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| 1 | 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 |
| 2 | Research on the resource utilization of Baosteel steel slag as concrete material显示文摘The utilization of steel slag has been a worldwide issue for a long time.Attention is increasingly being paid to the technological innovation and development of steel slag.Aiming at the development of environmentally friendly steel slag concrete materials and their use in a recyclable economy,Baosteel has recently been conducting research on and using many new building materials,including steel slag powder concrete,steel slag pervious concrete,steel slag counter weight concrete and so on.In this way,steel slag has been turned from a kind of solid waste into a value-added material.The technology of steel slag utilization has been enriched and developed,while a new model of using Baosteel steel slag in a recyclable economy has also been explored and practised. | JIN Qiang HE Hongzhu YANG Gang ZHANG Chao WANG Youqin | 2009 | Baosteel Technical Research2009，3，4： | 4 |
| 3 | 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 |
| 4 | Decreased Endogenous Production of Hydrogen Sulfide Accelerates Atherosclerosis显示文摘 | Sarathi Mani Hongzhu Li Ashley Untereiner Lingyun Wu Guangdong Yang Richard C. Austin Jeffrey G. Dickhout ?árka Lhoták Qing H. Meng Rui Wang | 2013 | Circulation2013，，25： | 2 |
| 5 | CSE/H_2S通路缺失影响小鼠肝脏胆固醇和脂肪酸代谢(英文)显示文摘肝脂质代谢异常导致过度肝脂肪沉积和脂肪变性是脂肪肝发展的关键环节.胱硫脒-伽马-裂解酶(CSE)是在肝脏中催化硫化氢(H2S)生成的酶之一.本研究的目的是研究CSE/H2S在调控肝脏胆固醇和脂肪酸代谢中的作用.用高脂饮食(HFD)喂食野生型(WT)和CSE敲除(KO)小鼠后,对小鼠肝形态学和生物化学变化进行了分析.与WT小鼠不同,HFD喂食显著增加CSE-KO小鼠的血浆和肝脏胆固醇水平以及肝和胆囊的大小.这些CSE-KO小鼠呈现典型的脂肪肝组织学和生物化学变化以及肝功能损害.血浆和肝脏甘油三酯水平也比HFD喂养WT小鼠显著降低.核受体转录因子LXRα以及它的靶基因,CYP7A1,在对照组和HFD组CSE-KO小鼠肝脏中的表达都低于相应WT小鼠的水平.这些异常阻碍胆固醇分解成胆汁并导致胆固醇蓄积在肝脏和胆囊.由于CSE/H2S通路缺失造成对HFD诱导的脂肪肝的高易感性,肝脏CSE/H2S通路可能是治疗脂肪肝损伤的一个新的靶向. | Sarathi Mani Hongzhu Li Guangdong Yang Lingyun Wu Rui Wang | 2015 | Science Bulletin2015，60，3： | 2 |
| 6 | Short-term effects of organic amendments on soil fertility and root growth of rubber trees on Hainan Island, China显示文摘Rubber[Hevea brasiliensis(Willd.ex A.Juss.)Müll.Arg.]plantations are the largest cultivated forest type in tropical China.Returning organic materials to the soil will help to maintain the quality and growth of rubber trees.Although many studies have demonstrated that organic waste materials can be used to improve soil fertility and structure to promote root growth,few studies have studied the eff ects of organic amendments on soil fertility and root growth in rubber tree plantations.Here,bagasse,coconut husk or biochar were applied with a chemical fertilizer to test their eff ects on soil properties after 6 months and compared with the eff ects of only the chemical fertilizer.Results showed that the soil organic matter content,total nitrogen,available phosphorus and available potassium after the chemical fertilizer(F)treatment were all signifi cantly lower than after the chemical fertilizer+bagasse(Fba),chemical fertilizer+coconut husk(Fco)or chemical fertilizer+biochar(Fbi)(p<0.05).Soil pH in all organic amendments was higher than in the F treatment,but was only signifi cantly higher in the Fbi treatment.In contrast,soil bulk density in the F treatment was signifi cantly higher than in treatments with the organic amendments(p<0.05).When compared with the F treatment,soil root dry mass increased signifi-cantly by 190%,176%and 33%in Fba,Fco and Fbi treatments,respectively(p<0.05).Similar results were found for root activity,number of root tips,root length,root surface area and root volume.Conclusively,the application of bagasse,coconut husk and biochar increased soil fertility and promoted root growth of rubber trees in the short term.However,bagasse and coconut husk were more eff ective than biochar in improving root growth of rubber trees. | Yanyan Huang Yudan Jing Meirong Bei Hongzhu Yang Zhengzao Cha Qinghuo Lin Wei Luo | 2020 | Journal of Forestry Research2020，31，6： | 1 |
| 7 | Anthraquinones from hairy root cultures of Cassia obtusifolia显示文摘 | Guo Hongzhu Chang Zhenzhan Yang Rujun | 1998 | Phytochemistry1998，49，6： | 1 |
| 8 | Increased neointimal formation in cystathionine gamma-lyase deficient mice: Role of hydrogen sulfide in α5β1-integrin and matrix metalloproteinase-2 expression in smooth muscle cells显示文摘 | Guangdong Yang Hongzhu Li Guanghua Tang Lingyun Wu Kexin Zhao Qiuhui Cao Changqing Xu Rui Wang | 2011 | Journal of Molecular and Cellular Cardiology2011，，3： | 1 |
| 9 | GliomaDB: A Web Server for Integrating Glioma Omics Data and Interactive Analysis显示文摘Gliomas are one of the most common types of brain cancers.Numerous efforts have been devoted to studying the mechanisms of glioma genesis and identifying biomarkers for diagnosis and treatment.To help further investigations,we present a comprehensive database named GliomaDB.GliomaDB includes 21,086 samples from 4303 patients and integrates genomic,transcriptomic,epigenomic,clinical,and gene-drug association data regarding glioblastoma multiforme(GBM)and low-grade glioma(LGG)from The Cancer Genome Atlas(TCGA),Gene Expression Omnibus(GEO),the Chinese Glioma Genome Atlas(CGGA),the Memorial Sloan Kettering Cancer Center Integrated Mutation Profiling of Actionable Cancer Targets(MSK-IMPACT),the US Food and Drug Administration(FDA),and Pharm GKB.GliomaDB offers a user-friendly interface for two main types of functionalities.The first comprises queries of(i)somatic mutations,(ii)gene expression,(iii)microRNA(miRNA)expression,and(iv)DNA methylation.In addition,queries can be executed at the gene,region,and base level.Second,GliomaDB allows users to perform survival analysis,coexpression network visualization,multi-omics data visualization,and targeted drug recommendations based on personalized variations.GliomaDB bridges the gap between glioma genomics big data and the delivery of integrated information for end users,thus enabling both researchers and clinicians to effectively use publicly available data and empowering the progression of precision medicine in glioma.GliomaDB is freely accessible at http://gffzzdbc7b6aaae734bddh9x66qc0wobxx6opu.ffgz.tsg.suse.edu.cn/glioma DB. | Yadong Yang Yang Sui Bingbing Xie Hongzhu Qu Xiangdong Fang | 2019 | Genomics, Proteomics & Bioinformatics2019，17，4： | 0 |
| 10 | Biological Databases for Hematology Research显示文摘With the advances of genome-wide sequencing technologies and bioinformatics approaches, a large number of datasets of normal and malignant erythropoiesis have been generated and made public to researchers around the world. Collection and integration of these datasets greatly facilitate basic research and clinical diagnosis and treatment of blood disorders. Here we provide a brief introduction of the most popular omics data resources of normal and malignant hematopoiesis, including some integrated web tools, to help users get better equipped to perform common analyses. We hope this review will promote the awareness and facilitate the usage of public database resources in the hematology research. | Qian Zhang Nan Ding Lu Zhang Xuetong Zhao Yadong Yang Hongzhu Qu Xiangdong Fang | 2016 | Genomics, Proteomics & Bioinformatics2016，14，6： | 0 |
| 11 | Common Postzygotic Mutational Signatures in Healthy Adult Tissues Related to Embryonic Hypoxia显示文摘Postzygotic mutations are acquired in normal tissues throughout an individual’s lifetime and hold clues for identifying mutagenic factors.Here,we investigated postzygotic mutation spectra of healthy individuals using optimized ultra-deep exome sequencing of the time-series samples from the same volunteer as well as the samples from different individuals.In blood,sperm,and muscle cells,we resolved three common types of mutational signatures.Signatures A and B represent clocklike mutational processes,and the polymorphisms of epigenetic regulation genes influence the proportion of signature B in mutation profiles.Notably,signature C,characterized by C>T transitions at GpCpN sites,tends to be a feature of diverse normal tissues.Mutations of this type are likely to occur early during embryonic development,supported by their relatively high allelic frequencies,presence in multiple tissues,and decrease in occurrence with age.Almost none of the public datasets for tumors feature this signature,except for 19.6%of samples of clear cell renal cell carcinoma with increased activation of the hypoxia-inducible factor 1(HIF-1)signaling pathway.Moreover,the accumulation of signature C in the mutation profile was accelerated in a human embryonic stem cell line with drug-induced activation of HIF-1α.Thus,embryonic hypoxia may explain this novel signature across multiple normal tissues.Our study suggests that hypoxic condition in an early stage of embryonic development is a crucial factor inducing C>T transitions at GpCpN sites;and individuals’genetic background may also influence their postzygotic mutation profiles. | Yaqiang Hong Dake Zhang Xiangtian Zhou Aili Chen Amir Abliz Jian Bai Liang Wang Qingtao Hu Kenan Gong Xiaonan Guan Mengfei Liu Xinchang Zheng Shujuan Lai Hongzhu Qu Fuxin Zhao Shuang Hao Zhen Wu Hong Cai Shaoyan Hu Yue Ma Junting Zhang Yang Ke Qian-Fei Wang Wei Chen Changqing Zeng | 2022 | Genomics, Proteomics & Bioinformatics2022，20，1： | 0 |
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