Viral Detection by Reverse Transcriptase Polymerase Chain Reaction in Upper Respiratory Tract and Metagenomic RNA Sequencing in Lower Respiratory Tract in Critically Ill Children With Suspected Lower Respiratory Tract Infection Society of Pediatric Critical Care Medicine, 2024
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Validation of a murine proteome-wide phage display library for identification of autoantibody specificities JCI Insight, 2023
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Implementation of California COVIDNet - a multi-sector collaboration for statewide SARS-CoV-2 genomic surveillance Frontiers in Public Health, 2023
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The antibiotic resistance reservoir of the lung microbiome expands with age in a population of critically ill patients Nature Journal, 2023
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Challenges and advances in the medical treatment of granulomatous amebic encephalitis Sage Journals, 2024
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ZSCAN1 autoantibodies are associated with pediatric paraneoplastic ROHHAD Annals of Neurology, 2022
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Autoantibodies to Perilipin-1 Define a Subset of Acquired Generalized Lipodystrophy Diabetes, Jan 2023
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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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