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| 1 | The Genome Sequence Archive Family: Toward Explosive Data Growth and Diverse Data Types显示文摘The Genome Sequence Archive(GSA)is a data repository for archiving raw sequence data,which provides data storage and sharing services for worldwide scientific communities.Considering explosive data growth with diverse data types,here we present the GSA family by expanding into a set of resources for raw data archive with different purposes,namely,GSA(http://gffzz77e3413bc06540eds0vovcx65q5pu66nn.ffgz.tsg.suse.edu.cn/gsa/),GSA for Human(GSA-Human,http://gffzz77e3413bc06540eds0vovcx65q5pu66nn.ffgz.tsg.suse.edu.cn/gsa-human/),and Open Archive for Miscellaneous Data(OMIX,http://gffzz77e3413bc06540eds0vovcx65q5pu66nn.ffgz.tsg.suse.edu.cn/omix/).Compared with the 2017 version,GSA has been significantly updated in data model,online functionalities,and web interfaces.GSA-Human,as a new partner of GSA,is a data repository specialized in human genetics-related data with controlled access and security.OMIX,as a critical complement to the two resources mentioned above,is an open archive for miscellaneous data.Together,all these resources form a family of resources dedicated to archiving explosive data with diverse types,accepting data submissions from all over the world,and providing free open access to all publicly available data in support of worldwide research activities. | Tingting Chen Xu Chen Sisi Zhang Junwei Zhu Bixia Tang Anke Wang Lili Dong Zhewen Zhang Caixia Yu Yanling Sun Lianjiang Chi Huanxin Chen Shuang Zhai Yubin Sun Li Lan Xin Zhang Jingfa Xiao Yiming Bao Yanqing Wang Zhang Zhang Wenming Zhao | 2021 | Genomics, Proteomics & Bioinformatics2021，19，4： | 38 |
| 2 | 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://gffzzdbc7b6aaae734bddh0vovcx65q5pu66nn.ffgz.tsg.suse.edu.cn/gsa or http://gffzz4eaf941a184140e3h0vovcx65q5pu66nn.ffgz.tsg.suse.edu.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 |
| 3 | Basin filling algorithm for the circular packing problem with equilibrium behavioral constraints显示文摘With the background of the satellite module layout design, the circular packing problem with equilibrium behavioral constraints is a layout optimization problem and NP-hard problem in math. For lack of a powerful optimization method, this problem is hard to solve. The energy landscape paving (ELP) method is a class of stochastic global optimization algorithms based on the Monte Carlo sampling. Based on the quasiphysical strategy and the penalty function method, the problem is converted into an unconstrained optimization problem. Here by combining the improved ELP method, the gradient method based on local search and the heuristic configuration update mechanism, a new global search algorithm, basin filling algorithm, is put forward. The numerical results show that the proposed algorithm is effective to solving the circular packing problem with equilibrium behavioral constraints, and is easy to be popularized to other layout optimization problems. | LIU JingFa LI Gang | 2010 | Science China(Information Sciences)2010，53，5： | 12 |
| 4 | Genome Warehouse: A Public Repository Housing Genome-scale Data显示文摘The Genome Warehouse(GWH)is a public repository housing genome assembly data for a wide range of species and delivering a series of web services for genome data submission,storage,release,and sharing.As one of the core resources in the National Genomics Data Center(NGDC),part of the China National Center for Bioinformation(CNCB;http://gffzz77e3413bc06540eds0vovcx65q5pu66nn.ffgz.tsg.suse.edu.cn),GWH accepts both full and partial(chloroplast,mitochondrion,and plasmid)genome sequences with different assembly levels,as well as an update of existing genome assemblies.For each assembly,GWH collects detailed genome-related metadata of biological project,biological sample,and genome assembly,in addition to genome sequence and annotation.To archive high-quality genome sequences and annotations,GWH is equipped with a uniform and standardized procedure for quality control.Besides basic browse and search functionalities,all released genome sequences and annotations can be visualized with JBrowse.By May 21,2021,GWH has received 19,124 direct submissions covering a diversity of 1108 species and has released 8772 of them.Collectively,GWH serves as an important resource for genomescale data management and provides free and publicly accessible data to support research activities throughout the world.GWH is publicly accessible at http://gffzz77e3413bc06540eds0vovcx65q5pu66nn.ffgz.tsg.suse.edu.cn/gwh. | Meili Chen Yingke Ma Song Wu Xinchang Zheng Hongen Kang Jian Sang Xingjian Xu Lili Hao Zhaohua Li Zheng Gong Jingfa Xiao Zhang Zhang Wenming Zhao Yiming Bao | 2021 | Genomics, Proteomics & Bioinformatics2021，19，4： | 12 |
| 5 | Land Subsidence in Xiong’an New Area,China Revealed by InSAR Observations显示文摘In 2017,China’s central government approved the national strategy to build Xiong’an New Area(XNA,100 km southwest to Beijing),which was announced as a'millennium strategy'and a'demo area'for a sustainable,modern,and innovative urban model.Xiong’an will draw in as much as$380 billion investment and is expected to help accelerate the development of the wider Beijing-Tianjin-Hebei(Jingjinji)Area.In this paper,present subsidence in the XNA area is investigated using InSAR observations for the first time.The 24 SAR images acquired by European Space Agency’s Sentinel-1 satellites during the period from June 2017 to July 2018 suggest that in the north of Xiong County,the subsidence rate reaches up to 90 mm/y,which is highly correlated with the exploitation of geothermal drilling.As the construction in the XNA area will significantly accelerate and its high-quality development,the InSAR findings could provide valuable information for future sustainable urban planning and underground infrastructure construction. | Keren DAI Peilian RAN Zhenhong LI Julian AUSTIN Jan-Peter MULLER Qiming ZENG Jingfa ZHANG Leyin HU | 2021 | Journal of Geodesy and Geoinformation Science2021，4，1： | 8 |
| 6 | Successful Applications of Generic Atmospheric Correction Online Service for InSAR (GACOS) to the Reduction of Atmospheric Effects on InSAR Observations显示文摘The tremendous development of Synthetic Aperture Radar(SAR)missions in recent years facilitates the study of smaller amplitude ground deformation over greater spatial scales using longer time series.However,this poses greater challenges for correcting atmospheric effects due to the wider coverage of SAR imagery than ever.Previous attempts have used observations from Global Positioning System(GPS)and Numerical Weather Models(NWMs)to separate atmospheric delays,but they are limited by(1)The availability(and distribution)of GPS stations;(2)The low spatial resolution of NWM;And(3)The difficulties in quantifying their performance.To overcome these limitations,we have developed the Generic Atmospheric Correction Online Service for InSAR(GACOS)which utilizes the high-resolution European Centre for Medium-Range Weather Forecasts(ECMWF)products using an Iterative Tropospheric Decomposition(ITD)model.This enables the reduction of the coupling effects of the troposphere turbulence and stratification and hence achieves equivalent performances over flat and mountainous terrains.GACOS comprises a range of notable features:(1)Global coverage;(2)All-weather,all-time usability;(3)Available with a maximum of two-day latency;And(4)Indicators available to assess the model’s performance and feasibility.In this paper,we demonstrate some successful applications of the GACOS online service to a variety of geophysical studies. | Chen YU Zhenhong LI Lin BAI Jan-Peter MULLER Jingfa ZHANG Qiming ZENG | 2021 | Journal of Geodesy and Geoinformation Science2021，4，1： | 8 |
| 7 | Study on microscope hyperspectral medical imaging method for biomedical quantitative analysis显示文摘A microscopic pushbroom hyperspectral imaging system was developed based on the microscopic technology and spectral imaging technology according to the principle of spectral imager in remote sensing. The basic principle and key technologies of this system were presented and the system per- formance was also analyzed. Some methods and algorithms were proposed to preprocess and nor- malize the microscopic hyperspectral data and retrieve the transmittance spectrum of samples. As a case study, the microscopic hyperspectral imaging system was used to image the retina sections of different rats and get some significant results. Experiment results show that the system can be used for the quantitative assessment and evaluating the effect of medication in biomedical research. | LI QingLi XUE YongQi XIAO GongHai ZHANG JingFa | 2008 | Chinese Science Bulletin2008，53，9： | 5 |
| 8 | Catalyzing the polysulfide conversion for promoting lithium sulfur battery performances:A review显示文摘Lithium-sulfur batteries(LSBs)are being recognized as potential successor to ubiquitous LIBs in daily life due to their higher theoretical energy density and lower cost effectiveness.However,the development of the LSB is beset with some tenacious issues,mainly including the insulation nature of the S or Li_(2)S(the discharged product),the unavoidable dissolution of the reaction intermediate products(mainly as lithium polysulfides(LiPSs)),and the subsequent LiPSs shuttling across the separator,resulting in the continuous loss of active material,anode passivation,and low coulombic efficiency.Containment methods by introducing the high-electrical conductivity host are commonly used in improving the electrochemical performances of LSBs.However,such prevalent technologies are in the price of reduced energy density since they require more addition of amount of host materials.Adding trace of catalysts that catalyze the redox reaction between S/Li_(2)S and Li_(2)Sn(3 | Jingfa Li Zhihao Niu Cong Guo Min Li Weizhai Bao | 2021 | Journal of Energy Chemistry2021，30，3： | 5 |
| 9 | A new heuristic algorithm for the circular packing problem with equilibrium constraints显示文摘The circular packing problem with equilibrium constraints is an optimization problem about simplified satellite module layout design.A heuristic algorithm based on tabu search is put forward for solving this problem.The algorithm begins from a random initial configuration and applies the gradient method with an adaptive step length to search for the minimum energy configuration.To jump out of the local minima and avoid the search doing repeated work,the algorithm adopts the strategy of tabu search.In the process of tabu search,we improve the traditional neighboring solutions,tabu objects and the acceptance criteria of the current solution effectively.We test two sets of benchmarks consisting of 11 representative instances from the current literature.The numerical results show that the proposed algorithm breaks the records in seven out of 11 instances,and obtains the optimal solutions for the other four instances. | LIU JingFa LI Gang GENG HuanTong | 2011 | Science China(Information Sciences)2011，54，8： | 5 |
| 10 | 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 |
| 11 | The Global Landscape of SARS-CoV-2 Genomes, Variants, and Haplotypes in 2019nCoVR显示文摘On January 22,2020,China National Center for Bioinformation(CNCB)released the 2019 Novel Coronavirus Resource(2019nCoVR),an open-access information resource for the severe acute respiratory syndrome coronavirus 2(SARS-CoV-2).2019nCoVR features a comprehensive integration of sequence and clinical information for all publicly available SARS-CoV-2 isolates,which are manually curated with value-added annotations and quality evaluated by an automated in-house pipeline.Of particular note,2019nCoVR offers systematic analyses to generate a dynamic landscape of SARS-CoV-2 genomic variations at a global scale.It provides all identified variants and their detailed statistics for each virus isolate,and congregates the quality score,functional annotation,and population frequency for each variant.Spatiotemporal change for each variant can be visualized and historical viral haplotype network maps for the course of the outbreak are also generated based on all complete and high-quality genomes available.Moreover,2019nCoVR provides a full collection of SARS-CoV-2 relevant literature on the coronavirus disease 2019(COVID-19),including published papers from PubMed as well as preprints from services such as bioRxiv and medRxiv through Europe PMC.Furthermore,by linking with relevant databases in CNCB,2019nCoVR offers data submission services for raw sequence reads and assembled genomes,and data sharing with NCBI.Collectively,SARS-CoV-2 is updated daily to collect the latest information on genome sequences,variants,haplotypes,and literature for a timely reflection,making 2019nCoVR a valuable resource for the global research community.2019nCoVR is accessible at http://gffzzdbc7b6aaae734bdds0vovcx65q5pu66nn.ffgz.tsg.suse.edu.cn/ncov/. | Shuhui Song Lina Ma Dong Zou Dongmei Tian Cuiping Li Junwei Zhu Meili Chen Anke Wang Yingke Ma Mengwei Li Xufei Teng Ying Cui Guangya Duan Mochen Zhang Tong Jin Chengmin Shi Zhenglin Du Yadong Zhang Chuandong Liu Rujiao Li Jingyao Zeng Lili Hao Shuai Jiang Hua Chen Dali Han Jingfa Xiao Zhang Zhang Wenming Zhao Yongbiao Xue Yiming Bao | 2020 | Genomics, Proteomics & Bioinformatics2020，18，6： | 4 |
| 12 | 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 |
| 13 | Transient deformation during the Milashan Tunnel construction in northern Sangri-Cuona Rift,southern Tibet,China observed by Sentinel-1 satellites显示文摘Using 3-year Sentinel-1 C-band synthetic aperture radar(SAR) data, we observed prominent ground subsidence around the construction site of the Milashan Tunnel, which is on top of the northern SangriCuona Rift(SCR) in southern Tibet. The most deformed area extends ~7 km in the north-south direction and ~6 km in the east-west direction, with a peak subsidence rate of over 10 mm/a in the line of sight direction of both the descending and ascending satellites. Aside from the long-term ground subsidence arising directly from underground water outflow and rock excavation, a regional aseismic fault slip episode is also evident. The aseismic slip event began in May 2016 and ended in July 2016. The surface aseismic displacements can be explained by normal faulting with mainly down-dip movement and a modest right-lateral strike-slip component on a nearly north-south trending fault. The aseismic deformation triggered by the Milashan Tunnel construction demonstrates the sensitive response of crustal-scale tectonics to human activity, which poses high seismic hazards for the heavily populated region. | Yunfeng Tian Jing Liu-Zeng Yi Luo Yongsheng Li Yingshun Hu Bin Gong Lizheng Liu Ping Guo Jingfa Zhang | 2018 | Science Bulletin2018，63，21： | 3 |
| 14 | The crystallization process of ultrafine Ni-B amorphous alloy 显示文摘 | Li Hui Li Hexing Deng Jingfa | 2001 | Materials Letters2001，50，： | 1 |
| 15 | Compositional Variability and Mutation Spectra of Monophyletic SARS-CoV-2 Clades显示文摘COVID-19 and its causative pathogen SARS-CoV-2 have rushed the world into a staggering pandemic in a few months,and a global fight against both has been intensifying.Here,we describe an analysis procedure where genome composition and its variables are related,through the genetic code to molecular mechanisms,based on understanding of RNA replication and its feedback loop from mutation to viral proteome sequence fraternity including effective sites on the replicase-transcriptase complex.Our analysis starts with primary sequence information,identity-based phylogeny based on 22,051 SARS-CoV-2 sequences,and evaluation of sequence variation patterns as mutation spectra and its 12 permutations among organized clades.All are tailored to two key mechanisms:strand-biased and function-associated mutations.Our findings are listed as follows:1)The most dominant mutation is C-to-U permutation,whose abundant second-codon-position counts alter amino acid composition toward higher molecular weight and lower hydrophobicity,albeit assumed most slightly deleterious.2)The second abundance group includes three negative-strand mutations(U-to-C,A-to-G,and G-to-A)and a positive-strand mutation(G-to-U)due to DNA repair mechanisms after cellular abasic events.3)A clade-associated biased mutation trend is found attributable to elevated level of negative-sense strand synthesis.4)Within-clade permutation variation is very informative for associating non-synonymous mutations and viral proteome changes.These findings demand a platform where emerging mutations are mapped onto mostly subtle but fast-adjusting viral proteomes and transcriptomes,to provide biological and clinical information after logical convergence for effective pharmaceutical and diagnostic applications.Such actions are in desperate need,especially in the middle of the War against COVID-19. | Xufei Teng Qianpeng Li Zhao Li Yuansheng Zhang Guangyi Niu Jingfa Xiao Jun Yu Zhang Zhang Shuhui Song | 2020 | Genomics, Proteomics & Bioinformatics2020，18，6： | 1 |
| 16 | Glucose hydro- genation to sorbitol over a skeletal Ni-P amorphous alloy catalyst显示文摘 | Li Hexing Wang Weijiang Deng Jingfa | 2000 | Journal of Catalysis2000，191，： | 1 |
| 17 | Precision Medicine:What Challenges Are We Facing?显示文摘Following the publication of the US National Research Council(NRC)report‘‘Toward Precision Medicine:Building a Knowledge Network for Biomedical Research and a New Taxonomy of Diseases'in 2011[1],several nations have announced that their national research programs would definitely head toward this direction.Now,precision medicine(PM)became a banner for many large-scale | Yu Xue Eric-Wubbo Lameijer Kai Ye Kunlin Zhang Suhua Chang Xiaoyue Wang Jianmin Wu Ge Gao Fangqing Zhao Jian Li Chunsheng Han Shuhua Xu Jingfa Xiao Xuerui Yang Xiaomin Ying Xuegong Zhang Wei-Hua Chen Yun Liu Zhang Zhang Kun Huang Jun Yu | 2016 | Genomics, Proteomics & Bioinformatics2016，14，5： | 1 |
| 18 | Uniform LiNi1/3Co1/3Mn1/3O2 hollow microspheres:designed synthesis,topotactical structural transformation and their enhanced electrochemical performance显示文摘 | Li Jingfa Xiong Shenglin LiuYurong | 2013 | Nano Energy2013，2，6： | 1 |
| 19 | Influence on the reduction degree of Ni-B/SiO2 amorphous catalyst and its role in selective hydrogenation of acrylonitrile显示文摘 | Li Hui Li Hexing Deng Jingfa | 2000 | Applied Catalysis A: General2000，193，： | 1 |
| 20 | The crystallization process of ultrafine Ni-B amorphous alloy显示文摘 | Li Hui Li Hexing Deng Jingfa | 2001 | Materials Letters2001，50，： | 1 |
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