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| 1 | GSA:Genome Sequence Archive显示文摘With the rapid development of sequencing technologies towards higher throughput and lower cost, sequence data are generated at an unprecedentedly explosive rate. To provide an efficient and easy-to-use platform for managing huge sequence data, here we present Genome Sequence Archive(GSA; http://bigd.big.ac.cn/gsa or http://gsa.big.ac.cn), a data repository for archiving raw sequence data. In compliance with data standards and structures of the International Nucleotide Sequence Database Collaboration(INSDC), GSA adopts four data objects(Bio Project, Bio Sample,Experiment, and Run) for data organization, accepts raw sequence reads produced by a variety of sequencing platforms, stores both sequence reads and metadata submitted from all over the world,and makes all these data publicly available to worldwide scientific communities. In the era of big data, GSA is not only an important complement to existing INSDC members by alleviating the increasing burdens of handling sequence data deluge, but also takes the significant responsibility for global big data archive and provides free unrestricted access to all publicly available data in support of research activities throughout the world. | Yanqing Wang Fuhai Song Junwei Zhu Sisi Zhang Yadong Yang Tingting Chen Bixia Tang Lili Dong Nan Ding Qian Zhang Zhouxian Bai Xunong Dong Huanxin Chen Mingyuan Sun Shuang Zhai Yubin Sun Lei Yu Li Lan Jingfa Xiao Xiangdong Fang Hongxing Lei Zhang Zhang Wenming Zhao | 2017 | Genomics, Proteomics & Bioinformatics2017，15，1： | 13 |
| 2 | Timing and splitting of nitrogen fertilizer supply to increase crop yield and efficiency of nitrogen utilization in a wheat–peanut relay intercropping system in China显示文摘Agronomically optimizing the timing and rates of nitrogen(N) fertilizer application can increase crop yield and decrease N loss to the environment. Wheat(Triticum aestivum L.)–peanut(Arachis hypogaea L.) relay intercropping systems are a mainstay of economic and food security in China. We performed a field experiment to investigate the effects of N fertilizer on N recovery efficiency, crop yield, and N loss rate in wheat–peanut relay intercropping systems in the Huang-Huai-Hai Plain, China during 2015–2017. The N was applied on the day before sowing, the jointing stage(G30) or the booting stage(G40) of winter wheat, and the anthesis stage(R1) of peanut in the following percentage splits: 50-50-0-0(N1), 35-35-0-30(N2), and 35-0-35-30(N3), using 300 kg N ha-1, with 0 kg N ha-1(N0) as control. ^(15)N-labeled(20.14 atom %) urea was used to trace the fate of N in microplots. The yields of wheat and peanut increased by 12.4% and 15.4% under the N2 and N3 treatments, relative to those under the N1 treatment. The ^(15)N recovery efficiencies( ^(15)NRE) were 64.9% and 58.1% for treatments N2 and N3, significantly greater than that for the N1 treatment(45.3%). The potential N loss rates for the treatments N2 and N3 were23.7% and 7.0%, significantly lower than that for treatment N1(30.1%). Withholding N supply until the booting stage(N3) did not reduce the wheat grain yield; however, it increased the N content derived from ^(15)N-labeled urea in peanuts, promoted the distribution of ^(15)N to pods, and ultimately increased pod yields in comparison with those obtained by topdressing N at jointing stage(N2). In comparison with N2, the N uptake and N recovery efficiency(NRE) of N3 was increased by 12.0% and 24.1%,respectively, while the apparent N loss decreased by 16.7%. In conclusion, applying N fertilizer with three splits and delaying topdressing fertilization until G40 of winter wheat increased total grain yields and NRE and reduced N loss. This practice could be an environment-friendly N management strategy for wheat–peanut relay intercropping systems in China. | Zhaoxin Liu Fang Gao Yan Liu Jianqun Yang Xiaoyu Zhen Xinxin Li Ying Li Jihao Zhao Jinrong Li Bichang Qian Dongqing Yang Xiangdong Li | 2019 | The Crop Journal2019，7，1： | 12 |
| 3 | First dark matter search results from the PandaX-Ⅰ experiment显示文摘We report on the first dark-matter(DM)search results from PandaX-I,a low threshold dual-phase xenon experiment operating at the China JinPing Underground Laboratory.In the 37-kg liquid xenon target with 17.4 live-days of exposure,no DM particle candidate event was found.This result sets a stringent limit for low-mass DM particles and disfavors the interpretation of previously-reported positive experimental results.The minimum upper limit,3.7×10-44cm2,for the spin-independent isoscalar DM-particle-nucleon scattering cross section is obtained at a DM-particle mass of 49 GeV/c2at 90%confidence level. | XIAO MengJiao XIAO Xiang ZHAO Li CAO XiGuang CHEN Xun CHEN YunHua CUI XiangYi FANG DeQing FU ChangBo GIBONI Karl L. GONG HaoWei GUO GuoDong HU Jie HUANG XingTao JI XiangDong JU YongLin LEI SiAo LI ShaoLi LIN Qing LIU HuaXuan LIU JiangLai LIU Xiang LORENZON Wolfgang MA YuGang MAO YaJun NI KaiXuan PUSHKIN Kirill REN XiangXiang SCHUBNELL Michael SHEN ManBing STEPHENSON Scott TAN AnDi TARL Greg WANG HongWei WANG JiMin WANG Meng WANG XuMing WANG Zhou WEI YueHuan WU ShiYong XIE PengWei YOU YingHui ZENG XiongHui ZHANG Hua ZHANG Tao ZHU ZhongHua | 2014 | Science China(Physics,Mechanics & Astronomy)2014，57，11： | 10 |
| 4 | PandaX: a liquid xenon dark matter experiment at CJPL显示文摘PandaX is a large liquid-xenon detector experiment usable for direct dark-matter detection and 136Xe double-beta decay search.The central vessel was designed to accommodate a staged target volume increase from initially 120 kg(stage I)to 0.5 t(stage II)and eventually to a multi-ton scale.The experiment is located in the Jinping Deep-Underground Laboratory in Sichuan,China.The detector operates in dual-phase mode,allowing detection of both prompt scintillation,and ionization charge through proportional scintillation.In this paper a detailed description of the stage I detector design and performance as well as results established during the commissioning phase are presented. | CAO XiGuang CHEN Xun CHEN YunHua CUI XiangYi FANG DeQing FU ChangBo GIBONI Karl L. GONG HaoWei GUO GuoDong HE Ming HU Jie HUANG XingTao JI XiangDong JU YongLin LI ShaoLi LIN Qing LIU HuaXuan LIU JiangLai LIU Xiang LORENZON Wolfgang MA YuGang MAO YaJun NI KaiXuan PUSHKIN Kirill REN XiangXiang SCHUBNELL Michael SHEN ManBing SHI YuJie STEPHENSON Scott TAN AnDi TARLé Greg WANG HongWei WANG JiMing WANG Meng WANG XuMing WANG Zhou WEI YueHuan WU ShiYong XIAO MengJiao XIAO Xiang XIE PengWei YE Tao YOU YingHui ZEN XiongHui ZHANG Hua ZHANG Tao ZHAO HaiYing ZHAO Li ZHOU XiaoPeng ZHU ZhongHua | 2014 | Science China(Physics,Mechanics & Astronomy)2014，57，8： | 9 |
| 5 | A Brief Review on the Human Encyclopedia of DNA Elements (ENCODE) Project显示文摘The ENCyclopedia Of DNA Elements (ENCODE) project is an international research consortium that aims to identify all functional elements in the human genome sequence. The second phase of the project comprised 1640 datasets from 147 different cell types, yielding a set of 30 publications across several journals. These data revealed that 80.4% of the human genome displays some functionality in at least one cell type. Many of these regulatory elements are physically associated with one another and further form a network or three-dimensional conformation to affect gene expression. These elements are also related to sequence variants associated with diseases or traits. All these findings provide us new insights into the organization and regulation of genes and genome, and serve as an expansive resource for understanding human health and disease. | Hongzhu Qu Xiangdong Fang | 2013 | Genomics, Proteomics & Bioinformatics2013，11，3： | 7 |
| 6 | Global transcriptome analysis for identification of interactions between coding and noncoding RNAs during human erythroid differentiation显示文摘在 erythroid 开发期间编码基因, miRNAs,和 lncRNAs 上的研究在最近的年里被执行了。然而,集中于三种 RNA 类型的集成的分析还得被做。在现在的学习,我们比较了编码基因, miRNA,和 lncRNA 表示侧面的动力学。为了在在 transcriptome 控制这些变化的红血球生成和潜在的机制探索动态变化,铺平,我们利用了定序技术从绳索血获得 transcriptome 数据的高产量造血的干细胞和下列四个 erythroid 区别阶段,以及从成熟的红血房间。结果显示 lncRNAs 为 erythroid 区别正在答应房间标记候选人。聚类分析分类差别表示基因进在 stemness 维护期间对应于动态变化的四种子类型,中间区别,并且成熟。综合分析揭示了 RNA 潜在地参予了控制血细胞成熟的那 noncoding,并且特别与到氧种类和 DNA 损坏的 heme 新陈代谢和回答联系了。这些规章的相互作用在一个全面网络,在 RNA 之间的从而推断的关联和他们的联系功能被显示。这些数据为正常红血球生成的学习提供了一个大量的资源,它将允许 erythroid 开发的进一步的调查和理解并且获得 erythroid 混乱。 | Nan Ding Jiafei Xi Yanming Li Xiaoyan Xie Jian Shi Zhaojun Zhang Yanhua Li Fang Fang Sihan Wang Wen Yue Xuetao Pei Xiangdong Fang | 2016 | Frontiers of Medicine2016，10，3： | 6 |
| 7 | Characterization of miRNomes in Acute and Chronic Myeloid Leukemia Cell Lines显示文摘Myeloid leukemias are highly diverse diseases and have been shown to be associated with microRNA(miRNA) expression aberrations. The present study involved an in-depth miRNome analysis of two human acute myeloid leukemia(AML) cell lines, HL-60 and THP-1, and one human chronic myeloid leukemia(CML) cell line, K562, via massively parallel signature sequencing. mRNA expression profiles of these cell lines that were established previously in our lab facilitated an integrative analysis of miRNA and mRNA expression patterns. miRNA expression profiling followed by differential expression analysis and target prediction suggested numerous miRNA signatures in AML and CML cell lines. Some miRNAs may act as either tumor suppressors or oncomiRs in AML and CML by targeting key genes in AML and CML pathways. Expression patterns of cell type-specific miRNAs could partially reflect the characteristics of K562, HL-60 and THP-1 cell lines, such as actin filament-based processes, responsiveness to stimulus and phagocytic activity. miRNAs may also regulate myeloid differentiation, since they usually suppress differentiation regulators. Our study provides a resource to further investigate the employment of miRNAs in human leukemia subtyping, leukemogenesis and myeloid development. In addition, the distinctive miRNA signatures may be potential candidates for the clinical diagnosis, prognosis and treatment of myeloid leukemias. | Qian Xiong Yadong Yang Hai Wang Jie Li Shaobin Wang Yanming Li Yaran Yang Kan Cai Xiuyan Ruan Jiangwei Yan Songnian Hu Xiangdong Fang | 2014 | Genomics, Proteomics & Bioinformatics2014，12，2： | 6 |
| 8 | Dark matter direct search sensitivity of the PandaX-4T experiment显示文摘The Panda X-4T experiment, a 4-ton scale dark matter direct detection experiment, is being planned at the China Jinping Underground Laboratory. In this paper we present a simulation study of the expected background in this experiment. In a 2.8-ton fiducial mass and the signal region between 1-10 keV electron equivalent energy, the total electron recoil background is found to be 4.9 × 10^(-5) kg^(-1) d^(-1) keV^(-1). The nuclear recoil background in the same region is 2.8 × 10^(-7) kg^(-1) d^(-1) keV^(-1). With an exposure of 5.6 ton-years, the sensitivity of Panda X-4 T could reach a minimum spin-independent dark matter-nucleon cross section of 6 × 10^(-48) cm^2 at a dark matter mass of 40 Ge V/c^2. | HongGuang Zhang Abdusalam Abdukerim Wei Chen Xun Chen YunHua Chen XiangYi Cui BinBin Dong DeQing Fang ChangBo Fu Karl Giboni Franco Giuliani LinHui Gu XuYuan Guo ZhiFan Guo Ke Han ChangDa He ShengMing He Di Huang XingTao Huang Zhou Huang Peng Ji XiangDong Ji YongLin Ju ShaoLi Li Yao Li Heng Lin HuaXuan Liu JiangLai Liu YuGang Ma YaJun Mao KaiXiang Ni JinHua Ning XiangXiang Ren Fang Shi AnDi Tan AnQing Wang Cheng Wang HongWei Wang Meng Wang QiuHong Wang SiGuang Wang XiuLi Wang XuMing Wang Zhou Wang MengMeng Wu ShiYong Wu JingKai Xia MengJiao Xiao PengWei Xie BinBin Yan JiJun Yang Yong Yang ChunXu Yu JuMin Yuan JianFeng Yue Dan Zhang Tao Zhang Li Zhao QiBin Zheng JiFang Zhou Ning Zhou XiaoPeng Zhou | 2019 | Science China(Physics,Mechanics & Astronomy)2019，62，3： | 6 |
| 9 | 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 |
| 10 | The Tibetan Plateau Surface–Atmosphere Coupling System and Its Weather and Climate Effects: The Third Tibetan Plateau Atmospheric Science Experiment显示文摘The Tibetan Plateau(TP) is a key area affecting forecasts of weather and climate in China and occurrences of extreme weather and climate events over the world. The China Meteorological Administration, the National Natural Science Foundation of China, and the Chinese Academy of Sciences jointly initiated the Third Tibetan Plateau Atmospheric Science Experiment(TIPEX-Ⅲ) in 2013, with an 8–10-yr implementation plan. Since its preliminary field measurements conducted in 2013, routine automatic sounding systems have been deployed at Shiquanhe, Gaize, and Shenzha stations in western TP, where no routine sounding observations were available previously. The observational networks for soil temperature and soil moisture in the central and western TP have also been established. Meanwhile, the plateau-scale and regional-scale boundary layer observations, cloud–precipitation microphysical observations with multiple radars and aircraft campaigns, and tropospheric–stratospheric air composition observations at multiple sites, were performed. The results so far show that the turbulent heat exchange coefficient and sensible heat flux are remarkably lower than the earlier estimations at grassland, meadow, and bare soil surfaces of the central and western TP. Climatologically, cumulus clouds over the main body of the TP might develop locally instead of originating from the cumulus clouds that propagate northward from South Asia. The TIPEX-Ⅲ observations up to now also reveal diurnal variations, macro-and microphysical characteristics, and water-phase transition mechanisms, of cumulus clouds at Naqu station. Moreover, TIPEX-Ⅲ related studies have proposed a maintenance mechanism responsible for the Asian 'atmospheric water tower' and demonstrated the effects of the TP heating anomalies on African, Asian, and North American climates. Additionally, numerical modeling studies show that the Γ distribution of raindrop size is more suitable for depicting the TP raindrop characteristics compared to the M–P distribution, the overestimation of sensible heat flux can be reduced via modifying the heat transfer parameterization over the TP, and considering climatic signals in some key areas of the TP can improve the skill for rainfall forecast in the central and eastern parts of China. Furthermore, the TIPEX-Ⅲ has been promoting the technology in processing surface observations, soundings, and radar observations, improving the quality of satellite retrieved soil moisture and atmospheric water vapor content products as well as high-resolution gauge–radar–satellite merged rainfall products, and facilitating the meteorological monitoring, forecasting, and data sharing operations. | Ping ZHAO Yueqing LI Xueliang GUO Xiangde XU Yimin LIU Shihao TANG Wenming XIAO Chunxiang SHI Yaoming MA Xing YU Huizhi LIU La JIA Yun CHEN Yanju LIU Jian LI Dabiao LUO Yunchang CAO Xiangdong ZHENG Junming CHEN An XIAO Fang YUAN Donghui CHEN Yang PANG Zhiqun HU Shengjun ZHANG Lixin DONG Juyang HU Shuai HAN Xiuji ZHOU | 2019 | Journal of Meteorological Research2019，33，3： | 4 |
| 11 | Wheat breeding history reveals synergistic selection of pleiotropic genomic sites for plant architecture and grain yield显示文摘Diversity surveys of crop germplasm are important for gaining insights into the genomic basis for plant architecture and grain yield improvement,which is still poorly understood in wheat.In this study,we exome sequenced 287 wheat accessions that were collected in the past 100 years.Population genetics analysis identified that 6.7%of the wheat genome falls within the selective sweeps between landraces and cultivars,which harbors the genes known for yield improvement.These regions were asymmetrically distributed on the A and B subgenomes with regulatory genes being favorably selected.Genome-wide association study(GWAS)identified genomic loci associated with traits for yield potential,and two underlying genes,TaARF12 encoding an auxin response factor and TaDEP1 encoding the G-proteinγ-subunit,were located and characterized to pleiotropically regulate both plant height and grain weight.Elite single-nucleotide haplotypes with increased allele frequency in cultivars relative to the landraces were identified and found to have accumulated over the course of breeding.Interestingly,we found that TaARF12 and TaDEP1 function in epistasis with the classical plant height Rht-1 locus,leading to propose a“Green Revolution”-based working model for historical wheat breeding.Collectively,our study identifies selection signatures that fine-tune the gibberellin pathway during modern wheat breeding and provides a wealth of genomic diversity resources for the wheat research community. | Aili Li Chenyang Hao Zhenyu Wang Shuaifeng Geng Meiling Jia Fang Wang Xiang Han Xingchen Kong Lingjie Yin Shu Tao Zhongyin Deng Ruyi Liao Guoliang Sun Ke Wang Xingguo Ye Chengzhi Jiao Hongfeng Lu Yun Zhou Dengcai Liu Xiangdong Fu Xueyong Zhang Long Mao | 2022 | Molecular Plant2022，15，3： | 4 |
| 12 | Identification of HSC/MPP expansion units in fetal liver by single-cell spatiotemporal transcriptomics显示文摘Limited knowledge of cellular and molecular mechanisms underlying hematopoietic stem cell and multipotent progenitor(HSC/MPP)expansion within their native niche has impeded the application of stem cell-based therapies for hematological malignancies.Here,we constructed a spatiotemporal transcriptome map of mouse fetal liver(FL)as a platform for hypothesis generation and subsequent experimental validation of novel regulatory mechanisms.Single-cell transcriptomics revealed three transcriptionally heterogeneous HSC/MPP subsets,among which a CD93-enriched subset exhibited enhanced stem cell properties.Moreover,by employing integrative analysis of single-cell and spatial transcriptomics,we identified novel HSC/MPP‘pocket-like’units(HSC PLUS),composed of niche cells(hepatoblasts,stromal cells,endothelial cells,and macrophages)and enriched with growth factors.Unexpectedly,macrophages showed an 11-fold enrichment in the HSC PLUS.Functionally,macrophage-HSC/MPP co-culture assay and candidate molecule testing,respectively,validated the supportive role of macrophages and growth factors(MDK,PTN,and IGFBP5)in HSC/MPP expansion.Finally,cross-species analysis and functional validation showed conserved cell-cell interactions and expansion mechanisms but divergent transcriptome signatures between mouse and human FL HSCs/MPPs.Taken together,these results provide an essential resource for understanding HSC/MPP development in FL,and novel insight into functional HSC/MPP expansion ex vivo. | Suwei Gao Qiang Shi Yifan Zhang Guixian Liang Zhixin Kang Baofeng Huang Dongyuan Ma Lu Wang Jianwei Jiao Xiangdong Fang Cheng-Ran Xu Longqi Liu Xun Xu Berthold Gottgens Cheng Li Feng Liu | 2022 | Cell Research2022，32，1： | 4 |
| 13 | MS1 is essential for male fertility by regulating the microsporocyte cell plate expansion in soybean显示文摘Male sterility is an essential trait in hybrid seed production,especially for monoclinous and autogamous food crops.Soybean male-sterile ms1 mutant has been known for more than 50 years and could be instrumental in making hybrid seeds.However,the gene responsible for the male-sterile phenotype has remained unknown.Here,we report the map-based cloning and characterization of the MS1 gene in soybean.MS1 encodes a kinesin protein and localizes to the nucleus,where it is required for the male meiotic cytokinesis after telophase Ⅱ.We further substantiated that MS1 colocalizes with microtubules and is essential for cell plate formation in soybean male gametogenesis through immunostaining.Both ms1 and CRISPR/Cas9 knockout mutants show complete male sterility but are otherwise phenotypically normal,making them perfect tools for producing hybrid seeds.The identification of MS1 has the practical potential for assembling the sterility system and speeding up hybrid soybean breeding. | Xiaolong Fang Xiaoyuan Sun Xiangdong Yang Qing Li Chunjing Lin Jie Xu Wenjun Gong Yifan Wang Lu Liu Limei Zhao Baohui Liu Jun Qin Mengchen Zhang Chunbao Zhang Fanjiang Kong Meina Li | 2021 | Science China(Life Sciences)2021，64，9： | 4 |
| 14 | Effects of the Different Supports on the Activity and Selectivity of Iron-Cobalt Bimetallic Catalyst for Fischer-Tropsch Synthesis显示文摘硅石,氧化铝,和活性炭支持了铁钴催化剂被早期的湿受精准备。这些催化剂被赌注, X 射线衍射(XRD ) ,和规划温度的减小(TPR ) 描绘了。为公司加氢在不同搬运人上支持的铁钴的活动和选择在 1.5 MPa 的条件下面被学习, 493 K, 630 h (? 1 ) ,并且 1.6 的 H2/CO 比率。结果显示这项活动, C4 olefin/(C4 olefin+C4 石蜡) 在 Fe-Co/SiO2, Fe-Co/AC1, Fe-Co/A12O3 和 Fe-Co/AC2 的顺序的比率,和 C5 olefin/(C5 olefin+C5 石蜡) 减少。Fe-Co/SiO2 的活动到达了最大值。TPR 的结果证明 Fe-Co/SiO2 催化剂,到某程度不同。XRD 模式证明 Fe-Co/SiO2 催化剂与其它显著地不同;它有二衍射峰。活跃尖晶石阶段与支持被相关。给词调音:Fischer-Tropsch;二金属的催化剂;铁;钴;支持;硅石;氧化铝;活性炭; | Xiangdong Ma Qiwen Sun Fahai Cao Weiyong Ying Dingye Fang | 2006 | Journal of Natural Gas Chemistry2006，15，4： | 3 |
| 15 | Databases and Web Tools for Cancer Genomics Study显示文摘Publicly-accessible resources have promoted the advance of scientific discovery. The era of genomics and big data has brought the need for collaboration and data sharing in order to make effective use of this new knowledge. Here, we describe the web resources for cancer genomics research and rate them on the basis of the diversity of cancer types, sample size, omics data comprehensiveness, and user experience. The resources reviewed include data repository and analysis tools; and we hope such introduction will promote the awareness and facilitate the usage of these resources in the cancer research community. | Yadong Yang Xunong Dong Bingbing Xie Nan Ding Juan Chen Yongjun Li Qian Zhang Hongzhu Qu Xiangdong Fang | 2015 | Genomics, Proteomics & Bioinformatics2015，13，1： | 3 |
| 16 | Effects of the ratio of Fe to Co over Fe-Co/SiO_2 bimetallic catalysts on their catalytic performance for Fischer-Tropsch synthesis显示文摘The Fe-Co/SiO2 bimetallic catalysts with different ratios of Fe to Co were prepared by aqueous incipient wetness impregnation. The catalysts of 10%Fe:0%Co/SiO2, 10%Fe:6%Co/SiO2, 10%Fe:2%Co/SiO2, 10%Fe:10%Co/SiO2, 6%Fe:10%Co/SiO2, 2%Fe:10%Co/SiO2 and 0%Fe: 10%Co/SiO2 by mass were tested in a fixed reactor by the Fischer-Tropsch synthesis. Activity and hydrocarbon distribution were found to be determined by the ratio of iron to cobalt of the catalysts. Higher iron content inhibited the activity, whereas higher cobalt content enhanced the activity of the Fe-Co/SiO2 catalysts. On the other hand, for the catalysts of 10%Fe:6%Co/SiO2, 10%Fe:10%Co/SiO2, 6%Fe:10%Co/SiO2, and 2%Fe:10%Co/SiO2, the total C2-C4 fraction increased (from 10.65% to 26.78%) and C5+ fraction decreased (from 75.75% to 57.63%) at 523 K. Temperature programmed reduction revealed that the addition of cobalt enhanced the reducibility of the Fe-Co/SiO2 catalyst. Metal oxides were present in those catalysts as shown by XRD. The Fe-Co alloy phase was found in the 2%Fe:10%Co/SiO2, 6%Fe:10%Co/SiO2, 10%Fe:10%Co/SiO2, 10%Fe:6%Co/SiO2 catalysts and their crystals were perfect. | Xiangdong Ma Qiwen Sun Weiyong Ying Dingye Fang | 2009 | Journal of Natural Gas Chemistry2009，18，2： | 2 |
| 17 | Effects of promoters on catalytic performance of Fe-Co/SiO_2 catalyst for Fischer-Tropsch synthesis显示文摘2%Fe-10%Co/SiO2 catalysts with different potassium or zirconium loadings were prepared by aqueous incipient wetness impregnation and tested for Fischer-Tropsch synthesis in a flow reactor, using H2/CO = 1.6 (molar ratio) in the feed, under the condition of an overall pressure of 1 MPa, GHSV of 600 h-1 and temperature of 503 K. The zirconium and potassium promoters remarkably influenced hydrocarbon distribution of the products. CO conversion increased on the catalysts with the increase of zirconium loadings, which indicated that zirconium enhanced the activity of iron-cobalt catalysts. Low potassium loadings also enhanced the activity of the catalysts. However, high potassium loading made CO conversion on the catalysts decrease and weakened the secondary hydrogenations. The catalyst was characterized by BET, XRD and TPR. The catalyst characterization revealed that the Co3O4 phase was presented on the fresh catalyst, whereas the spinel phase of Fe-Co alloy and CoO existed on the used catalyst. | Xiangdong Ma Qiwen Sun Weiyong Ying Dingye Fang | 2009 | Journal of Natural Gas Chemistry2009，18，3： | 2 |
| 18 | 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 |
| 19 | Mapping Human Pluripotent Stem Cell-derived Erythroid Differentiation by Single-cell Transcriptome Analysis显示文摘There is an imbalance between the supply and demand of functional red blood cells(RBCs)in clinical applications.This imbalance can be addressed by regenerating RBCs using several in vitro methods.Induced pluripotent stem cells(iPSCs)can handle the low supply of cord blood and the ethical issues in embryonic stem cell research,and provide a promising strategy to eliminate immune rejection.However,no complete single-cell level differentiation pathway exists for the iPSC-derived erythroid differentiation system.In this study,we used iPSC line BC1 to establish a RBC regeneration system.The 10X Genomics single-cell transcriptome platform was used to map the cell lineage and differentiation trajectory on day 14 of the regeneration system.We observed that iPSC differentiation was not synchronized during embryoid body(EB)culture.The cells(on day 14)mainly consisted of mesodermal and various blood cells,similar to the yolk sac hematopoiesis.We identified six cell classifications and characterized the regulatory transcription factor(TF)networks and cell-cell contacts underlying the system.iPSCs undergo two transformations during the differentiation trajectory,accompanied by the dynamic expression of cell adhesion molecules and estrogen-responsive genes.We identified erythroid cells at different stages,such as burst-forming unit erythroid(BFU-E)and orthochromatic erythroblast(ortho-E)cells,and found that the regulation of TFs(e.g.,TFDP1 and FOXO3)is erythroid-stage specific.Immune erythroid cells were identified in our system.This study provides systematic theoretical guidance for optimizing the iPSC-derived erythroid differentiation system,and this system is a useful model for simulating in vivo hematopoietic development and differentiation. | Zijuan Xin Wei Zhang Shangjin Gong Junwei Zhu Yanming Li Zhaojun Zhang Xiangdong Fang | 2021 | Genomics, Proteomics & Bioinformatics2021，19，3： | 2 |
| 20 | Biomarker Profiling for Lupus Nephritis显示文摘Lupus nephritis (LN) is one of the most severe manifestations of systemic lupus erythematosus (SLE), which is associated with significant morbidity and mortality of SLE patients. The pathogenesis of LN involves multiple factors, including genetic predisposition, epigenetic regulation and environmental interaction. Over the last decade, omics-based techniques have been extensively utilized for biomarker screening and a wide variety of variations which are associated with SLE and LN have been identified at the levels of genomics, transcriptomics and proteomics. These studies and discoveries have expanded our understanding of the molecular basis of the disease and are important for identification of potential therapeutic targets for disease prediction and early treatment. In this review, we summarize some of the recent studies targeted at the identification of LN-associated biomarkers using genomics and proteomic approaches. | Yajuan Li Xiangdong Fang Quan-Zhen Li | 2013 | Genomics, Proteomics & Bioinformatics2013，11，3： | 1 |
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