C, Dellicour S, Bajaj S, McCrone JT, Baele G, Parag KV, Lindstrom Battle A, Gutierrez B, Jackson B, Colquhoun R, O’Toole A, Klein B, Vespignani A, The COVID-19 Genomics UK (CoG-UK) consortium, Volz E, Faria NR, Aanensen D, Loman NJ, du Plessis L, Cauchemez S, Rambaut A, and Pybus OG). Science.

(2021) Modeling disease transmission & interventions. In: Krakauer DC & West G (ed.), The Complex Alternative: Complexity Scientists on the COVID-19 Pandemic. Santa Fe Institute Press.

(2021) A review and agenda for integrated disease models including social and behavioural factors. (with Bedson J, Skrip LA, Pedi D, Abramowitz S, Carter S, Jalloh MF, Funk S, Gobat N, Giles-Vernick Tamara, Chowell G, Rangel de Almeida J, Elessawi R, Hammond RA, Briand S, Epstein JM, Hébert-Dufresne L, and Althouse BM). Nature Human Behaviour.

(2021) The effect of eviction moratoria on the transmission of SARS-CoV-2. (with Nande A, Sheen J, Walters EL, Klein B, Chinazzi M, Gheorghe A, Adlam B, Shinnick J, Tejeda MF, Vespignani A, Greenlee AJ, Schneider D, Levy MZ, and Hill AL). Nature Communications.

(2021) Immunotranscriptomic profiling the acute and clearance phases of a human challenge dengue virus serotype 2 infection model. (with Hanley J, Tu HA, Dragon JA, Dickson DM, Selig N, Tighe S, Eckstrom KM, Whitehead SS, Durbin AP, Pierce KK, Kirkpatrick BD, Rizzo DM, Frietze S, and Diehl SA). Nature Communications.

(2021) Seeding COVID-19 across sub-Saharan Africa: an analysis of reported importation events across 40 countries. (with Skrip LA, Selvaraj P, Hagedorn B, Ouédraogo AL, Noori N, Orcutt A, Mistry D, Bedson J, Hébert-Dufresne L, and Althouse BM). The American Journal of Tropical Medicine and Hygiene.

(2021) Mask-wearing and control of SARS-CoV-2 transmission in the USA: a cross-sectional study (with Rader B, White LF, Burns MR, Chen J, Brilliant J, Cohen J, Shaman J, Brilliant L, Kraemer MUG, Hawkins JB, Scarpino SV, Astley C, Brownstein JS). The Lancet Digital Health.

(2020) Crowding and the shape of COVID-19 epidemics. (with Rader B, Nande A, Hill A, Dalziel B, Reiner Jr. R, Pigott D, Gutierrez B, Zarebski AE, Shrestha M, open COVID-19 data working group, Brownstein J, Castro MC, Dye C, Tian H, Pybus O, Kraemer MUG). Nature Medicine.

(2020) The effect of human mobility and control measures on the COVID-19 epidemic in China. (with Kraemer MUG, Yang CH, Gutierrez B, Wu CH, Klein B, Pigott DM, open COVID-19 data working group, Plessis LD, Faria NR, Li R, Hanage WP, Brownstein JS, Layan M, Vespignani A, Tian H, Dye C, and Pybus OG). Science.

(2020) Variation in microparasite free-living survival and indirect transmission can modulate the intensity of emerging outbreaks. (with Ogbunugafor B, Meszaros VA, Miller-Dickson MD, Gomez LM, Murillo AL). Scientific Reports.

(2020) Superspreading events in the transmission dynamics of SARS-CoV-2: Opportunities for interventions and control (with Althouse BM, Wenger EA, Miller JC, Allard A, Hebert-Dufresne L, Hu H). PLoS Biology.

(2020) Beyond R0: heterogeneity in secondary infections and probabilistic epidemic forecasting. (with Hebert-Dufresne L, Althouse BM, and Allard A). Proc. Roy. Soc. Interface.

(2020) Socioeconomic bias in influenza surveillance. (with Scott JG, Eggo RM, Clements B, Dimitrov NB, and Meyers LA). PLoS Computational Biology.

(2020) Macroscopic patterns of interacting contagions are indistinguishable from social reinforcement. (with Young JG and Hebert-Dufresne L). Nature Physics.

(2020) Epidemiological data from the COVID-19 outbreak: early descriptions and open release. (with Xu B, Gutierrez B, Mekaru S, Sewalk K, Loskill A, Wang L, Cohn E, Hill SC, Zabreski A, Li S, Wu C-H, Hulland E, Morgan J, Brownstein JS, Pybus OG, Pigott DM, and Kraemer MUG). Nature Scientific Data.

(2020) Asymptomatic infection and transmission of pertussis in households: a systematic review. (with Craig R, Kunkel E, Crowcroft N, Fitzpatrick MC, de Melker H, Althouse BM, Merkel T, Koelle K, Friedman L, Arnold C, and Bolotin S). Clinical Infectious Diseases.

(2019) Proteostasis environment shapes higher-order epistasis operating on antibiotic resistance. (with Guerrero RF, Rodrigues JV, Hartl D, and Ogbunugafor DB). Genetics.

(2019) Development and initial validation of a frontline health worker mHealth assessment platform (MEDSINC®) for children 2-60 months of age. (with Finette B, McLaughlin M, Canning J, Grunauer M, Teran E, Bahamonde M, Quizhpe E, Shah R, Swedberg E, Rahman K, Khondker H, Chakma I, Muhoza D, Seck A, Kabore A, Nibitanga S, and Heath B). American Journal of Tropical Medicine and Hygiene.

(2019) On the predictability of infectious disease outbreaks. (with Petri G). Nature Communications.

(2019) Food insecure cancer survivors continue to smoke after their diagnosis despite not having enough to eat: implications for policy and clinical interventions. (with Poghosyan H). Cancer Causes & Control.

(2018) Comparison of crowd-sourced, electronic health records based, and traditional health-care based influenza-tracking systems at multiple spatial resolutions in the United States of America. (with Baltrusaitis K, Brownstein JS, Bakota E, Crawley AW, Conidi G, Gunn J, Gray J, Zink A, and Santillana M). BMC Infectious Diseases.

(2018) The interhospital transfer network for very low birth weight infants in the United States. (with Shrestha M, Edwards EM, Greenberg LT, and Horbar JD). EPJ Data Science.

(2018) Single Nucleotide Polymorphism Analyses Reveal Potential Vancomycin-Resistant Enterococci Transmission Networks between Rooms and Patients on Stem Cell Transplant and Leukemia Units (with El Haddad L, Ghantoji SS, Otero G, Harb CP, Stibich M, & Chemaly RF.) Biology of Blood and Marrow Transplantation.

(2018) Automated collection of pathogen-specific diagnostic data for real-time syndromic epidemiological studies. (with Meyers L, Ginocchio CC, Faucett AN, Nolte FS, Gesteland PH, Leber A, Janowiak D, Donovan V, Bard JD, Spitzer S, Stellrecht KA, Salimnia H, Selvarangan R, Juretschko S, Daly JA, Wallentine JC, Lindsey K, Moore F, Reed SL, Aguero-Rosenfeld M, Fey PD, Storch GA, Melnick SL, Cook CV, Nelson RK, Jones JD, Althouse BM, Ririe KM, Malin BA, and Poritz MA). Journal of Internet Medical Research.

(2017) The risk of sustained sexual transmission of Zika is underestimated. (with Allard A, Althouse BM, and Hebert-Dufresne L). PLoS Pathogens.

(2017) Asymmetric percolation drives a double transition in sexual contact networks. (with Allard A, Althouse BM, and Hebert-Dufresne L). Proc. Natl. Acad. Sci. USA.

(2017) Topological features of a gene co-expression network predict patterns of natural diversity in environmental response. (with Des Marais DL, Guerrero R, and Lasky JR) Proceedings of the Royal Society B.

(2017) Design strategies for efficient arbovirus surveillance (with Meyers LA and Johansson MA) Emerging Infectious Diseases.

(2017) On the young age of intraspecific herbaceous taxa. (with Levin D) New Phytologist.

(2016) The effect of a prudent adaptive behaviour on disease transmission. (with Allard A and Hebert-Dufresne L) Nature Physics. Supplement.

(2016) Modeling the Effects of Priming With the Whole-Cell Bordetella Pertussis Vaccine—Reply (with DeAngelis H and Althouse BM) JAMA Pediatrics.

(2016) Cost-effectiveness of a next-generation pertussis vaccine. (with Fitzpatrick MC, Wenzel NS, Althouse BM, Galvani AP, and Townsend JP) Vaccine.

(2016) Evolution and the emergence of novel pathogens. Encyclopedia of Evolutionary Biology.

(2016) Epidemiological and economic effects of priming with the whole-cell Bordetella pertussis vaccine. (with DeAngelis H, Fitzpatrick MC, Galvani AP, and Althouse BM) JAMA Pediatrics.

(2015) Enhancing disease surveillance with novel data streams (with Althouse BM and the participants of the Santa Fe Institute workshop Next Generation Surveillance for the Next Pandemic) EPJ Data Science.

(2015) Estimating trait heritability in highly fecund species (with Davies SW, Pongwarin T, Scott J, and Matz M) Genes Genomes Genetics.

(2015) A Message-Passing Approach for Recurrent-State Epidemic Models on Networks (with Shrestha M and Moore C) Physical Review E.

(2015) Asymptomatic transmission and the resurgence of Bordetella pertussis (with Althouse BM) BMC Medicine.

(2015) Epidemiological and viral genomic sequence analysis of the 2014 Ebola outbreak reveals clustered transmission. (with Iamarino A, Wells C, Yamin D, Ndeffo-Mbah M, Wenzel N, Fox SJ, Nyenswah T, Altice FL, Galvani A, Meyers LA, and Townsend JP) Clinical Infectious Diseases . Supplement.

(2015) Robust Estimation of Inequality from Binned Incomes. (with von Hippel P and Holas I) Sociological Methodology. R Package

(2014) Polyploid formation shapes flowering plant diversity. (with Levin DA and Meyers LA) American Naturalist.

(2013) Evolution of a genetic incompatibility in the genus Xiphophorus. (with Hunt PJ, Garcia-De-Leon FJ, Juenger TE, Schartl M, and Kirkpatrick M) Molecular Biology and Evolution.

(2012) Epigenetic Transgenerational Alterations to Stress Response in Brain Gene Networks and Behavior. (with Crews D, Gillette R, Scarpino SV, Manikkam M, Savenkova MI, and Skinner MK) Proc. Natl. Acad. Sci. USA.

(2012) Optimizing Provider Recruitment for Influenza Surveillance Networks. (with Dimitrov NB and Meyers LA) PLoS Comp. Biol.A.

(2011) About PAR: The distinct evolutionary dynamics of the Pseudoautosomal Region. (with Otto SP, Pannell JR, Peichel CL, Ashman TL, Charlesworth D, Chippindale AK, Delph LF, Guerrero RF, and McAllister BF) Trends in Genetics.

(2011) Environment-dependent intralocus sexual conflict in a dioecious plant. (with Delph LF, Andicoechea J, Steven J, Herlihy C, and Bell D) New Phytologist.

(2010) Modeling the spatial distribution and fruiting pattern of a key tree species in a neotropical forest: methodology and potential applications. (with Caillaud D, Crofoot MC, Jansen P, Garzon-Lopez CX, Winkelhagen A, Bohlman SA, and Walsh PD) PLoS ONE.

(2010) Patterns of neutral genetic variation on recombining sex chromosomes. (with Kirkpatrick M and Guerrero RF) Genetics.

(2009) Initial human transmission dynamics of the pandemic (H1N1) 2009 virus in North America. (with Pourbohloul B, Ahued A, Davoudi B, Meza R, Meyers LA, Skowronski DM, Villasenor I, Galvan F, Cravioto P, Earn DJ, Dushoff J, Fisman D, Edmunds WJ, Hupert N, Trujillo J, Lutzow M, Morales J, Contreras A, Chavez C, Patrick DM, and Brunham RC) Influenza and Other Respiratory Viruses.

Preprints (not published elsewhere)

Spatial scales of COVID-19 transmission in Mexico (with Klein B, Hartle H, Shrestha M, Zenteno AC, Barros Sierra Cordera D, Nicolas-Carlock JR, Bento AI, Althouse BM, Gutierrez B, Escalera-Zamudio M, Reyes-Sandoval A, Pybus OG, Vespignani A, Diaz-Quiñonez JA, and Kraemer MUG).

Early risk-assessment of pathogen genomic variants emergence (with Susswein Z, Johnson KE, Kassa R, Parastaran M, Peng V, Wolansky L, and Bento AI).

Spatio-temporal heterogeneity and the spread of lineage B.1.1.7 in the United Kingdom(with Kraemer MUG, Hill V, Ruis C, Parag KV, Lindstrom Battle A, O’Toole A, Vespignani A, The COVID-19 Genomics UK (CoG-UK) consortium, Loman NJ, Rambaut A, and Pybus OG).

Reproductive Barriers as a Byproduct of Gene Network Evolution (with Yang CH).

Preliminary estimates of the international spreading risk associated with the SARS-CoV-2 VUI 202012/01 (with Chinazzi M, Davis JT, MU K, Pastore y Piontti A, Perra N, and Vespignani A).

Assessing changes in commuting and individual mobility in major metropolitan areas in the United States during the COVID-19 outbreak. (with Klein B, LaRock T, McCabe S, Torres L, Privitera F, Lake B, Kraemer MUG, Brownstein JS, Lazer D, Eliassi-Rad T, Chinazzi M, and Vespignani A).

Google searches accurately forecast RSV hospitalizations. (with Althouse BM, Weinberger DM, Pitzer VE, Ayers JW, Wenger W, Chun-Hai Fung I, Dredze M, and Hu H).

Analysis of clinical Bordetella pertussis isolates using whole genome sequences reveals novel genomic regions associated with recent outbreaks in the United States. (with Otero G and Althouse BM).

The Moose of Isle Royale: An Unnatural Condition? (with Guerrero RF and Scarpino PV).

multiDimBio: An R package for the design, analysis, and visualization of systems biology experiments. (with Crews D and Gillette R).

Perspectives, Opinions, and Outreach Publications

(2023) Wastewater surveillance of pathogens can inform public health action. Nature Medicine (with Diamond MB, Keshaviah A, Bento AI, Conroy-Ben O, Driver EM, Ensor KB, Halden RU, Hopkins LP, Kuhn KG, Moe CL, Rouchka EC, Smith T, Stadler LB, Stevenson BS, Susswein Z, Vogel JR, and Wolfe MK).

(2022) Tracking the 2022 monkeypox outbreak with epidemiological data in real-time. The Lancet Infectious Diseases (with Moritz U G Kraemer MUG, Tegally H, Pigott DM, Dasgupta A, Sheldon J, Wilkinson E, Schiltheiss M, Han A, Oglia M, Marks S, Kanner J, O’Brien K, Dandamudi S, Rader B, Sewalk K, Bento AI, de Oliveria T, Bogoch II, Katz R, and Brownstein JS).

(2022) Innovations in public health surveillance: updates from a forum convened by the WHO Hub for Pandemic and Epidemic Intelligence, 2 and 3 February 2022. Eurosurveillance (with Morgan O, Redies I, Rioja ZBL, Brownstein J, George D, Golding J, Hanefeld J, Horby P, Lee C, Mikhailov D, Philip W, Scarpino SV, Tessema SK, and Ihekweazu C).

(2022) Variants, Sublineages, and Recombinants: The Constantly Changing Genome of SARS-CoV-2. The Rockefeller Foundation: Case Studies. (with Houtman J, Shutlz L, Malaty Rivera J, Gilmour J, Luo D, and Bright RA).

(2021) One outstanding path from A to B. Nature Physics (with Shugars S).

(2021) Data curation during a pandemic and lessons learned from COVID-19. Nature Computational Science (with Kraemer MUG, Scarpino SV, Marivate V, Gutierrez B, Xu B, Lee G, Hawkins JB, Rivers C, Pigott DM, Katz R, and Brownstein JS).

(2020) Probing COVID’s complexity in real time. Science.

(2020) Leading with data on the path to normalcy. Tableau Blog.

(2020) Applications of predictive modeling during the early stages of the COVID-19 epidemic The Lancet Digital Health (with Poletto C and Volz E).

(2020) Modelling COVID-19: Realistic models require better data. Nature Reviews Physics (with Shrestha M).

(2020) Sampling bias and incorrect rooting make phylogenetic network tracing of SARS-COV-2 infections unreliable. PNAS (with Mavian C, Pond SK, Marini S, Magalis BR, Vandamme AM, Dellicour S, Houldcroft C, Villabona-Arenas J, Paisie TK, Trovao NS, Boucher C, Zhang Y, Scheuermann RH, Gascuel O, Tsan-Yuk Lam T, Suchard MA, Abecasis A, Wilkinson E, de Oliveira T, Bento AI, Schmidt KA, Martin D, Hadfield J, Faria N, Grubaugh ND, Neher RA, Baele G, Lemey P, Stadler T, Albert J, Crandall KA, Leitner T, Stamatakis A, Prosperi M, & Salemi M).

(2020) Aggregated Mobility Data Could Help Fight COVID-19. Science (with Buckee CO, Balsari S, Chan J, Crosas M, Dominici F, Gasser U, Grad YH, Grenfell B, Halloran ME, Kraemer MUG, Lipsitch M, Metcalf CJE, Meyers LA, Perkins TA, Santillana M, Scarpino SV, Viboud C, Wesolowski A, & Schroeder A).

(2020) Mobile phone data and COVID-19: Missing an opportunity? Science Advances (with Oliver N, Letouzé E, Sterly H, Delataille S, Nadai MD, Lepri B, Lambiotte R, Benjamins R, Cattuto C, Colizza V, de Cordes N, Fraiberger SP, Koebe T, Lehmann S, Murillo J, Pentland A, Pham PN, Pivetta F, Salah AA, Saramäki J, Tizzoni M, Verhulst S, Vinck P).

(2020) COVID-19: Keep calm and wash your hands. Medium.

(2020) Open access epidemiological data from the COVID-19 outbreak. The Lancet Infectious Diseases (with Xu B, Kraemer MUG, and the Open COVID-19 Data Curation Group).

(2019) Uncovering the hidden cost of bed bugs. PNAS (with Althouse BM).

(2019) Why it’s so difficult for scientists to predict the next outbreak of a dangerous disease. The Conversation (with Ogbunu CB and Harp R).

(2018) Modelling the trajectory of disease outbreaks works. Nature (with Rivers CM).

(2018) Epidemic Spreading: Don’t Close the Gates. Nature Physics.

(2017) The flu vaccine is effective. Medium.

(2015) 3 graphs that help show why Ebola goes viral or dies out. Nautilus.

(2014) Mathematical models: A key tool for outbreak response.(with Lofgren ET, Halloran ME, Rivers CM, Drake JM, Porco TC, Lewis BL, Yang W, Vespignani A, Shaman J, Eisenberg JNS, Eisenberg MC, Marathe MV, Alexander KA, Meza R, Ferrari MJ, Hyman JM, Meyers LA, and Eubank SG) Proc. Natl. Acad. Sci. USA.

(2014) Ebola: models do more than forecast. (with Rivers C, Alexander K, Bellan S, Del Valle S, Drake JM, Eisenberg JN, Eubank S, Ferrari M, Halloran ME, Galvani A, Lewis BL, Lewnard J, Lofgren E, Macal C, Marathe M, Ndeffo Mbah M, Meyers LA, Meza R, Park A, Porco T, Shaman J, Vespignani A, and Yang W) Nature.

(2014) Ebola: Mobility data. (with Halloran EM, Vespignani A, Bharti N, Feldstein LR, Alexander K, Ferrari M, Shaman J, Drake JM, Porco T, Eisenberg J, DeValle S, Lofgren E, Eisenberg M, Gao D, Hyman JM, Eubank S, and Longini IM) Science.

(2014) The mathematics of stopping Ebola. Santa Fe New Mexican.