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| 1 | TBtools: An Integrative Toolkit Developed for Interactive Analyses of Big Biological Data显示文摘The rapid development of high-throughput sequencing techniques has led biology into the big-data era.Data analyses using various bioinformatics tools rely on programming and command-line environments,which are challenging and time-consuming for most wet-lab biologists.Here,we present TBtools(a Toolkit for Biologists integrating various biological data-handling tools),a stand-alone software with a userfriendly interface.The toolkit incorporates over 130 functions,which are designed to meet the increasing demand for big-data analyses,ranging from bulk sequence processing to interactive data visualization.A wide variety of graphs can be prepared in TBtools using a new plotting engine('JIGplot')developed to maximize their interactive ability;this engine allows quick point-and-click modification of almost every graphic feature.TBtools is platform-independent software that can be run under all operating systems with Java Runtime Environment 1.6 or newer.It is freely available to non-commercial users at http://gffzz188fe103f8f1460ascfw06nubko5v6bfp.ffgz.tsg.suse.edu.cn/CJ-Chen/TBtools/releases. | Chengjie Chen Hao Chen Yi Zhang Hannah R.Thomas Margaret H.Frank Yehua He Rui Xia | 2020 | Molecular Plant2020，13，8： | 805 |
| 2 | Identification and characterization of putative CIPK genes in maize显示文摘当在细胞内部的发信号的第二个送信人由发展、环境的暗示得到了,钙(Ca ) 起一个关键作用。Calcineurin 象 B 一样蛋白质(CBL ) 和他们的目标蛋白质,交往 CBL 蛋白质 kinases (CIPK ) 在植物响应压力作为一个关键调停 Ca2+ 的发信号网络出现了。生物信息的分析被用来识别 43 通常认为的 ZmCIPK (Zea mays CIPK ) 在玉米的染色体的基因生来的线 B73。基于基因结构,这些 ZmCIPKs 被划分成 intron 富有、 intron 差的组。种系发生的分析显示 ZmCIPK 家庭与 30 个成员的米饭 CIPK 家庭一起有一种高进化的关系。Microarray 数据和 RT-PCR 试金显示出基因 transcriptionally 回答了到不能生活的压力,和基因是的那 24, 31, 20 和 19 ZmCIPK 的那 ZmCIPK 由盐,干旱,热和冷压力起来调整分别地。在冷应力下面有在寒冷容忍的生来的线 B73 和寒冷敏感的生来的线 Mo17 之间的 ZmCIPKs 的不同表示模式。我们的调查结果将在玉米帮助 CIPK 的生物功能的进一步分子的解剖,并且提供新卓见进在植物表明网络的 CBLCIPK。 | Xifeng Chen Zhimin Gu Dedong Xin Liang Hao Chengjie Liu Ji Huang Bojun Ma Hongsheng Zhang | 2011 | Journal of Genetics and Genomics2011，38，2： | 40 |
| 3 | Small RNAs, emerging regulators critical for the development of horticultural traits显示文摘Small RNAs(sRNAs)have been recently recognized as key genetic and epigenetic regulators in various organisms,ranging from the modification of DNA and histone methylations to the modulation of the abundance of coding or non-coding RNAs.In plants,major regulatory sRNAs are classified as respective microRNA(miRNA)and small interfering RNA(siRNA)species,with the former primarily engaging in posttranscriptional regulation while the latter in transcriptional one.Many of these characterized sRNAs are involved in regulation of diverse biological programs,processes,and pathways in response to developmental cues,environmental signals/stresses,pathogen infection,and pest attacks.Recently,sRNAs-mediated regulations have also been extensively investigated in horticultural plants,with many novel mechanisms unveiled,which display far more mechanistic complexity and unique regulatory features compared to those studied in model species.Here,we review the recent progress of sRNA research in horticultural plants,with emphasis on mechanistic aspects as well as their relevance to trait regulation.Given that major and pioneered sRNA research has been carried out in the model and other plants,we also discuss ongoing sRNA research on these plants.Because miRNAs and phased siRNAs(phasiRNAs)are the most studied sRNA regulators,this review focuses on their biogenesis,conservation,function,and targeted genes and traits as well as the mechanistic relation between them,aiming at providing readers comprehensive information instrumental for future sRNA research in horticulture crops. | Chengjie Chen Zaohai Zeng Zongrang Liu Rui Xia | 2018 | Horticulture Research2018，5，1： | 12 |
| 4 | Coexpression network analysis reveals an MYB transcriptional activator involved in capsaicinoid biosynthesis in hot peppers显示文摘Plant biosynthesis involves numerous specialized metabolites with diverse chemical natures and biological activities.The biosynthesis of metabolites often exclusively occurs in response to tissue-specific combinatorial developmental cues that are controlled at the transcriptional level.Capsaicinoids are a group of specialized metabolites that confer a pungent flavor to pepper fruits.Capsaicinoid biosynthesis occurs in the fruit placenta and combines its developmental cues.Although the capsaicinoid biosynthetic pathway has been largely characterized,the regulatory mechanisms that control capsaicinoid metabolism have not been fully elucidated.In this study,we combined fruit placenta transcriptome data with weighted gene coexpression network analysis(WGCNA)to generate coexpression networks.A capsaicinoid-related gene module was identified in which the MYB transcription factor CaMYB48 plays a critical role in regulating capsaicinoid in pepper.Capsaicinoid biosynthetic gene(CBG)and CaMYB48 expression primarily occurs in the placenta and is consistent with capsaicinoid biosynthesis.CaMYB48 encodes a nucleus-localized protein that primarily functions as a transcriptional activator through its C-terminal activation motif.CaMYB48 regulates capsaicinoid biosynthesis by directly regulating the expression of CBGs,including AT3a and KasIa.Taken together,the results of this study indicate ways to generate robust networks optimized for the mining of CBG-related regulators,establishing a foundation for future research elucidating capsaicinoid regulation. | Binmei Sun Xin Zhou Changming Chen Chengjie Chen Kunhao Chen Muxi Chen Shaoqun Liu Guoju Chen Bihao Cao Fanrong Cao Jianjun Lei Zhangsheng Zhu | 2020 | Horticulture Research2020，7，1： | 5 |
| 5 | Influence of co-solvent hydroxyl group number on properties of water-based conductive carbon pastes显示文摘 | Chengjie Hua Xiaoming Li Lijuan Shen Hong Lei Xiaoqian Guo Zhuo Liu Qingqiang Kong Lijing Xie cheng-Meng Chen | 2017 | Particuology2017，15，4： | 3 |
| 6 | Comprehensive test stand for high-intensity cyclotron development显示文摘A comprehensive test stand for high-intensity cyclotron development,a 10 MeV 430 μA cyclotron,has been successfully constructed at China Institute of Atomic Energy (CIAE) for the experimental verification of the viability of a 100 MeV high-intensity cyclotron (CYCIAE-100) being constructed at CIAE.The verification includes the overall design technology,detail design and engineering technology for the crucial parts of the machine,e.g.main magnet and beam diagnostics.It will also pave the way for future enhancement of the beam intensity.The test stand consists of a H-ion source,axial injection system,central region,main magnet and coil,RF resonator,stripping extraction,and auxiliary systems,which include the RF power amplifier,high voltage and DC power supplies,electric apparatus,beam diagnostics,control,vacuum,water cooling,pneumatic system,and safety interlock.This paper presents the work regarding the design and sub-system development of the test sand,and the results of the beam commissioning of the machine. | ZHANG TianJue LI ZhenGuo CHU ChengJie XING JianSheng GUAN FengPing ZHONG JunQing JI Bin GE Tao YIN ZhiGuo HOU ShiGang PAN GaoFeng YAO HongJuan LU YinLong WANG ZhenHui WU LongCheng LIN Jun JIA XianLu WEI SuMin WEN LiPeng WANG Feng XIA Le CAI HongRu XIE HuaiDong CHEN RongFan ZHANG Yan ZHANG SuPing LIU GengShou ZOU Jian AN ShiZhong YANG JianJun BI YuanJie YANG Fang | 2011 | Chinese Science Bulletin2011，56，3： | 3 |
| 7 | Circulation Features Associated with the Record-breaking Typhoon Silence in August 2014显示文摘Climatologically, August is the month with the most tropical cyclone(TC) formation over the western North Pacific(WNP) during the typhoon season. In this study, the reason for abnormal TC activity during August is discussed—especially August 2014, when no TCs formed. The large-scale background of August 2014 is presented, with low-level large-scale easterly anomalies and anticyclonic anomalies dominating over the main TC genesis region, a weak monsoon trough system,and a strong WNP subtropical high(WPSH), leading to significantly reduced low-level convergence, upper-level divergence,and mid-level upward motion. These unfavorable large-scale conditions suppressed convection and cyclogenesis. In August2014, equatorial waves were inactive within the negative phase of the Madden–Julian Oscillation(MJO), with fewer tropical disturbances. Although the low-level vorticity and convection of those disturbances were partly promoted by the convective envelopes of equatorial waves, the integral evolution of disturbances, as well as the equatorial waves, were suppressed when propagating into the negative MJO phase. Moreover, the upper-level potential vorticity(PV) streamers associated with anticyclonic Rossby wave breaking events imported extratropical cold and dry air into the tropics. The peripheral tropospheric dryness and enhanced vertical wind shear by PV streamer intrusion combined with the negative MJO phase were responsible for the absence of TC formation over the WNP in August 2014. | Jianpu BIAN Juan FANG Guanghua CHEN Chengji LIU | 2018 | Advances in Atmospheric Sciences2018，35，10： | 2 |
| 8 | Video-Assisted Thoracoscopic Surgery (VATS) for Patients with Solitary Fibrous Tumors of the Pleura显示文摘 | Jun Liu Chengjie Cai Daoyuan Wang Hanzhang Chen Linling Cheng Wenlong Shao Shuben Li Yubao Guan Yingying Gu Jianxing He | 2010 | Journal of Thoracic Oncology2010，，2： | 2 |
| 9 | Origin of High Efficiency and Long-Term Stability in Ionic Liquid Perovskite Photovoltaic显示文摘Environment-friendly protic amine carboxylic acid ionic liquids(ILs)as solvents is a significant breakthrough with respect to traditional highly coordinating and toxic solvents in achieving efficient and stable perovskite solar cells(PSCs)with a simple one-step air processing and without an antisolvent treatment approach.However,it remains mysterious for the improved efficiency and stability of PSCs without any passivation strategy.Here,we unambiguously demonstrate that the three functions of solvents,additive,and passivation are present for protic amine carboxylic acid ILs.We found that the ILs have the capability to dissolve a series of perovskite precursors,induce oriented crystallization,and chemically passivate the grain boundaries.This is attributed to the unique molecular structure of ILs with carbonyl and amine groups,allowing for strong interaction with perovskite precursors by forming C=O…Pb chelate bonds and N-H…I hydrogen bonds in both solution and film.This finding is generic in nature with extension to a wide range of IL-based perovskite optoelectronics. | Lingfeng Chao Tingting Niu Hao Gu Yingguo Yang Qi Wei Yingdong Xia Wei Hui Shouwei Zuo Zhaohua Zhu Chengjie Pei Xiaodong Li Jing Zhang Junfeng Fang Guichuan Xing Hai Li Xiao Huang Xingyu Gao Chenxin Ran Lin Song Li Fu Yonghua Chen Wei Huang | 2020 | Research2020，，1： | 2 |
| 10 | sRNAanno-a database repository of uniformly annotated small RNAs in plants显示文摘Small RNAs(sRNAs)are essential regulatory molecules,and there are three major sRNA classes in plants:microRNAs(miRNAs),phased small interfering RNAs(phased siRNAs or phasiRNAs),and heterochromatic siRNAs(hc-siRNAs).Excluding miRNAs,the other two classes are not well annotated or available in public databases for most sequenced plant genomes.We performed a comprehensive sRNA annotation of 143 plant species that have fully sequenced genomes and next-generation sequencing sRNA data publicly available.The results are available via an online repository called sRNAanno(www.plantsRNAs.org).Compared with other public plant sRNA databases,we obtained was much more miRNA annotations,which are more complete and reliable because of the consistent and highly stringent criteria used in our miRNA annotations.sRNAanno also provides free access to genomic information for>22,721 PHAS loci and>22 million hc-siRNA loci annotated from these 143 plant species.Both miRNA and PHAS loci can be easily browsed to view their main features,and a collection of archetypal trans-acting siRNA 3(TAS3)genes were annotated separately for quick access.To facilitate the ease of sRNA annotation,sRNAanno provides free service for sRNA annotations to the community.In summary,the sRNAanno database is a great resource to facilitate genomic and genetic research on plant small RNAs. | Chengjie Chen Jiawei Li Junting Feng Bo Liu Lei Feng Xiaoling Yu Guanliang Li Jixian Zhai Blake C.Meyers Rui Xia | 2021 | Horticulture Research2021，8，1： | 1 |
| 11 | Quantum discord of two-qubit X states显示文摘 | Chen Qing Zhang Chengjie Yu Sixia | 2011 | Phys Rev A2011，84，4： | 1 |
| 12 | Personalized recommendation based on implicit social network of re- searchers 显示文摘 | CHEN Cheng MAO Chengjie TANG Yong | 2013 | Pervasive Computing and the Networked World2013，7719，10： | 1 |
| 13 | Numer-ical simulationon combustion processes of a diesel engineunder ()2/C02 atmosphere 显示文摘 | Hanyu Chen Chengji Zuo Haichun Ding | 2013 | HKIE Transactions2013，20，3： | 1 |
| 14 | Numerical simulation on combustion processes of a diesel engine under O2/CO2atmosphere显示文摘 | Chen Hanyu Zuo Chengji Ding Haichun | 2013 | Source:HKIE Transactions2013，20，： | 1 |
| 15 | Species-specific regulatory pathways of small RNAs play sophisticated roles in flower development in Dimocarpus longan Lour.显示文摘Flower development plays vital role in horticultural plants.Post-transcriptional regulation via small RNAs is important for plant flower development.To uncover post-transcriptional regulatory networks during the flower development in Dimocarpus longan Lour.‘Shixia’,an economically important fruit crop in subtropical regions,we collected and analyzed sRNA deep-sequencing datasets and degradome libraries Apart from identifying miRNAs and phased siRNA generating loci(PHAS loci),120 hairpin loci,producing abundant sRNAs,were identified by in-house protocols.Our results suggested that 56 miRNA-target pairs,2221-nt-PHAS loci,and 111 hairpin loci are involved in posttranscriptional gene silencing during longan reproductive development.Lineage-specific or species-specific post-transcriptional regulatory modules have been unveiled,including miR482-PHAS and miRN15.miR482-PHAS might be involved in longan flower development beyond their conserved roles in plant defense,and miRN15 is a novel miRNA likely associated with a hairpin locus(HPL-056)to regulate strigolactone receptor gene DWARF14(D14)and the biogenesis of phasiRNAs from D14.These small RNAs are enriched in flower buds,suggesting they are likely involved in post-transcriptional regulatory networks essential for longan flower development via the strigolactone signaling pathway. | Bo Liu Guanliang Li Chengjie Chen Zaohai Zeng Jing Xu Jisen Zhang Rui Xia Yuanlong Liu | 2023 | Horticultural Plant Journal2023，9，2： | 1 |
| 16 | Numerical simulation on combustion processes of a diesel engine under O2/CO2 atmosphere显示文摘 | Chen Hanyu Zuo Chengji Ding Haichun | | 0，，03： | 1 |
| 17 | Julia’s lemma and bloch constants显示文摘 | Huaihui Chen Chengji Xiong | 2003 | Science in China Series A: Mathematics2003，，3： | 1 |
| 18 | Jack of Many Trades: The Multifaceted Role of miR528 in Monocots显示文摘MicroRNAs (miRNAs) are essential regulators,involved in almost all aspects of plant growth and development.In plants,miRNAs prese nt in all an giosperms are regarded as con served miRNAs;in contrast,miRNAs restricted to certain lineages (lessconserved) or a single species (species-specific) constitute the non-conserved miRNAs (Cuperus et al.,2011).Different members of a miRNA family usually target similar target genes from a gene family among different species.For in stance,in most analyzed plants,the well-known miR156 family,usually consist!ng of a number of members in a given species,collectively target SQUAMOSA-PROMOTER BINDING PROTEINLIKE (SPL) genes.Gen erally,con served miRNAs target genes encoding transcript factors which function in diverse biological processes.This functional diversity of miRNAs is mainly achieved by the plasticity of their target genes from the same family,such as miR156-targeted SPLs and miR167-targeted ARF (AUXIN RESPONSIVE FACTOR) genes,on regulating distinct downstream gen es. | Chengjie Chen Yuanlong Liu Rui Xia | 2019 | Molecular Plant2019，12，8： | 1 |
| 19 | TBtools-II: A “one for all, all for one” bioinformatics platform for biological big-data mining显示文摘Since the official release of the stand-alone bioinformatics toolkit TBtools in 2020,its superior functionality in data analysis has been demonstrated by its widespread adoption by many thousands of users and references in more than 5000 academic articles.Now,TBtools is a commonly used tool in biological laboratories.Over the past 3 years,thanks to invaluable feedback and suggestions from numerous users,we have optimized and expanded the functionality of the toolkit,leading to the development of an upgraded version—TBtools-II.In this upgrade,we have incorporated over 100 new features,such as those for comparative genomics analysis,phylogenetic analysis,and data visualization.Meanwhile,to better meet the increasing needs of personalized data analysis,we have launched the plugin mode,which enables users to develop their own plugins and manage their selection,installation,and removal according to individual needs.To date,the plugin store has amassed over 50 plugins,with more than half of them being independently developed and contributed by TBtools users.These plugins offer a range of data analysis options including co-expression network analysis,single-cell data analysis,and bulked segregant analysis sequencing data analysis.Overall,TBtools is now transforming from a stand-alone software to a comprehensive bioinformatics platform of a vibrant and cooperative community in which users are also developers and contributors.By promoting the theme“one for all,all for one”,we believe that TBtools-II will greatly benefit more biological researchers in this big-data era. | Chengjie Chen Ya Wu Jiawei Li Xiao Wang Zaohai Zeng Jing Xu Yuanlong Liu Junting Feng Hao Chen Yehua He Rui Xia | 2023 | Molecular Plant2023，16，11： | 0 |
| 20 | Timing and Single-pulse Study of Pulsar J1909+0122 Discovered by CRAFTS显示文摘We report the discovery of PSR J1909+0122 by the Five-hundred-meter Aperture Spherical Radio Telescope(FAST)as part of the Commensal Radio Astronomy FAST Survey.PSR J1909+0122 has a spin period of 1.257 s and a dispersion measure of 186.2 pc cm^(-3).The averaged pulse profile shows two distinct components.We performed a single-pulse study based on a one-hour observation at 1.25 GHz on 2021 August 23.We used a threshold of 5σ_(ep) to measure the nulling fraction(NF)as 63%±1.5%.The longitude-resolved fluctuation spectra and fast Fourier transform spectra of the binary sequences revealed the quasi-periodicity of nulling with a period of 30 rotation periods.We examined the reliability of the periodicity by comparing it to random noise injection.The NF,E,and modulation periodicity P_(M) of PSR J1909+0122 were compared with other periodic nulling pulsars,showing that the source of J1909+0122 has the second largest NF in the population.Long-term timing observations over six months were used to derive the phase-connected ephemeris of this pulsar.The measured P and P values disfavor dipolar geometry for polar gap models,and the prediction for a space-charge-limited flow model in the case of inverse Compton scattering is only just above the death line.In this work,PSR J1909+0122 has revealed possible correlations between nulling behavior and pulsar properties,which will help to shed light on the pulsar emission mechanism and its temporal evolution in future observations. | Yutong Chen Pei Wang Di Li Erbil Gügercinoğlu Rushuang Zhao Lingqi Meng Jianping Yuan Jiarui Niu Weiwei Zhu Yi Feng Chenchen Miao Chenhui Niu Qingdong Wu Na Wang Shen Wang Xiaoyao Xie Mengyao Xue Jumei Yao Mao Yuan Shanping You Xuhong Yu Youling Yue Jie Zhang Junshuo Zhang Lei Zhang Yabiao Wang Zhenye Gan Yuxi Li Zhongyi Sun Chengjie Wang | 2023 | Research in Astronomy and Astrophysics2023，23，8： | 0 |
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