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View article: Developing and Benchmarking One Health Genomic Surveillance Tools for Influenza A Virus in Wastewater
Developing and Benchmarking One Health Genomic Surveillance Tools for Influenza A Virus in Wastewater Open
Influenza A viruses (IAV) remain a persistent One Health threat, and whole-genome sequencing from wastewater offers a promising surveillance tool. However, IAV is at low abundance in wastewater, making it difficult to sequence. We benchmar…
View article: Developing and Benchmarking One Health Genomic Surveillance Tools for Influenza A Virus in Wastewater
Developing and Benchmarking One Health Genomic Surveillance Tools for Influenza A Virus in Wastewater Open
Influenza A viruses (IAV) remain a persistent One Health threat, and whole-genome sequencing from wastewater offers a promising surveillance tool. However, IAV is at low abundance in wastewater, making it difficult to sequence. We benchmar…
View article: A rapid phylogeny-based method for accurate community profiling of large-scale metabarcoding datasets
A rapid phylogeny-based method for accurate community profiling of large-scale metabarcoding datasets Open
Environmental DNA (eDNA) is becoming an increasingly important tool in diverse scientific fields from ecological biomonitoring to wastewater surveillance of viruses. The fundamental challenge in eDNA analyses has been the bioinformatical a…
View article: Author response: A rapid phylogeny-based method for accurate community profiling of large-scale metabarcoding datasets
Author response: A rapid phylogeny-based method for accurate community profiling of large-scale metabarcoding datasets Open
View article: Tracking SARS-CoV-2 variants of concern in wastewater: an assessment of nine computational tools using simulated genomic data
Tracking SARS-CoV-2 variants of concern in wastewater: an assessment of nine computational tools using simulated genomic data Open
Wastewater-based surveillance (WBS) is an important epidemiological and public health tool for tracking pathogens across the scale of a building, neighbourhood, city, or region. WBS gained widespread adoption globally during the SARS-CoV-2…
View article: Tracking SARS-CoV-2 variants of concern in wastewater: an assessment of nine computational tools using simulated genomic data
Tracking SARS-CoV-2 variants of concern in wastewater: an assessment of nine computational tools using simulated genomic data Open
Wastewater-based surveillance (WBS) is an important epidemiological and public health tool for tracking pathogens across the scale of a building, neighbourhood, city, or region. WBS gained widespread adoption globally during the SARS-CoV-2…
View article: A rapid phylogeny-based method for accurate community profiling of large-scale metabarcoding datasets
A rapid phylogeny-based method for accurate community profiling of large-scale metabarcoding datasets Open
Environmental DNA (eDNA) is becoming an increasingly important tool in diverse scientific fields from ecological biomonitoring to wastewater surveillance of viruses. The fundamental challenge in eDNA analyses has been the bioinformatical a…
View article: A rapid phylogeny-based method for accurate community profiling of large-scale metabaroding datasets
A rapid phylogeny-based method for accurate community profiling of large-scale metabaroding datasets Open
Tronko-build Cytochrome Oxidase I (COI) and 16S databases
View article: Estimating the relative proportions of SARS-CoV-2 haplotypes from wastewater samples
Estimating the relative proportions of SARS-CoV-2 haplotypes from wastewater samples Open
Wastewater surveillance has become essential for monitoring the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The quantification of SARS-CoV-2 RNA in wastewater correlates with the coronavirus disease 2019 (COVID-…
View article: Estimating the relative proportions of SARS-CoV-2 strains from wastewater samples
Estimating the relative proportions of SARS-CoV-2 strains from wastewater samples Open
Wastewater surveillance has become essential for monitoring the spread of SARS-CoV-2. The quantification of SARS-CoV-2 RNA in wastewater correlates with the Covid-19 caseload in a community. However, estimating the proportions of different…
View article: Imputed Multiple Sequence Alignment used in 'Estimating the relative proportions of SARS-CoV-2 strains from wastewater samples'
Imputed Multiple Sequence Alignment used in 'Estimating the relative proportions of SARS-CoV-2 strains from wastewater samples' Open
Multiple Sequence Alignment of imputed SARS-CoV-2 sequences used in 'Estimating the relative proportions of SARS-CoV-2 strains from wastewater samples'
View article: Simulations from 'Estimating the relative proportions of SARS-CoV-2 strains from wastewater samples'
Simulations from 'Estimating the relative proportions of SARS-CoV-2 strains from wastewater samples' Open
Simulations used in "Estimating the relative proportions of SARS-CoV-2 strains from wastewater samples"
View article: Simulations from 'Estimating the relative proportions of SARS-CoV-2 strains from wastewater samples'
Simulations from 'Estimating the relative proportions of SARS-CoV-2 strains from wastewater samples' Open
Simulations used in "Estimating the relative proportions of SARS-CoV-2 strains from wastewater samples"
View article: Imputed Multiple Sequence Alignment used in 'Estimating the relative proportions of SARS-CoV-2 strains from wastewater samples'
Imputed Multiple Sequence Alignment used in 'Estimating the relative proportions of SARS-CoV-2 strains from wastewater samples' Open
Multiple Sequence Alignment of imputed SARS-CoV-2 sequences used in 'Estimating the relative proportions of SARS-CoV-2 strains from wastewater samples'
View article: Estimating the Relative Proportions of SARS-CoV-2 Strains from Wastewater Samples
Estimating the Relative Proportions of SARS-CoV-2 Strains from Wastewater Samples Open
View article: Data for AncestralClust manuscript
Data for AncestralClust manuscript Open
Data underlying AncestralClust manuscript
View article: Data for AncestralClust manuscript
Data for AncestralClust manuscript Open
Data underlying AncestralClust manuscript
View article: AncestralClust: clustering of divergent nucleotide sequences by ancestral sequence reconstruction using phylogenetic trees
AncestralClust: clustering of divergent nucleotide sequences by ancestral sequence reconstruction using phylogenetic trees Open
Motivation Clustering is a fundamental task in the analysis of nucleotide sequences. Despite the exponential increase in the size of sequence databases of homologous genes, few methods exist to cluster divergent sequences. Traditional clus…
View article: The CALeDNA program: Citizen scientists and researchers inventory California's biodiversity
The CALeDNA program: Citizen scientists and researchers inventory California's biodiversity Open
Climate change is leading to habitat shifts that threaten species persistence throughout California's unique ecosystems. Baseline biodiversity data would provide opportunities for habitats to be managed under short-term and long-term envir…
View article: AncestralClust: Clustering of Divergent Nucleotide Sequences by Ancestral Sequence Reconstruction using Phylogenetic Trees
AncestralClust: Clustering of Divergent Nucleotide Sequences by Ancestral Sequence Reconstruction using Phylogenetic Trees Open
Motivation Clustering is a fundamental task in the analysis of nucleotide sequences. Despite the exponential increase in the size of sequence databases of homologous genes, few methods exist to cluster divergent sequences. Traditional clus…
View article: Assessing Uncertainty in the Rooting of the SARS-CoV-2 Phylogeny
Assessing Uncertainty in the Rooting of the SARS-CoV-2 Phylogeny Open
The rooting of the SARS-CoV-2 phylogeny is important for understanding the origin and early spread of the virus. Previously published phylogenies have used different rootings that do not always provide consistent results. We investigate se…
View article: Synonymous mutations and the molecular evolution of SARS-CoV-2 origins
Synonymous mutations and the molecular evolution of SARS-CoV-2 origins Open
Human severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is most closely related, by average genetic distance, to two coronaviruses isolated from bats, RaTG13 and RmYN02. However, there is a segment of high amino acid similarity …
View article: Assessing uncertainty in the rooting of the SARS-CoV-2 phylogeny
Assessing uncertainty in the rooting of the SARS-CoV-2 phylogeny Open
The rooting of the SARS-CoV-2 phylogeny is important for understanding the origin and early spread of the virus. Previously published phylogenies have used different rootings that do not always provide consistent results. We investigate se…
View article: Synonymous mutations and the molecular evolution of SARS-Cov-2 origins
Synonymous mutations and the molecular evolution of SARS-Cov-2 origins Open
Human severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is most closely related, by average genetic distance, to two coronaviruses isolated from bats, RaTG13 and RmYN02. However, there is a segment of high amino acid similarity …
View article: <i>Anacapa Toolkit</i> : An environmental DNA toolkit for processing multilocus metabarcode datasets
<i>Anacapa Toolkit</i> : An environmental DNA toolkit for processing multilocus metabarcode datasets Open
Environmental DNA (eDNA) metabarcoding is a promising method to monitor species and community diversity that is rapid, affordable and non‐invasive. The longstanding needs of the eDNA community are modular informatics tools, comprehensive a…
View article: The California environmental DNA “CALeDNA” program
The California environmental DNA “CALeDNA” program Open
Global change is leading to habitat shifts that threaten species persistence throughout California’s unique ecosystems. Baseline biodiversity data provide opportunities for ecosystems to be managed for community complexity and connectivity…
View article: <i>Anacapa Toolkit</i>: an environmental DNA toolkit for processing multilocus metabarcode datasets
<i>Anacapa Toolkit</i>: an environmental DNA toolkit for processing multilocus metabarcode datasets Open
1. Environmental DNA (eDNA) metabarcoding is a promising method to monitor species and community diversity that is rapid, affordable, and non-invasive. Longstanding needs of the eDNA community are modular informatics tools, comprehensive a…
View article: Genomic responses to selection for tame/aggressive behaviors in the silver fox ( <i>Vulpes vulpes</i> )
Genomic responses to selection for tame/aggressive behaviors in the silver fox ( <i>Vulpes vulpes</i> ) Open
Significance The behavior of domesticated animals differs dramatically from that of wild relatives, and the Russian tame fox experiment demonstrated clearly that these changes can occur in just a few generations of selection. Analysis of g…
View article: Sooty mangabey genome sequence provides insight into AIDS resistance in a natural SIV host
Sooty mangabey genome sequence provides insight into AIDS resistance in a natural SIV host Open
View article: Genomic responses to selection for tame/aggressive behaviors in the silver fox (<i>Vulpes vulpes</i>)
Genomic responses to selection for tame/aggressive behaviors in the silver fox (<i>Vulpes vulpes</i>) Open
Animal domestications have led to a shared spectrum of striking behavioral and morphological changes. To recapitulate this process, silver foxes have been selectively bred for tame and aggressive behaviors for over 50 generations at the In…