Dakota Howard
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View article: Patterns of genomic deletions in monkeypox virus during the 2022 outbreak in the United States
Patterns of genomic deletions in monkeypox virus during the 2022 outbreak in the United States Open
View article: NAVIP: Unraveling the influence of neighboring small sequence variants on functional impact prediction
NAVIP: Unraveling the influence of neighboring small sequence variants on functional impact prediction Open
Once a suitable reference sequence has been generated, intra-species variation is often assessed by re-sequencing. Variant calling processes can reveal all differences between strains, accessions, genotypes, or individuals. These variants …
View article: Reoccurring <i>Escherichia coli</i> O157:H7 Strain Linked to Leafy Greens–Associated Outbreaks, 2016–2019
Reoccurring <i>Escherichia coli</i> O157:H7 Strain Linked to Leafy Greens–Associated Outbreaks, 2016–2019 Open
Genomic characterization of an Escherichia coli O157:H7 strain linked to leafy greens-associated outbreaks dates its emergence to late 2015. One clade has notable accessory genomic content and a previously described mutation putatively ass…
View article: Genomic Surveillance for SARS-CoV-2 Variants: Circulation of Omicron Lineages — United States, January 2022–May 2023
Genomic Surveillance for SARS-CoV-2 Variants: Circulation of Omicron Lineages — United States, January 2022–May 2023 Open
CDC has used national genomic surveillance since December 2020 to monitor SARS-CoV-2 variants that have emerged throughout the COVID-19 pandemic, including the Omicron variant. This report summarizes U.S. trends in variant proportions from…
View article: Genomic deletions and rearrangements in monkeypox virus from the 2022 outbreak, USA
Genomic deletions and rearrangements in monkeypox virus from the 2022 outbreak, USA Open
Genomic surveillance of monkeypox virus (MPXV) during the 2022 outbreak has been mainly focused on single nucleotide polymorphism (SNP) changes. DNA viruses, including MPXV, have a lower SNP mutation rate than RNA viruses due to higher fid…
View article: Analysis of the initial lot of the CDC 2019-Novel Coronavirus (2019-nCoV) real-time RT-PCR diagnostic panel
Analysis of the initial lot of the CDC 2019-Novel Coronavirus (2019-nCoV) real-time RT-PCR diagnostic panel Open
At the start of the COVID-19 pandemic, the Centers for Disease Control and Prevention (CDC) designed, manufactured, and distributed the CDC 2019-Novel Coronavirus (2019-nCoV) Real-Time RT-PCR Diagnostic Panel for SARS-CoV-2 detection. The …
View article: Network analysis of intra- and interspecific freshwater fish interactions using year-around tracking
Network analysis of intra- and interspecific freshwater fish interactions using year-around tracking Open
A long-term, yet detailed view into the social patterns of aquatic animals has been elusive. With advances in reality mining tracking technologies, a proximity-based social network (PBSN) can capture detailed spatio-temporal underwater int…
View article: Complete Genome Sequence of<i>Rhodococcus</i>sp. Strain W8901, a Human Clinical Specimen, Assembled Using MiSeq and MinION Sequence Data
Complete Genome Sequence of<i>Rhodococcus</i>sp. Strain W8901, a Human Clinical Specimen, Assembled Using MiSeq and MinION Sequence Data Open
Rhodococcus sp. strain W8901 is a Gram-positive, aerobic, mycolic acid-containing coccobacillus obtained from a patient with acute lymphocytic leukemia. Here, we report on the complete, circular genome sequence obtained using Illumina MiSe…
View article: Clade-specific chromosomal rearrangements and loss of subtelomeric adhesins in <i>Candida auris</i>
Clade-specific chromosomal rearrangements and loss of subtelomeric adhesins in <i>Candida auris</i> Open
Candida auris is an emerging fungal pathogen of rising concern due to global spread, the ability to cause healthcare-associated outbreaks, and antifungal resistance. Genomic analyses revealed that early contemporaneously detected cases of …
View article: Complete and Circularized Genome Assemblies of the Kroppenstedtia eburnea Genus Type Strain and the Kroppenstedtia pulmonis Species Type Strain with MiSeq and MinION Sequence Data
Complete and Circularized Genome Assemblies of the Kroppenstedtia eburnea Genus Type Strain and the Kroppenstedtia pulmonis Species Type Strain with MiSeq and MinION Sequence Data Open
Kroppenstedtia eburnea DSM 45196 T and Kroppenstedtia pulmonis W9323 T are aerobic, Gram-positive, filamentous, chemoorganotrophic thermoactinomycetes. Here, we report on the complete and circular genome assemblies generated using Illumina…
View article: Soundscape shifts during the 2017 total solar eclipse: an application of dispersed automated recording units to study ephemeral acoustic events
Soundscape shifts during the 2017 total solar eclipse: an application of dispersed automated recording units to study ephemeral acoustic events Open
Shifts in soundscapes often reflect diurnal patterns. In 2017 a total solar eclipse occurred in the US, resulting in a period of 3 h with the sun partially covered by the moon and 2 min of total darkness. We hypothesised this would create …
View article: NAVIP: Unraveling the Influence of Neighboring Small Sequence Variants on Functional Impact Prediction
NAVIP: Unraveling the Influence of Neighboring Small Sequence Variants on Functional Impact Prediction Open
Once a suitable reference sequence has been generated, intraspecific variation is often assessed by re-sequencing. Variant calling processes can reveal all differences between strains, accessions, genotypes, or individuals. These variants …