Samuel Scarpino bio photo

Samuel Scarpino

Assistant Professor in the Network Science Institute at Northeastern University.

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Publications

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Preprints

On the predictability of infectious disease outbreaks. (with Petri G) Supplement.

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).

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).

Journal Articles

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

(in press) 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.