|
|
|
题名
|
作者
|
年代
|
出处
|
被引量
|
| 1 | Biomonitoring for traditional herbal medicinal products using DNA metabarcoding and single molecule, real-time sequencing显示文摘Global concerns have been paid to the potential hazard of traditional herbal medicinal products(THMPs). Substandard and counterfeit THMPs, including traditional Chinese patent medicine, health foods, dietary supplements, etc. are potential threats to public health. Recent marketplace studies using DNA barcoding have determined that the current quality control methods are not sufficient for ensuring the presence of authentic herbal ingredients and detection of contaminants/adulterants. An efficient biomonitoring method for THMPs is of great needed. Herein, metabarcoding and single-molecule, realtime(SMRT) sequencing were used to detect the multiple ingredients in Jiuwei Qianghuo Wan(JWQHW), a classical herbal prescription widely used in China for the last 800 years. Reference experimental mixtures and commercial JWQHW products from the marketplace were used to confirm the method. Successful SMRT sequencing results recovered 5416 and 4342 circular-consensus sequencing(CCS) reads belonging to the ITS2 and psb A-trn H regions. The results suggest that with the combination of metabarcoding and SMRT sequencing, it is repeatable, reliable, and sensitive enough to detect species in the THMPs, and the error in SMRT sequencing did not affect the ability to identify multiple prescribed species and several adulterants/contaminants. It has the potential for becoming a valuable tool for the biomonitoring of multi-ingredient THMPs. | Tianyi Xin Zhichao Xu Jing Jia Christine Leon Songnian Hu Yulin Lin Subramanyam Ragupathy Jingyuan Song Steven G.Newmaster | 2018 | Acta Pharmaceutica Sinica B2018，8，3： | 22 |
| 2 | Rice Expression Database(RED):An integrated RNA-Seq-derived gene expression database for rice显示文摘Rice is one of the most important stable food as well as a monocotyledonous model organism for the plant research community.Here,we present RED(Rice Expression Database;http://gffzzd1bc3ab4bbbc4005hf5vf0xuf9qk66qxx.ffgz.tsg.suse.edu.cn),an integrated database of rice gene expression profiles derived entirely from RNA-Seq data.RED features a comprehensive collection of 284 high-quality RNA-Seq experiments,integrates a large number of gene expression profiles and covers a wide range of rice growth stages as well as various treatments.Based on massive expression profiles,RED provides a list of housekeeping and tissue-specific genes and dynamically constructs co-expression networks for gene(s) of interest.Besides,it provides user-friendly web interfaces for querying,browsing and visualizing expression profiles of concerned genes.Together,as a core resource in BIG Data Center,RED bears great utility for characterizing the function of rice genes and better understanding important biological processes and mechanisms underlying complex agronomic traits in rice. | Lin Xia Dong Zou Jian Sang Xingjian Xu Hongyan Yin Mengwei Li Shuangyang Wu Songnian Hu Lili Hao Zhang Zhang | 2017 | Journal of Genetics and Genomics2017，44，5： | 12 |
| 3 | Transcriptome profiling of the developing postnatal mouse testis using next-generation sequencing显示文摘Mammalian testis development is a complex and highly sophisticated process. To study the dynamic change of normal testis development at the transcriptional level, we investigated mouse testes at three postnatal ages: 6 days postnatal, 4 weeks old, and 10 weeks old, representing infant (PN1), juvenile (PN2), and adult (PN3) stages, respectively. Using ultra high-throughput RNA sequencing (RNA-seq) technology, we obtained 211 million reads with a length of 35 bp. We identified 18837 genes that were expressed in mouse testes, and found that genes expressed at the highest level were involved in spermatogenesis. The gene expression pattern in PN1 was distinct from that in PN2 and PN3, which indicates that spermatogenesis has commenced in PN2. We analyzed a large number of genes related to spermatogenesis and somatic development of the testis, which play important roles at different developmental stages. We also found that the MAPK, Hedgehog, and Wnt signaling pathways were significantly involved at different developmental stages. These findings further our understanding of the molecular mechanisms that regulate testis development. Our study also demonstrates significant advantages of RNA-seq technology for studying transcriptome during development. | GONG Wei PAN LinLin LIN Qiang ZHOU YuanYuan XIN ChengQi YU XiaoMin CUI Peng HU SongNian YU Jun | 2013 | Science China(Life Sciences)2013，56，1： | 8 |
| 4 | A draft sequence of the rice (Oryza sativa ssp. indica) genome显示文摘The sequence of the rice genome holds fundamental information for its biology, including physiology, genetics, development, and evolution, as well as information on many beneficial phenotypes of economic significance. Using a 'whole genome shotgun' approach, we have pro-duced a draft rice genome sequence of Oryza sativa ssp. in-dica, the major crop rice subspecies in China and many other regions of Asia. The draft genome sequence is constructed from over 4.3 million successful sequencing traces with an accumulative total length of 2214.9 Mb. The initial assembly of the non-redundant sequences reached 409.76 Mb in length, based on 3.30 million successful sequencing traces with a total length of 1797.4 Mb from an indica variant cultivar 93-11, giving an estimated coverage of 95.29% of the rice genome with an average base accuracy of higher than 99%. The coverage of the draft sequence, the randomness of the sequence distribution, and the consistency of BIG-ASSEM-BLER, a custom-designed software package | YU Jun, HU Songnian, WANG Jun,LI Songgang WONG Ka-Shu Gane, LIU Bin,DENG Yajun, DAI Li, ZHOU Yan,ZHANG Xiuqing, CAO Mengliang, LIU Jing,SUN Jiandong , TANG Jiabin, CHEN Yanjiong,HUANG Xiaobing, LIN Wei, YE Chen, TONG Wei,CONG Lijuan, GENG Jianing, HAN Yujun, LI Lin,LI Wei, HU Guangqiang, HUANG Xiangang,LI Wenjie, LI Jian, LIU Zhanwei, LI Long,LIU Jianping, Ql Qiuhui, LIU Jinsong, LI Li,WANG Xuegang, LU Hong, WU Tingling,ZHU Miao, Nl Peixiang, HAN Hua, DONG Wei,REN Xiaoyu, FENG Xiaoli, GUI Peng,LI Xianran, WANG Hao, XU Xin, ZHAI Wenxue,XU Zhao, ZHANG Jinsong, HE Sijie,ZHANG Jianguo, XU Jichen, ZHANG Kunlin,ZHENG Xianwu, DONG Jianhai, ZENG Wanyong,TAO Lin, CHEN Xuewei, HE Jun, LIU Daofeng,TIAN Wei, TIAN Chaoguang, XIA Hongai,LI Gang, GAO Hui, LI Ping, CHEN Wei ,WANG Xudong, ZHANG Yong, HU Jianfei,WANG Jing, LIU Song, YANG Jian,ZHANG Guangyu, XIONG Yuqing, LI Zhijie,MAO Long, ZHOU Chengshu, ZHU Zhen,CHEN Runsheng, HAO Bailin,ZHENG Weimou, CHEN Shouyi, QUO Wei,LI Guojie, LIU Siqi, HUANG Guyang,TAO Ming, WANG Jian, ZHU Lihuang,YUAN Longping& YANG HuanmingBeijing Genomics Institute/Center of Genomics & Bioinformatics, Chinese Academy of Sciences, Beijing 101300, China Hangzhou Genomics Institute/Institute of Bioinformatics of Zhejiang University/Key Laboratory of Bioinformatics of Zhejiang Province, Hangzhou 310007, China Institute of Genetics, Chinese Academy of Sciences, Beijing 100101, China National Hybrid Rice R & D Center, Changsha 410125, China Laboratory of Bioinformatics, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China College of Life Sciences, Peking University, Beijing 100871, China Institute of Theoretical Physics, Chinese Academy of Sciences, Beijing 1Q0080, China Digital China Ltd., Beijing 100080, China Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100080, China Medical College, Xi’an Jiaotong University, Xi’an 710061, ChinaThese authors contributed equally to this work.Corresponding author.Corresponden | 2001 | Chinese Science Bulletin2001，46，23： | 6 |
| 5 | Distinct Contributions of Replication and Transcription to Mutation Rate Variation of Human Genomes显示文摘Here, we evaluate the contribution of two major biological processes-DNA replication and transcription-to mutation rate variation in human genomes. Based on analysis of the public human tissue transcriptomics data, high-resolution replicating map of Hela cells and dbSNP data, we present significant correlations between expres-sion breadth, replication time in local regions and SNP density. SNP density of tissue-specific (TS) genes is sig-nificantly higher than that of housekeeping (HK) genes. TS genes tend to locate in late-replicating genomic re-gions and genes in such regions have a higher SNP density compared to those in early-replication regions. In addi-tion, SNP density is found to be positively correlated with expression level among HK genes. We conclude that the process of DNA replication generates stronger mutational pressure than transcription-associated biological processes do, resulting in an increase of mutation rate in TS genes while having weaker effects on HK genes. In contrast, transcription-associated processes are mainly responsible for the accumulation of mutations in highly-expressed HK genes. | Peng Cui Feng Ding Qiang Lin Lingfang Zhang Ang Li Zhang Zhang Songnian Hu Jun Yu | 2012 | Genomics, Proteomics & Bioinformatics2012，10，1： | 5 |
| 6 | Genome-wide mapping of conserved microRNAs and their host transcripts in Tribolium castaneum显示文摘MicroRNAs (miRNAs) are endogenous 22-nt RNAs,which play important regulatory roles by post-transcriptional gene silencing. A computational strategy has been developed for the identification of conserved miRNAs based on features of known metazoan miRNAs in red flour beetle (Tribolium castaneum),which is regarded as one of the major laboratory models of arthropods. Among 118 putative miRNAs,47% and 53% of the predicted miRNAs from the red flour beetle are harbored by known protein-coding genes (intronic) and genes located outside (intergenic miRNA),respectively. There are 31 intronic miRNAs in the same transcriptional orientation as the host genes,which may share RNA polymerase Ⅱ and spliceosomal machinery with their host genes for their biogenesis. A hypothetical feed-back model has been proposed based on the analysis of the relationship between intronic miRNAs and their host genes in the develop-ment of red flour beetle. | Qibin Luo Qing Zhoub Xiaomin Yu Hongbin Lin Songnian Hu Jun Yu | 2008 | Journal of Genetics and Genomics2008，35，6： | 3 |
| 7 | High-performance polarization management devices based on thin-film lithium niobate显示文摘High-speed polarization management is highly desirable for many applications,such as remote sensing,telecommunication,and medical diagnosis.However,most of the approaches for polarization management rely on bulky optical components that are slow to respond,cumbersome to use,and sometimes with high drive voltages.Here,we overcome these limitations by harnessing photonic integrated circuits based on thin-film lithium niobate platform.We successfully realize a portfolio of thin-film lithium niobate devices for essential polarization management functionalities,including arbitrary polarization generation,fast polarization measurement,polarization scrambling,and automatic polarization control.The present devices feature ultra-fast control speeds,low drive voltages,low optical losses and compact footprints.Using these devices,we achieve high fidelity polarization generation with a polarization extinction ratio up to 41.9 dB and fast polarization scrambling with a scrambling rate up to 65 Mrad s−1,both of which are best results in integrated optics.We also demonstrate the endless polarization state tracking operation in our devices.The demonstrated devices unlock a drastically new level of performance and scales in polarization management devices,leading to a paradigm shift in polarization management. | Zhongjin Lin Yanmei Lin Hao Li Mengyue Xu Mingbo He Wei Ke Heyun Tan Ya Han Zhaohui Li Dawei Wang X.Steve Yao Songnian Fu Siyuan Yu Xinlun Cai | 2022 | Light(Science & Applications)2022，11，5： | 3 |
| 8 | CYP2A6 Polymorphisms Associate with Outcome of S-1 Plus Oxaliplatin Chemotherapy in Chinese Gastric Cancer Patients显示文摘Gastric carcinoma is a heterogeneous malignant disease involving genetic factors. To identify predictive markers for gastric cancer treatment in Chinese patients, we evaluated the association between polymorphisms of the gene encoding cytochrome P450 2A6(CYP2A6) and outcomes of S-1 plus oxaliplatin(SOX) chemotherapy treatment. Clinical data on 60 consecutive gastric cancer patients receiving SOX regimen were collected prospectively. We sequenced all exons of CYP2A6 and a total of 22 different polymorphisms were detected in the present study. Comprehensive analyses of these genetic polymorphisms were performed to determine their association with both safety and efficacy of SOX regimen. Our results showed that polymorphisms of CYP2A6 were associated with the safety and efficacy of SOX treatment. Among them, missense mutations CYP2A6 rs60823196 and rs138978736 could be possible risk factors(P < 0.05) for severe diarrhea induced by SOX, whereas CYP2A6 rs138978736 could be a conceivable predictor for overall survival of patients treated with SOX adjuvant chemotherapy. Further large-scale randomized prospective studies are warranted to confirm these findings. | Lin Yang Shanshan Zou Chang Shu Yan Song Yong-Kun Sun Wen Zhang Aiping Zhou Xinghua Yuan Yi Yang Songnian Hu | 2017 | Genomics, Proteomics & Bioinformatics2017，15，4： | 2 |
| 9 | A simple and efficient procedure for the synthesis of benzimidazoles using air as the oxidant显示文摘 | Lin Songnian Yang Lihu | | 0，，： | 1 |
| 10 | A simple and efficient procedure for the synthesis of benzimidazoles using air as the oxidant 显示文摘 | Lin Songnian Yang Lihu | 2005 | Tetrahedron Letters2005，46，： | 1 |
| 11 | 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://gffzz6ccd80d7270b40f2sf5vf0xuf9qk66qxx.ffgz.tsg.suse.edu.cn/projects/rgaat/and http://gffzz188fe103f8f1460asf5vf0xuf9qk66qxx.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 |
| 12 | Geographic information science in the era of geospatial big data: A cyberspace perspective显示文摘The advent of information and communication technology and the Internet of Things have led our society toward a digital era.The proliferation of personal computers,smartphones,intelligent autonomous sensors,and pervasive network interactions with individuals have gradually shifted human activities from offline to online and from in person to virtual.This transformation has brought a series of challenges in a variety of fields,such as the dilemma of placelessness,some aspects of timelessness(no time relevance),and the changing relevance of distance in the field of geographic information science(GIScience).In the last two decades,“cyber thinking”in GIScience has received significant attention from different perspectives.For instance,human activities in“cyberspace”need to be reconsidered when coupled with the geographic space to observe the first law of geography. | Xintao Liu Min Chen Christophe Claramunt Michael Batty Mei-Po Kwan Ahmad MSenousi Tao Cheng Josef Strobl Arzu Cöltekin John Wilson Temenoujka Bandrova Milan Konecny Paul MTorrens Fengyuan Zhang Li He Jinfeng Wang Carlo Ratti Olaf Kolditz Alexander Klippel Songnian Li Hui Lin Guonian Lu | 2022 | The Innovation2022，3，5： | 1 |
| 13 | A simple and efficient procedure for the synthesis ofbenzimidazoles using air as the oxidant显示文摘 | Lin Songnian Yang Lihu | 2005 | Tetrahedron Letters2005，46，： | 1 |
| 14 | A simple and efficient procedure for the\ssynthesis of benzimidazoles using air as the oxidant显示文摘 | Songnian Lin Lihu Yang | 2005 | Tetrahedron\sLetters2005，，46： | 1 |
| 15 | A simple and efficient procedure for the synthesis ofbenzimidazoles using air as the oxidant显示文摘 | Lin Songnian Yang Lihu | 2005 | Tetrahedron Letters[J]2005，46，： | 1 |
| 16 | The Association Between H3K4me3 and Antisense Transcription显示文摘Histone H3 lysine 4 trimethylation(H3K4me3) is well known to occur in the promoter region of genes for transcription activation.However,when investigating the H3K4me3 profiles in the mouse cerebrum and testis,we discovered that H3K4me3 also has a significant enrichment at the 3 0 end of actively transcribed(sense) genes,named as 3 0-H3K4me3.3 0-H3K4me3 is associated with 15% of protein-coding genes in both tissues.In addition,we examined the transcriptional initiation signals including RNA polymerase II(RNAPII) binding sites and 5 0-CAGE-tag that marks transcriptional start sites.Interestingly,we found that 3 0-H3K4me3 is associated with the initiation of antisense transcription.Furthermore,3 0-H3K4me3 modification levels correlate positively with the antisense expression levels of the associated sense genes,implying that 3 0-H3K4me3 is involved in the activation of antisense transcription.Taken together,our findings suggest that H3K4me3 may be involved in the regulation of antisense transcription that initiates from the 3 0 end of sense genes.In addition,a positive correlation was also observed between the expression of antisense and the associated sense genes with 3 0-H3K4me3 modification.More importantly,we observed the 3 0-H3K4me3 enrichment among genes in human,fruitfly and Arabidopsis,and found that the sequences of 3 0-H3K4me3-marked regions are highly conserved and essentially indistinguishable from known promoters in vertebrate.Therefore,we speculate that these 3 0-H3K4me3-marked regions may serve as potential promoters for antisense transcription and 3 0-H3K4me3 appear to be a universal epigenetic feature in eukaryotes.Our results provide a novel insight into the epigenetic roles of H3K4me3 and the regulatory mechanism of antisense transcription. | Peng Cui Wanfei Liu Yuhui Zhao Qiang Lin Feng Ding Chengqi Xin Jianing Geng Shuhui Song Fanglin Sun Songnian Hu Jun Yu | 2012 | Genomics, Proteomics & Bioinformatics2012，10，2： | 1 |
| 17 | Comparative Analyses of H3K4 and H3K27 Trimethylations Between the Mouse Cerebrum and Testis显示文摘The global features of H3K4 and H3K27 trimethylations(H3K4me3 and H3K27me3) have been well studied in recent years,but most of these studies were performed in mammalian cell lines.In this work,we generated the genome-wide maps of H3K4me3 and H3K27me3 of mouse cerebrum and testis using ChIP-seq and their high-coverage transcriptomes using ribominus RNA-seq with SOLiD technology.We examined the global patterns of H3K4me3 and H3K27me3 in both tissues and found that modifications are closely-associated with tissue-specific expression,function and development.Moreover,we revealed that H3K4me3 and H3K27me3 rarely occur in silent genes,which contradicts the findings in previous studies.Finally,we observed that bivalent domains,with both H3K4me3 and H3K27me3,existed ubiquitously in both tissues and demonstrated an invariable preference for the regulation of developmentally-related genes.However,the bivalent domains tend towards a 'winner-takes-all' approach to regulate the expression of associated genes.We also verified the above results in mouse ES cells.As expected,the results in ES cells are consistent with those in cerebrum and testis.In conclusion,we present two very important findings.One is that H3K4me3 and H3K27me3 rarely occur in silent genes.The other is that bivalent domains may adopt a 'winner-takes-all' principle to regulate gene expression. | Peng Cui Wanfei Liu Yuhui Zhao Qiang Lin Daoyong Zhang Feng Ding Chengqi Xin Zhang Zhang Shuhui Song Fanglin Sun Jun Yu Songnian Hu | 2012 | Genomics, Proteomics & Bioinformatics2012，10，2： | 1 |
| 18 | Adolescent Mouse Takes on An Active Transcriptomic Expression During Postnatal Cerebral Development显示文摘Postnatal cerebral development is a complicated biological process precisely controlled by multiple genes. To understand the molecular mechanism of cerebral development, we compared dynamics of mouse cerebrum transcriptome through three developmental stages using high-throughput RNA-seq technique. Three libraries were generated from the mouse cerebrum at infancy, adolescence and adulthood, respectively. Consequently, 44,557,729(infancy), 59,257,530(adolescence) and 72,729,636(adulthood) reads were produced, which were assembled into15,344, 16,048 and 15,775 genes, respectively. We found that the overall gene expression level increased from infancy to adolescence and decreased later on upon reaching adulthood. The adolescence cerebrum has the most active gene expression, with expression of a large number of regulatory genes up-regulated and some crucial pathways activated. Transcription factor(TF) analysis suggested the similar dynamics as expression pro?ling, especially those TFs functioning in neurogenesis differentiation, oligodendrocyte lineage determination and circadian rhythm regulation. Moreover, our data revealed a drastic increase in myelin basic protein(MBP)-coding gene expression in adolescence and adulthood, suggesting that the brain myelin may be generated sincemouse adolescence. In addition, differential gene expression analysis indicated the activation of rhythmic pathway, suggesting the function of rhythmic movement since adolescence; Furthermore,during infancy and adolescence periods, gene expression related to axon repulsion and attraction showed the opposite trends, indicating that axon repulsion was activated after birth, while axon attraction might be activated at the embryonic stage and declined during the postnatal development. Our results from the present study may shed light on the molecular mechanism underlying the postnatal development of the mammalian cerebrum. | Wei Xu Chengqi Xin Qiang Lin Feng Ding Wei Gong Yuanyuan Zhou Jun Yu Peng Cui Songnian Hu | 2014 | Genomics, Proteomics & Bioinformatics2014，12，3： | 0 |
| 19 | The Transcript-centric Mutations in Human Genomes显示文摘Since the human genome is mostly transcribed, genetic variations must exhibit sequence signatures reflecting the relationship between transcription processes and chromosomal structures as we have observed in unicellular or-ganisms. In this study, a set of 646 ubiquitous expression-invariable genes (EIGs) which are present in germline cells were defined and examined based on RNA-sequencing data from multiple high-throughput transcriptomic data. We demonstrated a relationship between gene expression level and transcript-centric mutations in the human genome based on single nucleotide polymorphism (SNP) data. A significant positive correlation was shown be-tween gene expression and mutation, where highly-expressed genes accumulate more mutations than low-ly-expressed genes. Furthermore, we found four major types of transcript-centric mutations: C→T, A→G, C→G, and G→T in human genomes and identified a negative gradient of the sequence variations aligning from the 5' end to the 3' end of the transcription units (TUs). The periodical occurrence of these genetic variations across TUs is associated with nucleosome phasing. We propose that transcript-centric mutations are one of the major driving forces for gene and genome evolution along with creation of new genes, gene/genome duplication, and horizontal gene transfer. | Peng Cui Qiang Lin Feng Ding Songnian Hu Jun Yu | 2012 | Genomics, Proteomics & Bioinformatics2012，10，1： | 0 |
| 20 | Optimal Model and Solution of Railway Hub Shift Working Plan显示文摘OptimalModelandSolutionofRailwayHubShiftWorkingPlanHeShiweiZhuSongnianLinBoliangDepartmentofTransportationEngineering,Southwe... | He Shiwei Zhu Songnian Lin Boliang Department of Transportation Engineering,Southwest Jiaotong University,Chengdu 610031,China | 1996 | Journal of Modern Transportation1996，13，2： | 0 |
您所在的机构暂未开通此部分的功能，请联系管理员