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| 1 | Low-dose quercetin positively regulates mouse healthspan显示文摘Dear Editor,Aging is the leading risk factor for many chronic diseases,accounting for almost 60%of all deaths worldwide.How to achieve healthy aging,alleviate aging-related diseases,and extend healthspan has become a main topic of biomedical research(He et al.,2019).Geroprotective compounds,such as metformin and rapamycin,have been shown to improve both healthspan and lifespan in mice(Martin-Montalvo et al.,2013;Bitto et al.,2016),whereas nicotinamide partially improves healthspan in mice(Mitchell et al.,2018). | Lingling Geng Zunpeng Liu Si Wang Shuhui Sun Shuai Ma Xiaoqian Liu Piu Chan Liang Sun Moshi Song Weiqi Zhang Guang-Hui Liu Jing Qu | 2019 | Protein & Cell2019，10，10： | 12 |
| 2 | Single-cell transcriptomic atlas of primate cardiopulmonary aging显示文摘Aging is a major risk factor for many diseases,especially in highly prevalent cardiopulmonary comorbidities and infectious diseases including Coronavirus Disease 2019(COVID-19).Resolving cellular and molecular mechanisms associated with aging in higher mammals is therefore urgently needed.Here,we created young and old non-human primate single-nucleus/cell transcriptomic atlases of lung,heart and artery,the top tissues targeted by SARS-CoV-2.Analysis of cell type-specific aging-associated transcriptional changes revealed increased systemic inflammation and compromised virus defense as a hallmark of cardiopulmonary aging.With age,expression of the SARS-CoV-2 receptor angiotensin-converting enzyme 2(ACE2)was increased in the pulmonary alveolar epithelial barrier,cardiomyocytes,and vascular endothelial cells.We found that interleukin 7(IL7)accumulated in aged cardiopulmonary tissues and induced ACE2 expression in human vascular endothelial cells in an NF-κB-dependent manner.Furthermore,treatment with vitamin C blocked IL7-induced ACE2 expression.Altogether,our findings depict the first transcriptomic atlas of the aged primate cardiopulmonary system and provide vital insights into age-linked susceptibility to SARS-CoV-2,suggesting that geroprotective strategies may reduce COVID-19 severity in the elderly. | Shuai Ma Shuhui Sun Jiaming Li Yanling Fan Jing Qu Liang Sun Si Wang Yiyuan Zhang Shanshan Yang Zunpeng Liu Zeming Wu Sheng Zhang Qiaoran Wang Aihua Zheng Shuguang Duo Yang Yu Juan Carlos Izpisua Belmonte Piu Chan Qi Zhou Moshi Song Weiqi Zhang Guang-Hui Liu | 2021 | Cell Research2021，31，4： | 10 |
| 3 | Modeling CADASIL vascular pathologies with patient-derived induced pluripotent stem cells显示文摘Cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy(CADASIL)is a rare hereditary cerebrovascular disease caused by a NOTCH3 mutation.However,the underlying cellular and molecular mechanisms remain unidentified.Here,we generated non-integrative induced pluripotent stem cells(iPSCs)from fibroblasts of a CADASIL patient harboring a heterozygous NOTCH3 mutation(c.3226C>T,p.R1076C).Vascular smooth muscle cells(VSMCs)differentiated from CADASIL-specific iPSCs showed gene expression changes associated with disease phenotypes,including activation of the NOTCH and NF-kB signaling pathway,cytoskeleton disorganization,and excessive cell proliferation.In comparison,these abnormalities were not observed in vascular endothelial cells(VECs)derived from the patients iPSCs.Importantly,the abnormal upregulation of NF-kB target genes in CADASIL VSMCs was diminished by a NOTCH pathway inhibitor,providing a potential therapeutic strategy for CADASIL.Overall,using this iPSCbased disease model,our study identified clues for studying the pathogenic mechanisms of CADASIL and developing treatment strategies for this disease. | Chen Ling Zunpeng Liu Moshi Song Weiqi Zhang Si Wang Xiaoqian Liu Shuai Ma Shuhui Sun Lina Fu Qun Chu Juan Carlos Izpisua Belmonte Zhaoxia Wang Jing Qu Yun Yuan Guang-Hui Liu | 2019 | Protein & Cell2019，10，4： | 7 |
| 4 | Telomere-dependent and telomereindependent roles of RAP1 in regulating human stem cell homeostasis显示文摘RAP1 is a well-known telomere-binding protein, but its functions in human stem cells have remained unclea匚 Here we generated RAP1 -deficient human embryonic stem cells (hESCs) by using CRISPR/Cas9 technique and obtained RAP1-deficient human mesenchymal stem cells (hMSCs) and neural stem cells (hNSCs) via directed differentiation. In both hMSCs and hNSCs, RAP1 not only negatively regulated telomere length but also acted as a transcriptional regulator of RELN by tuning the methylation status of its gene promoter. RAP1 deficiency enhanced self-renewal and delayed senescence in hMSCs, but not in hNSCs, suggesting complicated lineage-specific effects of RAP1 in adult stem cells.Altogether, these results demonstrate for the first time that RAP1 plays both telomeric and nontelomeric roles in regulating human stem cell homeostasis. | Xing Zhang Zunpeng Liu Xiaoqian Liu Si Wang Yiyuan Zhang Xiaojuan He Shuhui Sun Shuai Ma Ng Shyh-Chang Feng Liu Qiang Wang Xiaoqun Wang Lin Liu Weiqi Zhang Moshi Song Guang-Hui Liu Jing Qu | 2019 | Protein & Cell2019，10，9： | 7 |
| 5 | A MyD88-JAK1-STAT1 complex directly induces SOCS-1 expression in macrophages infected with Group A Streptococcus显示文摘一些病原体能使用表明 1 的 cytokine (SOCS-1 ) 的主人 suppressor,一个重要否定反馈的分子,有免疫力的避免的主要模式。这里,我们发现那个组 A 链球菌(气体) 能够在 RAW264.7 和 BMDM 巨噬细胞导致 SOCS-1 表示。IFN-β在由气体跟随 cytokine 表示的正式就职的巨噬细胞在导致气体的 SOCS-1 表示起一个作用,代表 SOCS-1 表示的古典小径。然而,当感染气体的房间与 anti-IFN-β 被孵化时,气体也导致了 STAT1 激活和 SOCS-1 表示;在这研究的 monoclonal 抗体。而且,在把 TLR4 −/− BMDM 巨噬细胞与作比较之上野类型(WT ) 房间,我们发现 TLR4 也在 SOCS-1 的正式就职起一个必要作用。MyD88,是为 TLR4 的适配器蛋白质,由与 Janus kinase 形成建筑群贡献 STAT1 激活和 phosphorylation 1 (JAK1 ) 并且信号变换器和在巨噬细胞的抄写 1 的使活跃之物(STAT1 ) 。而 JAK1 的表示是未受影响的, STAT1 的刺激气体的表示严重地在 MyD88 −/− 巨噬细胞被损害,建议 MyD88 涉及 STAT1 表示和 phosphorylation。一起,这些数据除了 IFN-β 表明了那;发信号并且 MyD88 复杂形成, JAK1 和 STAT1 在一条新奇小径行动直接在感染气体的巨噬细胞导致 SOCS-1 表示,它可能对快速的细菌的感染更导致。 | Jinghua Wu Cuiqing Ma Haixin Wang Shuhui Wu Gao Xue Xinli Shi Zhang Song Lin Wei | 2015 | Cellular & Molecular Immunology2015，12，3： | 5 |
| 6 | Whole Genome Analyses of Chinese Population and De Novo Assembly of A Northern Han Genome显示文摘To unravel the genetic mechanisms of disease and physiological traits,it requires comprehensive sequencing analysis of large sample size in Chinese populations.Here,we report the primary results of the Chinese Academy of Sciences Precision Medicine Initiative(CASPMI)project launched by the Chinese Academy of Sciences,including the de novo assembly of a northern Han reference genome(NH1.0)and whole genome analyses of 597 healthy people coming from most areas in China.Given the two existing reference genomes for Han Chinese(YH and HX1)were both from the south,we constructed NH1.0,a new reference genome from a northern individual,by combining the sequencing strategies of PacBio,10×Genomics,and Bionano mapping.Using this integrated approach,we obtained an N50 scaffold size of 46.63 Mb for the NH1.0 genome and performed a comparative genome analysis of NH1.0 with YH and HX1.In order to generate a genomic variation map of Chinese populations,we performed the whole-genome sequencing of 597 participants and identified 24.85 million(M)single nucleotide variants(SNVs),3.85 M small indels,and 106,382 structural variations.In the association analysis with collected phenotypes,we found that the T allele of rs1549293 in KAT8 significantly correlated with the waist circumference in northern Han males.Moreover,significant genetic diversity in MTHFR,TCN2,FADS1,and FADS2,which associate with circulating folate,vitamin B12,or lipid metabolism,was observed between northerners and southerners.Especially,for the homocysteine-increasing allele of rs1801133(MTHFR 677T),we hypothesize that there exists a “comfort”zone for a high frequency of 677T between latitudes of 35–45 degree North.Taken together,our results provide a high-quality northern Han reference genome and novel population-specific data sets of genetic variants for use in the personalized and precision medicine. | Zhenglin Du Liang Ma Hongzhu Qu Wei Chen Bing Zhang Xi Lu Weibo Zhai Xin Sheng Yongqiao Sun Wenjie Li Meng Lei Qiuhui Qi Na Yuan Shuo Shi Jingyao Zeng Jinyue Wang Yadong Yang Qi Liu Yaqiang Hong Lili Dong Zhewen Zhang Dong Zou Yanqing Wang Shuhui Song Fan Liu Xiangdong Fang Hua Chen Xin Liu Jingfa Xiao Changqing Zeng | 2019 | Genomics, Proteomics & Bioinformatics2019，17，3： | 4 |
| 7 | Discovery of β-Dihydroagarofuran-Type Sesquiterpenoids from the Leaves of Tripterygium wilfordii with Neuroprotective Activities显示文摘Nine undescribed dihydro-β-agarofuran sesquiterpenoid derivatives(1—9),along with a known analogue(10),were obtained from the leaves of Tripterygium wilfordii.Their gross structures were determined via extensive spectroscopic data,and the absolute configurations were elucidated by means of single-crystal X-ray diffraction analysis and electron circular dichroism(ECD)techniques,which include ECD exciton chirality,octant rule of saturated cyclohexanone and comparison between the experimental and calculated ECD spectra.All the isolated compounds were tested for their neuroprotective activities against H2O2-induced cell injury in human neuroblastoma SH-SY5Y cells.Compounds 5 and 6 improved cell viability by 16.15%and 15.12%compared with the H2O2 treated group at 25μmol·L^(-1),respectively. | Shuhui Dong Bin Lin Xiaobian Xue Ming Bai Xiaoxiao Huang Shaojiang Song | 2021 | Chinese Journal of Chemistry2021，39，2： | 4 |
| 8 | Rice Genomics: over the Past Two Decades and into the Future显示文摘Domestic rice(Oryza sativa L.) is one of the most important cereal crops, feeding a large number of worldwide populations. Along with various high-throughput genome sequencing projects, rice genomics has been making great headway toward direct ?eld applications of basic research advances in understanding the molecular mechanisms of agronomical traits and utilizing diverse germplasm resources. Here, we brie?y review its achievements over the past two decades and present the potential for its bright future. | Shuhui Song Dongmei Tian Zhang Zhang Songnian Hu Jun Yu | 2018 | Genomics, Proteomics & Bioinformatics2018，16，6： | 4 |
| 9 | Discovery,Identification and Comparative Analysis of Non-Specific Lipid Transfer Protein (nsLtp) Family in Solanaceae显示文摘Plant non-specific lipid transfer proteins (nsLtps) have been reported to be involved in plant defense activity against bacterial and fungal pathogens. In this study, we identified 135 (122 putative and 13 previously identified) Solanaceae nsLtps, which are clustered into 8 different groups. By comparing with Boutrot's nsLtp classification, we classified these eight groups into five types (I, II, IV, IX and X). We compared Solanaceae nsLtps with Arabidopsis and Gramineae nsLtps and found that (1) Types I, II and IV are shared by Solanaceae, Gramineae and Arabidopsis; (2) Types III, V, VI and VIII are shared by Gramineae and Arabidopsis but not detected in Solanaceae so far; (3) Type VII is only found in Gramineae whereas type IX is present only in Arabidopsis and Solanaceae; (4) Type X is a new type that accounts for 52.59% Solanaceae nsLtps in our data, and has not been reported in any other plant so far. We further built and compared the three-dimensional structures of the eight groups, and found that the major functional diversification within the nsLtp family could be predated to the monocot/dicot divergence, and many gene duplications and sequence variations had happened in the nsLtp family after the monocot/dicot divergence, especially in Solanaceae. | Wanfei Liu Dawei Huang Kan Liu Songnian Hu Jun Yu Gang Gao Shuhui Song | 2010 | Genomics, Proteomics & Bioinformatics2010，8，4： | 4 |
| 10 | The Global Landscape of SARS-CoV-2 Genomes, Variants, and Haplotypes in 2019nCoVR显示文摘On January 22,2020,China National Center for Bioinformation(CNCB)released the 2019 Novel Coronavirus Resource(2019nCoVR),an open-access information resource for the severe acute respiratory syndrome coronavirus 2(SARS-CoV-2).2019nCoVR features a comprehensive integration of sequence and clinical information for all publicly available SARS-CoV-2 isolates,which are manually curated with value-added annotations and quality evaluated by an automated in-house pipeline.Of particular note,2019nCoVR offers systematic analyses to generate a dynamic landscape of SARS-CoV-2 genomic variations at a global scale.It provides all identified variants and their detailed statistics for each virus isolate,and congregates the quality score,functional annotation,and population frequency for each variant.Spatiotemporal change for each variant can be visualized and historical viral haplotype network maps for the course of the outbreak are also generated based on all complete and high-quality genomes available.Moreover,2019nCoVR provides a full collection of SARS-CoV-2 relevant literature on the coronavirus disease 2019(COVID-19),including published papers from PubMed as well as preprints from services such as bioRxiv and medRxiv through Europe PMC.Furthermore,by linking with relevant databases in CNCB,2019nCoVR offers data submission services for raw sequence reads and assembled genomes,and data sharing with NCBI.Collectively,SARS-CoV-2 is updated daily to collect the latest information on genome sequences,variants,haplotypes,and literature for a timely reflection,making 2019nCoVR a valuable resource for the global research community.2019nCoVR is accessible at https://bigd.big.ac.cn/ncov/. | Shuhui Song Lina Ma Dong Zou Dongmei Tian Cuiping Li Junwei Zhu Meili Chen Anke Wang Yingke Ma Mengwei Li Xufei Teng Ying Cui Guangya Duan Mochen Zhang Tong Jin Chengmin Shi Zhenglin Du Yadong Zhang Chuandong Liu Rujiao Li Jingyao Zeng Lili Hao Shuai Jiang Hua Chen Dali Han Jingfa Xiao Zhang Zhang Wenming Zhao Yongbiao Xue Yiming Bao | 2020 | Genomics, Proteomics & Bioinformatics2020，18，6： | 4 |
| 11 | Deciphering primate retinal aging at single-cell resolution显示文摘Dear Editor, The retina is a light-sensitive highly-organized tissue,which is vulnerable to aging and age-related retinal diseases.Specifically,progressive retinal degeneration leads to visual function deterioration and vision impairment in the elderly(Lin et al.,2016).In diseases such as age-related macular degeneration(AMD),retinitis pigmentosa(RP)and diabetic retinopathy(DR),pathological process lacking effective treatments profoundly and negatively impact on the quality of life in the elderly(Lin et al.,2016;Chen et al.,2019).Thus,an in-depth molecular assessment of the mechanisms driv-ing retinal aging is of urgent scientific and medical importance. | Si Wang Yuxuan Zheng Qingqing Li Xiaojuan He Ruotong Ren Weiqi Zhang Moshi Song Huifang Hu Feifei Liu Guoqiang Sun Shuhui Sun Zunpeng Liu Yang Yu Piu Chan Guo-Guang Zhao Qi Zhou Guang-Hui Liu Fuchou Tang Jing Qu | 2021 | Protein & Cell2021，12，11： | 4 |
| 12 | Mobility in China,2020:a tale of four phases显示文摘2020 was an unprecedented year;with rapid and drastic changes in human mobility due to the COVID-19 pandemic.To understand the variation in commuting patterns among the Chinese population across stable and unstable periods,we used nationwide mobility data from 318 million mobile phone users in China to examine the extreme fluctuations of population movements in 2020,ranging from the Lunar New Year travel season(chunyun),to the exceptional calm of COVID-19 lockdown,and then to the recovery period.We observed that cross-city movements;which increased substantially in chunyun and then dropped sharply during the lockdown,are primarily dependent on travel distance and the socio-economic development of cities.Following the Lunar New Year holiday,national mobility remained low until mid-February,and COVID-19 interventions delayed more than 72.89 million people returning to large cities.Mobility network analysis revealed clusters of highly connected cities,conforming to the social-economic division of urban agglomerations in China.While the mass migration back to large cities was delayed,smaller cities connected more densely to form new clusters.During the recovery period after travel restrictions were lifted,the netflows of over 55%city pairs reversed in direction compared to before the lockdown.These findings offer the most comprehensive picture of Chinese mobility at fine resolution across various scenarios in China and are of critical importance for decision making regarding future public-health-emergency response,transportation planning and regional economic development,among others. | Suoyi Tan Shengjie Lai Fan Fang Ziqiang Cao Bin Sai Bing Song Bitao Dai Shuhui Guo Chuchu Liu Mengsi Cai Tong Wang Mengning Wang Jiaxu Li Saran Chen Shuo Qin Jessica R.Floyd Zhidong Cao Jing Tan Xin Sun Tao Zhou Wei Zhang Andrew J.Tatem Petter Holme Xiaohong Chen Xin Lu | 2021 | National Science Review2021，8，11： | 3 |
| 13 | Database Resources in BIG Data Center:Submission, Archiving, and Integration of Big Data in Plant Science显示文摘With the rapid advancement of sequencing technologies and the growing volume of omics data in plants, there is much anticipation in digging out the treasure from such big data and accordingly refining the current agricultural practice to be applied in the near future. Toward this end, database resources that deliver web services for plant omics data submission, archiving, and integration are urgently needed. As a part of Beijing Institute of Genomics (BIG) of the Chinese Academy of Sciences (CAS), BIG Data Center (http://bigd.big.ac.cn) provides open access to a suite of database resources (Table 1), with the aim of supporting plant research activities for domestic and international users in both academia and industry to translate big data into big discoveries (BIG Data Center Members, 2017;BIG Data Center Members, 2018;BIG Data Center Members, 2019). Here, we give a brief introduction of plant-related database resources in BIG Data Center and appeal to plant research com丒 munities to make full use of these resources for plant data submission, archiving, and integration. | Shuhui Song Zhang Zhang | 2019 | Molecular Plant2019，12，3： | 3 |
| 14 | Seroprevalence of SARS-CoV-2 infections among children visiting a hospital显示文摘Importance:In this study,we retrospectively investigated the seroprevalence of severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)antibodies within serum samples from children in Beijing,China.These findings provide preliminary guidance regarding population susceptibility to SARS-CoV-2,which will aid in establishing policy toward coronavirus disease 2019(COVID-19)prevention and control.Objective:To understand the seropositivity of anti-SARS-CoV-2 IgM/IgG antibodies among children in Beijing,China,evaluate the susceptibility of children in Beijing to SARS-CoV-2,and provide prima facie evidence to guide SARS-CoV-2 prevention and control.Methods:IgM/IgG antibody kits(colloidal gold)were used to conduct preliminary screening of SARS-CoV-2 IgM/IgG antibodies in serum samples of children who presented to Beijing Children’s Hospital,Capital Medical University,having fever or requiring hospitalization,from March 2020 to August 2020.Statistical analysis of anti-SARS-CoV-2 antibody seropositivity was performed according to the children’s general demographic characteristics,timing of admission to hospital,presence of pneumonia,and viral nucleic acid test results.Results:The study included 19797 children with both IgM and IgG antibody results.Twenty-four children had anti-SARS-CoV-2 IgM-positive results(positive rate of 1.2‰),twelve children had anti-SARS-CoV-2 IgG-positive results(positive rate of 0.6‰).Viral nucleic acid test results were negative for the above-mentioned children with positive antibody findings;during the study,two children exhibited positive viral nucleic acid test results,but their anti-SARS-CoV-2 IgM/IgG antibody results were negative.Anti-SARS-CoV-2 IgM antibody seropositivity was higher in the<1-year-old group than in the≥6-year-old group.The rates of anti-SARS-CoV-2 IgM seropositivity was highest in August from March to August;IgG results did not significantly differ over time.The rates of anti-SARS-CoV-2 IgM or IgG seropositivity among children with and without suspected pneumonia did not significantly differ between groups.Interpretation:During the study period,the rates of anti-SARS-CoV-2 IgM/IgG antibody seropositivity were low among children who presented to Beijing Children’s Hospital,Capital Medical University.The findings suggest that children in Beijing are generally susceptible to SARS-CoV-2 infection;COVID-19 prevention and control measures should be strengthened to prevent disease in children. | Ran Wang Fang Jin Shuhui Cao Hong Yuan Jingchen Qu Jiaqi Zhang Yuxuan Li Xiangpeng Chen Wenqi Song Zhengde Xie | 2020 | Pediatric Investigation2020，4，4： | 2 |
| 15 | An RNA-seq-based Gene Expression Profiling of Radiation-induced Tumorigenic Mammary Epithelial Cells显示文摘Immortality and tumorigenicity are two distinct characteristics of cancers. Immortalization has been suggested to precede tumorigenesis. To understand the molecular mechanisms of tumorigenicity and cancer progression in mammary epithelium, we established a tumorigenic cell model by means of heavy-ion radiation of an immortal cell model, which was created by overexpressing the human telomerase reverse transcriptase (hTERT) in normal human mammary epithelial cells. We examined the expression profile of this tumorigenic cell line (T_hMEC) using the hTERT-overexpressing immortal cell line (I_hMEC) as a control. In-depth RNA-seq data was generated by using the next-generation sequencing (NGS) platform (Life Technologies SOLiD3). We found that house-keeping (HK) and tissue-specific (TS) genes were differentially regulated during the tumorigenic process. HK genes tended to be activated while TS genes tended to be repressed. In addition, the HK genes and TS genes tended to contribute differentially to the variation of gene expression at different RPKM (gene expression in reads per exon kilobase per million mapped sequence reads) levels. Based on transcriptome analysis of the two cell lines, we defined 7053 differentially-expressed genes (DEGs) between immortality and tumorigenicity. Differential expression of 20 manually-selected genes was further validated using qRT-PCR. Our observations may help to further our understanding of cellular mechanism(s) in the transition from immortalization to tumorigenesis. | Lina Ma Linghu Nie Jing Liu Bing Zhang Shuhui Song Min Sun Jin Yang Yadong Yang Xiangdong Fang Songnian Hu Yongliang Zhao Jun Yu | 2012 | Genomics, Proteomics & Bioinformatics2012，10，6： | 2 |
| 16 | MPoxVR: A comprehensive genomic resource for monkeypox virus variant surveillance显示文摘Monkeypox is a viral zoonotic disease endemic in Central and West Africa.Since January 1,2022,3413 laboratory-confirmed monkeypox cases and one death have been reported from 50 countries/territories in five WHO regions(as of June 22,2022;https://www.who.int/emergencies/disease-outbreak-news/item/2022-DON396),and 1310 new cases and eight new countries have been reported in the past week.Genomic epidemiology is vital to determine the similarity between viruses and suggest possible links between cases,origins of infection,and transmission dynamics when combined with epidemiological information.However,one of the priority evidence gaps relating to the monkeypox outbreak is genome sequencing and in-host variation analysis.1 So,timely sharing both raw sequence data and consensus genomic data are useful to public health investigators and academic partners undertaking related studies. | Yingke Ma Meili Chen Yiming Bao Shuhui Song MPoxVR Team | 2022 | The Innovation2022，3，5： | 2 |
| 17 | Population Genetics of SARS-CoV-2: Disentangling Effects of Sampling Bias and Infection Clusters显示文摘A novel RNA virus,the severe acute respiratory syndrome coronavirus 2(SARS-CoV-2),is responsible for the ongoing outbreak of coronavirus disease 2019(COVID-19).Population genetic analysis could be useful for investigating the origin and evolutionary dynamics of COVID-19.However,due to extensive sampling bias and existence of infection clusters during the epidemic spread,direct applications of existing approaches can lead to biased parameter estimations and data misinterpretation.In this study,we first present robust estimator for the time to the most recent common ancestor(TMRCA)and the mutation rate,and then apply the approach to analyze 12,909 genomic sequences of SARS-CoV-2.The mutation rate is inferred to be 8.69×10^(−4) per site per year with a 95%confidence interval(CI)of[8.61×10^(−4),8.77×10^(−4)],and the TMRCA of the samples inferred to be Nov 28,2019 with a 95%CI of[Oct 20,2019,Dec 9,2019].The results indicate that COVID-19 might originate earlier than and outside of Wuhan Seafood Market.We further demonstrate that genetic polymorphism patterns,including the enrichment of specific haplotypes and the temporal allele frequency trajectories generated from infection clusters,are similar to those caused by evolutionary forces such as natural selection.Our results show that population genetic methods need to be developed to efficiently detangle the effects of sampling bias and infection clusters to gain insights into the evolutionary mechanism of SARS-CoV-2.Software for implementing VirusMuT can be downloaded at https://bigd.big.ac.cn/biocode/tools/BT007081. | Qi Liu Shilei Zhao Cheng-Min Shi Shuhui Song Sihui Zhu Yankai Su Wenming Zhao Mingkun Li Yiming Bao Yongbiao Xue Hua Chen | 2020 | Genomics, Proteomics & Bioinformatics2020，18，6： | 1 |
| 18 | Compositional Variability and Mutation Spectra of Monophyletic SARS-CoV-2 Clades显示文摘COVID-19 and its causative pathogen SARS-CoV-2 have rushed the world into a staggering pandemic in a few months,and a global fight against both has been intensifying.Here,we describe an analysis procedure where genome composition and its variables are related,through the genetic code to molecular mechanisms,based on understanding of RNA replication and its feedback loop from mutation to viral proteome sequence fraternity including effective sites on the replicase-transcriptase complex.Our analysis starts with primary sequence information,identity-based phylogeny based on 22,051 SARS-CoV-2 sequences,and evaluation of sequence variation patterns as mutation spectra and its 12 permutations among organized clades.All are tailored to two key mechanisms:strand-biased and function-associated mutations.Our findings are listed as follows:1)The most dominant mutation is C-to-U permutation,whose abundant second-codon-position counts alter amino acid composition toward higher molecular weight and lower hydrophobicity,albeit assumed most slightly deleterious.2)The second abundance group includes three negative-strand mutations(U-to-C,A-to-G,and G-to-A)and a positive-strand mutation(G-to-U)due to DNA repair mechanisms after cellular abasic events.3)A clade-associated biased mutation trend is found attributable to elevated level of negative-sense strand synthesis.4)Within-clade permutation variation is very informative for associating non-synonymous mutations and viral proteome changes.These findings demand a platform where emerging mutations are mapped onto mostly subtle but fast-adjusting viral proteomes and transcriptomes,to provide biological and clinical information after logical convergence for effective pharmaceutical and diagnostic applications.Such actions are in desperate need,especially in the middle of the War against COVID-19. | Xufei Teng Qianpeng Li Zhao Li Yuansheng Zhang Guangyi Niu Jingfa Xiao Jun Yu Zhang Zhang Shuhui Song | 2020 | Genomics, Proteomics & Bioinformatics2020，18，6： | 1 |
| 19 | MeRIP-PF:An Easy-to-use Pipeline for High-resolution Peak-finding in MeRIP-Seq Data显示文摘RNA modifications, especially methylation of the N6 position of adenosine (A)--m 6A, represent an emerging research frontier in RNA biology. With the rapid development of high-throughput sequencing technology, in-depth study of m 6A distribution and function relevance becomes feasible. However, a robust method to effectively identify m 6A-modified regions has not been available yet. Here, we present a novel high-efficiency and user-friendly analysis pipeline called MeRIP-PF for the signal identification of MeRIP-Seq data in reference to controls. MeRIP-PF provides a statistical P-value for each identified m 6A region based on the difference of read distribution when compared to the controls and also calculates false discovery rate (FDR) as a cut off to differentiate reliable m 6A regions from the background. Furthermore, MeRIP-PF also achieves gene annotation of m 6A signals or peaks and produce outputs in both XLS and graphical format, which are useful for further study. MeRIP-PF is implemented in Perl and is freely available at http://software.big.ac.cn/MeRIP-PF.html. | Yuli Li Shuhui Song Cuiping Li Jun Yu | 2013 | Genomics, Proteomics & Bioinformatics2013，11，1： | 1 |
| 20 | Preparation and adsorption properties of chelating resins containing 3-aminopyridine and hydrophilic spacer arms for Hg(Ⅱ)显示文摘 | Chunnuan Ji Shuhui Song Chunrong Wang | 2010 | Chemical Engineering Journal2010，165，2： | 1 |
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