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Samuel Scarpino

Assistant Professor in the Network Science Institute at Northeastern University.

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Preprints (unpublished)

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

Stochasticity and heterogeneity in the transmission dynamics of SARS-CoV-2 (with Althouse BM, Wenger EA, Miller JC, Allard A, Hebert-Dufresne L, Hu H).

Reshaping a nation: Mobility, commuting, and contact patterns 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, Vespignani A, and Chinazzi M).

The intensity of COVID-19 outbreaks is modulated by SARS-CoV-2 free-living survival and environmental transmission. (with Ogbunugafor B, Meszaros VA, Miller-Dickson MD, Gomez LM, Murillo AL).

Crowding and the epidemic intensity of COVID-19 transmission. (with Rader B, Nande A, Hill A, Dalziel B, Reiner Jr. R, Pigott D, Gutierrez B, Shrestha M, open COVID-19 data working group, Brownstein J, Castro M, Tian H, Grenfell B, Pybus O, Metcalf J, Kraemer MUG.).

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).

Beyond R0: the importance of contact tracing when predicting epidemics. (with Hebert-Dufresne L, Althouse BM, and Allard A).

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, Mistry D, Bedson J, Hébert-Dufresne L, and Althouse BM).

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).

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


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


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

(in press) 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, Cauchemez S, and Pybus OG). Science.

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

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

(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.

(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.