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Author Details

Stephen F Schaffner
Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard
1988
141
57
PMIDPaper TitleJournal TitlePublished Year
36268576Distinguishing Severe Acute Respiratory Syndrome Coronavirus 2 Persistence and Reinfection: A Retrospective Cohort Study.Clin Infect Dis2023
36268576Distinguishing Severe Acute Respiratory Syndrome Coronavirus 2 Persistence and Reinfection: A Retrospective Cohort Study.Clin Infect Dis2023
36656774The 2022 RSV surge was driven by multiple viral lineages.medRxiv2023
36812457Viral Lineages in the 2022 RSV Surge in the United States.N Engl J Med2023
36732505High-depth sequencing characterization of viral dynamics across tissues in fatal COVID-19 reveals compartmentalized infection.Nat Commun2023
37542071Metagenomic surveillance uncovers diverse and novel viral taxa in febrile patients from Nigeria.Nat Commun2023
36781860Emergence and spread of two SARS-CoV-2 variants of interest in Nigeria.Nat Commun2023
37542071Metagenomic surveillance uncovers diverse and novel viral taxa in febrile patients from Nigeria.Nat Commun2023
36656774The 2022 RSV surge was driven by multiple viral lineages.medRxiv2023
36812457Viral Lineages in the 2022 RSV Surge in the United States.N Engl J Med2023
36781860Emergence and spread of two SARS-CoV-2 variants of interest in Nigeria.Nat Commun2023
36732505High-depth sequencing characterization of viral dynamics across tissues in fatal COVID-19 reveals compartmentalized infection.Nat Commun2023
35051367Transmission from vaccinated individuals in a large SARS-CoV-2 Delta variant outbreak.Cell2022
36246152R H: a genetic metric for measuring intrahost Plasmodium falciparum relatedness and distinguishing cotransmission from superinfection.PNAS Nexus2022
36198312Multimodal surveillance of SARS-CoV-2 at a university enables development of a robust outbreak response framework.Med2022
35608456Analysis of 6.4 million SARS-CoV-2 genomes identifies mutations associated with fitness.Science2022
35051367Transmission from vaccinated individuals in a large SARS-CoV-2 Delta variant outbreak.Cell2022
35608456Analysis of 6.4 million SARS-CoV-2 genomes identifies mutations associated with fitness.Science2022
36246152R H: a genetic metric for measuring intrahost Plasmodium falciparum relatedness and distinguishing cotransmission from superinfection.PNAS Nexus2022
36198312Multimodal surveillance of SARS-CoV-2 at a university enables development of a robust outbreak response framework.Med2022
33303686Phylogenetic analysis of SARS-CoV-2 in Boston highlights the impact of superspreading events.Science2021
33534888Biomarkers to Distinguish Bacterial From Viral Pediatric Clinical Pneumonia in a Malaria-Endemic Setting.Clin Infect Dis2021
33850016Repeated mutation of a developmental enhancer contributed to human thermoregulatory evolution.Proc Natl Acad Sci U S A2021
34049977Development of a qualitative real-time RT-PCR assay for the detection of SARS-CoV-2: a guide and case study in setting up an emergency-use, laboratory-developed molecular microbiological assay.J Clin Pathol2021
33303686Phylogenetic analysis of SARS-CoV-2 in Boston highlights the impact of superspreading events.Science2021
34452470The Origins and Future of Sentinel: An Early-Warning System for Pandemic Preemption and Response.Viruses2021
34704102Evidence of transmission from fully vaccinated individuals in a large outbreak of the SARS-CoV-2 Delta variant in Provincetown, Massachusetts.medRxiv2021
33850016Repeated mutation of a developmental enhancer contributed to human thermoregulatory evolution.Proc Natl Acad Sci U S A2021
33534888Biomarkers to Distinguish Bacterial From Viral Pediatric Clinical Pneumonia in a Malaria-Endemic Setting.Clin Infect Dis2021
34704102Evidence of transmission from fully vaccinated individuals in a large outbreak of the SARS-CoV-2 Delta variant in Provincetown, Massachusetts.medRxiv2021
34452470The Origins and Future of Sentinel: An Early-Warning System for Pandemic Preemption and Response.Viruses2021
34049977Development of a qualitative real-time RT-PCR assay for the detection of SARS-CoV-2: a guide and case study in setting up an emergency-use, laboratory-developed molecular microbiological assay.J Clin Pathol2021
32869040Phylogenetic analysis of SARS-CoV-2 in the Boston area highlights the role of recurrent importation and superspreading events.medRxiv2020
31952352Reporter Assays for Ebola Virus Nucleoprotein Oligomerization, Virion-Like Particle Budding, and Minigenome Activity Reveal the Importance of Nucleoprotein Amino Acid Position 111.Viruses2020
32045407Combining genomics and epidemiology to track mumps virus transmission in the United States.PLoS Biol2020
32991842Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant.Cell2020
32869040Phylogenetic analysis of SARS-CoV-2 in the Boston area highlights the role of recurrent importation and superspreading events.medRxiv2020
32807807Deployable CRISPR-Cas13a diagnostic tools to detect and report Ebola and Lassa virus cases in real-time.Nat Commun2020
32746830Genetic evidence for imported malaria and local transmission in Richard Toll, Senegal.Malar J2020
32958025Use of a Plasmodium vivax genetic barcode for genomic surveillance and parasite tracking in Sri Lanka.Malar J2020
32909014Development of a qualitative real-time RT-PCR assay for the detection of SARS-CoV-2: A guide and case study in setting up an emergency-use, laboratory-developed molecular assay.medRxiv2020
32618255Evidence for Reduced Malaria Parasite Population after Application of Population-Level Antimalarial Drug Strategies in Southern Province, Zambia.Am J Trop Med Hyg2020
33159858Single-Cell Profiling of Ebola Virus Disease In Vivo Reveals Viral and Host Dynamics.Cell2020
32045407Combining genomics and epidemiology to track mumps virus transmission in the United States.PLoS Biol2020
31952352Reporter Assays for Ebola Virus Nucleoprotein Oligomerization, Virion-Like Particle Budding, and Minigenome Activity Reveal the Importance of Nucleoprotein Amino Acid Position 111.Viruses2020
33159858Single-Cell Profiling of Ebola Virus Disease In Vivo Reveals Viral and Host Dynamics.Cell2020
32807807Deployable CRISPR-Cas13a diagnostic tools to detect and report Ebola and Lassa virus cases in real-time.Nat Commun2020
32746830Genetic evidence for imported malaria and local transmission in Richard Toll, Senegal.Malar J2020
32909014Development of a qualitative real-time RT-PCR assay for the detection of SARS-CoV-2: A guide and case study in setting up an emergency-use, laboratory-developed molecular assay.medRxiv2020
32991842Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant.Cell2020
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Collaborators

Harvard University
Co-authored papers 59
Broad Institute of MIT and Harvard
Co-authored papers 33
Co-authored papers 26
Vanderbilt-Ingram Cancer Center, Vanderbilt University
Co-authored papers 24
University of Kentucky
Co-authored papers 21
The Broad Institute
Co-authored papers 20
Massachusetts General Hospital
Co-authored papers 14
Broad Institute of Harvard and Massachusetts Institute of Technology (MIT)
Co-authored papers 14
Co-authored papers 12
Tulane University School of Medicine
Co-authored papers 12
The Scripps Research Institute
Co-authored papers 9
Broad Institute of MIT and Harvard
Co-authored papers 9
Co-authored papers 9
Harvard T.H. Chan School of Public Health
Co-authored papers 8
The Center for Genome Architecture, Baylor College of Medicine
Co-authored papers 8
Harvard University
Co-authored papers 7
Co-authored papers 7
Massachusetts General Hospital
Co-authored papers 6
Ontario Institute for Cancer Research
Co-authored papers 6
Institute of Ecology and Evolution, University of Edinburgh
Co-authored papers 6
Co-authored papers 6
University of Massachusetts Medical School
Co-authored papers 6
Broad Institute of MIT and Harvard
Co-authored papers 6
Co-authored papers 6
Hinton State Laboratory Institute
Co-authored papers 5
Tulane University
Co-authored papers 5
The Broad Institute of MIT and Harvard
Co-authored papers 5
Vertex Pharmaceuticals
Co-authored papers 5
Broad Institute of Harvard and the Massachusetts Institute of Technology
Co-authored papers 5
Broad Institute of MIT and Harvard
Co-authored papers 5