Lydia A. Krasilnikova
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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: JUNIPER: Reconstructing Transmission Events from Next-Generation Sequencing Data at Scale
JUNIPER: Reconstructing Transmission Events from Next-Generation Sequencing Data at Scale Open
Transmission reconstruction––the inference of who infects whom in disease outbreaks––offers critical insights into how pathogens spread and provides opportunities for targeted control measures. We developed JUNIPER (Joint Underlying Networ…
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: Cobain, Hemingway, Sinatra and me
Cobain, Hemingway, Sinatra and me Open
A postdoc explains how being medicated for bipolar changed her life and the way she conducts research.
View article: Author Correction: Multiplexed CRISPR-based microfluidic platform for clinical testing of respiratory viruses and identification of SARS-CoV-2 variants
Author Correction: Multiplexed CRISPR-based microfluidic platform for clinical testing of respiratory viruses and identification of SARS-CoV-2 variants Open
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: Multiplexed CRISPR-based microfluidic platform for clinical testing of respiratory viruses and identification of SARS-CoV-2 variants
Multiplexed CRISPR-based microfluidic platform for clinical testing of respiratory viruses and identification of SARS-CoV-2 variants Open
View article: Transmission from vaccinated individuals in a large SARS-CoV-2 Delta variant outbreak
Transmission from vaccinated individuals in a large SARS-CoV-2 Delta variant outbreak Open
View article: Evidence of transmission from fully vaccinated individuals in a large outbreak of the SARS-CoV-2 Delta variant in Provincetown, Massachusetts
Evidence of transmission from fully vaccinated individuals in a large outbreak of the SARS-CoV-2 Delta variant in Provincetown, Massachusetts Open
Multiple summer events, including large indoor gatherings, in Provincetown, Massachusetts (MA), in July 2021 contributed to an outbreak of over one thousand COVID-19 cases among residents and visitors. Most cases were fully vaccinated, man…
View article: SARS-CoV-2 Reinfection in a Liver Transplant Recipient
SARS-CoV-2 Reinfection in a Liver Transplant Recipient Open
Letters20 April 2021SARS-CoV-2 Reinfection in a Liver Transplant RecipientFREEChristopher H. Tomkins-Tinch, BS, Jennifer S. Daly, MD, Adrianne Gladden-Young, MS, Nicole M. Theodoropoulos, MD, MS, Michael P. Madaio, DO, Neng Yu, MD, Vijay K…
View article: Phylogenetic analysis of SARS-CoV-2 in Boston highlights the impact of superspreading events
Phylogenetic analysis of SARS-CoV-2 in Boston highlights the impact of superspreading events Open
Phylogenetics of superspreading One important characteristic of coronavirus epidemiology is the occurrence of superspreading events. These are marked by a disproportionate number of cases originating from often-times asymptomatic individua…
View article: Phylogenetic analysis of SARS-CoV-2 in the Boston area highlights the role of recurrent importation and superspreading events
Phylogenetic analysis of SARS-CoV-2 in the Boston area highlights the role of recurrent importation and superspreading events Open
SARS-CoV-2 has caused a severe, ongoing outbreak of COVID-19 in Massachusetts with 111,070 confirmed cases and 8,433 deaths as of August 1, 2020. To investigate the introduction, spread, and epidemiology of COVID-19 in the Boston area, we …
View article: Combining genomics and epidemiology to track mumps virus transmission in the United States
Combining genomics and epidemiology to track mumps virus transmission in the United States Open
Unusually large outbreaks of mumps across the United States in 2016 and 2017 raised questions about the extent of mumps circulation and the relationship between these and prior outbreaks. We paired epidemiological data from public health i…
View article: Supplementary Data for "Combining genomics and epidemiology to track mumps virus transmission in the United States"
Supplementary Data for "Combining genomics and epidemiology to track mumps virus transmission in the United States" Open
Supplementary data and scripts used to produce figures for "Combining genomics and epidemiology to track mumps virus transmission in the United States." Files are divided into "code" and "data" directories and a README is provided for each.
View article: Supplementary Data for "Combining genomics and epidemiology to track mumps virus transmission in the United States"
Supplementary Data for "Combining genomics and epidemiology to track mumps virus transmission in the United States" Open
Supplementary data and scripts used to produce figures for "Combining genomics and epidemiology to track mumps virus transmission in the United States." Files are divided into "code" and "data" directories and a README is provided for each.
View article: Co-circulating mumps lineages at multiple geographic scales
Co-circulating mumps lineages at multiple geographic scales Open
Despite widespread vaccination, eleven thousand mumps cases were reported in the United States (US) in 2016–17, including hundreds in Massachusetts, primarily in college settings. We generated 203 whole genome mumps virus (MuV) sequences f…