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19篇 您的检索式:作者名="Jingfa Xiao"
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1The 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://gffzz77e3413bc06540edsc0bbubb9o9no6cxc.ffgz.tsg.suse.edu.cn/gsa/),GSA for Human(GSA-Human,http://gffzz77e3413bc06540edsc0bbubb9o9no6cxc.ffgz.tsg.suse.edu.cn/gsa-human/),and Open Archive for Miscellaneous Data(OMIX,http://gffzz77e3413bc06540edsc0bbubb9o9no6cxc.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 2021Genomics, Proteomics & Bioinformatics2021,19,4:38
2GSA: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://gffzzdbc7b6aaae734bddhc0bbubb9o9no6cxc.ffgz.tsg.suse.edu.cn/gsa or http://gffzz4eaf941a184140e3hc0bbubb9o9no6cxc.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 2017Genomics, Proteomics & Bioinformatics2017,15,1:13
3Genome 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://gffzz77e3413bc06540edsc0bbubb9o9no6cxc.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://gffzz77e3413bc06540edsc0bbubb9o9no6cxc.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 2021Genomics, Proteomics & Bioinformatics2021,19,4:12
4Study 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 2008Chinese Science Bulletin2008,53,9:5
5Whole 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 2019Genomics, Proteomics & Bioinformatics2019,17,3:4
6DNA 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 2011Science China(Life Sciences)2011,54,3:4
7The 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://gffzzdbc7b6aaae734bddsc0bbubb9o9no6cxc.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 2020Genomics, Proteomics & Bioinformatics2020,18,6:4
8Transcriptomic 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 2014Science China(Life Sciences)2014,57,3:4
9Systematic 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 2013Science China(Life Sciences)2013,56,10:4
10Coevolution 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 2011Journal of Genetics and Genomics2011,38,5:3
11Transcriptome-wide evolutionary analysis on essential brown algae(Phaeophyceae)in China显示文摘Brown algae(Chromista,Ochrophyta,Phaeophyceae) are a large group of multicellular algae that play important roles in the ocean's ecosystem and biodiversity.However,poor molecular bases for studying their phylogenetic evolutions and novel metabolic characteristics have hampered progress in the field.In this study,we sequenced the de novo transcriptome of 18 major species of brown algae in China,covering six orders and seven families,using the high-throughput sequencing platform Illumina HiSeq 2000.From the transcriptome data of these 18 species and publicly available genome data of Ectocarpus siliculosus and Phaeodactylum tricornutum,we identified 108 nuclear-generated orthologous genes and clarified the phylogenetic relationships among these brown algae based on a multigene method.These brown algae could be separated into two clades: Clade Ishigeales-Dictyotales and Clade Ectocarpales-Laminariales-Desmarestiale-Fucales.The former was at the base of the phylogenetic tree,indicating its early divergence,while the latter was divided into two branches,with Order Fucales diverging from Orders Ectocarpales,Laminariales,and Desmarestiale.In our analysis of taxonomy-contentious species,Sargassum fusiforme and Saccharina sculpera were found to be closely related to genera Sargassum and Saccharina,respectively,while Petalonia fascia showed possible relation to genus Scytosiphon.The study provided molecular evidence for the phylogenetic taxonomy of brown algae.SUN Jing WANG Liang WU Shuangxiu WANG Xumin XIAO Jingfa CHI Shan LIU Cui REN Lufeng ZHAO Yuhui LIU Tao YU Jun 2014Acta Oceanologica Sinica2014,33,2:2
12Ribogenomics: 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 2014Genomics, Proteomics & Bioinformatics2014,12,2:2
13Compositional 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 2020Genomics, Proteomics & Bioinformatics2020,18,6:1
14Precision 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-scaleYu 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 2016Genomics, Proteomics & Bioinformatics2016,14,5:1
15A 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 2015Genomics, Proteomics & Bioinformatics2015,13,1:1
16ParaAT: A parallel tool for constructing multiple protein-coding DNA alignments显示文摘Zhang Zhang Xiao Jingfa Wu Jiayan 2012Biochemical Biophysical Research Communications2012,419,4:1
17Microscopic hyperspectral imaging studies of normal and diabetic retina of rats显示文摘A microscopic hyperspectral imager was developed based on the microscopic technology and the spectral imaging technology. Some microscopic hyperspectral images of retina sections of the normal, the diabetic, and the treated rats were collected by the new imager. Single-band images and pseudo-color images of each group were obtained and the typical transmittance spectrums were ex-tracted. The results showed that the transmittance of outer nuclear layer cells of the diabetic group was generally higher than that of the normal. A small absorption peak appeared near the 180th band in the spectrum of the diabetic group and this peak weakened or disappeared in the spectrum of the treated group. Our findings indicate that the microscopic hyperspectral images include wealthy information of retina sections which is helpful for the ophthalmologist to reveal the pathogenesis of diabetic reti-nopathy and explore the therapeutic effect of drugs.LI QingLi XUE YongQi ZHANG JingFa XIAO GongHai 2008Science China(Life Sciences)2008,51,9:1
18Latest notable achievements in genomics显示文摘Within the past 10 years, the progress of genomics development in China exhibited a frogleap in terms of scale,quality, organization, and international collaboration.WU JiaYan XIAO JingFa YU Jun 2012Science China(Life Sciences)2012,55,7:0
19Database Commons:A Catalog of Worldwide Biological Databases显示文摘Biological databases serve as a global fundamental infrastructure for the worldwide scientific community,which dramatically aid the transformation of big data into knowledge discovery and drive significant innovations in a wide range of research fields.Given the rapid data production,biological databases continue to increase in size and importance.To build a catalog of worldwide biological databases,we curate a total of 5825 biological databases from 8931 publications,which are geographically distributed in 72 countries/regions and developed by 1975 institutions(as of September 20,2022).We further devise a z-index,a novel index to characterize the scientific impact of a database,and rank all these biological databases as well as their hosting institutions and countries in terms of citation and z-index.Consequently,we present a series of statistics and trends of worldwide biological databases,yielding a global perspective to better understand their status and impact for life and health sciences.An up-to-date catalog of worldwide biological databases,as well as their curated meta-information and derived statistics,is publicly available at Database Commons(http://gffzz77e3413bc06540edsc0bbubb9o9no6cxc.ffgz.tsg.suse.edu.cn/databasecommons/).Lina Ma Dong Zou Lin Liu Huma Shireen Amir AAbbasi Alex Bateman Jingfa Xiao Wenming Zhao Yiming Bao Zhang Zhang 2023Genomics, Proteomics & Bioinformatics2023,21,5:0
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