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S. Schaffner · SciRah

Researcher profile · Semantic Scholar

S. Schaffner

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S. Schaffner — researcher profile on SciRah

h-index: 64
Works: 356
Citations: 64K

Most-cited papers

A global reference for human genetic variation
Taras K. Oleksyk, Adam Gonçalo R. David M. Richard M. Gonçalo R. David R. Auton Abecasis Altshuler Durbin Abecasis Bentley C, Adam Gonçalo R. Auton Abecasis, Adam Auton +496 more
2015Nature17K citations Open access
Semantic Scholar
A second generation human haplotype map of over 3.1 million SNPs
K. Frazer, D. Ballinger, D. Cox, D. Hinds +233 more
2007Nature4,713 citations Open access
Semantic Scholar
Integrating common and rare genetic variation in diverse human populations
D. Altshuler, R. Gibbs, L. Peltonen, E. Dermitzakis +65 more
2010Nature3,065 citations Open access
Semantic Scholar
Genome-wide detection and characterization of positive selection in human populations
Pardis C Sabeti, P. Varilly, B. Fry, J. Lohmueller +8 more
2007Nature2,072 citations Open access
Semantic Scholar
Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak
Stephen Gire, A. Goba, K. Andersen, Rachel S. G. Sealfon +54 more
2014Science1,233 citations Open access
Semantic Scholar
Searching for missing heritability: Designing rare variant association studies
O. Zuk, S. Schaffner, K. Samocha, R. Do +6 more
2014Proceedings of the National Academy of Sciences of the United States of America640 citations Open access
Semantic Scholar
Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant
L. Yurkovetskiy, Xue Wang, Kristen E. Pascal, C. Tomkins-Tinch +18 more
2020Cell625 citations Open access
Semantic Scholar
SARS-CoV-2 Spike protein variant D614G increases infectivity and retains sensitivity to antibodies that target the receptor binding domain
L. Yurkovetskiy, Xue Wang, Kristen E. Pascal, C. Tomkins-Tinch +18 more
2020bioRxiv585 citations Open access
Semantic Scholar
A Composite of Multiple Signals Distinguishes Causal Variants in Regions of Positive Selection
Sharon R. Grossman, Ilya Shylakhter, E. Karlsson, E. Byrne +9 more
2010Science539 citations Open access
Semantic Scholar
Clinical Illness and Outcomes in Patients with Ebola in Sierra Leone
John S. Schieffelin, Jeffrey G. Shaffer, A. Goba, Michael A Gbakie +43 more
2014New England Journal of Medicine525 citations Open access
Semantic Scholar
Direct identification of hundreds of expression-modulating variants using a multiplexed reporter assay
R. Tewhey, Dylan Kotliar, Daniel S. Park, Brandon Liu +7 more
2016Cell465 citations Open access
Semantic Scholar
Virus genomes reveal factors that spread and sustained the Ebola epidemic
G. Dudas, L. Carvalho, T. Bedford, A. Tatem +92 more
2017Nature398 citations Open access
Semantic Scholar
Identifying Recent Adaptations in Large-scale Genomic Data
Sharon R. Grossman, K. Andersen, I. Shlyakhter, S. Tabrizi +15 more
2013Cell361 citations Open access
Semantic Scholar
A genome-wide map of diversity in Plasmodium falciparum
S. Volkman, Pardis C Sabeti, David Decaprio, D. Neafsey +24 more
2007Nature Genetics326 citations
Semantic Scholar
Genomic epidemiology reveals multiple introductions of Zika virus into the United States
N. Grubaugh, J. Ladner, M. Kraemer, G. Dudas +65 more
2017Nature321 citations Open access
Semantic Scholar
Ebola Virus Epidemiology, Transmission, and Evolution during Seven Months in Sierra Leone
Daniel J. Park, G. Dudas, Shirlee Wohl, A. Goba +82 more
2015Cell290 citations Open access
Semantic Scholar
Phylogenetic analysis of SARS-CoV-2 in Boston highlights the impact of superspreading events
J. Lemieux, K. Siddle, B. Shaw, Christine Loreth +49 more
2020Science277 citations Open access
Semantic Scholar
Clinical sequencing uncovers origins and evolution of Lassa virus
K. Andersen, B. Shapiro, C. B. Matranga, Rachel S. G. Sealfon +67 more
2015Cell272 citations Open access
Semantic Scholar
Analysis of 6.4 million SARS-CoV-2 genomes identifies mutations associated with fitness
F. Obermeyer, M. Jankowiak, Nikolaos Barkas, S. Schaffner +9 more
2022Science209 citations Open access
Semantic Scholar
Ebola virus glycoprotein with increased infectivity dominated the 2013–2016 epidemic
W. Diehl, A. Lin, N. Grubaugh, L. Carvalho +12 more
2016Cell204 citations Open access
Semantic Scholar
Modeling malaria genomics reveals transmission decline and rebound in Senegal
Rachel F. Daniels, S. Schaffner, E. Wenger, J. L. Proctor +14 more
2015Proceedings of the National Academy of Sciences of the United States of America185 citations Open access
Semantic Scholar
Deployable CRISPR-Cas13a diagnostic tools to detect and report Ebola and Lassa virus cases in real-time
K. Barnes, Anna E. Lachenauer, Adam N. Nitido, S. Siddiqui +35 more
2020Nature Communications160 citations Open access
Semantic Scholar
hmmIBD: software to infer pairwise identity by descent between haploid genotypes
S. Schaffner, Aimee R. Taylor, W. Wong, D. Wirth +1 more
2017Malaria Journal155 citations Open access
Semantic Scholar
Data sharing: Make outbreak research open access
N. Yozwiak, S. Schaffner, Pardis C Sabeti
2015Nature135 citations Open access
Semantic Scholar
Genome-wide SNP genotyping highlights the role of natural selection in Plasmodium falciparum population divergence
D. Neafsey, S. Schaffner, S. Volkman, Daniel J. Park +24 more
2008Genome Biology133 citations Open access
Semantic Scholar
Longitudinal genomic surveillance of Plasmodium falciparum malaria parasites reveals complex genomic architecture of emerging artemisinin resistance
G. Cerqueira, Ian H. Cheeseman, S. Schaffner, S. Nair +9 more
2017Genome Biology130 citations Open access
Semantic Scholar
Genomic analysis of Lassa virus from the 2018 surge in Nigeria
K. Siddle, Philomena E. Eromon, K. Barnes, Samar B. Mehta +47 more
2018New England Journal of Medicine126 citations Open access
Semantic Scholar
Clinical and laboratory predictors of Lassa fever outcome in a dedicated treatment facility in Nigeria: an observational cohort study
P. Okokhere, A. Colubri, C. Azubike, C. Iruolagbe +21 more
2018Lancet. Infectious Diseases (Print)125 citations Open access
Semantic Scholar
Artemisinin resistance without pfkelch13 mutations in Plasmodium falciparum isolates from Cambodia
A. Mukherjee, S. Bopp, P. Magistrado, W. Wong +14 more
2017Malaria Journal121 citations Open access
Semantic Scholar
Plasmepsin II–III copy number accounts for bimodal piperaquine resistance among Cambodian Plasmodium falciparum
S. Bopp, P. Magistrado, W. Wong, S. Schaffner +13 more
2018Nature Communications120 citations Open access
Semantic Scholar
Sequence-based association and selection scans identify drug resistance loci in the Plasmodium falciparum malaria parasite
Daniel J. Park, A. Lukens, D. Neafsey, S. Schaffner +14 more
2012Proceedings of the National Academy of Sciences of the United States of America119 citations Open access
Semantic Scholar
Development of a Single Nucleotide Polymorphism Barcode to Genotype Plasmodium vivax Infections
M. Baniecki, Aubrey Faust, S. Schaffner, Daniel J. Park +16 more
2015PLoS Neglected Tropical Diseases116 citations Open access
Semantic Scholar
Quantifying connectivity between local Plasmodium falciparum malaria parasite populations using identity by descent
Aimee R. Taylor, S. Schaffner, G. Cerqueira, Standwell C. Nkhoma +6 more
2017PLoS Genetics113 citations Open access
Semantic Scholar
Harnessing genomics and genome biology to understand malaria biology
S. Volkman, D. Neafsey, S. Schaffner, Daniel J. Park +1 more
2012Nature reviews genetics112 citations
Semantic Scholar
Single-Cell Profiling of Ebola Virus Disease In Vivo Reveals Viral and Host Dynamics
Dylan Kotliar, A. Lin, James P. Logue, T. Hughes +23 more
2020Cell106 citations Open access
Semantic Scholar
Genetic Surveillance Detects Both Clonal and Epidemic Transmission of Malaria following Enhanced Intervention in Senegal
Rachel F. Daniels, Hsiao-Han Chang, P. Séne, D. C. Park +11 more
2013PLoS ONE104 citations Open access
Semantic Scholar
A global map of genetic diversity in Babesia microti reveals strong population structure and identifies variants associated with clinical relapse
J. Lemieux, Alice Tran, Lisa M. Freimark, S. Schaffner +13 more
2016Nature Microbiology93 citations Open access
Semantic Scholar
Natural Selection in a Bangladeshi Population from the Cholera-Endemic Ganges River Delta
E. Karlsson, J. Harris, S. Tabrizi, Atiqur Rahman +16 more
2013Science Translational Medicine90 citations Open access
Semantic Scholar
Comment on "Ongoing Adaptive Evolution of ASPM, a Brain Size Determinant in Homo sapiens"
Fu-Li Yu, R. Hill, S. Schaffner, Pardis C Sabeti +6 more
2007Science81 citations
Semantic Scholar
Searching for signals of evolutionary selection in 168 genes related to immune function
E. Walsh, Pardis C Sabeti, H. Hutcheson, B. Fry +12 more
2006Human Genetics80 citations
Semantic Scholar
Discovery of Novel Rhabdoviruses in the Blood of Healthy Individuals from West Africa
M. Stremlau, K. Andersen, O. Folarin, Jessica N Grove +23 more
2015PLoS Neglected Tropical Diseases68 citations Open access
Semantic Scholar
Genomic sequencing of Plasmodium falciparum malaria parasites from Senegal reveals the demographic history of the population.
Hsiao-Han Chang, Daniel J. Park, K. Galinsky, S. Schaffner +9 more
2012Molecular biology and evolution62 citations Open access
Semantic Scholar
GENOMIC ANALYSIS OF VIRAL OUTBREAKS
Shirlee Wohl, S. Schaffner, Pardis C Sabeti
2016Annual Review of Virology61 citations Open access
Semantic Scholar
Genetic relatedness analysis reveals the cotransmission of genetically related Plasmodium falciparum parasites in Thiès, Senegal
W. Wong, A. Griggs, Rachel F. Daniels, S. Schaffner +8 more
2017Genome Medicine55 citations Open access
Semantic Scholar
Phylogenetic analysis of SARS-CoV-2 in the Boston area highlights the role of recurrent importation and superspreading events.
J. Lemieux, K. Siddle, B. Shaw, Christine Loreth +49 more
2020medRxiv52 citations Open access
Semantic Scholar
Repeated mutation of a developmental enhancer contributed to human thermoregulatory evolution
D. Aldea, Y. Atsuta, B. Kokalari, S. Schaffner +5 more
2021Proceedings of the National Academy of Sciences of the United States of America49 citations Open access
Semantic Scholar
Cosi2 : An efficient simulator of exact and approximate coalescent with selection
I. Shlyakhter, Pardis C Sabeti, S. Schaffner
2014bioRxiv49 citations Open access
Semantic Scholar
Transmission from vaccinated individuals in a large SARS-CoV-2 Delta variant outbreak
K. Siddle, L. Krasilnikova, G. Moreno, S. Schaffner +76 more
2021Cell46 citations Open access
Semantic Scholar
RSV Surge in the USA and Viral Lineages, 2022
G. Adams, G. Moreno, B. Petros, R. Uddin +18 more
2023New England Journal of Medicine44 citations Open access
Semantic Scholar
Combining genomics and epidemiology to track mumps virus transmission in the United States
Shirlee Wohl, Hayden C. Metsky, S. Schaffner, A. Piantadosi +26 more
2020PLoS Biology44 citations Open access
Semantic Scholar

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