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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 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   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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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.

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

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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   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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A cytoprotective graphene oxide-polyelectrolytes nanoshell for single-cell encapsulation

Luanying He, Yulin Chang, Junhao Zhu, Ying Bi, Wenlin An, Yiyang Dong, Jia-Hui Liu, Shihui Wang

Frontiers of Chemical Science and Engineering 2021, Volume 15, Issue 2,   Pages 410-420 doi: 10.1007/s11705-020-1950-9

Abstract: Graphene oxide (GO) has been increasingly utilized in the fields of food, biomedicine, environment and other fields because of its benign biocompatible. We encapsulated two kinds of GO with different sizes on yeast cells with the assistance of polyelectrolytes poly (styrene sulfonic acid) sodium salt (PSS) and polyglutamic acid (PGA) (termed as Y@GO). The result does not show a significant difference between the properties of the two types of Y@GO (namely Y@GO1 and Y@GO2). The encapsulation layers are optimized as Yeast/PGA/PSS/PGA/GO/PGA/PSS based on the morphology, dispersity, colony-forming unit, and zeta potential. The encapsulation of GO increases the roughness of the yeast. It is proved that the Y@GO increases the survival time and enhance the activity of yeast cells. The GO shell improves the resistance of yeast cells against pH and salt stresses and extends the storage time of yeast cells.

Keywords： GO     yeast     polyelectrolyte     cytoprotection     nanomaterials    

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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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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: both ways of thinking and technological platforms: ① a shift from dissecting microbiota structureby sequencing

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

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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.In 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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Identification of Monocytes Associated with Severe COVID-19 in the PBMCs of Severely Infected Patients Through Single-CellTranscriptome Sequencing Article

Yan Zhang, Shuting Wang, He Xia, Jing Guo, Kangxin He, Chenjie Huang, Rui Luo, Yanfei Chen, Kaijin Xu, Hainv Gao, Jifang Sheng, Lanjuan Li

Engineering 2022, Volume 17, Issue 10,   Pages 161-169 doi: 10.1016/j.eng.2021.05.009

Abstract: In this study, we performed single-cell transcriptomic sequencing of peripheral blood samples collected

Keywords： COVID-19     Severe infection     Critically ill     Monocytes     Fibrosis    

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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.In 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: Moreover, 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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Clinical characteristics and prognostic factors of patients with mature T-cell lymphoid malignancies:a single-institution study of 225 cases

Wen Xue,Yan Sheng,Xiangqin Weng,Yongmei Zhu,Yan Zhao,Pengpeng Xu,Xiaochun Fei,Xiaoyan Chen,Li Wang,Weili Zhao

Frontiers of Medicine 2015, Volume 9, Issue 4,   Pages 468-477 doi: 10.1007/s11684-015-0419-6

Abstract:

Mature T-cell lymphoid malignancies comprise a group of heterogeneous diseases that vary in clinicopathologicalBone marrow (BM) infiltration is more commonly present in mature T-cell lymphoid malignancies comparedwith their B-cell counterparts and hence important for differential diagnosis.lymphoid malignancies treated in a single institution.These included 29 cases of T-cell lymphoproliferative disorders (T-LPD, all with BM infiltration) and

Keywords： mature T-cell lymphoid malignancies     clonal T-cell population     bone marrow infiltration     prognostic factors    

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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

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

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

A cytoprotective graphene oxide-polyelectrolytes nanoshell for single-cell encapsulation

Luanying He, Yulin Chang, Junhao Zhu, Ying Bi, Wenlin An, Yiyang Dong, Jia-Hui Liu, Shihui Wang

Journal Article

Information Science Should Take a Lead in Future Biomedical Research

Kenta Nakai

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

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

Journal Article

Identification of Monocytes Associated with Severe COVID-19 in the PBMCs of Severely Infected Patients Through Single-CellTranscriptome Sequencing

Yan Zhang, Shuting Wang, He Xia, Jing Guo, Kangxin He, Chenjie Huang, Rui Luo, Yanfei Chen, Kaijin Xu, Hainv Gao, Jifang Sheng, Lanjuan Li

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

Clinical characteristics and prognostic factors of patients with mature T-cell lymphoid malignancies:a single-institution study of 225 cases

Wen Xue,Yan Sheng,Xiangqin Weng,Yongmei Zhu,Yan Zhao,Pengpeng Xu,Xiaochun Fei,Xiaoyan Chen,Li Wang,Weili Zhao

Journal Article