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PathogenTrack and Yeskit: tools for identifying intracellular pathogens from single-cell RNA-sequencing

Frontiers of Medicine 2022, Volume 16, Issue 2,   Pages 251-262 doi: 10.1007/s11684-021-0915-9

Abstract: Taking advantage of single-cell RNA-sequencing (scRNA-seq) analysis, we can assess the transcriptomicfeatures at the single-cell level.Still, the tools used to interpret pathogens (such as viruses, bacteria, and fungi) at the single-cellcomputational pipeline that uses unmapped scRNA-seq data to identify intracellular pathogens at the single-cellthe state-of-the-art tools such as Viral-Track, and the first tools for identifying bacteria at the single-cell

Keywords： scRNA-seq     intracellular pathogen     microbe     COVID-19     SARS-CoV-2    

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Distinct immune escape and microenvironment between RG-like and pri-OPC-like glioma revealed by single-cellRNA-seq analysis

Frontiers of Medicine 2024, Volume 18, Issue 1,   Pages 147-168 doi: 10.1007/s11684-023-1017-7

Abstract: By conducting single-cell RNA-seq analyses on 26 gliomas, we reported their classification into primitiveoligodendrocyte precursor cell (pri-OPC)-like and radial glia (RG)-like tumors and validated it in aFor example, glial/glioma stem cell markers OLIG1/PTPRZ1 and B cell-specific receptors

Keywords： single-cell RNA-seq     glioma     radial glia     primitive oligodendrocyte precursor cell     immune escape    

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Distinct mononuclear diploid cardiac subpopulation with minimal cell–cell communications persists in

Frontiers of Medicine 2023, Volume 17, Issue 5,   Pages 939-956 doi: 10.1007/s11684-023-0987-9

Abstract: end, 12 645 cardiac cells were generated from embryonic day 17.5 and postnatal days 2 and 8 mice by single-cellRNA sequencing.MNDCMs having interactions with macrophages and non-proliferative MNDCMs (non-pMNDCMs) with minimal cell–cell Single-nucleus RNA sequencing and immunohistochemical staining further proved that the Myl4single-cell transcriptomic data.

Keywords： mononuclear diploid cardiomyocytes     cell–cell communication     cardiac fibroblast     single-cell RNA sequencing    

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Dysregulated N-methyladenosine modification in peripheral immune cells contributes to the pathogenesis of amyotrophic lateral sclerosis

Frontiers of Medicine 2024, Volume 18, Issue 2,   Pages 285-302 doi: 10.1007/s11684-023-1035-5

Abstract: Methylated RNA immunoprecipitation sequencing (MeRIP-seq) and liquid chromatography–mass spectrometrywere utilized for m6A profiling in peripheral immune cells and serum proteome analysis, respectivelyThe single-cell transcriptomic dataset (GSE174332) of primary motor cortex was further analyzed to illuminateAnalysis of peripheral immune cells revealed extensive RNA hypermethylation, highlighting candidate genesSerum proteome analysis demonstrated the role of dysregulated immune cell migration in ALS.

Keywords： amyotrophic lateral sclerosis     N6-methyladenosine     epi-transcriptome     proteome     single cellRNA sequencing analysis     CX3CR1    

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Single-cell RNA-seq data analysis on the receptor ACE2 expression reveals the potential risk of different

Xin Zou, Ke Chen, Jiawei Zou, Peiyi Han, Jie Hao, Zeguang Han

Frontiers of Medicine 2024, Volume 18, Issue 1,   Pages 185-192 doi: 10.1007/s11684-020-0754-0

Abstract: To construct a risk map of different human organs, we analyzed the single-cell RNA sequencing (scRNA-seqthe organs at risk, such as lung, heart, esophagus, kidney, bladder, and ileum, and located specific cell

Keywords： 2019-nCoV     ACE2     single-cell RNA-seq    

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Effects of vitrification and cryostorage duration on single-cell RNA-Seq profiling of vitrified-thawed

Ying Huo, Peng Yuan, Qingyuan Qin, Zhiqiang Yan, Liying Yan, Ping Liu, Rong Li, Jie Yan, Jie Qiao

Frontiers of Medicine 2021, Volume 15, Issue 1,   Pages 144-154 doi: 10.1007/s11684-020-0792-7

Abstract: RNA-Seq profiles of 3 fresh oocytes and 13 surviving vitrified-thawed oocytes (3, 3, 4, and 3 oocyteswere cryostored for 1, 2, 3, and 12 months) were analyzed at a single-cell resolution.Further analysis revealed that the aberrant genes in the vitrified oocytes were closely related to oogenesis

Keywords： human metaphase II oocyte     vitrification     cryostorage duration     single-cell RNA-Seq     lncRNA    

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BULKED SEGREGANT RNA SEQUENCING (BSR-SEQ) IDENTIFIES A NOVEL ALLELE ASSOCIATED WITH WEEPING TRAITS IN

Frontiers of Agricultural Science and Engineering 2021, Volume 8, Issue 2,

Abstract: Bulked segregant RNA sequencing was used and five QTLs on Chromosome 7 were identified.Weighted correlation network analysis indicates that genes neighboring Pm024074 wereIn addition, a reliable single nucleotide polymorphism marker was developed based on the variation in

Keywords： BSR-seq / PmUGT72B3 / Prunus mume / UDP-glycosyltransferase / weeping shoots / WGCNA    

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Effect on proliferation and apoptosis of T24 cell lines via silencing DNMT1 with RNA interference

ZHANG Shilong, ZENG Fuqing, PENG Shibo, WANG Liang

Frontiers of Medicine 2008, Volume 2, Issue 4,   Pages 374-379 doi: 10.1007/s11684-008-0072-4

Abstract: and protein effectively, and to some extent, it also can inhibit the proliferation of bladder cancer cell
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Nucleic acid crystallization and X-ray crystallography facilitated by single selenium atom

Wen Zhang,Jack W. Szostak,Zhen Huang

Frontiers of Chemical Science and Engineering 2016, Volume 10, Issue 2,   Pages 196-202 doi: 10.1007/s11705-016-1565-3

Abstract: X-ray crystallography is a powerful strategy for 3-D structure determination of macromolecules, such as nucleic acids and protein-nucleic acid complexes. However, the crystallization and phase determination are the major bottle-neck problems in crystallography. Recently we have successfully developed synthesis and strategy of selenium-derivatized nucleic acids (SeNA) for nucleic acid crystallography. SeNA might not only provide the rational strategies to solve the phase determination problem, but also offer a potential strategy to explore crystallization solutions.

Keywords： selenium     DNA     RNA     nucleic acid     crystallization    

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BULKED SEGREGANT RNA SEQUENCING (BSR-SEQ) IDENTIFIES A NOVEL ALLELE ASSOCIATED WITH WEEPING TRAITS IN

Xiaokang ZHUO, Tangchun ZHENG, Zhiyong ZHANG, Suzhen LI, Yichi ZHANG, Lidan SUN, Weiru YANG, Jia WANG, Tangren CHENG, Qixiang ZHANG

Frontiers of Agricultural Science and Engineering   Pages 196-214 doi: 10.15302/J-FASE-2020379

Abstract: Bulked segregant RNA sequencing was used and five QTLs on Chromosome 7 were identified.Weighted correlation network analysis indicates that genes neighboring were significantly associatedIn addition, a reliable single nucleotide polymorphism marker was developed based on the variation in

Keywords： BSR-seq     PmUGT72B3     Prunus mume     UDP-glycosyltransferase     weeping shoots     WGCNA    

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Long non-coding RNA SAP30-2:1 is downregulated in congenital heart disease and regulates cell proliferation

Jing Ma, Shiyu Chen, Lili Hao, Wei Sheng, Weicheng Chen, Xiaojing Ma, Bowen Zhang, Duan Ma, Guoying Huang

Frontiers of Medicine 2021, Volume 15, Issue 1,   Pages 91-100 doi: 10.1007/s11684-020-0778-5

Abstract: We used Gene Expression Omnibus data mining, bioinformatics analysis, and analysis of clinical tissueMoreover, lncRNA SAP30-2:1 was associated with HAND2 by RNA immunoprecipitation.these results suggest that lncRNA SAP30-2:1 may be involved in heart development through affecting cell

Keywords： congenital heart disease     Gene Expression Omnibus     lncRNA SAP30-2:1     cell proliferation     RNA immunoprecipitation    

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Transcriptome analysis of wheat grain using RNA-Seq

Liu WEI,Zhihui WU,Yufeng ZHANG,Dandan GUO,Yuzhou XU,Weixia CHEN,Haiying ZHOU,Mingshan YOU,Baoyun LI

Frontiers of Agricultural Science and Engineering 2014, Volume 1, Issue 3,   Pages 214-222 doi: 10.15302/J-FASE-2014024

Abstract: Transcriptome analysis is a powerful approach to research grain traits and elucidate their genetic regulationThe analysis of the 61393 unigenes involved in the biological processes of the grain showed that thereGene ontology enrichment and the Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis

Keywords： transcriptome analysis     wheat grain     differentially expressed genes     enrichment analysis    

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Information Science Should Take a Lead in Future Biomedical Research Perspective

Kenta Nakai

Engineering 2019, Volume 5, Issue 6,   Pages 1155-1158 doi: 10.1016/j.eng.2019.07.023

Abstract: Recently, the explosive development of next-generation sequencing (NGS) has been producing massive dataused for "reading" DNA sequences, but also for obtaining various types of information at the single-cell

Keywords： Data science     Artificial intelligence     Next-generation sequencing     DNA     Cancer genome     Single-cell transcriptomics    

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Global transcriptome analysis for identification of interactions between coding and noncoding RNAs during

Nan Ding,Jiafei Xi,Yanming Li,Xiaoyan Xie,Jian Shi,Zhaojun Zhang,Yanhua Li,Fang Fang,Sihan Wang,Wen Yue,Xuetao Pei,Xiangdong Fang

Frontiers of Medicine 2016, Volume 10, Issue 3,   Pages 297-310 doi: 10.1007/s11684-016-0452-0

Abstract: However, analysis focusing on the integration of the three RNA types has yet to be done.mechanisms that control these changes in the transcriptome level, we took advantage of high throughput sequencingResults indicated that lncRNAs were promising cell marker candidates for erythroid differentiation.Clustering analysis classified the differentially expressed genes into four subtypes that correspondedIntegrated analysis revealed that noncoding RNAs potentially participated in controlling blood cell maturation

Keywords： erythroid differentiation     hematopoietic stem cell     RNA-seq     miRNA     lncRNA    

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Emerging Trends for Microbiome Analysis: From Single-Cell Functional Imaging to Microbiome Big Data

Jian Xu, Bo Ma, Xiaoquan Su, Shi Huang, Xin Xu, Xuedong Zhou, Wei Huang, Rob Knight

Engineering 2017, Volume 3, Issue 1,   Pages 66-70 doi: 10.1016/J.ENG.2017.01.020

Abstract: In this perspective, we argue that in the next decade, method development in microbiome analysis willboth ways of thinking and technological platforms: ① a shift from dissecting microbiota structureby sequencinga consortium or population of cells to probing individual cells; and ③ a shift from microbiome data analysis

Keywords： Microbiome     Methoddevelopment     Single-cell analysis     Big data     China Microbiome Initiative    

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Title Author Date Type Operation

PathogenTrack and Yeskit: tools for identifying intracellular pathogens from single-cell RNA-sequencing

Journal Article

Distinct immune escape and microenvironment between RG-like and pri-OPC-like glioma revealed by single-cellRNA-seq analysis

Journal Article

Distinct mononuclear diploid cardiac subpopulation with minimal cell–cell communications persists in

Journal Article

Dysregulated N-methyladenosine modification in peripheral immune cells contributes to the pathogenesis of amyotrophic lateral sclerosis

Journal Article

Single-cell RNA-seq data analysis on the receptor ACE2 expression reveals the potential risk of different

Xin Zou, Ke Chen, Jiawei Zou, Peiyi Han, Jie Hao, Zeguang Han

Journal Article

Effects of vitrification and cryostorage duration on single-cell RNA-Seq profiling of vitrified-thawed

Ying Huo, Peng Yuan, Qingyuan Qin, Zhiqiang Yan, Liying Yan, Ping Liu, Rong Li, Jie Yan, Jie Qiao

Journal Article

BULKED SEGREGANT RNA SEQUENCING (BSR-SEQ) IDENTIFIES A NOVEL ALLELE ASSOCIATED WITH WEEPING TRAITS IN

Journal Article

Effect on proliferation and apoptosis of T24 cell lines via silencing DNMT1 with RNA interference

ZHANG Shilong, ZENG Fuqing, PENG Shibo, WANG Liang

Journal Article

Nucleic acid crystallization and X-ray crystallography facilitated by single selenium atom

Wen Zhang,Jack W. Szostak,Zhen Huang

Journal Article

BULKED SEGREGANT RNA SEQUENCING (BSR-SEQ) IDENTIFIES A NOVEL ALLELE ASSOCIATED WITH WEEPING TRAITS IN

Xiaokang ZHUO, Tangchun ZHENG, Zhiyong ZHANG, Suzhen LI, Yichi ZHANG, Lidan SUN, Weiru YANG, Jia WANG, Tangren CHENG, Qixiang ZHANG

Journal Article

Long non-coding RNA SAP30-2:1 is downregulated in congenital heart disease and regulates cell proliferation

Jing Ma, Shiyu Chen, Lili Hao, Wei Sheng, Weicheng Chen, Xiaojing Ma, Bowen Zhang, Duan Ma, Guoying Huang

Journal Article

Transcriptome analysis of wheat grain using RNA-Seq

Liu WEI,Zhihui WU,Yufeng ZHANG,Dandan GUO,Yuzhou XU,Weixia CHEN,Haiying ZHOU,Mingshan YOU,Baoyun LI

Journal Article

Information Science Should Take a Lead in Future Biomedical Research

Kenta Nakai

Journal Article

Global transcriptome analysis for identification of interactions between coding and noncoding RNAs during

Nan Ding,Jiafei Xi,Yanming Li,Xiaoyan Xie,Jian Shi,Zhaojun Zhang,Yanhua Li,Fang Fang,Sihan Wang,Wen Yue,Xuetao Pei,Xiangdong Fang

Journal Article

Emerging Trends for Microbiome Analysis: From Single-Cell Functional Imaging to Microbiome Big Data

Jian Xu, Bo Ma, Xiaoquan Su, Shi Huang, Xin Xu, Xuedong Zhou, Wei Huang, Rob Knight

Journal Article