 Estimation of secondary household attack rates for emergent spike L452R SARS-CoV-2 variants detected by genomic surveillance at a community-based testing site in San Francisco. Clin Infect Dis. 2021
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 Performance Characteristics of a Rapid SARS-CoV-2 Antigen Detection Assay at a Public Plaza Testing Site in San Francisco J. of Infect. Disease, 2020
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 Rapid deployment of SARS-CoV-2 testing: The CLIAHUB PLOS Pathogens, 2020
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 Community Transmission of Severe Acute Respiratory Syndrome Coronavirus 2 Disproportionately Affects the Latinx Population During Shelter-in-Place in San Francisco Infectious Disease Society of America, 2020
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 IDseq-An open source cloud-based pipeline and analysis service for metagenomic pathogen detection and monitoring Oxford Academic, 2020
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 Temporal airway microbiome changes related to ventilator associated pneumonia in children European Respiratory Journal, 2020
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 ReScan, a Multiplex Diagnostic Pipeline, Pans Human Sera for SARS-CoV-2 Antigens Cell Reports Medicine, 2020
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|  Here we introduce HMMSplicer, an accurate and efficient algorithm for discovering canonical and non-canonical splice junctions in short read datasets. HMMSplicer identifies more splice junctions than currently available algorithms when tested on publicly available A. thaliana, P. falciparum, and H. sapiens datasets without a reduction in specificity. HMMSplicer was found to perform especially well in compact genomes and on genes with low expression levels, alternative splice isoforms, or non-canonical splice junctions. Because HHMSplicer does not rely on pre-built gene models, the products of inexact splicing are also detected. In addition, HMMSplicer provides a score for every predicted junction allowing the user to set a threshold to tune false positive rates depending on the needs of the experiment. HMMSplicer is implemented in Python. Code and documentation are freely available at the link below. Download HMMSplicer! (Updated Nov 25th 2010 - Version: 0.9.5) |
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