S. F. Schaffner
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View article: Phenotypic assessment and genetic validation of <i>Plasmodium falciparum</i> molecular markers associated with malaria chemoprevention in Senegal
Phenotypic assessment and genetic validation of <i>Plasmodium falciparum</i> molecular markers associated with malaria chemoprevention in Senegal Open
Drug resistance in Plasmodium falciparum threatens to undermine malaria control and elimination efforts. Senegal is a malaria-endemic country that has implemented successive antimalarial and chemopreventive drug-based strategies for two de…
View article: Rapunzel Syndrome Resulting in Multiple Sites of Simultaneous Intussusception
Rapunzel Syndrome Resulting in Multiple Sites of Simultaneous Intussusception Open
We present a case of Rapunzel syndrome in a nine-year-old girl with nonverbal autism, pica, and trichotillomania, who presented for acute worsening of abdominal pain and vomiting. Imaging revealed a bezoar extending from the stomach throug…
View article: hmmibd-rs: An enhanced hmmIBD implementation for parallelizable identity-by-descent detection from large-scale Plasmodium genomic data
hmmibd-rs: An enhanced hmmIBD implementation for parallelizable identity-by-descent detection from large-scale Plasmodium genomic data Open
View article: Geospatial and demographic patterns of SARS-CoV-2 spread in Massachusetts from over 130,000 genomes
Geospatial and demographic patterns of SARS-CoV-2 spread in Massachusetts from over 130,000 genomes Open
Despite intensive study, gaps remain in our understanding of SARS-CoV-2 transmission patterns during the COVID-19 pandemic, in part due to limited contextual metadata accompanying most large genomic surveillance datasets. We analyzed over …
View article: Towards an open analysis ecosystem for<i>Plasmodium</i>genomic epidemiology
Towards an open analysis ecosystem for<i>Plasmodium</i>genomic epidemiology Open
Major advances in Plasmodium sequencing approaches, bioinformatic pipelines, and data analysis tools have provided valuable insights into malaria epidemiology from parasite genomic data. However, translating genetic data into actionable in…
View article: JUNIPER: Reconstructing Transmission Events from Next-Generation Sequencing Data at Scale
JUNIPER: Reconstructing Transmission Events from Next-Generation Sequencing Data at Scale Open
View article: Delphy: scalable, near-real-time Bayesian phylogenetics for outbreaks
Delphy: scalable, near-real-time Bayesian phylogenetics for outbreaks Open
Pathogen genomic analysis is central to tracking, understanding, and containing outbreaks, but complexity and high costs of state-of-the-art (SOTA) phylogenetic tools limit global access and impact. We introduce Delphy, an exact reformulat…
View article: Complex exchanges among plasmids and clonal expansion of lineages shape the population structure and virulence of <i>Borrelia burgdorferi</i>
Complex exchanges among plasmids and clonal expansion of lineages shape the population structure and virulence of <i>Borrelia burgdorferi</i> Open
Background In the United States, Borrelia burgdorferi ( Bb ) is the principal etiologic agent of Lyme disease. The complex structure of Bb genomes has posed challenges for genomic studies because homology among the bacterium’s many plasmid…
View article: Polyphonia: detecting inter-sample contamination in viral genomic sequencing data
Polyphonia: detecting inter-sample contamination in viral genomic sequencing data Open
Summary In viral genomic research and surveillance, inter-sample contamination can affect variant detection, analysis of within-host evolution, outbreak reconstruction, and detection of superinfections and recombination events. While sampl…
View article: <i>MalKinID</i>: A classification model for identifying malaria parasite genealogical relationships using identity-by-descent
<i>MalKinID</i>: A classification model for identifying malaria parasite genealogical relationships using identity-by-descent Open
Pathogen genomics is a powerful tool for tracking infectious disease transmission. In malaria, identity-by-descent is used to assess the genetic relatedness between parasites and has been used to study transmission and importation. In theo…
View article: MalKinID: A Likelihood-Based Model for Identifying Malaria Parasite Genealogical Relationships Using Identity-by-Descent
MalKinID: A Likelihood-Based Model for Identifying Malaria Parasite Genealogical Relationships Using Identity-by-Descent Open
Pathogen genomics is a powerful tool for tracking infectious disease transmission. In malaria, identity-by-descent (IBD) is used to assess the genetic relatedness between parasites and has been used to study transmission and importation. I…
View article: Two decades of molecular surveillance in Senegal reveal rapid changes in known drug resistance mutations over time
Two decades of molecular surveillance in Senegal reveal rapid changes in known drug resistance mutations over time Open
Background Drug resistance in Plasmodium falciparum is a major threat to malaria control efforts. Pathogen genomic surveillance could be invaluable for monitoring current and emerging parasite drug resistance. Methods Data from two decades…
View article: Genotypic analysis of RTS,S/AS01E malaria vaccine efficacy against parasite infection as a function of dosage regimen and baseline malaria infection status in children aged 5–17 months in Ghana and Kenya: a longitudinal phase 2b randomised controlled trial
Genotypic analysis of RTS,S/AS01E malaria vaccine efficacy against parasite infection as a function of dosage regimen and baseline malaria infection status in children aged 5–17 months in Ghana and Kenya: a longitudinal phase 2b randomised controlled trial Open
View article: Evaluating the performance of Plasmodium falciparum genetic metrics for inferring National Malaria Control Programme reported incidence in Senegal
Evaluating the performance of Plasmodium falciparum genetic metrics for inferring National Malaria Control Programme reported incidence in Senegal Open
Background Genetic surveillance of the Plasmodium falciparum parasite shows great promise for helping National Malaria Control Programmes (NMCPs) assess parasite transmission. Genetic metrics such as the frequency of polygenomic (multiple …
View article: Genome-wide association study identifies human genetic variants associated with fatal outcome from Lassa fever
Genome-wide association study identifies human genetic variants associated with fatal outcome from Lassa fever Open
View article: Investigating the etiologies of non-malarial febrile illness in Senegal using metagenomic sequencing
Investigating the etiologies of non-malarial febrile illness in Senegal using metagenomic sequencing Open
View article: Historic Building Case Study: Measuring Differential Settlement Combined with Experiential Learning
Historic Building Case Study: Measuring Differential Settlement Combined with Experiential Learning Open
Sagging floors along with cracked interior finishes and exterior masonry is commonplace for structures that have been in service for an extended period of time. Differential settlement is a phenomenon that many structures undergo. A histor…
View article: Baseline malaria infection status and RTS,S/AS01E malaria vaccine efficacy
Baseline malaria infection status and RTS,S/AS01E malaria vaccine efficacy Open
Background The only licensed malaria vaccine, RTS,S/AS01 E , confers moderate protection against symptomatic disease. Because many malaria infections are asymptomatic, we conducted a large-scale longitudinal parasite genotyping study of sa…
View article: Malaria surveillance reveals parasite relatedness, signatures of selection, and correlates of transmission across Senegal
Malaria surveillance reveals parasite relatedness, signatures of selection, and correlates of transmission across Senegal Open
We here analyze data from the first year of an ongoing nationwide program of genetic surveillance of Plasmodium falciparum parasites in Senegal. The analysis is based on 1097 samples collected at health facilities during passive malaria ca…
View article: Evaluating the performance of Plasmodium falciparum genetics for inferring National Malaria Control Program reported incidence in Senegal
Evaluating the performance of Plasmodium falciparum genetics for inferring National Malaria Control Program reported incidence in Senegal Open
Genetic surveillance of the Plasmodium falciparum parasite shows great promise for helping National Malaria Control Programs (NMCPs) assess parasite transmission. Genetic metrics such as the frequency of polygenomic (multiple strain) infec…
View article: Three linked variants have opposing regulatory effects on isovaleryl-CoA dehydrogenase gene expression
Three linked variants have opposing regulatory effects on isovaleryl-CoA dehydrogenase gene expression Open
While genome-wide association studies (GWAS) and positive selection scans identify genomic loci driving human phenotypic diversity, functional validation is required to discover the variant(s) responsible. We dissected the IVD gene locus—w…
View article: Inferring Viral Transmission Pathways from Within-Host Variation
Inferring Viral Transmission Pathways from Within-Host Variation Open
Genome sequencing can offer critical insight into pathogen spread in viral outbreaks, but existing transmission inference methods use simplistic evolutionary models and only incorporate a portion of available genetic data. Here, we develop…
View article: Improving diagnosis of non-malarial fevers in Senegal:<i>Borrelia</i>and the contribution of tick-borne bacteria
Improving diagnosis of non-malarial fevers in Senegal:<i>Borrelia</i>and the contribution of tick-borne bacteria Open
The worldwide decline in malaria incidence is revealing the extensive burden of non-malarial febrile illness (NMFI), which remains poorly understood and difficult to diagnose. To characterize NMFI in Senegal, we collected venous blood and …
View article: Metagenomic surveillance uncovers diverse and novel viral taxa in febrile patients from Nigeria
Metagenomic surveillance uncovers diverse and novel viral taxa in febrile patients from Nigeria Open
Effective infectious disease surveillance in high-risk regions is critical for clinical care and pandemic preemption; however, few clinical diagnostics are available for the wide range of potential human pathogens. Here, we conduct unbiase…
View article: Two decades of molecular surveillance in Senegal reveal changes in known drug resistance mutations associated with historical drug use and seasonal malaria chemoprevention
Two decades of molecular surveillance in Senegal reveal changes in known drug resistance mutations associated with historical drug use and seasonal malaria chemoprevention Open
Drug resistance in Plasmodium falciparum is a major threat to malaria control efforts. We analyzed data from two decades (2000-2020) of continuous molecular surveillance of P. falciparum parasite strains in Senegal to determine how histori…
View article: Malaria surveillance reveals parasite relatedness, signatures of selection, and correlates of transmission across Senegal
Malaria surveillance reveals parasite relatedness, signatures of selection, and correlates of transmission across Senegal Open
Parasite genetic surveillance has the potential to play an important role in malaria control. We describe here an analysis of data from the first year of an ongoing, nationwide program of genetic surveillance of Plasmodium falciparum paras…
View article: Viral Lineages in the 2022 RSV Surge in the United States
Viral Lineages in the 2022 RSV Surge in the United States Open
View article: High-depth sequencing characterization of viral dynamics across tissues in fatal COVID-19 reveals compartmentalized infection
High-depth sequencing characterization of viral dynamics across tissues in fatal COVID-19 reveals compartmentalized infection Open
View article: The 2022 RSV surge was driven by multiple viral lineages
The 2022 RSV surge was driven by multiple viral lineages Open
The US experienced an early and severe respiratory syncytial virus (RSV) surge in autumn 2022. Despite the pressure this has put on hospitals and care centers, the factors promoting the surge in cases are unknown. To investigate whether vi…
View article: Three linked opposing regulatory variants under selection associate with<i>IVD</i>
Three linked opposing regulatory variants under selection associate with<i>IVD</i> Open
While genome-wide association studies (GWAS) and selection scans identify genomic loci driving human phenotypic diversity, functional validation is required to discover the variant(s) responsible. We dissected the IVD locus, implicated by …