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| 1 | The first metagenome of activated sludge from full-scale anaerobic/anoxic/oxic(A2O) nitrogen and phosphorus removal reactor using Illumina sequencing显示文摘The anaerobic/anoxic/oxic(A2O) process is globally one of the widely used biological sewage treatment processes. This is the first report of a metagenomic analysis using Illumina sequencing of full-scale A2O sludge from a municipal sewage treatment plant.With more than 530,000 clean reads from different taxa and metabolic categories, the metagenome results allow us to gain insight into the functioning of the biological community of the A2O sludge. There are 51 phyla and nearly 900 genera identified from the A2O activated sludge ecosystem. Proteobacteria, Bacteroidetes, Nitrospirae and Chloroflexi are predominant phyla in the activated sludge, suggesting that these organisms play key roles in the biodegradation processes in the A2O sewage treatment system.Nitrospira, Thauera, Dechloromonas and Ignavibacterium, which have abilities to metabolize nitrogen and aromatic compounds, are most prevalent genera. The percent of nitrogen and phosphorus metabolism in the A2O sludge is 2.72% and 1.48%, respectively. In the current A2O sludge, the proportion of Candidatus Accumulibacter is 1.37%, which is several times more than that reported in a recent study of A2O sludge. Among the four processes of nitrogen metabolism, denitrification related genes had the highest number of sequences(76.74%), followed by ammonification(15.77%), nitrogen fixation(3.88%) and nitrification(3.61%). In phylum Planctomycetes, four genera(Planctomyces, Pirellula, Gemmata and Singulisphaera) are included in the top 30 abundant genera, suggesting the key role of ANAMMOX in nitrogen metabolism in the A2O sludge. | Mei Tian Fangqing Zhao Xin Shen Kahou Chu Jinfeng Wang Shuai Chen Yan Guo Hanhu Liu | 2015 | Journal of Environmental Sciences2015，27，9： | 20 |
| 2 | Single-cell metagenomics: challenges and applications显示文摘与高产量定序和单个房间的 genomics 技术的发展,许多未耕作的细菌的社区被联合这二种技术把了。由同时单个房间的 genomics 和 metagenomics 利用,特别,研究人员们能极大地改进从复杂微生物引起的社区获得整个染色体信息的效率和精确性,它允许我们识别微生物而且连接功能到种类不仅,识别亚种变化,学习主人病毒相互作用和等等。这里,我们考察最近的开发,挑战需要在单个房间的 metagenomics 被探讨,包括潜在的污染,不平的顺序范围,顺序怪物,染色体集会和注解。与定序和计算方法的开发,单个房间的 metagenomics 将无疑在各种各样的 microbiome 研究拓宽它的应用程序。 | Yuan Xu Fangqing Zhao | 2018 | Protein & Cell2018，9，5： | 8 |
| 3 | Small RNA transcriptome investigation based on next-generation sequencing technology显示文摘在过去的十年,有学习小 RNA transcriptome 为理解 transcriptional 规定的复杂性是必要的一条成长认识。与增加的产量和减少的费用,下一代的定序技术提供了一个崭新的机会测量小 RNA transcriptome 的程度和复杂性。同时,大量获得的数据和改变的技术平台也为有效数据分析和采矿提出了多重挑战。提供某卓见进小 RNA transcriptome 调查,这评论描述主要小 RNA 班,识别小 RNA 的试验性的方法,和可得到的生物信息学工具和数据库。 | Linglin Zhou Xueying Li Qi Liu Fangqing Zhao Jinyu Wu | 2011 | Journal of Genetics and Genomics2011，38，11： | 5 |
| 4 | eGPS 1.0: comprehensive software for multi-omic and evolutionary analyses显示文摘It has become increasingly challenging for researchers to analyze the exponentially expanding amount of multi-omic data.Here,we describe multi-functional software named evolutionary GenotypePhenotype Systems(eGPS)that enables users to perform comprehensive multiomic and evolutionary analyses.The eGPS combines the power of cloud computing and the advantage of desktop application,has a user-friendly graphic interface and is highly interactive. | Dalang Yu Lili Dong Fangqi Yan Hailong Mu Bixia Tang Xiao Yang Tao Zeng Qing Zhou Feng Gao Zhonghuang Wang Ziqian Hao Hongen Kang Yi Zheng Hongwei Huang Yuzhang Wei Wei Pan Yaochen Xu Junwei Zhu Shilei Zhao Ciran Wang Pengyu Wang Long Dai Mushan Li Li Lan Yiwei Wang Hua Chen Yi-Xue Li Yun-Xin Fu Zhen Shao Yiming Bao Fangqing Zhao Luo-Nan Chen Guo-Qing Zhang Wenming Zhao Haipeng Li | 2019 | National Science Review2019，6，5： | 4 |
| 5 | Microbiota-gut-brain axis in autism spectrum disorder显示文摘Extensive studies, largely during the past decade, identify the dynamic and bidirectional interaction between the bacteria resident in the intestines and their host brain along the 'microbiota-gut-brain axis'. This interaction modulates the development and function of the central nervous system and is implicated in neurological disorders. As a neurodevelopmental disorder, autism spectrum disorder (ASD) is considered a historically defect in the brain. With accumulating evidence showing how the microorganisms modulate neural activities, more and more research is focusing on the role of the gut microbiota in mitigating ASD symptoms and the underlying mechanisms. In this review, we describe the intricate and crucial pathways via which the gut microbiota communicates with the brain, the microbiota-gut-brain axis, and summarize the specific pathways that mediate the crosstalk of the gut microbiota to the brain in ASD. | You Yu Fangqing Zhao | 2021 | Journal of Genetics and Genomics2021，48，9： | 4 |
| 6 | Phylogenomics of non-model ciliates based on transcriptomic analyses显示文摘Ciliates 是最旧的生活真核细胞的单细胞的有机体之一,在水里广泛地分布式在全世界。作为典型海洋的 oligotrich 有睫, Strombidium sulcatum 在海洋的食物网和精力流动起一个重要作用。这里,我们报导第一从 Strombidium sulcatum 的深定序和 RNA-Seq 数据的分析。我们在 de novo 汇编和搬迁 rRNA 以后与 1,451 bp 的 N50 产生了 42,640 unigenes, mitochondrial 和细菌沾染物。我们采用了 SPOCS 从 S 检测 orthologs。sulcatum 和 17 另外的 ciliates,然后用 127 单个拷贝 orthologs 执行了 phylogenomic 重建。在 phylogenomic 分析,并置树在班水平上与词语索引树有类似的拓扑的结构。和种系发生的网络分析,它关于 Protocruzia, Mesodinium 和 Myrionecta 的放置引起了更多的疑问。当 epiplasmic 蛋白质被知道与词法特征有关时,我们发现了在 epiplasmic 蛋白质和词法特征的基因表示之间的潜在的关系。这个工作象在目标基因和词法特征的表示水平之间的关联分析一样为 phylogenomic 分析支持高产量途径的使用。 | Xiao Chen Xiaolu Zhao Xiaohui Liu Alan Warren Fangqing Zhao Miao Miao | 2015 | Protein & Cell2015，6，5： | 4 |
| 7 | Variation of the Vaginal Microbiome During and After Pregnancy in Chinese Women显示文摘A comprehensive profiling of the vaginal microbial communities and their variability enables an accurate description of the microbiome in women.However,there is a lack of studies available on Chinese women.In the present study,the composition of the vaginal microbiota during pregnancy and the 6-week postpartum period of 454 Chinese women was characterized by sequencing the V3-V4 region of the 16S ribosomal RNA(rRNA)gene.The vaginal microbiome showed variations during pregnancy and the postpartum period based on the abortion history,hypertensive disorders,delivery mode,and maternal age.Co-variation of 22 bacterial taxa,including the Lactobacillus genus and two of its species,may account for the common characteristics of the vaginal microbiome under scenarios of different medical histories and pregnancy outcomes.In contrast,discriminant bacterial species were significantly different between women who had preterm birth(PTB)with and without premature rupture of membranes(PROM),and the community state type(CST)IV-A without any predominant Lactobacillus species in the microbiota was more prevalent during pregnancy in the PROM-PTB cases,suggesting that specific bacterial species could be considered to distinguish between different types of PTB.By providing data on Chinese women,this study will enrich the knowledge of the human microbiome and contribute to a better understanding of the association between the vaginal microbiome and reproductive health. | Xiaoai Zhang Qingzhi Zhai Jinfeng Wang Xiuling Ma Bo Xing Hang Fan Zhiying Gao Fangqing Zhao Wei Liu | 2022 | Genomics, Proteomics & Bioinformatics2022，20，2： | 2 |
| 8 | CRISPRs provide broad and robust protection to oral microbial flora of gingival health against bacteriophage challenge显示文摘 | Huiyue Zhou (1) (2) Hui Zhao (3) Jiayong Zheng (3) Yuan Gao (1) (2) Yanming Zhang (1) Fangqing Zhao (1) Jinfeng Wang (1) | 2015 | Protein & Cell2015，6，7： | 2 |
| 9 | Genome-wide survey of putative serine/threonine pro rein kinases in Cyanobaeterla显示文摘 | Zhang Xiaowen Zhao Fangqing Guan Xiangyu | 2007 | BMC Genomics2007，8，： | 1 |
| 10 | Characterization of human αβTCR repertoire and discovery of D-D fusion in TCRβ chains显示文摘 | Peipei Liu Di Liu Xi Yang Jing Gaoai Ma3, Fangqing Zhaos, Xuyu Zhou~'2~, George F. Gao1'2'4'5~, Baoli Zhu~'2~ Yan Chen Xue Xiao Fei Liu Jing Zou Jun Wu Juncai Ma Fangqing Zhao Xuyu Zhou George F. Gao Baoli Zhu | 2014 | Protein & Cell2014，5，8： | 1 |
| 11 | Precision Medicine:What Challenges Are We Facing?显示文摘Following the publication of the US National Research Council(NRC)report‘‘Toward Precision Medicine:Building a Knowledge Network for Biomedical Research and a New Taxonomy of Diseases'in 2011[1],several nations have announced that their national research programs would definitely head toward this direction.Now,precision medicine(PM)became a banner for many large-scale | Yu Xue Eric-Wubbo Lameijer Kai Ye Kunlin Zhang Suhua Chang Xiaoyue Wang Jianmin Wu Ge Gao Fangqing Zhao Jian Li Chunsheng Han Shuhua Xu Jingfa Xiao Xuerui Yang Xiaomin Ying Xuegong Zhang Wei-Hua Chen Yun Liu Zhang Zhang Kun Huang Jun Yu | 2016 | Genomics, Proteomics & Bioinformatics2016，14，5： | 1 |
| 12 | Scale-up of fermentation and purification of recombinant allophycocyanin over-expressed in Escherichia coli显示文摘 | Baosheng Ge Zhihong Tang Fangqing Zhao Yuhong Ren Yu Yang Song Qin | 2005 | Process Biochemistry2005，，： | 1 |
| 13 | Combinational Biosynthesis of a Fluorescent Cyanobacterial Holo-α-Phycocyanin in Escherichia coli by Using One Expression Vector显示文摘 | Xiangyu Guan Song Qin Zhongliang Su Fangqing Zhao Baosheng Ge Fuchao Li Xuexi Tang | 2007 | Applied Biochemistry and Biotechnology2007，，： | 1 |
| 14 | Screening Linear and Circular RNA Transcripts from Stress Granules显示文摘Stress granules(SGs)are cytoplasmic ribonucleoprotein assemblies formed under stress conditions and are related to various biological processes and human diseases.Previous studies have reported the regulatory role of some proteins and linear RNAs in SG assembly.However,the relationship between circular RNAs(circRNAs)and SGs has not been discovered.Here,we screened both linear RNAs and circRNAs in SGs using improved total RNA sequencing of purified SG cores in mammalian cells and identified circular transcripts specifically localized in SGs.circRNAs with higher SG-related RNA-binding protein(RBP)binding abilities are more likely to be enriched in SGs.Furthermore,some SG-enriched circRNAs are differentially expressed in hepatocellular carcinoma(HCC)and adjacent tissues.These results suggest the regulatory role of circRNAs in SG formation and provide insights into the biological function of circRNAs and SGs in HCC. | Shuai Chen Jinyang Zhang Fangqing Zhao | 2023 | Genomics, Proteomics & Bioinformatics2023，21，4： | 1 |
| 15 | Scale-up of fermentation and purification of recombinant allophyeoeyanin over-expressed in Escherichia coli显示文摘 | Ge Baosheng Tang Zhihong Zhao Fangqing | 2005 | Process Biochemistry2005，40，： | 1 |
| 16 | First Glimpse of Gut Microbiota of Quarantine Insects in China显示文摘Quarantine insects are economically important pests that frequently invade new habitats.A rapid and accurate monitoring method to trace the geographical sources of invaders is required for their prevention,detection,and eradication.Current methods based on genetics are typically time-consuming.Here,we developed a novel tracing method based on insect gut microbiota.The source location of the insect gut microbiota can be used to rapidly determine the geographical origin of the insect.We analyzed 179 gut microbiota samples from 591 individuals of 22 quarantine insect species collected from 36 regions in China.The gut microbiota of these insects primarily included Actinobacteria,Bacteroidetes,Cyanobacteria,Firmicutes,Proteobacteria,and Tenericutes.The diversity of the insect gut microbiota was closely associated with geographical and environmental factors.Different insect species could be distinguished based on the composition of gut microbiota at the phylum level.Populations of individual insect species from different regions could be distinguished based on the composition of gut microbiota at the phylum,class,and order levels.A method for determining the geographical origins of invasive insect species has been established;however,its practical application requires further investigations before implementation. | Yanxue Yu Qi Wang Ping Zhou Na Lv Wei Li Fangqing Zhao Shuifang Zhu Di Liu | 2022 | Genomics, Proteomics & Bioinformatics2022，20，2： | 0 |
| 17 | Was Wuhan the early epicenter of the COVID-19 pandemic?——a critique显示文摘Recently, Worobey et al.(2022) published a report entitled ‘The Huanan Seafood Wholesale Market in Wuhan was the early epicenter of the COVID-19 pandemic' that succinctly summarizes their study [1]. A pre-print version of this study had earlier elicited a series of highprofile media coverages [2,3]. All these reports deliver a social-political message that the Huanan market is the epicenter of COVID-19. | Yanan Cao Lingling Chen Hua Chen Yupeng Cun Xiaofeng Dai Hongli Du Feng Gao Fengbiao Guo Yalong Guo Pei Hao Shunmin He Shunping He XiongLei He Zheng Hu Boon-Peng Hoh Xin Jin Qian Jiang Qinghua Jiang Asifullah Khan Hong-Zhi Kong Jinchen Li Shuai Cheng Li Ying Li Qiang Lin Jianquan Liu Qi Liu Jian Lu Xuemei Lu Shujin Luo Qinghua Nie Zilong Qiu Tieliu Shi Xiaofeng Song Jianzhong Su Sheng-ce Tao Chaolong Wang Chuan-Chao Wang Guo-Dong Wang Jiguang Wang Qi Wu Shaoyuan Wu Shuhua Xu Yu Xue Wenjun Yang Zhaohui Yang Kai Ye Yuan-Nong Ye Li Yu Fangqing Zhao Yiqiang Zhao Weiwei Zhai Dandan Zhang Liye Zhang Houfeng Zheng Qi Zhou Tianqi Zhu Ya-ping Zhang | 2023 | National Science Review2023，10，4： | 0 |
| 18 | Bioinformatics Commons: The Cornerstone of Life and Health Sciences显示文摘Bioinformatics, an interdisciplinary field that combines biology, mathematics, computer science, medicine, and health science, to integrate, analyze, and interpret biological data, is now becoming increasingly data-intensive. To dig out the treasure from big data powered by high-throughput sequencing technologies, it is highly dependent on Bioinformatics Commons that involves a variety of fundamental resources, includ- | Zhang Zhang Yu Xue Fangqing Zhao | 2018 | Genomics, Proteomics & Bioinformatics2018，16，4： | 0 |
| 19 | Maternal and neonatal viromes indicate the risk of offspring's gastrointestinal tract exposure to pathogenic viruses of vaginal origin during delivery显示文摘A cumulative effect of enterovirus and gluten intake on the risk of celiac disease autoimmunity in infants highlights the significance of viral exposure in early life on the health of children.However,pathogenic viruses may be transmitted to the offspring in an earlier period,raising the possibility that women whose vaginas are inhabited by such viruses may have had their babies infected as early as the time of delivery.A high‐resolution intergenerational virome atlas was obtained by metagenomic sequencing and virome analysis on 486 samples from six body sites of 99 mother–neonate pairs.We found that neonates had less diverse oral and enteric viruses than mothers.Vaginally delivered newborns seconds after birth had a more similar oral virome and more viruses of vaginal origin than cesarean‐section(C‐section)newborns(56.9%vs.5.8%).Such viruses include both Lactobacillus phage and potentially pathogenic viruses,such as herpesvirus,vaccinia virus,and hepacivirus,illustrating a relatively high variety of the pioneer viral taxa at the time of delivery and a delivery‐dependent mother‐to‐neonate transmission along the vaginal–oral–intestinal route.Neonates are exposed to vaginal viruses as they pass through the reproductive tract,and viruses of vaginal origin may threaten their health.These findings challenge the conventional notion that vaginal delivery is definitely better than cesarean delivery from the perspective of microbial transmission.Screening for vaginal virome before delivery is a worthwhile step to advocate in normal labor to eliminate the risk of intergenerational transmission of pathogenic viruses to offspring. | Jinfeng Wang Liwen Xiao Baichuan Xiao Bing Zhang Zhenqiang Zuo Peifeng Ji Jiayong Zheng Xiaoqing Li Fangqing Zhao | 2022 | mLife2022，1，3： | 0 |
| 20 | MBRidge: an accurate and cost-effective method for profiling DNA methylome at single-base resolution显示文摘Organisms and cells,in response to environmental influences or during development,undergo considerable changes in DNA methylation on a genome-wide scale,which are linked to a variety of biological processes.Using MethylC-seq to decipher DNA methylome at single-base resolution is prohibitively costly.In this study,we develop a novel approach,named MBRidge,to detect the methylation levels of repertoire CpGs,by innovatively introducing C-hydroxylmethylated adapters and bisulfate treatment into the MeDIP-seq protocol and employing ridge regression in data analysis.A systematic evaluation of DNA methylome in a human ovarian cell line T29 showed that MBRidge achieved high correlation(R>0.90)with much less cost(∼10%)in comparison with MethylC-seq.We further applied MBRidge to profiling DNA methylome in T29H,an oncogenic counterpart of T29’s.By comparing methylomes of T29H and T29,we identified 131790 differential methylation regions(DMRs),which are mainly enriched in carcinogenesis-related pathways.These are substantially different from7567 DMRs that were obtained by RRBS and related with cell development or differentiation.The integrated analysis ofDMRsin the promoterand expression of DMR-corresponding genes revealed thatDNAmethylation enforced reverse regulation of gene expression,depending on the distance fromthe proximalDMRto transcription starting sites in both mRNA and lncRNA.Taken together,our results demonstrate that MBRidge is an efficient and cost-effective method that can be widely applied to profiling DNA methylomes. | Wanshi Cai Fengbiao Mao Huajing Teng Tao Cai Fangqing Zhao Jinyu Wu Zhong Sheng Sun | 2015 | Journal of Molecular Cell Biology2015，7，4： | 0 |
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