Andrew Y. S. Cheng
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View article: Analyzing RNA-Seq data from Chlamydia with super broad transcriptomic activation: challenges, solutions, and implications for other systems
Analyzing RNA-Seq data from Chlamydia with super broad transcriptomic activation: challenges, solutions, and implications for other systems Open
This study highlights the limitations of standard RNA-Seq analysis tools in scenarios with extensive transcriptomic activation, such as in Chlamydia spp. during early infection. Our revised normalization methods, incorporating host reads o…
View article: Analyzing RNA-Seq Data from<i>Chlamydia</i>with Super Broad Transcriptomic Activation: Challenges, Solutions, and Implications for Other Systems
Analyzing RNA-Seq Data from<i>Chlamydia</i>with Super Broad Transcriptomic Activation: Challenges, Solutions, and Implications for Other Systems Open
Motivation RNA sequencing (RNA-Seq) offers profound insights into the complex transcriptomes of diverse biological systems. However, standard differential expression analysis pipelines based on DESeq2 and edgeR encounter challenges when ap…
View article: Methylene blue dose-dependently induces cutaneous inflammation and heat hyperalgesia in a novel rat model
Methylene blue dose-dependently induces cutaneous inflammation and heat hyperalgesia in a novel rat model Open
Methylene blue (MB) has been shown to reduce mortality and morbidity in vasoplegic patients after cardiac surgery. Though MB is considered to be safe, extravasation of MB leading to cutaneous toxicity has been reported. In this study, we s…
View article: Requirement of GrgA for<i>Chlamydia</i>infectious progeny production, optimal growth, and efficient plasmid maintenance
Requirement of GrgA for<i>Chlamydia</i>infectious progeny production, optimal growth, and efficient plasmid maintenance Open
Chlamydia , an obligate intracellular bacterial pathogen, has a unique developmental cycle involving the differentiation of invading elementary bodies (EBs) to noninfectious reticulate bodies (RBs), replication of RBs, and redifferentiatio…
View article: Identification and structural modeling of the chlamydial RNA polymerase omega subunit
Identification and structural modeling of the chlamydial RNA polymerase omega subunit Open
Gene transcription in bacteria is carried out by the multisubunit RNA polymerase (RNAP), which is composed of a catalytic core enzyme and a promoter-recognizing σ factor. RNAP core enzyme comprises two α subunits, one β subunit, one β’ s s…
View article: Nonlinear Vibrations of Variable-Stiffness Plates using Different Semi-Analytical Models
Nonlinear Vibrations of Variable-Stiffness Plates using Different Semi-Analytical Models Open