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| 1 | Exploration of the formation mechanism and source attribution of ambient ozone in Chongqing with an observation-based model显示文摘An intensive field campaign was conducted in Chongqing during the summer of 2015 to explore the formation mechanisms of ozone pollution. The sources of ozone, the local production rates, and the controlling factors, as well as key species of volatile organic compounds(VOCs), were quantified by integrating a local ozone budget analysis, calculations of the relative incremental reactivity, and an empirical kinetic model approach. It was found that the potential for rapid local ozone formation exists in Chongqing. During ozone pollution episodes, the ozone production rates were found to be high at the upwind station Nan Quan, the urban station Chao Zhan, and the downwind station Jin-Yun Shan. The average local ozone production rate was 30×10^(-9) V/V h^(-1) and the daily integration of the produced ozone was greater than 180×10^(-9) V/V. High ozone concentrations were associated with urban and downwind air masses. At most sites, the local ozone production was VOC-limited and the key species were aromatics and alkene, which originated mainly from vehicles and solvent usage. In addition, the air masses at the northwestern rural sites were NO_x-limited and the local ozone production rates were significantly higher during the pollution episodes due to the increased NOx concentrations. In summary, the ozone abatement strategies of Chongqing should be focused on the mitigation of VOCs. Nevertheless, a reduction in NO_x is also beneficial for reducing the regional ozone peak values in Chongqing and the surrounding areas. | SU Rong LU KeDing YU JiaYan TAN ZhaoFeng JIANG MeiQing LI Jing XIE ShaoDong WU YuSheng ZENG LiMin ZHAI ChongZhi ZHANG YuanHang | 2018 | Science China Earth Sciences2018，61，1： | 24 |
| 2 | Adenovirus-mediated gene delivery:Potential applications for gene and cell-based therapies in the new era of personalized medicine显示文摘With rapid advances in understanding molecular pathogenesis of human diseases in the era of genome sciences and systems biology,it is anticipated that increasing numbers of therapeutic genes or targets will become available for targeted therapies.Despite numerous setbacks,efficacious gene and/or cell-based therapies still hold the great promise to revolutionize the clinical management of human diseases.It is wildly recognized that poor gene delivery is the limiting factor for most in vivo gene therapies.There has been a long-lasting interest in using viral vectors,especially adenoviral vectors,to deliver therapeutic genes for the past two decades.Among all currently available viral vectors,adenovirus is the most efficient gene delivery system in a broad range of cell and tissue types.The applications of adenoviral vectors in gene delivery have greatly increased in number and efficiency since their initial development.In fact,among over 2000 gene therapy clinical trials approved worldwide since 1989,a significant portion of the trials have utilized adenoviral vectors.This review aims to provide a comprehensive overview on the characteristics of adenoviral vectors,including adenoviral biology,approaches to engineering adenoviral vectors,and their applications in clinical and preclinical studies with an emphasis in the areas of cancer treatment,vaccination and regenerative medicine.Current challenges and future directions regarding the use of adenoviral vectors are also discussed.It is expected that the continued improvements in adenoviral vectors should provide great opportunities for cell and gene therapies to live up to its enormous potential in personalized medicine. | Cody S.Lee Elliot S.Bishop Ruyi Zhang Xinyi Yu Evan M.Farina Shujuan Yan Chen Zhao Zongyue Zeng Yi Shu Xingye Wu Jiayan Lei Yasha Li Wenwen Zhang Chao Yang Ke Wu Ying Wu Sherwin Ho Aravind Athiviraham Michael J.Lee Jennifer Moriatis Wolf Russell R.Reid Tong-Chuan He | 2017 | Genes & Diseases2017，4，2： | 19 |
| 3 | Spinel MnCo2O4 nanoparticles cross-linked with two-dimensional porous carbon nanosheets as a high-efficiency oxygen reduction electrocatalyst显示文摘为氧减小反应(ORR ) 的催化剂在燃料房间起一个重要作用。有到基于磅的催化剂的可比较的 ORR 活动的其他的非宝贵的金属催化剂为燃料房间的发展是高度合乎需要的。在这个工作,我们第一次报导尖晶石 MnCo 2 O 4/C ORR 催化剂由一致 MnCo 2 O 4 nanoparticles cross-linked 与二维( 2D )多孔的碳 nanosheets (缩短的同样多孔的 MnCo 2 O 4/C nanosheets ),在哪个葡萄糖作为模板被用作碳来源和 NaCl 。获得的多孔的 MnCo 2 在场的 O 4/C nanosheets 互连的多孔的体系结构和一个大表面区域的联合性质(175.3 m 2( | Gengtao Fu Zhenyuan Liu Jingfei Zhang Jiayan Wu Lin Xu Dongmei Sun Jubing Zhang Yawen Tang Pei Chen | 2016 | Nano Research2016，9，7： | 7 |
| 4 | Characterization of atomic defects on the photoluminescence in two-dimensional materials using transmission electron microscope显示文摘Two-dimensional material(2D)that possesses atomic thin geometry and remarkable properties is a star material for the fundamental researches and advanced applications.Defects in 2D materials are critical and fundamental to understand the chemical,physical,and optical properties.Photoluminescence arises in 2D materials owing to various physical phenomena including activator/dopant-induced luminescence and defect-related emissions,and so forth.With the advanced transmission electron microscopy(TEM)technologies,such as aberration correction and low voltage technologies,the morphology,chemical compositions and electronic structures of defects in 2D material could be directly characterized at the atomic scale.In this review,we introduce the applications of state-of-the-art TEM technologies on the studies of the role of atomic defects in the photoluminescence characteristics in 2D material.The challenges in spatial and time resolution are also discussed.It is proved that TEM is a powerful tool to pinpoint the relationship between the defects and the photoluminescence characteristics. | Jiayan Zhang Ye Yu Peng Wang Chen Luo Xing Wu Ziqi Sun Jianlu Wang Wei Da Hu Guozhen Shen | 2019 | InfoMat2019，1，1： | 6 |
| 5 | Dendritic platinum-copper bimetallic nanoassemblies with tunable composition and structure: Arginine-driven self-assembly and enhanced electrocatalytic activity显示文摘 | Gengtao Fu Huimin Liu Nika You Jiayan Wu Dongmei Sun Lin Xu Yawen Tang Yu Chen | 2016 | Nano Research2016，9，3： | 6 |
| 6 | Establishment and functional characterization of the reversibly immortalized mouse glomerular podocytes(imPODs)显示文摘Glomerular podocytes are highly specialized epithelial cells and play an essential role in establishing the selective permeability of the glomerular filtration barrier of kidney.Maintaining the viability and structural integrity of podocytes is critical to the clinical management of glomerular diseases,which requires a thorough understanding of podocyte cell biology.As mature podocytes lose proliferative capacity,a conditionally SV40 mutant tsA58-immortalized mouse podocyte line(designated as tsPC)was established from the Immortomouse over 20 years ago.However,the utility of the tsPC cells is hampered by the practical inconvenience of culturing these cells.In this study,we establish a user-friendly and reversibly-immortalized mouse podocyte line(designated as imPOD),on the basis of the tsPC cells by stably expressing the wildtype SV40 T-antigen,which is flanked with FRT sites.We show the imPOD cells exhibit long-term high proliferative activity,which can be effectively reversed by FLP recombinase.The imPOD cells express most podocyte-related markers,including WT-1,Nephrin,Tubulin and Vinculin,but not differentiation marker Synaptopodin.The imPOD cells do not form tumor-like masses in vivo.We further demonstrate that TGFb1 induces a podocyte injury-like response in the FLP-reverted imPOD cells by suppressing the expression of slit diaphragm-associated proteins P-Cadherin and ZO-1 and upregulating the expression of mesenchymal markers,a-SMA,Vimentin and Nestin,as well as fibrogenic factors CTGF and Col1a1.Collectively,our results strongly demonstrate that the newly engineered im-POD cells should be a valuable tool to study podocyte biology both under normal and under pathological conditions. | Xinyi Yu Liqun Chen Ke Wu Shujuan Yan Ruyi Zhang Chen Zhao Zongyue Zeng Yi Shu Shifeng Huang Jiayan Lei Xiaojuan Ji Chengfu Yuan Linghuan Zhang Yixiao Feng Wei Liu Bo Huang Bo Zhang Wenping Luo Xi Wang Bo Liu Rex C.Haydon Hue H.Luu Tong-Chuan He Hua Gan | 2018 | Genes & Diseases2018，5，2： | 5 |
| 7 | Arginine-mediated synthesis of cube-like platinum nanoassemblies as efficient electrocatalysts显示文摘可控制高贵金属 nanocrystals 自己组装具有为高度活跃的 electrocatalysts 的发展的宽广兴趣。这里,我们与多孔的洞和不平的表面为像立方体的磅 nanoassemblies (Pt-CNAs ) 的产量很高的合成报导一条有效调停精氨酸的热水的途径基于零维的磅 nanocrystals 自己组装。在这进程,精氨酸充当在邻近的 nanocrystals 之间的 reductant,结构指导代理人,和连接器。有趣地, Pt-CNAs 展览单个水晶的结构与主导 { 100 } 方面由 X 光检查衍射证实了。把研究基于 electrocatalytic,同样综合的 Pt-CNAs 展览在甲醇氧化反应改进了 electrocatalytic 活动以及好稳定性和公司忍耐。Pt-CNAs 好表演被归因于他们的唯一的形态学和表面结构。我们相信这里构画出的合成策略能被递讲道理地设计的其它为在高效燃料房间的使用的一金属或二金属的 nanoassemblies。 | Gengtao Fu Qian Zhang Jiayan Wu Dongmei Sun Lin Xu Yawen Tang Yu Chen | 2015 | Nano Research2015，8，12： | 4 |
| 8 | DNA sequencing leads to genomics progress in China显示文摘1 Science in the large-scale sequencing era Ten years ago,the first draft sequence assembly of the human genome was completed [1],bringing biomedical research one-step closer toward the goal of revolutionizing diagnosis,prevention,and treatment of human diseases.Recently,journalists from the journal Nature surveyed more than 1000 life scientists regarding this laudable aim [2],obtaining substantially negative responses [3].However,almost all of those surveyed had been influenced,in one way or another,by the availability of the human genome sequence,and they also agreed with the notion that the 'sequence is the start.' The complexity of genome biology and almost every aspect of human biology is far greater than previously thought [4]. | WU JiaYan XIAO JingFa ZHANG RuoSi YU Jun | 2011 | Science China(Life Sciences)2011，54，3： | 4 |
| 9 | The development of a sensitive fluorescent protein-based transcript reporter for high throughput screening of negative modulators of lncRNAs显示文摘While the human genome is pervasively transcribed,<2%of the human genome is transcribed into protein-coding mRNAs,leaving most of the transcripts as noncoding RNAs,such as microRNAs and long-noncoding RNAs(lncRNAs),which are critical components of epigenetic regulation.lncRNAs are emerging as critical regulators of gene expression and genomic stability.However,it remains largely unknown about how lncRNAs are regulated.Here,we develop a highly sensitive and dynamic reporter that allows us to identify and/or monitor negative modulators of lncRNA transcript levels in a high throughput fashion.Specifically,we engineer a fluorescent fusion protein by fusing three copies of the PEST destruction domain of mouse ornithine decarboxylase(MODC)to the C-terminal end of the codon-optimized bilirubin-inducible fluorescent protein,designated as dBiFP,and show that the dBiFP protein is highly destabilized,compared with the commonly-used eGFP protein.We further demonstrate that the dBiFP signal is effectively down-regulated when the dBiFP and mouse lncRNA H19 chimeric transcript is silenced by mouse H19-specific siRNAs.Therefore,our results strongly suggest that the dBiFP fusion protein may serve as a sensitive and dynamic transcript reporter to monitor the inhibition of lncRNAs by microRNAs,synthetic regulatory RNA molecules,RNA binding proteins,and/or small molecule inhibitors so that novel and efficacious inhibitors targeting the epigenetic circuit can be discovered to treat human diseases such as cancer and other chronic disorders. | Zongyue Zeng Bo Huang Shifeng Huang Ruyi Zhang Shujuan Yan Xinyi Yu Yi Shu Chen Zhao Jiayan Lei Wenwen Zhang Chao Yang Ke Wu Ying Wu Liping An Xiaojuan Ji Cheng Gong Chengfu Yuan Linghuan Zhang Wei Liu Yixiao Feng Bo Zhang Zhengyu Dai Yi Shen Xi Wang Wenping Luo Rex C.Haydon Hue H.Luu Lan Zhou Russell R.Reid Tong-Chuan He Xingye Wu | 2018 | Genes & Diseases2018，5，1： | 4 |
| 10 | Transcriptomic analysis reveals key regulators of mammogenesis and the pregnancy-lactation cycle显示文摘An organ unique to mammals,the mammary gland develops 90%of its mass after birth and experiences the pregnancy-lactation-involution cycle(PL cycle)during reproduction.To understand mammogenesis at the transcriptomic level and using a ribo-minus RNA-seq protocol,we acquired greater than 50 million reads each for the mouse mammary gland during pregnancy(day 12 of pregnancy),lactation(day 14 of lactation),and involution(day 7 of involution).The pregnancy-,lactation-and involution-related sequencing reads were assembled into 17344,10160,and 13739 protein-coding transcripts and1803,828,and 1288 non-coding RNAs(ncRNAs),respectively.Differentially expressed genes(DEGs)were defined in the three samples,which comprised 4843 DEGs(749 up-regulated and 4094 down-regulated)from pregnancy to lactation and4926 DEGs(4706 up-regulated and 220 down-regulated)from lactation to involution.Besides the obvious and substantive upand down-regulation of the DEGs,we observe that lysosomal enzymes were highly expressed and that their expression coincided with milk secretion.Further analysis of transcription factors such as Trps1,Gtf2i,Tcf7l2,Nupr1,Vdr,Rb1,and Aebp1,and ncRNAs such as mir-125b,Let7,mir-146a,and mir-15 has enabled us to identify key regulators in mammary gland development and the PL cycle. | ZHOU YuanYuan GONG Wei XIAO JingFa WU JiaYan PAN LinLin LI XiaoNuan WANG XuMin WANG WeiWei HU SongNian YU Jun | 2014 | Science China(Life Sciences)2014，57，3： | 4 |
| 11 | Systematic analysis of intron size and abundance parameters in diverse lineages显示文摘All eukaryotic genomes have genes with introns in variable sizes.As far as spliceosomal introns are concerned,there are at least three basic parameters to stratify introns across diverse eukaryotic taxa:size,number,and sequence context.The number parameter is highly variable in lower eukaryotes,especially among protozoan and fungal species,which ranges from less than4%to 78%of the genes.Over greater evolutionary time scales,the number parameter undoubtedly increases as observed in higher plants and higher vertebrates,reaching greater than 12.5 exons per gene in average among mammalian genomes.The size parameter is more complex,where multiple modes appear at work.Aside from intronless genes,there are three other types of intron-containing genes:half-sized,minimal,and size-expandable introns.The half-sized introns have only been found in a limited number of genomes among protozoan and fungal lineages and the other two types are prevalent in all animal and plant genomes.Among the size-expandable introns,the sizes of plant introns are expansion-limited in that the large introns exceeding 1000 bp are fewer in numbers and transposon-free as compared to the large introns among animals,where the larger introns are filled with transposable elements and appear expansion-flexible,reaching several kilobasepairs(kbp)and even thousands of kbp in size.Most of the intron parameters can be studied as signatures of the specific splicing machineries of different eukaryotic lineages and are highly relevant to the regulation of gene expression and functionality.In particular,the transcription-splicing-export coupling of eukaryotic intron dispensing leads to a working hypothesis that all intron parameters are evolved to be efficient and function-related in processing and routing the spliced transcripts. | WU JiaYan XIAO JingFa WANG LingPing ZHONG Jun YIN HongYan WU ShuangXiu ZHANG Zhang YU Jun | 2013 | Science China(Life Sciences)2013，56，10： | 4 |
| 12 | Coevolution study of mitochondria respiratory chain proteins:Toward the understanding of protein-protein interaction显示文摘Coevolution can be seen as the interdependency between evolutionary histories.In the context of protein evolution,functional correlation proteins are ever-present coordinated evolutionary characters without disruption of organismal integrity.As to complex system,there are two forms of protein—protein interactions in vivo,which refer to inter-complex interaction and intra-complex interaction.In this paper,we studied the difference of coevolution characters between inter-complex interaction and intra-complex interaction using 'Mirror tree' method on the respiratory chain(RC) proteins.We divided the correlation coefficients of every pairwise RC proteins into two groups corresponding to the binary protein—protein interaction in intra-complex and the binary protein—protein interaction in inter-complex,respectively.A dramatical discrepancy is detected between the coevolution characters of the two sets of protein interactions(Wilcoxon test,p-value = 4.4×10^(-6)).Our finding reveals some critical information on coevolutionary study and assists the mechanical investigation of protein—protein interaction. Furthermore,the results also provide some unique clue for supramolecular organization of protein complexes in the mitochondrial inner membrane.More detailed binding sites map and genome information of nuclear encoded RC proteins will be extraordinary valuable for the further mitochondria dynamics study. | Ming Yang Yan Ge Jiayan Wu Jingfa Xiao Jun Yu | 2011 | Journal of Genetics and Genomics2011，38，5： | 3 |
| 13 | Metabolic risk factors associated with sudden cardiac death(SCD)during acute myocardial ischemia显示文摘Sudden cardiac death(SCD)is the leading cause of death worldwide.Myocardial ischemia(MI)is the most common underlying causal disorder for SCD.Metabolic risks leading to SCD during acute MI are still not fully understood.Here,using tissue metabolomics,we aimed to investigate myocardial metabolic alterations relevant to SCD events in an acute MI rat model induced by coronary artery ligation(CAL).Thirty-four rats were successfully performed CAL,of which 13 developed lethal ventricular tachyarrhythmia(LVTA)-SCD and 7 developed severe atrioventricular block(AB)-SCD.Fourteen rats that survived within 70 min after the ligation were served as peer controls.The partial least squares-discriminant analysis plots demonstrated clear separations between the SCD rats and controls,indicating obvious differences in myocardial metabolome between these rats.The levels of isoleucine,lactate,glutamate choline,phosphorylcholine,taurine and asparagine in ischemic myocardia were positively associated with LVTA-SCD events;in contrast,the levels of alanine,urea,phenylalanine,linoleic acid,elaidic acid and stearic acid were inversely correlated with LVTA-SCD events.The levels of glutamate and urea were positively and negatively relevant to AB-SCD events,respectively.The dangerous metabolites indicated that lower levels of energy substrates,severe hypoxia,the inhibition of transamination and hyper sympathetic excitement and reactive oxygen species in myocardia were vulnerable to SCD during acute MI.The results suggest fatal metabolic alterations correlated with SCD events during acute MI,which could offer novel clues for the prevention or treatment of acute MI-related SCD. | Dian Wang Xingxing Wang Jiayan Wu Ruibing Su Jing Kong Xiaojun Yu | 2017 | Forensic Sciences Research2017，2，3： | 2 |
| 14 | Vascular endothelial growth factor induces multidrug resistance-associated protein 1 overexpression through phosphatidylinositol-3-kinase/protein kinase B signaling pathway and transcription factor specificity protein 1 in BGC823 cell line显示文摘Multidrug 抵抗(MDR ) 是化疗失败和癌复发的最重要的原因之一。但是 rolesof 在 MDR 遗体的联系 MDR 的蛋白质 MRP1 糟糕理解。脉管的 endothelial 生长因素(VEGF ) , themost 之一活跃、特定的脉管的生长因素,在增长,区别,和 metastasisof 癌症起一个重要作用。在 MRP1 的表示上探索 VEGF 的效果,我们使用了 recombinant 人 VEGF 刺激 K562 andBGC-823 房间线。量的即时聚合酶链反应和西方的污点分析证明在 mRNA 和蛋白质层次的 expressionof MRP1 被增加。3-(4,5-Dimethylthiazol-2-yl )-2,5-diphenyl tetrazolium 溴化物 resultsalso 证明 VEGF 显著地提高了与 adriamycin 对待的房间的 IC 50 。探索内在的规章的机制,我们构造了 MRP1 倡导者和 theluciferase 记者基因 recombinant 向量。,酶记者基因试金证明 MRP1 倡导者的活动被 VEGF 刺激显著地增加 LY294002, phosphatidylinositol-3-kinase (PI3K ) 的一个禁止者表明小径的 /proteinkinase B (Akt ) ,减少了这效果。抄写因素特性蛋白质 1 (SP1 ) 有约束力的地点 mutationpartially 由 VEGF 堵住了 MRP1 倡导者活动的起来规定。在摘要,我们的结果表明了 MRP1 的那 VEGF enhancedthe 表情,并且表明小径和 SP1 的 PI3K/Akt 可以涉及这调整。 | Juan Li Xiaojun Wu Jinling Gong Jing Yang Jiayan Leng Qiaoyun Chen Wenlin Xu | 2013 | Acta Biochimica et Biophysica Sinica2013，45，8： | 2 |
| 15 | The 1 PW/0.1 Hz laser beamline in SULF facility显示文摘In this paper,we report the recent progress on the 1 PW/0.1 Hz laser beamline of Shanghai Superintense Ultrafast Laser Facility(SULF).The SULF-1 PW laser beamline is based on the double chirped pulse amplification(CPA)scheme,which can generate laser pulses of 50.8 J at 0.1 Hz after the final amplifier;the shot-to-shot energy fluctuation of the amplified pulse is as low as 1.2%(std).After compression,the pulse duration of 29.6 fs is achieved,which can support a maximal peak power of 1 PW.The contrast ratio at-80 ps before main pulse is measured to be 2.5×10^-11.The focused peak intensity is improved by optimizing the angular dispersion in the grating compressor.The maximal focused peak intensity can reach 2.7×10^19W/cm2 even with an f/26.5 off-axis parabolic mirror.The horizontal and vertical angular pointing fluctuations in 1 h are measured to be 1.89 and 2.45μrad,respectively.The moderate repetition rate and the good stability are desirable characteristics for lasermatter interactions.The SULF-1 PW laser beamline is now in the phase of commissioning,and preliminary experiments of particle acceleration and secondary radiation under 300–400 TW/0.1 Hz laser condition have been implemented.The progress on the experiments and the daily stable operation of the laser demonstrate the availability of the SULF-1 PW beamline. | Zongxin Zhang Fenxiang Wu Jiabing Hu Xiaojun Yang Jiayan Gui Penghua Ji Xingyan Liu Cheng Wang Yanqi Liu Xiaoming Lu Yi Xu Yuxin Leng Ruxin Li Zhizhan Xu | 2020 | High Power Laser Science and Engineering2020，8，1： | 2 |
| 16 | Combining mannose receptor mediated nanovaccines and gene regulated PD-L1 blockade for boosting cancer immunotherapy显示文摘Tumor nanovaccines have potential applications in the prevention and treatment of malignant tumors.However,it remains a longstanding challenge in exploiting efficient nanocarriers for inducing potent specifically cellular immune responses.Toward this objective,we herein explore an intensive tumor immunotherapeutic strategy by combining mannosylated nanovaccines and gene regulated PD-L1 blockade for immune stimulation and killing activity.Here,we fabricate a mannose modified PLL-RT(Man-PLL-RT)mediated nanovaccines with dendritic cells(DCs)targeting capacity.Man-PLL-RT is capable of co-encapsulating with antigen(ovalbumin,OVA)and adjuvant(unmethylated cytosine-phosphate-guanine,CpG)by electrostatic interaction.This positively charged Man-PLL-RT/OVA/CpG nanovaccines can facilitate the endocytosis,maturation and cross presentation in DCs.However,the nanovaccines arouse limited inhibition of tumor growth,which is mainly due to the immunosuppressed microenvironment of tumors.Combining tumor nanovaccines with gene regulated PD-L1 blockade leads to an obvious tumor remission in B16F10 melanoma bearing mice.The collaborative strategy provides essential insights to boost the benefits of tumor vaccines by regulating the checkpoint blockade with gene therapy. | Jie Chen Huapan Fang Yingying Hu Jiayan Wu Sijia Zhang Yuanji Feng Lin Lin Huayu Tian Xuesi Chen | 2022 | Bioactive Materials2022，7，1： | 2 |
| 17 | Ribogenomics: the Science and Knowledge of RNA显示文摘Ribonucleic acid(RNA) deserves not only a dedicated field of biological research –– a discipline or branch of knowledge –– but also explicit definitions of its roles in cellular processes and molecular mechanisms. Ribogenomics is to study the biology of cellular RNAs, including their origin, biogenesis, structure and function. On the informational track, messenger RNAs(mRNAs) are the major component of ribogenomes, which encode proteins and serve as one of the four major components of the translation machinery and whose expression is regulated at multiple levels by other operational RNAs. On the operational track, there are several diverse types of RNAs –– their length distribution is perhaps the most simplistic stratification –– involving in major cellular activities, such as chromosomal structure and organization, DNA replication and repair, transcriptional/ post-transcriptional regulation, RNA processing and routing, translation and cellular energy/ metabolism regulation. An all-out effort exceeding the magnitude of the Human Genome Project is of essence to construct just mammalian transcriptomes in multiple contexts including embryonic development, circadian and seasonal rhythms, defined life-span stages, pathological conditions and anatomy-driven tissue/organ/cell types. | Jiayan Wu Jingfa Xiao Zhang Zhang Xumin Wang Songnian Hu Jun Yu | 2014 | Genomics, Proteomics & Bioinformatics2014，12，2： | 2 |
| 18 | The Kuroshio Extension: a leading mechanism for the seasonal sea-level variability along the west coast of Japan显示文摘 | Chao Ma Jiayan Yang Dexing Wu Xiaopei Lin | 2010 | Ocean Dynamics2010，，3： | 1 |
| 19 | A Brief Review of Software Tools for Pangenomics显示文摘Since the proposal for pangenomic study, there have been a dozen software tools actively in use for pangenomic analysis. By the end of 2014, Panseq and the pan-genomes analysis pipeline(PGAP) ranked as the top two most popular packages according to cumulative citations of peerreviewed scientific publications. The functions of the software packages and tools, albeit variable among them, include categorizing orthologous genes, calculating pangenomic profiles, integrating gene annotations, and constructing phylogenies. As epigenomic elements are being gradually revealed in prokaryotes, it is expected that pangenomic databases and toolkits have to be extended to handle information of detailed functional annotations for genes and non-protein-coding sequences including non-coding RNAs, insertion elements, and conserved structural elements. To develop better bioinformatic tools, user feedback and integration of novel features are both of essence. | Jingfa Xiao Zhewen Zhang Jiayan Wu Jun Yu | 2015 | Genomics, Proteomics & Bioinformatics2015，13，1： | 1 |
| 20 | An invasive zone in human liver cancer identified by Stereo-seq promotes hepatocyte–tumor cell crosstalk,local immunosuppression and tumor progression显示文摘Dissecting and understanding the cancer ecosystem,especially that around the tumor margins,which have strong implications for tumor cell infiltration and invasion,are essential for exploring the mechanisms of tumor metastasis and developing effective new treatments.Using a novel tumor border scanning and digitization model enabled by nanoscale resolution-SpaTial Enhanced REsolution Omics-sequencing(Stereo-seq),we identified a 500µm-wide zone centered around the tumor border in patients with liver cancer,referred to as“the invasive zone”.We detected strong immunosuppression,metabolic reprogramming,and severely damaged hepatocytes in this zone.We also identified a subpopulation of damaged hepatocytes with increased expression of serum amyloid A1 and A2(referred to collectively as SAAs)located close to the border on the paratumor side.Overexpression of CXCL6 in adjacent malignant cells could induce activation of the JAK-STAT3 pathway in nearby hepatocytes,which subsequently caused SAAs’overexpression in these hepatocytes.Furthermore,overexpression and secretion of SAAs by hepatocytes in the invasive zone could lead to the recruitment of macrophages and M2 polarization,further promoting local immunosuppression,potentially resulting in tumor progression.Clinical association analysis in additional five independent cohorts of patients with primary and secondary liver cancer(n=423)showed that patients with overexpression of SAAs in the invasive zone had a worse prognosis.Further in vivo experiments using mouse liver tumor models in situ confirmed that the knockdown of genes encoding SAAs in hepatocytes decreased macrophage accumulation around the tumor border and delayed tumor growth.The identification and characterization of a novel invasive zone in human cancer patients not only add an important layer of understanding regarding the mechanisms of tumor invasion and metastasis,but may also pave the way for developing novel therapeutic strategies for advanced liver cancer and other solid tumors. | Liang Wu Jiayan Yan Yinqi Bai Feiyu Chen Xuanxuan Zou Jiangshan Xu Ao Huang Liangzhen Hou Yu Zhong Zehua Jing Qichao Yu Xiaorui Zhou Zhifeng Jiang Chunqing Wang Mengnan Cheng Yuan Ji Yingyong Hou Rongkui Luo Qinqin Li Liang Wu Jianwen Cheng Pengxiang Wang Dezhen Guo Waidong Huang Junjie Lei Shang Liu Yizhen Yan Yiling Chen Sha Liao Yuxiang Li Haixiang Sun Na Yao Xiangyu Zhang Shiyu Zhang Xi Chen Yang Yu Yao Li Fengming Liu Zheng Wang Shaolai Zhou Huanming Yang Shuang Yang Xun Xu Longqi Liu Qiang Gao Zhaoyou Tang Xiangdong Wang Jian Wang Jia Fan Shiping Liu Xinrong Yang Ao Chen Jian Zhou | 2023 | Cell Research2023，33，8： | 1 |
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