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Articles by Xinge Wang
Discovery and engineering of avian R2 retrotransposons for all-RNA-mediated targeted DNA integration in human cells
Abstract To discover unknown retrotransposons for genomic integration in human cells, we searched 1,139 avian genomes, identified 159 avian R2 retrotransposons and characterized conserved/nonconserved sequence features in their proteins and untranslated region elements. Engineered variants of these retrotransposons achieved up to 60% site-specific gene integration across human primary cells. This work expands the avian R2 resource and provides additional tools for all-RNA-mediated genome editing.
Best Practices: Developing career routes for the people who move us
Best Practices: Developing career routes for the people who move us Leveraging frontline operators and maintenance technicians can be the best recruiters for the public transit industry. Research supports what we see in the field: Our frontline workers are our most effective recruiters. As a past Mass Transit 40 Under 40 honoree, I am excited to share space in this issue with the newest cohort.
Employing the intravesical delivery route to target on the kidney
Abstract There is an unmet demand for kidney‐targeted non-invasive drug‐delivery systems to enhance the therapeutic index and at the same time reduce the systemic side effects. In the present study, we performed a proof-of-concept study to evaluate the validity and efficacy of intravesical delivery for kidney targeting in mice. We demonstrated that intravesical infusion was valid for a retrograde delivery of molecules up to 500 kDa to the kidney.
Unveiling the cell-type-specific landscape of cellular senescence through single-cell transcriptomics using SenePy - Nature Communications
Abstract Senescent cells accumulate in most tissues with organismal aging, exposure to stressors, or disease progression. It is challenging to identify senescent cells because cellular senescence signatures and phenotypes vary widely across distinct cell types and tissues. Here we developed an analytical algorithm that defines cell-type-specific and universal signatures of cellular senescence across a wide range of cell types and tissues.
Inhibitory Activity Against Rhizoctonia Solani and Chemical Composition of Extract from Moutan Cortex
Conflict of interests The authors declare no conflict of interest. Supporting Information As a service to our authors and readers, this journal provides supporting information supplied by the authors. Such materials are peer reviewed and may be re-organized for online delivery, but are not copy-edited or typeset. Technical support issues arising from supporting information (other than missing files) should be addressed to the authors.
SenePy: Unveiling the Cell-Type Specific Landscape of Cellular Senescence through Single-Cell Analysis in Living Organisms
Abstract Senescent cells accumulate in tissues with organismal age and contribute causally to multiple chronic diseases. In vivo senescent cell phenotypes are heterogeneous because cellular context and stressors vary by cell type and tissue. Due to the variability of senescence programs, there is no universal method to identify senescent cells and even widely used markers, such as CDKN2A, are not ubiquitous.
Trained immunity of alveolar macrophages enhances injury resolution via KLF4-MERTK-mediated efferocytosis
Subjects: Infectious disease and host defense, Innate immunity and inflammation, Tolerance Subjects: Infectious disease and host defense, Innate immunity and inflammation, Tolerance Immune memory as a consequence of repeated exposure to pathogens or pathogen components has been traditionally associated with the adaptive immune system and forms the basis of vaccine efficacy (Cupovic et al., 2021).
NetBID2 provides comprehensive hidden driver analysis - Nature Communications
Input datasets for NetBID2 The two required input datasets of NetBID2 include (1) a transcriptomic dataset in the relevant biological condition used for network construction and (2) an expression profiling dataset (at least one omics modality from RNA-seq, whole proteomics, and phosphoproteomics) with experimental design (e.g., case vs. control, phenotype groups) for driver inference.
Immunotoxicity in Vitro Assays for Environmental Pollutants under Paradigm Shift in Toxicity Tests
This is an early access version, the complete PDF, HTML, and XML versions will be available soon.
Synergistic engineering of CRISPR-Cas nucleases enables robust mammalian genome editing
Next, we investigated the efficacy of MIDAS in engineering Cas nucleases. MIDAS-engineered Cas12i variant N164Y/E178R/K238R/T447R/E563R/E323R/D362R, which was named Cas12iMax, was chosen to test (Figure 4A).
Systematic temporal analysis of peripheral blood transcriptomes using TrendCatcher identifies early and persistent neutrophil activation as a hallmark of severe COVID-19
Systematic temporal analysis of peripheral blood transcriptomes using TrendCatcher identifies early and persistent neutrophil activation as a hallmark of severe COVID-19 Xinge Wang, Mark Sanborn, Yang Dai, Jalees Rehman bioRxiv 2021.05.04.442617; doi: https://doi.org/10.1101/2021.05.04.442617
Systematic temporal analysis of transcriptomes using TrendCatcher identifies early and persistent neutrophil activation as an early hallmark of severe COVID-19
Abstract Studying the dynamic shifts in gene expression during disease progression may provide important insights into the biological mechanisms that distinguish adaptive and maladaptive responses. Existing computational tools for the analysis of transcriptomic data are not designed to optimally identify distinct temporal patterns when analyzing dynamic differentially expressed genes (DDEGs).
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