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| 1 | Distribution of Ambler class A,B and Dβ-lactamases among Pseudomonas aeruginosaisolates显示文摘 | Tawfik AF Shibl AM Aljohi MA | 2012 | Burns2012，38，6： | 1 |
| 2 | RGAAT: A Reference-based Genome Assembly and Annotation Tool for New Genomes and Upgrade of Known Genomes显示文摘The rapid development of high-throughput sequencing technologies has led to a dramatic decrease in the money and time required for de novo genome sequencing or genome resequencing projects, with new genome sequences constantly released every week. Among such projects, the plethora of updated genome assemblies induces the requirement of versiondependent annotation files and other compatible public dataset for downstream analysis. To handlethese tasks in an efficient manner, we developed the reference-based genome assembly and annotation tool(RGAAT), a flexible toolkit for resequencing-based consensus building and annotation update. RGAAT can detect sequence variants with comparable precision, specificity, and sensitivity to GATK and with higher precision and specificity than Freebayes and SAMtools on four DNAseq datasets tested in this study. RGAAT can also identify sequence variants based on cross-cultivar or cross-version genomic alignments. Unlike GATK and SAMtools/BCFtools, RGAAT builds the consensus sequence by taking into account the true allele frequency. Finally, RGAAT generates a coordinate conversion file between the reference and query genomes using sequence variants and supports annotation file transfer. Compared to the rapid annotation transfer tool(RATT),RGAAT displays better performance characteristics for annotation transfer between different genome assemblies, strains, and species. In addition, RGAAT can be used for genome modification,genome comparison, and coordinate conversion. RGAAT is available at http://gffzz6ccd80d7270b40f2scnkw5c09xkpk6fvo.ffgz.tsg.suse.edu.cn/projects/rgaat/and http://gffzz188fe103f8f1460ascnkw5c09xkpk6fvo.ffgz.tsg.suse.edu.cn/wushyer/RGAAT_v2 at no cost. | Wanfei Liu Shuangyang Wu Qiang Lin Shenghan Gao Feng Ding Xiaowei Zhang Hasan Awad Aljohi Jun Yu Songnian Hu | 2018 | Genomics, Proteomics & Bioinformatics2018，16，5： | 1 |
| 3 | Identification and analysis of mouse non-coding RNA using transcriptome data显示文摘Transcripts are expressed spatially and temporally and they are very complicated, precise and specific; however, most studies are focused on protein-coding related genes. Recently, massively parallel c DNA sequencing(RNA-seq) has emerged to be a new and promising tool for transcriptome research, and numbers of non-coding RNAs, especially linc RNAs, have been widely identified and well characterized as important regulators of diverse biological processes. In this study, we used ultra-deep RNA-seq data from 15 mouse tissues to study the diversity and dynamic of non-coding RNAs in mouse. Using our own criteria, we identified totally 16,249 non-coding genes(21,569 non-coding RNAs) in mouse. We annotated these non-coding RNAs by diverse properties and found non-coding RNAs are generally shorter, have fewer exons, express in lower level and are more strikingly tissue-specific compared with protein-coding genes. Moreover, these non-coding RNAs show significant enrichment with transcriptional initiation and elongation signals including histone modifications(H3K4me3, H3K27me3 and H3K36me3), RNAPII binding sites and CAGE tags. The gene set enrichment analysis(GSEA) result revealed several sets of linc RNAs associated with diverse biological processes such as immune effector process, muscle development and sexual reproduction. Taken together, this study provides a more comprehensive annotation of mouse non-coding RNAs and gives an opportunity for future functional and evolutionary study of mouse non-coding RNAs. | Yuhui Zhao Wanfei Liu Jingyao Zeng Shoucheng Liu Xinyu Tan Hasanawad Aljohi Songnian Hu | 2016 | Science China(Life Sciences)2016，59，6： | 1 |
| 4 | Distribution of Ambler class A,B and D 13-1actamases among Pseudomonas aeruginosa i- solates显示文摘 | Tawfik AF Shibl AM Aljohi MA | 2012 | Burns2012，38，6： | 1 |
| 5 | Monomeric C-reactive protein and Notch-3 co-operatively increase angiogenesis through PI3K signalling pathway显示文摘 | Emhamed Boras Mark Slevin M. Yvonne Alexander Ali Aljohi William Gilmore Jason Ashworth Jerzy Krupinski Lawrence A. Potempa Ibrahim Al Abdulkareem Adila Elobeid Sabine Matou-Nasri | 2014 | Cytokine2014，，2： | 1 |
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