List of works - Stephen F Schaffner

A composite of multiple signals distinguishes causal variants in regions of positive selection

scientific article

A genome-wide map of diversity in Plasmodium falciparum

scientific article published on 10 December 2006

A global map of genetic diversity in Babesia microti reveals strong population structure and identifies variants associated with clinical relapse

scientific article published on 13 June 2016

A second generation human haplotype map of over 3.1 million SNPs

scientific article

An emergent Ebola virus nucleoprotein variant influences virion budding, oligomerization, transcription and replication

An integrated haplotype map of the human major histocompatibility complex

scientific article

Analysis of 6.4 million SARS-CoV-2 genomes identifies mutations associated with fitness

scientific article published in 2022

Artemisinin resistance without pfkelch13 mutations in Plasmodium falciparum isolates from Cambodia

scientific article

Calibrating a coalescent simulation of human genome sequence variation

scientific article published on November 2005

Clinical Sequencing Uncovers Origins and Evolution of Lassa Virus

scientific article

Clinical and laboratory predictors of Lassa fever outcome in a dedicated treatment facility in Nigeria: a retrospective, observational cohort study

scientific article

Clinical illness and outcomes in patients with Ebola in Sierra Leone

scientific article

Co-circulating mumps lineages at multiple geographic scales

Combining genomics and epidemiology to track mumps virus transmission in the United States

scientific article published on 11 February 2020

Comment on "Ongoing adaptive evolution of ASPM, a brain size determinant in Homo sapiens".

scientific article published on April 2007

Cosi2: an efficient simulator of exact and approximate coalescent with selection

scientific article published on 22 August 2014

Data sharing: Make outbreak research open access

scientific article

Deployable CRISPR-Cas13a diagnostic tools to detect and report Ebola and Lassa virus cases in real-time

scientific article published on 17 August 2020

Detecting recent positive selection in the human genome from haplotype structure

scientific article

Development of a SNP barcode to genotype Babesia microti infections

article

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

scientific article published on 01 September 2020

Development of a single nucleotide polymorphism barcode to genotype Plasmodium vivax infections

scientific article

Direct Identification of Hundreds of Expression-Modulating Variants using a Multiplexed Reporter Assay

scientific article

Discovery of novel rhabdoviruses in the blood of healthy individuals from West Africa

scientific article

Ebola Virus Epidemiology and Evolution in Nigeria

scientific article published on 04 July 2016

Ebola Virus Epidemiology, Transmission, and Evolution during Seven Months in Sierra Leone

scientific article

Ebola Virus Glycoprotein with Increased Infectivity Dominated the 2013-2016 Epidemic

scientific article published on November 2016

Epidemiology. Emerging disease or diagnosis?

scientific article published on November 2012

Genetic relatedness analysis reveals the cotransmission of genetically related Plasmodium falciparum parasites in Thiès, Senegal

scientific article published on 24 January 2017

Genetic surveillance detects both clonal and epidemic transmission of malaria following enhanced intervention in Senegal

scientific article

Genome sequencing reveals Zika virus diversity and spread in the Americas

scientific article (publication date: 18 February 2017)

Genome-wide SNP genotyping highlights the role of natural selection in Plasmodium falciparum population divergence

scientific article published on 15 December 2008

Genome-wide detection and characterization of positive selection in human populations

scientific article

Genomic Analysis of Lassa Virus during an Increase in Cases in Nigeria in 2018

article by Katherine J Siddle et al published 17 October 2018 in The New England Journal of Medicine

Genomic Analysis of Viral Outbreaks

scientific article published on 3 August 2016

Genomic epidemiology reveals multiple introductions of Zika virus into the United States ⬇️

scientific article

Genomic sequencing of Plasmodium falciparum malaria parasites from Senegal reveals the demographic history of the population

scientific article

Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak

scientific article

Harnessing genomics and genome biology to understand malaria biology

scientific article published on 12 April 2012

High-resolution haplotype structure in the human genome

article

Human cerebral malaria and Plasmodium falciparum genotypes in Malawi

scientific article published on 7 February 2012

Human genome sequence variation and the influence of gene history, mutation and recombination

scientific article

Identification and functional validation of the novel antimalarial resistance locus PF10_0355 in Plasmodium falciparum

scientific article

Identifying recent adaptations in large-scale genomic data

scientific article

Integrating common and rare genetic variation in diverse human populations

scientific article (publication date: 2 September 2010)

Metagenomic sequencing of HIV-1 in the blood and female genital tract reveals little quasispecies diversity during acute infection

article

Modeling malaria genomics reveals transmission decline and rebound in Senegal

scientific article published on 4 May 2015

Multiple introductions of Zika virus into the United States revealed through genomic epidemiology

scientific article

Natural selection in a bangladeshi population from the cholera-endemic ganges river delta

scientific article

Phylogenetic analysis of SARS-CoV-2 in Boston highlights the impact of superspreading events

scientific article published on 10 December 2020

Plasmepsin II-III copy number accounts for bimodal piperaquine resistance among Cambodian Plasmodium falciparum.

scientific article published on 2 May 2018

Quantifying connectivity between local Plasmodium falciparum malaria parasite populations using identity by descent.

scientific article published on 27 October 2017

Reporter Assays for Ebola Virus Nucleoprotein Oligomerization, Virion-Like Particle Budding, and Minigenome Activity Reveal the Importance of Nucleoprotein Amino Acid Position 111

scientific article published on 15 January 2020

SNP genotyping identifies new signatures of selection in a deep sample of West African Plasmodium falciparum malaria parasites

scientific article published on 11 June 2012

Searching for missing heritability: designing rare variant association studies

scientific article published on 17 January 2014

Searching for signals of evolutionary selection in 168 genes related to immune function

scientific article published on 14 December 2005

Sequence-based association and selection scans identify drug resistance loci in the Plasmodium falciparum malaria parasite

scientific article

The Origins and Future of Sentinel: An Early-Warning System for Pandemic Preemption and Response

scientific article published in 2021

The X chromosome in population genetics

scientific article

The structure of haplotype blocks in the human genome

scientific article

Virus genomes reveal factors that spread and sustained the Ebola epidemic

scientific article (publication date: 12 April 2017)

Virus genomes reveal the factors that spread and sustained the West African Ebola epidemic

article published in 2016

Zika virus evolution and spread in the Americas

scientific article

hmmIBD: software to infer pairwise identity by descent between haploid genotypes.

scientific article published on 15 May 2018

List of works by Stephen F Schaffner

A composite of multiple signals distinguishes causal variants in regions of positive selection

A genome-wide map of diversity in Plasmodium falciparum

A global map of genetic diversity in Babesia microti reveals strong population structure and identifies variants associated with clinical relapse

A second generation human haplotype map of over 3.1 million SNPs

An emergent Ebola virus nucleoprotein variant influences virion budding, oligomerization, transcription and replication

An integrated haplotype map of the human major histocompatibility complex

Analysis of 6.4 million SARS-CoV-2 genomes identifies mutations associated with fitness

Artemisinin resistance without pfkelch13 mutations in Plasmodium falciparum isolates from Cambodia

Calibrating a coalescent simulation of human genome sequence variation

Clinical Sequencing Uncovers Origins and Evolution of Lassa Virus

Clinical and laboratory predictors of Lassa fever outcome in a dedicated treatment facility in Nigeria: a retrospective, observational cohort study

Clinical illness and outcomes in patients with Ebola in Sierra Leone

Co-circulating mumps lineages at multiple geographic scales

Combining genomics and epidemiology to track mumps virus transmission in the United States

Comment on "Ongoing adaptive evolution of ASPM, a brain size determinant in Homo sapiens".

Cosi2: an efficient simulator of exact and approximate coalescent with selection

Data sharing: Make outbreak research open access

Deployable CRISPR-Cas13a diagnostic tools to detect and report Ebola and Lassa virus cases in real-time

Detecting recent positive selection in the human genome from haplotype structure

Development of a SNP barcode to genotype Babesia microti infections

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

Development of a single nucleotide polymorphism barcode to genotype Plasmodium vivax infections

Direct Identification of Hundreds of Expression-Modulating Variants using a Multiplexed Reporter Assay

Discovery of novel rhabdoviruses in the blood of healthy individuals from West Africa

Ebola Virus Epidemiology and Evolution in Nigeria

Ebola Virus Epidemiology, Transmission, and Evolution during Seven Months in Sierra Leone

Ebola Virus Glycoprotein with Increased Infectivity Dominated the 2013-2016 Epidemic

Epidemiology. Emerging disease or diagnosis?

Genetic relatedness analysis reveals the cotransmission of genetically related Plasmodium falciparum parasites in Thiès, Senegal

Genetic surveillance detects both clonal and epidemic transmission of malaria following enhanced intervention in Senegal

Genome sequencing reveals Zika virus diversity and spread in the Americas

Genome-wide SNP genotyping highlights the role of natural selection in Plasmodium falciparum population divergence

Genome-wide detection and characterization of positive selection in human populations

Genomic Analysis of Lassa Virus during an Increase in Cases in Nigeria in 2018

Genomic Analysis of Viral Outbreaks

Genomic epidemiology reveals multiple introductions of Zika virus into the United States ⬇️

Genomic sequencing of Plasmodium falciparum malaria parasites from Senegal reveals the demographic history of the population

Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak

Harnessing genomics and genome biology to understand malaria biology

High-resolution haplotype structure in the human genome

Human cerebral malaria and Plasmodium falciparum genotypes in Malawi

Human genome sequence variation and the influence of gene history, mutation and recombination

Identification and functional validation of the novel antimalarial resistance locus PF10_0355 in Plasmodium falciparum

Identifying recent adaptations in large-scale genomic data

Integrating common and rare genetic variation in diverse human populations

Metagenomic sequencing of HIV-1 in the blood and female genital tract reveals little quasispecies diversity during acute infection

Modeling malaria genomics reveals transmission decline and rebound in Senegal

Multiple introductions of Zika virus into the United States revealed through genomic epidemiology

Natural selection in a bangladeshi population from the cholera-endemic ganges river delta

Phylogenetic analysis of SARS-CoV-2 in Boston highlights the impact of superspreading events

Plasmepsin II-III copy number accounts for bimodal piperaquine resistance among Cambodian Plasmodium falciparum.

Quantifying connectivity between local Plasmodium falciparum malaria parasite populations using identity by descent.

Reporter Assays for Ebola Virus Nucleoprotein Oligomerization, Virion-Like Particle Budding, and Minigenome Activity Reveal the Importance of Nucleoprotein Amino Acid Position 111

SNP genotyping identifies new signatures of selection in a deep sample of West African Plasmodium falciparum malaria parasites

Searching for missing heritability: designing rare variant association studies

Searching for signals of evolutionary selection in 168 genes related to immune function

Sequence-based association and selection scans identify drug resistance loci in the Plasmodium falciparum malaria parasite

The Origins and Future of Sentinel: An Early-Warning System for Pandemic Preemption and Response

The X chromosome in population genetics

The structure of haplotype blocks in the human genome

Virus genomes reveal factors that spread and sustained the Ebola epidemic

Virus genomes reveal the factors that spread and sustained the West African Ebola epidemic

Zika virus evolution and spread in the Americas

hmmIBD: software to infer pairwise identity by descent between haploid genotypes.