分类： 生物学 >> 生物学其他学科 分类： 计算机科学 >> 计算机应用技术 提交时间： 2023-02-09
摘要： Circular RNA (circRNAs) may mediate mRNA expression as miRNA sponge. Since the community has paid more attention on circRNAs, a lot of circRNA databases have been developed for plant. However, a comprehensive collection of circRNAs in crop response to abiotic stress is still lacking. In this work, we applied a big-data approach to take full advantage of large-scale sequencing data, and developed a rich circRNA resource: CropCircDB for maize and rice, later extending to incorporate more crop species. We also designed a metric: stress detections score, which is specifically for detecting circRNAs under stress condition. In summary, we systematically investigated 244 and 288 RNASeq samples for maize and rice, respectively, and found 38 785 circRNAs in maize, and 63 048 circRNAs in rice. This resource not only supports user-friendly JBrowser to visualize genome easily, but also provides elegant view of circRNA structures and dynamic profiles of circRNA expression in all samples. Together, this database will host all predicted and validated crop circRNAs response to abiotic stress.
分类： 生物学 >> 病毒学 分类： 计算机科学 >> 计算机科学技术其他学科 提交时间： 2020-02-21
摘要： 新发传染病爆发流行期间，亟需提出候选药物功效与机制的科学假说。疫苗或新药研发均需要一定时间，因而药物重定位（老药新用）策略有其独特价值。但是新发疾病其病原体、宿主反应的临床数据不充分，制约了候选药物假设的提出。此阶段常根据病人临床特征进行广谱抗病毒药物的尝试。本文借鉴人工智能领域常见的启发式搜索思路，提出一种新方法(aCODE)，基于前期有一定疗效提示的广谱抗病毒药，获得其宿主靶蛋白集合，在全基因组尺度上搜索与之相关性最高的基因模块组合，进而对候选化合物（如已批准上市药物、天然产物）进行模式匹配与统计检验排序。本方法可根据临床实践的进展更新输入药物，迭代输出更精准结果，输出的天然产物或中药、药食同源成分结合其它信息后可实施快速测试，形成敏捷研发测试闭环。本方法的第二版更新及其与文献证据的比对分析请参考：http://chinaxiv.org/abs/202002.00024。
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