Searching journal content for articles similar to Nguyen et al. 28 (7): 1053.

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  1. Method: Alignment of single-cell RNA-seq samples without overcorrection using kernel density matching
    • Mengjie Chen,
    • Qi Zhan,
    • Zepeng Mu,
    • Lili Wang,
    • Zhaohui Zheng,
    • Jinlin Miao,
    • Ping Zhu,
    • and Yang I. Li
    Genome Res. April 2021 31: 698-712; Published in Advance March 19, 2021, doi:10.1101/gr.261115.120
    ..., and improves the utility of scRNA-seq for several important applications. Dmatch is freely available online.Single cell RNA-sequencing (scRNA-seq) technology is transforming the study of cellular heterogeneity (Kumar et al. 2014; Villani et al. 2017), differentiation (Bendall et al. 2014; Durruthy-Durruthy et...
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  2. Method: Transcript assembly improves expression quantification of transposable elements in single-cell RNA-seq data
    • Wanqing Shao and
    • Ting Wang
    Genome Res. January 2021 31: 88-100; Published in Advance December 21, 2020, doi:10.1101/gr.265173.120
    ...of cells. Nat Biotechnol 33: 155–160. doi:10.1038/nbt.3102 ↵Cheng S, Pei Y, He L, Peng G, Reinius B, Tam PPL, Jing N, Deng Q. 2019. Single-cell RNA-seq reveals cellular heterogeneity of pluripotency transition and X chromosome dynamics during early mouse development. Cell Rep 26: 2593–2607.e3. doi:10...
  3. Resource: Murine single-cell RNA-seq reveals cell-identity- and tissue-specific trajectories of aging
    • Jacob C. Kimmel,
    • Lolita Penland,
    • Nimrod D. Rubinstein,
    • David G. Hendrickson,
    • David R. Kelley,
    • and Adam Z. Rosenthal
    Genome Res. December 2019 29: 2088-2103; Published in Advance November 21, 2019, doi:10.1101/gr.253880.119
    ...depend on cell identitySingle-cell analysis measures not only the mean expression of each gene, but also the variation within a cell population. Previous studies have reported that both gene expression variance and cell–cell heterogeneity increase with age using RNA-seq (Enge et al. 2017; Martinez...
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  4. Method: Characterizing and inferring quantitative cell cycle phase in single-cell RNA-seq data analysis
    • Chiaowen Joyce Hsiao,
    • PoYuan Tung,
    • John D. Blischak,
    • Jonathan E. Burnett,
    • Kenneth A. Barr,
    • Kushal K. Dey,
    • Matthew Stephens,
    • and Yoav Gilad
    Genome Res. April 2020 30: 611-621; Published in Advance April 20, 2020, doi:10.1101/gr.247759.118
    ..., even in otherwise homogeneous cell populations. Recent advances in single-cell RNA-sequencing (scRNA-seq) facilitate detailed characterization of gene expression heterogeneity and can thus shed new light on the processes driving heterogeneity. Here, we combined fluorescence imaging with scRNA-seq...
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  5. Method: Linking transcriptional and genetic tumor heterogeneity through allele analysis of single-cell RNA-seq data
    • Jean Fan,
    • Hae-Ock Lee,
    • Soohyun Lee,
    • Da-eun Ryu,
    • Semin Lee,
    • Catherine Xue,
    • Seok Jin Kim,
    • Kihyun Kim,
    • Nikolaos Barkas,
    • Peter J. Park,
    • Woong-Yang Park,
    • and Peter V. Kharchenko
    Genome Res. August 2018 28: 1217-1227; Published in Advance June 13, 2018, doi:10.1101/gr.228080.117
    ...associated with distinct genetic subclones. Single-cell RNA-sequencing (scRNA-seq) methods can provide detailed information on the transcriptional state of the cancer cells. However, integration with genotypic information at the single-cell level is necessary to establish correspondence between...
  6. Method: Data integration and inference of gene regulation using single-cell temporal multimodal data with scTIE
    • Yingxin Lin,
    • Tung-Yu Wu,
    • Xi Chen,
    • Sheng Wan,
    • Brian Chao,
    • Jingxue Xin,
    • Jean Y.H. Yang,
    • Wing H. Wong,
    • and Y.X. Rachel Wang
    Genome Res. January 2024 34: 119-133; Published in Advance December 15, 2023, doi:10.1101/gr.277960.123
    .... Corresponding authors: rachel.wang@sydney.edu.au, whwong@stanford.eduAbstractSingle-cell technologies offer unprecedented opportunities to dissect gene regulatory mechanisms in context-specific ways. Although there are computational methods for extracting gene regulatory relationships from scRNA-seq and sc...
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  7. Research: Characterization of transcript enrichment and detection bias in single-nucleus RNA-seq for mapping of distinct human adipocyte lineages
    • Anushka Gupta,
    • Farnaz Shamsi,
    • Nicolas Altemose,
    • Gabriel F. Dorlhiac,
    • Aaron M. Cypess,
    • Andrew P. White,
    • Nir Yosef,
    • Mary Elizabeth Patti,
    • Yu-Hua Tseng,
    • and Aaron Streets
    Genome Res. February 2022 32: 242-257; Published in Advance January 18, 2022, doi:10.1101/gr.275509.121
    ...of such metabolic diseases. Consequently, recent studies are beginning to elucidate cellular heterogeneity and developmental pathways in distinct adipose tissue lineages at the single-cell level (Deutsch et al. 2020; Ferrero et al. 2020; Shamsi et al. 2021).Over the last decade, single-cell RNA sequencing (scRNA-seq...
  8. Research: Single-cell gene expression analysis reveals regulators of distinct cell subpopulations among developing human neurons
    • Jiaxu Wang,
    • Piroon Jenjaroenpun,
    • Akshay Bhinge,
    • Vladimir Espinosa Angarica,
    • Antonio Del Sol,
    • Intawat Nookaew,
    • Vladimir A. Kuznetsov,
    • and Lawrence W. Stanton
    Genome Res. November 2017 27: 1783-1794; Published in Advance October 13, 2017, doi:10.1101/gr.223313.117
    ...72205, USA The stochastic dynamics and regulatory mechanisms that govern differentiation of individual human neural precursor cells (NPC) into mature neurons are currently not fully understood. Here, we used single-cell RNA-sequencing (scRNA-seq) of developing neurons to dissect/identify NPC subtypes...
  9. Research: Single-cell RNA-seq reveals changes in cell cycle and differentiation programs upon aging of hematopoietic stem cells
    • Monika S. Kowalczyk,
    • Itay Tirosh,
    • Dirk Heckl,
    • Tata Nageswara Rao,
    • Atray Dixit,
    • Brian J. Haas,
    • Rebekka K. Schneider,
    • Amy J. Wagers,
    • Benjamin L. Ebert,
    • and Aviv Regev
    Genome Res. December 2015 25: 1860-1872; Published in Advance October 1, 2015, doi:10.1101/gr.192237.115
    ...Single-cell RNA-seq reveals changes in cell cycle and differentiation programs upon aging of hematopoietic stem cells Monika S. Kowalczyk 1 , 8 , Itay Tirosh 1 , 8 , Dirk Heckl 2 , Tata Nageswara Rao 3 , 4 , Atray Dixit 1 , Brian J...
  10. Method: Parallel bimodal single-cell sequencing of transcriptome and chromatin accessibility
    • Qiao Rui Xing,
    • Chadi A El Farran,
    • Ying Ying Zeng,
    • Yao Yi,
    • Tushar Warrier,
    • Pradeep Gautam,
    • James J. Collins,
    • Jian Xu,
    • Peter Dröge,
    • Cheng-Gee Koh,
    • Hu Li,
    • Li-Feng Zhang,
    • and Yuin-Han Loh
    Genome Res. July 2020 30: 1027-1039; Published in Advance July 22, 2020, doi:10.1101/gr.257840.119
    ...ASTAR-seq libraries at a comparable sequencing depth (40 single-cell libraries per lane of HiSeq 4000) (Supplemental Table 1). scCAT-seq libraries showed a significantly lower alignment rate to the human in comparison with ASTAR-seq (scATAC-seq: 67.6% vs. 85.8%; scRNA-seq: 54.9% vs. 73.8%) (Supplemental...
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