 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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 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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 Deep profiling of protease substrate specificity enabled by dual random and scanned human proteome substrate phage libraries PNAS, 2020
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 Auto-antibodies against type I IFNs in patients with life-threatening COVID-19 Science, 2020
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 High resolution epitope mapping of anti-Hu and anti-Yo autoimmunity by programmable phage display Oxford Academic, 2020
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 Detection of Pneumonia Pathogens from PlasmaCell-Free DNA American Journal of Respiratory Critical Care, 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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