Integrated host/microbe metagenomics enables accurate lower respiratory tract infection diagnosis in critically ill children JCI, 2023
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Autoantigen profiling reveals a shared post-COVID signature in fully recovered and long COVID patients JCI Insight, 2023
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Field assessment of BinaxNOW antigen tests as COVID-19 treatment entry point at a community testing site in San Francisco during evolving omicron surges PLOS One, 2023
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Prolonged silent carriage, genomic virulence potential and transmission between staff and patients characterize a neonatal intensive care unit (NICU) outbreak of methicillin-resistant Staphylococcus aureus (MRSA) Cambridge University Press, 2023
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Antibodies to repeat-containing antigens in Plasmodium falciparum are exposure-dependent and short-lived in children in natural malaria infections eLife, 2023
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Dual ankyrinG and subpial autoantibodies in a man with well-controlled HIV infection with steroid-responsive meningoencephalitis: A case report Frontiers, 2023
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Successful Treatment of Balamuthia mandrillaris Granulomatous Amebic Encephalitis with Nitroxoline Emerging Infectious Diseases, 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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