Zhang, Shi-Jian Liu, Lei Yang, Ruolin Wang, Xiangfeng
Published in
Genomics, proteomics & bioinformatics
The dynamic activity of transposable elements (TEs) contributes to the vast diversity of genome size and architecture among plants. Here, we examined the genomic distribution and transposition activity of long terminal repeat retrotransposons (LTR-RTs) in Arabidopsis thaliana (Ath) and three of its relatives, Arabidopsis lyrata (Aly), Eutrema salsu...
He, Song Wen, Yuqi Yang, Xiaoxi Liu, Zhen Song, Xinyu Huang, Xin Bo, Xiaochen
Published in
Genomics, proteomics & bioinformatics
The accumulation of various types of drug informatics data and computational approaches for drug repositioning can accelerate pharmaceutical research and development. However, the integration of multi-dimensional drug data for precision repositioning remains a pressing challenge. Here, we propose a systematic framework named PIMD to predict drug th...
Li, Ting Chen, Bing Yang, Pengcheng Wang, Depin Du, Baozhen Kang, Le
Published in
Genomics, proteomics & bioinformatics
Long non-coding RNAs (lncRNAs) regulate various biological processes ranging from gene expression to animal behavior. Although protein-coding genes, microRNAs, and neuropeptides play important roles in the regulation of phenotypic plasticity in migratory locust, empirical studies on the function of lncRNAs in this process remain limited. Here, we a...
Liang, Yuan Lu, Dengxue Wang, Sen Zhao, Yuhui Gao, Shenghan Han, Rongbing Yu, Jun Zheng, Weili Geng, Jianing Hu, Songnian
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Genomics, proteomics & bioinformatics
Agrocybe cylindracea, an edible mushroom, is widely cultivated for its abundance of nutrients and flavor, and many of its metabolites are reported to have beneficial roles, such as medicinal effects on tumors and chronical illnesses. However, the lack of genomic information has hindered further molecular studies on this fungus. Here, we present a g...
Guan, Jiantao Garcia, Diego F Zhou, Yun Appels, Rudi Li, Aili Mao, Long
Published in
Genomics, proteomics & bioinformatics
In the year 2018, the world witnessed the finale of the race to sequence the genome of the world's most widely grown crop, the common wheat. Wheat has been known to bear a notoriously large and complicated genome of a polyploidy nature. A decade competition to sequence the wheat genome initiated with a single consortium of multiple countries, takin...
Zhou, Zijian Cao, Yan Li, Tao Wang, Xinghao Chen, Jiafa He, Hang Yao, Wen Wu, Jianyu Zhang, Huiyong
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Genomics, proteomics & bioinformatics
Fusarium ear rot (FER) caused by Fusarium verticillioides is one of the most common diseases affecting maize production worldwide. FER results in severe yield losses and grain contamination with health-threatening mycotoxins. Although most studies to date have focused on comprehensive analysis of gene regulation in maize during defense responses ag...
Suo, Jinwei Zhang, Heng Zhao, Qi Zhang, Nan Zhang, Yongxue Li, Ying Song, Baohua Yu, Juanjuan Cao, Jianguo Wang, Tai
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Genomics, proteomics & bioinformatics
Alkali-salinity exerts severe osmotic, ionic, and high-pH stresses to plants. To understand the alkali-salinity responsive mechanisms underlying photosynthetic modulation and reactive oxygen species (ROS) homeostasis, physiological and diverse quantitative proteomics analyses of alkaligrass (Puccinellia tenuiflora) under Na2CO3 stress were conducte...
Zhang, Zhang Song, Shuhui Yu, Jun Zhao, Wenming Xiao, Jingfa Bao, Yiming
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Genomics, proteomics & bioinformatics
Chen, Ningbo Fu, Weiwei Zhao, Jianbang Shen, Jiafei Chen, Qiuming Zheng, Zhuqing Chen, Hong Sonstegard, Tad S Lei, Chuzhao Jiang, Yu
...
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Genomics, proteomics & bioinformatics
Next-generation sequencing has yielded a vast amount of cattle genomic data for global characterization of population genetic diversity and identification of genomic regions under natural and artificial selection. However, efficient storage, querying, and visualization of such large datasets remain challenging. Here, we developed a comprehensive da...
Sang, Jian Zou, Dong Wang, Zhennan Wang, Fan Zhang, Yuansheng Xia, Lin Li, Zhaohua Ma, Lina Li, Mengwei Xu, Bingxiang
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Published in
Genomics, proteomics & bioinformatics
Genome reannotation aims for complete and accurate characterization of gene models and thus is of critical significance for in-depth exploration of gene function. Although the availability of massive RNA-seq data provides great opportunities for gene model refinement, few efforts have been made to adopt these precious data in rice genome reannotati...