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edgeR v4: powerful differential analysis of sequencing data with expanded functionality and improved support for small counts and larger datasets.
Nucleic Acids Res
January 2025
Bioinformatics Division, WEHI, Parkville, VIC 3052, Australia.
edgeR is an R/Bioconductor software package for differential analyses of sequencing data in the form of read counts for genes or genomic features. Over the past 15 years, edgeR has been a popular choice for statistical analysis of data from sequencing technologies such as RNA-seq or ChIP-seq. edgeR pioneered the use of the negative binomial distribution to model read count data with replicates and the use of generalized linear models to analyze complex experimental designs.
View Article and Find Full Text PDFIntegrated metabolomics and transcriptomics reveal the role of calcium sugar alcohol in the regulation of phenolic acid biosynthesis in Torreya grandis nuts.
BMC Plant Biol
January 2025
State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, People's Republic of China.
Background: Torreya grandis, a prominent tree species of the autochthonous subtropical region of China, possesses a drupe-like fruit containing a nut that is rich in nutrients and bioactive compounds. However, the effect of calcium (Ca) sugar alcohol (CSA), a newly developed chelated Ca-fertilizer, on the secondary metabolism of phenolics in T. grandis nuts is largely unknown, for which transcriptomic and metabolomic analysis was carried out.
View Article and Find Full Text PDFCohort profile: A prospective cohort study on newlywed couples in rural and poor urban Bangladesh.
PLoS One
January 2025
Maternal and Child Health Division, icddr,b, Dhaka, Bangladesh.
Sexual and Reproductive Health and Rights (SRHR) aim to enhance quality of life through safe sexual experiences, reproductive autonomy, and protection against gender-based violence. However, existing SRHR research and interventions in low- and middle-income countries like Bangladesh predominantly focus on women, often understating men and neglecting the nuanced contextual issues faced by married couples. This study contributes to filling this gap by examining SRHR dynamics among newlyweds in rural and poor urban areas of Bangladesh, especially focusing on marital satisfaction, fertility preferences, and post-marriage adaptation mechanisms.
View Article and Find Full Text PDFExtreme Tolerance of Nanoparticle-Protein Corona to Ultra-High Abundance Proteins Enhances the Depth of Serum Proteomics.
Adv Sci (Weinh)
January 2025
Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang, 310022, China.
The serum nanoparticle-protein corona (NPC) provides specific disease information, thus opening a new avenue for high-throughput in-depth proteomics to facilitate biomarker discovery. Yet, little is known about the interactions between NPs and proteins, and its role in enhanced depth of serum proteomics. Herein, a series of protein spike-in experiments are conducted to systematically investigate protein depletion and enrichment during NPC formation.
View Article and Find Full Text PDFNew insight into the role of the pathway NLRP1 and NLRP3 inflammasomes and IL-33 in ultraviolet-induced cutaneous carcinogenesis.
Front Med (Lausanne)
January 2025
Department of Dermatology, Paediatric Dermatology and Oncology, Medical University of Łódź, Łódź, Poland.
Introduction: Inflammasomes NLRP1 (NLR family pyrin domain containing 1) and NLRP3 are pivotal regulators of the innate immune response, activated by a spectrum of endogenous and exogenous stressors, including ultraviolet radiation (UVR). The precise molecular mechanisms underlying the activation of these inflammasomes remain unclear. Furthermore, the involvement of interleukin-33 (IL-33) in UVR-induced skin carcinogenesis is not well defined.
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