Harvard Catalyst Profiles

Contact, publication, and social network information about Harvard faculty and fellows.

Stephen Schaffner, Ph.D.

Co-Author

This page shows the publications co-authored by Stephen Schaffner and Pardis Sabeti.
Connection Strength

5.221
  1. Transmission from vaccinated individuals in a large SARS-CoV-2 Delta variant outbreak. Cell. 2022 02 03; 185(3):485-492.e10.
    View in: PubMed
    Score: 0.244
  2. Evidence of transmission from fully vaccinated individuals in a large outbreak of the SARS-CoV-2 Delta variant in Provincetown, Massachusetts. medRxiv. 2021 Oct 20.
    View in: PubMed
    Score: 0.241
  3. Deployable CRISPR-Cas13a diagnostic tools to detect and report Ebola and Lassa virus cases in real-time. Nat Commun. 2020 08 17; 11(1):4131.
    View in: PubMed
    Score: 0.222
  4. Combining genomics and epidemiology to track mumps virus transmission in the United States. PLoS Biol. 2020 02; 18(2):e3000611.
    View in: PubMed
    Score: 0.215
  5. Reporter Assays for Ebola Virus Nucleoprotein Oligomerization, Virion-Like Particle Budding, and Minigenome Activity Reveal the Importance of Nucleoprotein Amino Acid Position 111. Viruses. 2020 01 15; 12(1).
    View in: PubMed
    Score: 0.214
  6. Development of a SNP barcode to genotype Babesia microti infections. PLoS Negl Trop Dis. 2019 03; 13(3):e0007194.
    View in: PubMed
    Score: 0.202
  7. Clinical and laboratory predictors of Lassa fever outcome in a dedicated treatment facility in Nigeria: a retrospective, observational cohort study. Lancet Infect Dis. 2018 06; 18(6):684-695.
    View in: PubMed
    Score: 0.188
  8. Direct Identification of Hundreds of Expression-Modulating Variants using a Multiplexed Reporter Assay. Cell. 2018 02 22; 172(5):1132-1134.
    View in: PubMed
    Score: 0.187
  9. Zika virus evolution and spread in the Americas. Nature. 2017 06 15; 546(7658):411-415.
    View in: PubMed
    Score: 0.178
  10. Genomic Analysis of Viral Outbreaks. Annu Rev Virol. 2016 09 29; 3(1):173-195.
    View in: PubMed
    Score: 0.168
  11. A global map of genetic diversity in Babesia microti reveals strong population structure and identifies variants associated with clinical relapse. Nat Microbiol. 2016 06 13; 1(7):16079.
    View in: PubMed
    Score: 0.166
  12. Direct Identification of Hundreds of Expression-Modulating Variants using a Multiplexed Reporter Assay. Cell. 2016 Jun 02; 165(6):1519-1529.
    View in: PubMed
    Score: 0.166
  13. Clinical Sequencing Uncovers Origins and Evolution of Lassa Virus. Cell. 2015 Aug 13; 162(4):738-50.
    View in: PubMed
    Score: 0.157
  14. Ebola Virus Epidemiology, Transmission, and Evolution during Seven Months in Sierra Leone. Cell. 2015 Jun 18; 161(7):1516-26.
    View in: PubMed
    Score: 0.155
  15. Development of a single nucleotide polymorphism barcode to genotype Plasmodium vivax infections. PLoS Negl Trop Dis. 2015 Mar; 9(3):e0003539.
    View in: PubMed
    Score: 0.153
  16. Data sharing: Make outbreak research open access. Nature. 2015 Feb 26; 518(7540):477-9.
    View in: PubMed
    Score: 0.152
  17. Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak. Science. 2014 Sep 12; 345(6202):1369-72.
    View in: PubMed
    Score: 0.147
  18. Cosi2: an efficient simulator of exact and approximate coalescent with selection. Bioinformatics. 2014 Dec 01; 30(23):3427-9.
    View in: PubMed
    Score: 0.147
  19. Identifying recent adaptations in large-scale genomic data. Cell. 2013 Feb 14; 152(4):703-13.
    View in: PubMed
    Score: 0.132
  20. Epidemiology. Emerging disease or diagnosis? Science. 2012 Nov 09; 338(6108):750-2.
    View in: PubMed
    Score: 0.130
  21. Identification and functional validation of the novel antimalarial resistance locus PF10_0355 in Plasmodium falciparum. PLoS Genet. 2011 Apr; 7(4):e1001383.
    View in: PubMed
    Score: 0.117
  22. A composite of multiple signals distinguishes causal variants in regions of positive selection. Science. 2010 Feb 12; 327(5967):883-6.
    View in: PubMed
    Score: 0.107
  23. Genome-wide detection and characterization of positive selection in human populations. Nature. 2007 Oct 18; 449(7164):913-8.
    View in: PubMed
    Score: 0.091
  24. Detecting recent positive selection in the human genome from haplotype structure. Nature. 2002 Oct 24; 419(6909):832-7.
    View in: PubMed
    Score: 0.065
  25. Analysis of 6.4 million SARS-CoV-2 genomes identifies mutations associated with fitness. medRxiv. 2022 Feb 16.
    View in: PubMed
    Score: 0.062
  26. A year of genomic surveillance reveals how the SARS-CoV-2 pandemic unfolded in Africa. Science. 2021 Oct 22; 374(6566):423-431.
    View in: PubMed
    Score: 0.060
  27. The Origins and Future of Sentinel: An Early-Warning System for Pandemic Preemption and Response. Viruses. 2021 08 13; 13(8).
    View in: PubMed
    Score: 0.060
  28. Development 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 Pathol. 2021 Aug; 74(8):496-503.
    View in: PubMed
    Score: 0.059
  29. Phylogenetic analysis of SARS-CoV-2 in Boston highlights the impact of superspreading events. Science. 2021 02 05; 371(6529).
    View in: PubMed
    Score: 0.057
  30. Single-Cell Profiling of Ebola Virus Disease In Vivo Reveals Viral and Host Dynamics. Cell. 2020 11 25; 183(5):1383-1401.e19.
    View in: PubMed
    Score: 0.056
  31. Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. Cell. 2020 10 29; 183(3):739-751.e8.
    View in: PubMed
    Score: 0.056
  32. Development 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. medRxiv. 2020 Sep 01.
    View in: PubMed
    Score: 0.056
  33. Phylogenetic analysis of SARS-CoV-2 in the Boston area highlights the role of recurrent importation and superspreading events. medRxiv. 2020 Aug 25.
    View in: PubMed
    Score: 0.056
  34. Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. bioRxiv. 2020 Jul 15.
    View in: PubMed
    Score: 0.055
  35. Real-time Metagenomic Analysis of Undiagnosed Fever Cases Unveils a Yellow Fever Outbreak in Edo State, Nigeria. Sci Rep. 2020 02 21; 10(1):3180.
    View in: PubMed
    Score: 0.054
  36. Metagenomic Sequencing of HIV-1 in the Blood and Female Genital Tract Reveals Little Quasispecies Diversity during Acute Infection. J Virol. 2019 01 15; 93(2).
    View in: PubMed
    Score: 0.050
  37. Genomic Analysis of Lassa Virus during an Increase in Cases in Nigeria in 2018. N Engl J Med. 2018 11 01; 379(18):1745-1753.
    View in: PubMed
    Score: 0.049
  38. Genomic epidemiology reveals multiple introductions of Zika virus into the United States. Nature. 2017 06 15; 546(7658):401-405.
    View in: PubMed
    Score: 0.044
  39. Virus genomes reveal factors that spread and sustained the Ebola epidemic. Nature. 2017 04 20; 544(7650):309-315.
    View in: PubMed
    Score: 0.044
  40. Ebola Virus Glycoprotein with Increased Infectivity Dominated the 2013-2016 Epidemic. Cell. 2016 11 03; 167(4):1088-1098.e6.
    View in: PubMed
    Score: 0.043
  41. Ebola Virus Epidemiology and Evolution in Nigeria. J Infect Dis. 2016 10 15; 214(suppl 3):S102-S109.
    View in: PubMed
    Score: 0.042
  42. Discovery of novel rhabdoviruses in the blood of healthy individuals from West Africa. PLoS Negl Trop Dis. 2015 Mar; 9(3):e0003631.
    View in: PubMed
    Score: 0.038
  43. Clinical illness and outcomes in patients with Ebola in Sierra Leone. N Engl J Med. 2014 Nov 27; 371(22):2092-100.
    View in: PubMed
    Score: 0.037
  44. Natural selection in a bangladeshi population from the cholera-endemic ganges river delta. Sci Transl Med. 2013 Jul 03; 5(192):192ra86.
    View in: PubMed
    Score: 0.034
  45. Genetic surveillance detects both clonal and epidemic transmission of malaria following enhanced intervention in Senegal. PLoS One. 2013; 8(4):e60780.
    View in: PubMed
    Score: 0.033
  46. Sequence-based association and selection scans identify drug resistance loci in the Plasmodium falciparum malaria parasite. Proc Natl Acad Sci U S A. 2012 Aug 07; 109(32):13052-7.
    View in: PubMed
    Score: 0.032
  47. Genomic sequencing of Plasmodium falciparum malaria parasites from Senegal reveals the demographic history of the population. Mol Biol Evol. 2012 Nov; 29(11):3427-39.
    View in: PubMed
    Score: 0.032
  48. Human cerebral malaria and Plasmodium falciparum genotypes in Malawi. Malar J. 2012 Feb 07; 11:35.
    View in: PubMed
    Score: 0.031
  49. Integrating common and rare genetic variation in diverse human populations. Nature. 2010 Sep 02; 467(7311):52-8.
    View in: PubMed
    Score: 0.028
  50. Genome-wide SNP genotyping highlights the role of natural selection in Plasmodium falciparum population divergence. Genome Biol. 2008; 9(12):R171.
    View in: PubMed
    Score: 0.025
  51. A second generation human haplotype map of over 3.1 million SNPs. Nature. 2007 Oct 18; 449(7164):851-61.
    View in: PubMed
    Score: 0.023
  52. Comment on "Ongoing adaptive evolution of ASPM, a brain size determinant in Homo sapiens". Science. 2007 Apr 20; 316(5823):370.
    View in: PubMed
    Score: 0.022
  53. A genome-wide map of diversity in Plasmodium falciparum. Nat Genet. 2007 Jan; 39(1):113-9.
    View in: PubMed
    Score: 0.022
  54. Searching for signals of evolutionary selection in 168 genes related to immune function. Hum Genet. 2006 Mar; 119(1-2):92-102.
    View in: PubMed
    Score: 0.020
Connection Strength
The connection strength for co-authors is the sum of the scores for each of their shared publications.

Publication scores are based on many factors, including how long ago they were written and whether the person is a first or senior author.
Funded by the NIH National Center for Advancing Translational Sciences through its Clinical and Translational Science Awards Program, grant number UL1TR002541.