Qingxiang Guo

Integrated transcriptomic and functional analyses identify PRR7 as a therapeutic target that associated with Wnt/β-catenin signaling and docetaxel resistance in prostate cancer

Wei Sun, Yuheng Si, Lu Hong, Qingxiang Guo et autres

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Tumor-specific lncRNA IGF1R-AS1 trans-regulates chromatin interactions associated with oncogenic MYC signaling

Yongyong Yang, Ting-You Wang, Joshua Fry, YINGMING LI et autres

LncRNAs have emerged as pivotal regulators in the development and progression of various human cancers. However, understanding the precise mechanisms by which lncRNAs influence cancer progression remains a substantial challenge, largely due to their cell type- and tissue-specific expression patterns and the …

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Genomic language model mitigates chimera artifacts in nanopore direct RNA sequencing

Yangyang Li, Ting-You Wang, Qingxiang Guo, Yanan Ren et autres

Chimera artifacts in nanopore direct RNA sequencing (dRNA-seq) introduce substantial inaccuracies, complicating downstream applications such as transcript annotation and gene fusion detection. Current basecalling models are unable to detect or mitigate these artifacts, limiting the reliability and utility of dRNA-seq for transcriptomics …

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OctopuSV and TentacleSV: a one-stop toolkit for multi-sample, cross-platform structural variant comparison and analysis

Qingxiang Guo, Yangyang Li, Ting-You Wang

MOTIVATION: Structural variants (SVs) influence gene regulation, disease progression, and diagnostics, yet integrating SV calls across platforms remains difficult due to inconsistent annotations, limited merging flexibility, and fragmented workflows. Ambiguous breakend (BND) annotations, which comprise many variant calls, are often discarded or …

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Androgen receptor–regulated lncRNA PRCAT71 promotes AR signaling through the interaction with KHSRP in prostate cancer

Yongyong Yang, Ting-You Wang, Jiawen Lu, Yanan Ren et autres

Mounting evidence indicates that long noncoding RNAs (lncRNAs) play vital roles in tumorigenesis and progression of cancers. However, the functions and regulatory mechanisms of lncRNAs in prostate cancer (PCa) are still largely unknown. In this study, we found an lncRNA, PCa-associated transcript …

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OctopusV and TentacleSV: a one-stop toolkit for multi-sample, cross-platform structural variant comparison and analysis

Qingxiang Guo, Yangyang Li, Tingyou Wang

Structural variants (SVs) significantly influence genomic variability and disease, but their accurate analysis across multiple samples and sequencing platforms remains challenging. We developed OctopusV, a tool that standardizes ambiguous breakend (BND) annotations into canonical SV types (inversions, duplications, translocations) and integrates variant …

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ScanNeo2: a comprehensive workflow for neoantigen detection and immunogenicity prediction from diverse genomic and transcriptomic alterations

Richard A Schäfer, Qingxiang Guo, Rendong Yang

MOTIVATION: Neoantigens, tumor-specific protein fragments, are invaluable in cancer immunotherapy due to their ability to serve as targets for the immune system. Computational prediction of these neoantigens from sequencing data often requires multiple algorithms and sophisticated workflows, which are currently restricted to …

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Identification of Myxobolus distalisensis n. sp. (Cnidaria: Myxozoa) infecting yellow catfish Tachysurus fulvidraco (Richardson), with a supplement description of M. voremkhai (Akhmerov, 1960) Landsberg and Lom, 1991

Bo Zhang, Qingxiang Guo, Xiao Tu, Zemao Gu

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Transcriptomic Insights into the Diversity and Evolution of Myxozoa (Cnidaria, Endocnidozoa) Toxin-like Proteins

Bin Xiao, Qingxiang Guo, Yanhua Zhai, Zemao Gu

Myxozoa is a speciose group of endoparasitic cnidarians that can cause severe ecological and economic effects. Their cnidarian affinity is affirmed by genetic relatedness and the presence of nematocysts, historically called “polar capsules”. Previous studies have revealed the presence of toxin-like proteins …

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A myxozoan genome reveals mosaic evolution in a parasitic cnidarian

Qingxiang Guo, Stephen D. Atkinson, Bin Xiao, Yanhua Zhai et autres

BACKGROUND: Parasite evolution has been conceptualized as a process of genetic loss and simplification. Contrary to this model, there is evidence of expansion and conservation of gene families related to essential functions of parasitism in some parasite genomes, reminiscent of widespread mosaic …

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Quantitative Insights into the Contribution of Nematocysts to the Adaptive Success of Cnidarians Based on Proteomic Analysis

Qingxiang Guo, Christopher M. Whipps, Yanhua Zhai, Dan Li et autres

Nematocysts are secretory organelles in cnidarians that play important roles in predation, defense, locomotion, and host invasion. However, the extent to which nematocysts contribute to adaptation and the mechanisms underlying nematocyst evolution are unclear. Here, we investigated the role of the nematocyst …

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Additional file 1 of A myxozoan genome reveals mosaic evolution in a parasitic cnidarian

Qingxiang Guo, Stephen D. Atkinson, Bin Xiao, Yanhua Zhai et autres

Additional file 1: Table S1. Statistics of the Pacbio sequencing and assembly of the Myxobolus honghuensis genome. Table S2. Length distribution of the Pacbio subreads. Table S3. Estimated genome characteristics. Table S4. Clean reads mapping result. Table S5. Details of the gene …

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