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基于Single—Sequence布图规划线长约束问题的研究
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作者 周永翔 刘陈 《电脑知识与技术》 2009年第1期247-250,共4页
布图规划是VLSI设计中非常重要的步骤。Single—Sequenc是一种非常有用的表示布图的编码方法。在实际的布图规划中,由于线长对芯片性能有较大的影响,因此为了使芯片的整体性能达到最优,考虑线长因素,使线长尽可能短。该论文提出了... 布图规划是VLSI设计中非常重要的步骤。Single—Sequenc是一种非常有用的表示布图的编码方法。在实际的布图规划中,由于线长对芯片性能有较大的影响,因此为了使芯片的整体性能达到最优,考虑线长因素,使线长尽可能短。该论文提出了在用模拟退火算法寻求最优布图的同时,通过对算法加以改进,考虑线长约束条件,有效地解决了布图规划的线长约束问题。 展开更多
关键词 VLSI 布图规划 模拟退火 singlesequence 线长 特征尺寸
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Single-cell transcriptomic dissection of the cellular and molecular events underlying the triclosan-induced liver fibrosis in mice 被引量:1
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作者 Yun-Meng Bai Fan Yang +12 位作者 Piao Luo Lu-Lin Xie Jun-Hui Chen Yu-Dong Guan Hong-Chao Zhou Teng-Fei Xu Hui-Wen Hao Bing Chen Jia-Hui Zhao Cai-Ling Liang Ling-Yun Dai Qing-Shan Geng Ji-Gang Wang 《Military Medical Research》 SCIE CAS CSCD 2023年第5期599-619,共21页
Background: Triclosan [5-chloro-2-(2,4-dichlorophenoxy) phenol, TCS], a common antimicrobial additive in many personal care and health care products, is frequently detected in human blood and urine. Therefore, it has ... Background: Triclosan [5-chloro-2-(2,4-dichlorophenoxy) phenol, TCS], a common antimicrobial additive in many personal care and health care products, is frequently detected in human blood and urine. Therefore, it has been considered an emerging and potentially toxic pollutant in recent years. Long-term exposure to TCS has been suggested to exert endocrine disruption effects, and promote liver fibrogenesis and tumorigenesis. This study was aimed at clarifying the underlying cellular and molecular mechanisms of hepatotoxicity effect of TCS at the initiation stage.Methods: C57BL/6 mice were exposed to different dosages of TCS for 2 weeks and the organ toxicity was evaluated by various measurements including complete blood count, histological analysis and TCS quantification. Single cell RNA sequencing(scRNA-seq) was then carried out on TCS-or mock-treated mice livers to delineate the TCS-induced hepatotoxicity. The acquired single-cell transcriptomic data were analyzed from different aspects including differential gene expression, transcription factor(TF) regulatory network, pseudotime trajectory, and cellular communication, to systematically dissect the cellular and molecular events after TCS exposure. To verify the TCS-induced liver fibrosis,the expression levels of key fibrogenic proteins were examined by Western blotting, immunofluorescence, Masson’s trichrome and Sirius red stainings. In addition, normal hepatocyte cell MIHA and hepatic stellate cell LX-2 were used as in vitro cell models to experimentally validate the effects of TCS by immunological, proteomic and metabolomic technologies.Results: We established a relatively short term TCS exposure murine model and found the TCS mainly accumulated in the liver. The scRNA-seq performed on the livers of the TCS-treated and control groups profiled the gene expressions of > 76,000 cells belonging to 13 major cell types. Among these types, hepatocytes and hepatic stellate cells(HSCs)were significantly increased in TCS-treated group. We found that TCS promoted fibrosis-associated proliferation of hepatocytes, in which Gata2 and Mef2c are the key driving TFs. Our data also suggested that TCS induced the proliferation and activation of HSCs, which was experimentally verified in both liver tissue and cell model. In addition,other changes including the dysfunction and capillarization of endothelial cells, an increase of fibrotic characteristics in B plasma cells, and M2 phenotype-skewing of macrophage cells, were also deduced from the scRNA-seq analysis, and these changes are likely to contribute to the progression of liver fibrosis. Lastly, the key differential ligand-receptor pairs involved in cellular communications were identified and we confirmed the role of GAS6_AXL interactionmediated cellular communication in promoting liver fibrosis.Conclusions: TCS modulates the cellular activities and fates of several specific cell types(including hepatocytes, HSCs,endothelial cells, B cells, Kupffer cells and liver capsular macrophages) in the liver, and regulates the ligand-receptor interactions between these cells, thereby promoting the proliferation and activation of HSCs, leading to liver fibrosis.Overall, we provide the first comprehensive single-cell atlas of mice livers in response to TCS and delineate the key cellular and molecular processes involved in TCS-induced hepatotoxicity and fibrosis. 展开更多
关键词 TRICLOSAN single cell RNA sequencing Liver fibrogenesis Hepatic stellate cell
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Single-cell RNA sequencing in cornea research:Insights into limbal stem cells and their niche regulation 被引量:1
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作者 Di Sun Wei-Yun Shi Sheng-Qian Dou 《World Journal of Stem Cells》 SCIE 2023年第5期466-475,共10页
The corneal epithelium is composed of stratified squamous epithelial cells on the outer surface of the eye,which acts as a protective barrier and is critical for clear and stable vision.Its continuous renewal or wound... The corneal epithelium is composed of stratified squamous epithelial cells on the outer surface of the eye,which acts as a protective barrier and is critical for clear and stable vision.Its continuous renewal or wound healing depends on the proliferation and differentiation of limbal stem cells(LSCs),a cell population that resides at the limbus in a highly regulated niche.Dysfunction of LSCs or their niche can cause limbal stem cell deficiency,a disease that is manifested by failed epithelial wound healing or even blindness.Nevertheless,compared to stem cells in other tissues,little is known about the LSCs and their niche.With the advent of single-cell RNA sequencing,our understanding of LSC characteristics and their microenvironment has grown considerably.In this review,we summarized the current findings from single-cell studies in the field of cornea research and focused on important advancements driven by this technology,including the heterogeneity of the LSC population,novel LSC markers and regulation of the LSC niche,which will provide a reference for clinical issues such as corneal epithelial wound healing,ocular surface reconstruction and interventions for related diseases. 展开更多
关键词 CORNEA Limbal stem cells single cell RNA sequencing HETEROGENEITY Novel markers Niche regulation
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Single cell RNA sequencing reveals mesenchymal heterogeneity and critical functions of Cd271 in tooth development
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作者 Yan-Yan Zhang Feng Li +6 位作者 Xiao-Ke Zeng Yan-Hui Zou Bing-Bing Zhu Jia-Jia Ye Yun-Xiao Zhang Qiu Jin Xin Nie 《World Journal of Stem Cells》 SCIE 2023年第6期589-605,共17页
BACKGROUND Accumulating evidence suggests that the maxillary process,to which cranial crest cells migrate,is essential to tooth development.Emerging studies indicate that Cd271 plays an essential role in odontogenesis... BACKGROUND Accumulating evidence suggests that the maxillary process,to which cranial crest cells migrate,is essential to tooth development.Emerging studies indicate that Cd271 plays an essential role in odontogenesis.However,the underlying mechanisms have yet to be elucidated.AIM To establish the functionally heterogeneous population in the maxillary process,elucidate the effects of Cd271 deficiency on gene expression differences.METHODS p75NTR knockout(Cd271-/-)mice(from American Jackson laboratory)were used to collect the maxillofacial process tissue of p75NTR knockout mice,and the wildtype maxillofacial process of the same pregnant mouse wild was used as control.After single cell suspension,the cDNA was prepared by loading the single cell suspension into the 10x Genomics Chromium system to be sequenced by NovaSeq6000 sequencing system.Finally,the sequencing data in Fastq format were obtained.The FastQC software is used to evaluate the quality of data and CellRanger analyzed the data.The gene expression matrix is read by R software,and Seurat is used to control and standardize the data,reduce the dimension and cluster.We search for marker genes for subgroup annotation by consulting literature and database;explore the effect of p75NTR knockout on mesenchymal stem cells(MSCs)gene expression and cell proportion by cell subgrouping,differential gene analysis,enrichment analysis and protein-protein interaction network analysis;understand the interaction between MSCs cells and the differentiation trajectory and gene change characteristics of p75NTR knockout MSCs by cell communication analysis and pseudo-time analysis.Last we verified the findings single cell sequencing in vitro.RESULTS We identified 21 cell clusters,and we re-clustered these into three subclusters.Importantly,we revealed the cell–cell communication networks between clusters.We clarified that Cd271 was significantly associated with the regulation of mineralization.CONCLUSION This study provides comprehensive mechanistic insights into the maxillary-process-derived MSCs and demonstrates that Cd271 is significantly associated with the odontogenesis in mesenchymal populations. 展开更多
关键词 Cd271 Mesenchymal stem cells single cell RNA sequencing OSTEOGENESIS MINERALIZATION Tooth development
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A SARS-CoV-2 neutralizing antibody discovery by single cell sequencing and molecular modeling
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作者 Zheyue Wang Qi Tang +14 位作者 Bende Liu Wenqing Zhang Yufeng Chen Ningfei Ji Yan Peng Xiaohui Yang Daixun Cui Weiyu Kong Xiaojun Tang Tingting Yang Mingshun Zhang Xinxia Chang Jin Zhu Mao Huang Zhenqing Feng 《The Journal of Biomedical Research》 CAS CSCD 2023年第3期166-178,共13页
Although vaccines have been developed,mutations of SARS-CoV-2,especially the dominant B.1.617.2(delta)and B.1.529(omicron)strains with more than 30 mutations on their spike protein,have caused a significant decline in... Although vaccines have been developed,mutations of SARS-CoV-2,especially the dominant B.1.617.2(delta)and B.1.529(omicron)strains with more than 30 mutations on their spike protein,have caused a significant decline in prophylaxis,calling for the need for drug improvement.Antibodies are drugs preferentially used in infectious diseases and are easy to get from immunized organisms.The current study combined molecular modeling and single memory B cell sequencing to assess candidate sequences before experiments,providing a strategy for the fabrication of SARS-CoV-2 neutralizing antibodies.A total of 128 sequences were obtained after sequencing 196 memory B cells,and 42 sequences were left after merging extremely similar ones and discarding incomplete ones,followed by homology modeling of the antibody variable region.Thirteen candidate sequences were expressed,of which three were tested positive for receptor binding domain recognition but only one was confirmed as having broad neutralization against several SARS-CoV-2 variants.The current study successfully obtained a SARS-CoV-2 antibody with broad neutralizing abilities and provided a strategy for antibody development in emerging infectious diseases using single memory B cell BCR sequencing and computer assistance in antibody fabrication. 展开更多
关键词 SARS-CoV-2 neutralizing antibody single B cell BCR sequencing molecular modeling
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Rapid and Accurate Sequencing of Enterovirus Genomes Using MinION Nanopore Sequencer 被引量:11
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作者 WANG Ji KE Yue Hua +6 位作者 ZHANG Yong HUANG Ke Qiang WANG Lei SHEN Xin Xin DONG Xiao Ping XU Wen Bo MA Xue Jun 《Biomedical and Environmental Sciences》 SCIE CAS CSCD 2017年第10期718-726,共9页
Objective Knowledge of an enterovirus genome sequence is very important in epidemiological investigation to identify transmission patterns and ascertain the extent of an outbreak. The MinION sequencer is increasingly ... Objective Knowledge of an enterovirus genome sequence is very important in epidemiological investigation to identify transmission patterns and ascertain the extent of an outbreak. The MinION sequencer is increasingly used to sequence various viral pathogens in many clinical situations because of its long reads, portability, real-time accessibility of sequenced data, and very low initial costs. However, information is lacking on MinION sequencing of enterovirus genomes. Methods In this proof-of-concept study using Enterovirus 71 (EV71) and Coxsackievirus A16 (CA16) strains as examples, we established an amplicon-based whole genome sequencing method using MinION. We explored the accuracy, minimum sequencing time, discrimination and high-throughput sequencing ability of MinION, and compared its performance with Sanger sequencing. Results Within the first minute (min) of sequencing, the accuracy of MinION was 98.5% for the single EV71 strain and 94.12%-97.33% for 10 genetically-related CA16 strains. In as little as 14 min, 99% identity was reached for the single EV71 strain, and in 17 min (on average), 99% identity was achieved for 10 CA16 strains in a single run. Conclusion MinION is suitable for whole genome sequencing of enteroviruses with sufficient accuracy and fine discrimination and has the potential as a fast, reliable and convenient method for routine use. 展开更多
关键词 Nanopore sequencing MinION Enterovirus single molecule sequencing Viral genome sequencing
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COVID-19 Related Research by Data Mining in Single Cell Transcriptome Profiles
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作者 Zi-Wei Wang Chi-Chang Chang Quan Zou 《Journal of Electronic Science and Technology》 CAS CSCD 2021年第1期1-5,共5页
The outbreak of coronavirus disease 2019(COVID-2019)has drawn public attention all over the world.As a newly emerging area,single cell sequencing also exerts its power in the battle over the epidemic.In this review,th... The outbreak of coronavirus disease 2019(COVID-2019)has drawn public attention all over the world.As a newly emerging area,single cell sequencing also exerts its power in the battle over the epidemic.In this review,the up-to-date knowledge of COVID-19 and its receptor is summarized,followed by a collection of the mining of single cell transcriptome profiling data for the information in aspects of the vulnerable cell types in humans and the potential mechanisms of the disease. 展开更多
关键词 Coronavirus disease 2019(COVID-19) BIOINFORMATICS data mining single cell sequencing
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Insights into the genetic architecture of congenital heart disease from animal modeling 被引量:1
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作者 Wenjuan Zhu Cecilia W.Lo 《Zoological Research》 SCIE CAS CSCD 2023年第3期577-590,共14页
Congenital heart disease(CHD)is observed in up to 1%of live births and is one of the leading causes of mortality from birth defects.While hundreds of genes have been implicated in the genetic etiology of CHD,their rol... Congenital heart disease(CHD)is observed in up to 1%of live births and is one of the leading causes of mortality from birth defects.While hundreds of genes have been implicated in the genetic etiology of CHD,their role in CHD pathogenesis is still poorly understood.This is largely a reflection of the sporadic nature of CHD,as well as its variable expressivity and incomplete penetrance.We reviewed the monogenic causes and evidence for oligogenic etiology of CHD,as well as the role of de novo mutations,common variants,and genetic modifiers.For further mechanistic insight,we leveraged single-cell data across species to investigate the cellular expression characteristics of genes implicated in CHD in developing human and mouse embryonic hearts.Understanding the genetic etiology of CHD may enable the application of precision medicine and prenatal diagnosis,thereby facilitating early intervention to improve outcomes for patients with CHD. 展开更多
关键词 Congenital heart disease Genetic modifier single cell sequencing De novo mutation Protective variant Common copy number variant
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System analysis based on the T cell exhaustion‑related genes identifies CD38 as a novel therapy target for ovarian cancer
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作者 TIANMING SHI RONGRONG YAN MI HAN 《Oncology Research》 SCIE 2023年第4期591-604,共14页
Ovarian cancer(OV)is highly heterogeneous tumor with a very poor prognosis.Studies increasingly show that T cell exhaustion is prognostically relevant in OV.The aim of this study was to dissect the heterogeneity of T ... Ovarian cancer(OV)is highly heterogeneous tumor with a very poor prognosis.Studies increasingly show that T cell exhaustion is prognostically relevant in OV.The aim of this study was to dissect the heterogeneity of T cell subclusters in OV through single cell transcriptomic analysis.The single RNA-sequencing(scRNA-seq)data of five OV patients were analyzed,and six major cell clusters were identified after threshold screening.Further clustering of T cell-associated clusters revealed four subtypes.Pathways related to oxidative phosphorylation,G2M checkpoint,JAK-STAT and MAPK signaling were significantly activated,while the p53 pathway was inhibited in the CD8+exhausted T cells.The standard marker genes of CD8+T cell exhaustion were screened to develop a T-cell related gene score(TRS)based on random forest plots in TCGA cohort.The patients with low TRS have better prognosis compared to the patients with high TRS in both TCGA and GEO.In addition,most genes included in the TRS showed significant differences in expression levels between the high-and low-risk groups.Immune cell infiltration was analyzed using the MCPcounter and xCell algorithms,which revealed significant differences between the two risk groups,indicating that the different prognoses may stem from the respective immune landscapes.In addition,CD38 knockdown in OV cell lines increased apoptosis and inhibited invasion in vitro.Finally,we performed a drug sensitivity analysis and identified six potential drug candidates for OV.To summarize,we identified the heterogeneity and clinical significance of T cell exhaustion in OV and built a superior prognostic model based on T cell exhaustion genes,which can contribute to the development of more precise and effective therapies. 展开更多
关键词 CD8+T exhausted Ovarian cancer Prognostic model single cell sequencing
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Explore potential biomarkers to provide a theoretical basis for the treatment of liver fibrosis with pirfenidone
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作者 Hao Li Xi-Yang Dong +3 位作者 Qin Zhou Zhi-Xiang Ding Qing-Hai Wang De-Hui Li 《Gastroenterology & Hepatology Research》 2023年第3期1-11,共11页
Background:Hepatic fibrosis is a common chronic liver disease in clinic,the purpose of our study is to explore potential biomarkers to provide a theoretical basis for the treatment of liver fibrosis with pirfenidone.M... Background:Hepatic fibrosis is a common chronic liver disease in clinic,the purpose of our study is to explore potential biomarkers to provide a theoretical basis for the treatment of liver fibrosis with pirfenidone.Methods:We downloaded a gene-sequencing dataset and a single-cell dataset from the GEO database and pirfenidone target genes from three different databases.First,we performed GO,KEGG,and DO analysis on pirfenidone target genes.Then,we grouped the liver tissue sequencing data(GSE162694)in the sequencing data set(N-F0 group and F1-F4 group)and performed gene expression differential analysis on these two groups,weighted gene co-expression network analysis and gene Enrichment analysis.Finally,we intersected the significantly upregulated genes in the F1-F4 group with the pirfenidone target genes and performed PPI network analysis.In order to further explore the expression of both pirfenidone drug target genes and liver fibrosis disease genes(PDLFG)in different immune cells of liver tissue,we used the CD45+cell data in the GSE136103 data set for further analysis.Results:A subnetwork consisting of CDC42,HNF4A,BHLHE40,CCDC71L,NR1H3,TNF,MGLL,GPT,SCD and PLIN1 was screened out,and by analysis,we finally identified the SCD as PDLFG.In single-cell sequencing analysis,we found that SCD was highly expressed in M2-polarized macrophages.Conclusion:SCD may be an important target protein to inhibit the progression of liver fibrosis. 展开更多
关键词 hepatic fibrosis pirfenidone target genes BIOMARKER GSEA WGCNA single cell sequencing analysis
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Sequence Information on Simple Sequence Repeats and Single Nucleotide Polymorphisms through Transcriptome Analysis of Mungbean 被引量:4
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作者 Kyaw Thu Moe Jong-Wook Chung +5 位作者 Young-Il Cho Jung-Kyung Moon Ja-Hwan Ku Jin-Kyo Jung Jungran Lee Yong-Jin Park 《Journal of Integrative Plant Biology》 SCIE CAS CSCD 2011年第1期63-73,共11页
Mungbean (Vigna radiata (L.) Wilczek) is a unique species in its ability to fix atmospheric nitrogen, with early maturity, and relatively good drought resistance. We used 454 sequencing technology for transcriptom... Mungbean (Vigna radiata (L.) Wilczek) is a unique species in its ability to fix atmospheric nitrogen, with early maturity, and relatively good drought resistance. We used 454 sequencing technology for transcriptome sequencing. A total of 150 159 and 142 993 reads produced 5 254 and 6 374 large contigs (〉_500 bp) with an average length of 833 and 853 for Sunhwa and Jangan, respectively. Functional annotation to known sequences yielded 41.34% and 41.74% unigenes for Jangan and Sunhwa. A higher number of simple sequence repeat (SSR) motifs was identified in Jangan (1 630) compared with that of Sunhwa (1 334). A similar SSR distribution pattern was observed in both varieties. A total of 8 249 single nucleotide polymorphisms (SNPs) and indels with 2 098 high-confidence candidates were identified in the two mungbean varieties. The average distance between individual SNPs was -860 bp. Our report demonstrates the utility of transcriptomic data for implementing a functional annotation and development of genetic markers. We also provide large resource sequence data for mungbean improvement programs. 展开更多
关键词 sequence Information on Simple sequence Repeats and single Nucleotide Polymorphisms through Transcriptome Analysis of Mungbean SNPS
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Complete genome of Cobetia marina JCM 21022T and phylogenomic analysis of the family Halomonadaceae 被引量:1
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作者 唐祥海 徐奎鹏 +2 位作者 韩晓娟 莫照兰 茅云翔 《Journal of Oceanology and Limnology》 SCIE CAS CSCD 2018年第2期528-536,共9页
Cobetia marina is a model proteobacteria in researches on marine biofouling. Its taxonomic nomenclature has been revised many times over the past few decades. ~To better understand the role of the surface-associated l... Cobetia marina is a model proteobacteria in researches on marine biofouling. Its taxonomic nomenclature has been revised many times over the past few decades. ~To better understand the role of the surface-associated lifestyle of C. marina and the phylogeny of the family Halomonadaceae, we sequenced the entire genome of C. marina JCM 21022 ~T using single molecule real-time sequencing technology(SMR^T) and performed comparative genomics and phylogenomics analyses. ~The circular chromosome was 4 176 300 bp with an average GC content of 62.44% and contained 3 611 predicted coding sequences, 72 t RNA genes, and 21 r RNA genes. ~The C. marina JCM 21022 ~T genome contained a set of crucial genes involved in surface colonization processes. ~The comparative genome analysis indicated the significant diff erences between C. marina JCM 21022 ~T and Cobetia amphilecti KMM 296(formerly named C. marina KMM 296) resulted from sequence insertions or deletions and chromosomal recombination. Despite these diff erences, pan and core genome analysis showed similar gene functions between the two strains. ~The phylogenomic study of the family Halomonadaceae is reported here for the first time. We found that the relationships were well resolved among every genera tested, including Chromohalobacter, Halomonas, Cobetia, Kushneria, Zymobacter, and Halotalea. 展开更多
关键词 Cobetia marina JCM 21022T Halomonadaceae complete genome sequence comparative genomics PHYLOGENOMICS surface colonization single molecule real-time sequencing technology(SMRT)
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基于SS序列集成电路不规则模块布图算法
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作者 徐敏 刘陈 《微型机与应用》 2010年第3期62-63,66,共3页
针对Single-Sequence的集成电路布图,在SS编解码应用对芯片中各单元的摆放进行优化,从而达到芯片面积利用率最大化。重点介绍了利用SS序列解决不规则模块摆放问题,使得SS布图功能更灵活多变。
关键词 singlesequence 水平/垂直约束图 ABLR关系
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基于SS序列集成电路布线技术
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作者 徐敏 刘陈 《电脑知识与技术》 2009年第4期2749-2750,共2页
集成电路(IC)是在半导体基片上形成的完整的电子线路。当前芯片里的电路与系统日趋复杂,超大规模集成电路(VLSI)设计技术水平也在逐渐提高。VLSI设计中一般采用分级设计的方法。布图设计过程是整个VLSI分级设计中非常关键的步骤之... 集成电路(IC)是在半导体基片上形成的完整的电子线路。当前芯片里的电路与系统日趋复杂,超大规模集成电路(VLSI)设计技术水平也在逐渐提高。VLSI设计中一般采用分级设计的方法。布图设计过程是整个VLSI分级设计中非常关键的步骤之一。基于Single-Sequence的集成电路布图就是在SS编解码的应用下对芯片中各单元的摆放进行优化从而达到芯片面积利用率最大化。本文重点介绍了在SS序列生成版图后各单元间连线的设计以及如何根据水平/垂直约束图提取版图中各单元的坐标。并根据要连模块的位置关系对其连线经过的模块进行有条件加线宽的处理。 展开更多
关键词 singlesequence 水平/垂直约束图 ABLR关系
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FSPAM:A Feature Construction Method to Identifying Cell Populations in ScRNA-seq Data
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作者 Amin Einipour Mohammad Mosleh Karim Ansari-Asl 《Computer Modeling in Engineering & Sciences》 SCIE EI 2020年第1期377-397,共21页
The emergence of single-cell RNA-sequencing(scRNA-seq)technology has introduced new information about the structure of cells,diseases,and their associated biological factors.One of the main uses of scRNA-seq is identi... The emergence of single-cell RNA-sequencing(scRNA-seq)technology has introduced new information about the structure of cells,diseases,and their associated biological factors.One of the main uses of scRNA-seq is identifying cell populations,which sometimes leads to the detection of rare cell populations.However,the new method is still in its infancy and with its advantages comes computational challenges that are just beginning to address.An important tool in the analysis is dimensionality reduction,which transforms high dimensional data into a meaningful reduced subspace.The technique allows noise removal,visualization and compression of high-dimensional data.This paper presents a new dimensionality reduction approach where,during an unsupervised multistage process,a feature set including high valuable markers is created which can facilitate the isolation of cell populations.Our proposed method,called fusion of the Spearman and Pearson affinity matrices(FSPAM),is based on a graph-based Gaussian kernel.Use of the graph theory can be effective to overcome the challenge of the nonlinear relations between cellular markers in scRNA-seq data.Furthermore,with a proper fusion of the Pearson and Spearman correlation coefficient criteria,it extracts a set of the most important features in a new space.In fact,the FSPAM aggregates the various aspects of cell-to-cell similarity derived from the Pearson and Spearman metrics,and reveals new aspects of cell-to-cell similarity,which can be used to extract new features.The results of the identification of cell populations via k-means++clustering method based on the features extracted from the FSPAM and different datasets of scRNA-seq suggested that the proposed method,regardless of the characteristics that govern each dataset,enjoys greater accuracy and better quality compared to previous methods. 展开更多
关键词 single cell RNA sequencing cell population feature extraction FUSION
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Full-length transcripts facilitates Portunus trituberculatus genome structure annotation
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作者 Fangrui LOU Zhiqiang HAN 《Journal of Oceanology and Limnology》 SCIE CAS CSCD 2022年第5期2042-2051,共10页
Portunus trituberculatus is an ide al model for elucidating crustacean genetic networks.Here we combined single molecule real-time(SMRT)sequencing and Illumina RNA-seq to characterize the coding genes,non-coding RNAs ... Portunus trituberculatus is an ide al model for elucidating crustacean genetic networks.Here we combined single molecule real-time(SMRT)sequencing and Illumina RNA-seq to characterize the coding genes,non-coding RNAs and pseudogenes and further to improve the genome annotation information of P.tritub erculatus.In this study,we assembled 9694 non-redundancy full-length transcripts,and 658737307-bp repetitive sequences were identified in the P.trituberculatus full-length transcriptome.We also predicted the P.tritub erculatus genome structure based on full-length transcripts,including 18602 genes,28686 non-coding RNAs,1407 pseudogenes,740 motif,and 26434 domain.Meanwhile,14460,10211,5412,7314,and 14448 genes had significant matches with sequences in the NR,KOG,GO,KEGG,and TrEMBL database,respectively.Overall,our work firstly provided the long-read transcriptome and we believed that these data are very necessary to improve the annotation information of P.trituberculatus genome structure,and useful information for the future studies on evolution and physiological regulation of P.trituberculatus. 展开更多
关键词 Portunus trituberculatus full-length transcripts single molecule real-time(SMRT)sequencing
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Single cell metabolic phenome and genome via the ramanome technology platform:Precision medicine of infectious diseases at the ultimate precision? 被引量:1
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作者 Jian Xu Jianzhong Zhang +3 位作者 Yingchun Xu Yi‐Wei Tang Bo Ma Yuzhang Wu 《iLABMED》 2023年第1期5-14,共10页
Due to the limitations of existing approaches,a rapid,sensitive,accurate,comprehensive,and generally applicable strategy to diagnose and treat bacterial and fungal infections remains a major challenge.Here,based on th... Due to the limitations of existing approaches,a rapid,sensitive,accurate,comprehensive,and generally applicable strategy to diagnose and treat bacterial and fungal infections remains a major challenge.Here,based on the ramanome technology platform,we propose a culture‐free,one cell resolution,phenome‐genome‐combined strategy called single‐cell identification,viability and vitality tests and source tracking(SCIVVS).For each cell directly extracted from a clinical specimen,the fingerprint region of the D2O‐probed single cell Raman spectrum(SCRS)enables species‐level identification based on a reference SCRS database of pathogen species,whereas the C‐D band accurately quantifies viability,metabolic vitality,phenotypic susceptibility to antimicrobials,and their intercellular heterogeneity.Moreover,to source track a cell,Raman‐activated cell sorting followed by sequencing or cultivation proceeds,producinging an indexed,high coverage genome assembly or a pure culture from precisely one pathogenic cell.Finally,an integrated SCIVVS workflow that features automated profiling and sorting of metabolic and morphological phenomes can complete the entire process in only a few hours.Because it resolves heterogeneity for both the metabolic phenome and genome,targets functions,can be automated,and is orders‐of‐magnitude faster while cost‐effective,SCIVVS is a new technological and data framework to diagnose and treat bacterial and fungal infections in various clinical and disease control settings. 展开更多
关键词 diagnosis of microbial infections phenome ramanome Raman‐activated cell sorting(RACS) single cell sequencing
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PN code generator based on generalized Bent function for SW/SFH System
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《Wuhan University Journal of Natural Sciences》 CAS 1996年第2期221-224,共4页
Generalized Bent function and generalized Bent function sequences are introduced in this paper.The main performance or these sequences used as SW/SFH(Short Wave/Slow Frequency Hopping) code are studied. And the hardwa... Generalized Bent function and generalized Bent function sequences are introduced in this paper.The main performance or these sequences used as SW/SFH(Short Wave/Slow Frequency Hopping) code are studied. And the hardware circuit and the soflware program flow chart of the SW/SFH PN code generator are also given,which is based on generalized Bent function sequence generator by using a single chip mlcrocomputer. 展开更多
关键词 SW/FH bent function sequence PN code generator single chip microcomputer
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VASC: Dimension Reduction and Visualization of Single-cell RNA-seq Data by Deep Variational Autoencoder 被引量:7
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作者 Dongfang Wang Jin Gu 《Genomics, Proteomics & Bioinformatics》 SCIE CAS CSCD 2018年第5期320-331,共12页
Single-cell RNA sequencing(scRNA-seq) is a powerful technique to analyze the transcriptomic heterogeneities at the single cell level. It is an important step for studying cell subpopulations and lineages, with an effe... Single-cell RNA sequencing(scRNA-seq) is a powerful technique to analyze the transcriptomic heterogeneities at the single cell level. It is an important step for studying cell subpopulations and lineages, with an effective low-dimensional representation and visualization of the original scRNA-Seq data. At the single cell level, the transcriptional fluctuations are much larger than the average of a cell population, and the low amount of RNA transcripts will increase the rate of technical dropout events. Therefore, scRNA-seq data are much noisier than traditional bulk RNA-seq data. In this study, we proposed the deep variational autoencoder for scRNA-seq data(VASC), a deep multi-layer generative model, for the unsupervised dimension reduction and visualization of scRNA-seq data. VASC can explicitly model the dropout events and find the nonlinear hierarchical feature representations of the original data. Tested on over 20 datasets, VASC shows superior performances in most cases and exhibits broader dataset compatibility compared to four state-of-the-art dimension reduction and visualization methods. In addition, VASC provides better representations for very rare cell populations in the 2D visualization. As a case study, VASC successfully re-establishes the cell dynamics in pre-implantation embryos and identifies several candidate marker genes associated with early embryo development. Moreover, VASC also performs well on a 10× Genomics dataset with more cells and higher dropout rate. 展开更多
关键词 single cell RNA sequencing Deep variational autoencoder Dimension reduction VISUALIZATION DROPOUT
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Biomonitoring for traditional herbal medicinal products using DNA metabarcoding and single molecule, real-time sequencing 被引量:23
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作者 Tianyi Xin Zhichao Xu +6 位作者 Jing Jia Christine Leon Songnian Hu Yulin Lin Subramanyam Ragupathy Jingyuan Song Steven G.Newmaster 《Acta Pharmaceutica Sinica B》 SCIE CAS CSCD 2018年第3期488-497,共10页
Global concerns have been paid to the potential hazard of traditional herbal medicinal products(THMPs). Substandard and counterfeit THMPs, including traditional Chinese patent medicine, health foods, dietary supplemen... Global concerns have been paid to the potential hazard of traditional herbal medicinal products(THMPs). Substandard and counterfeit THMPs, including traditional Chinese patent medicine, health foods, dietary supplements, etc. are potential threats to public health. Recent marketplace studies using DNA barcoding have determined that the current quality control methods are not sufficient for ensuring the presence of authentic herbal ingredients and detection of contaminants/adulterants. An efficient biomonitoring method for THMPs is of great needed. Herein, metabarcoding and single-molecule, realtime(SMRT) sequencing were used to detect the multiple ingredients in Jiuwei Qianghuo Wan(JWQHW), a classical herbal prescription widely used in China for the last 800 years. Reference experimental mixtures and commercial JWQHW products from the marketplace were used to confirm the method. Successful SMRT sequencing results recovered 5416 and 4342 circular-consensus sequencing(CCS) reads belonging to the ITS2 and psb A-trn H regions. The results suggest that with the combination of metabarcoding and SMRT sequencing, it is repeatable, reliable, and sensitive enough to detect species in the THMPs, and the error in SMRT sequencing did not affect the ability to identify multiple prescribed species and several adulterants/contaminants. It has the potential for becoming a valuable tool for the biomonitoring of multi-ingredient THMPs. 展开更多
关键词 Traditional herbal medic inal products(THMP) Species mixture Authentication DNA metabarcoding single molecule real-time(SMRT) sequencing Circular-consensus sequencing(CCS)
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