Searching journal content for articles similar to Pellegrino et al. 28 (9): 1345.

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  1. Review: Advancements in prospective single-cell lineage barcoding and their applications in research
    • Xiaoli Zhang,
    • Yirui Huang,
    • Yajing Yang,
    • Qi-En Wang,
    • and Lang Li
    Genome Res. December 2024 34: 2147-2162; Published in Advance November 21, 2024, doi:10.1101/gr.278944.124
    ...with the increased length and multiplicity of the random nucleotide sequence, providing a vast array of unique labels. When combined with current single-cell sequencing techniques, DNA lineage barcoding offers unlimited potential to study cell behavior and fate over space and time. This powerful combination allows...
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  2. 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
    ...importance to gain comprehensive understanding of cell states. To tackle this, multimodal single-cell methods have been developed for concurrent measurement of and transcriptome (Dey et al. 2015; Macaulay et al. 2015) and of transcriptome and DNA methylome within a single-cell (Angermueller et al. 2016...
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  3. Research: Integrated single-cell genetic and transcriptional analysis suggests novel drivers of chronic lymphocytic leukemia
    • Lili Wang,
    • Jean Fan,
    • Joshua M. Francis,
    • George Georghiou,
    • Sarah Hergert,
    • Shuqiang Li,
    • Rutendo Gambe,
    • Chensheng W. Zhou,
    • Chunxiao Yang,
    • Sheng Xiao,
    • Paola Dal Cin,
    • Michaela Bowden,
    • Dylan Kotliar,
    • Sachet A. Shukla,
    • Jennifer R. Brown,
    • Donna Neuberg,
    • Dario R. Alessi,
    • Cheng-Zhong Zhang,
    • Peter V. Kharchenko,
    • Kenneth J. Livak,
    • and Catherine J. Wu
    Genome Res. August 2017 27: 1300-1311; Published in Advance July 5, 2017, doi:10.1101/gr.217331.116
    ...and chromosomal abnormalities detected by single-cell DNA analysis and CCF inferred from bulk tumor whole-exome sequencing (WES). Single-cell analysis reveals cancer drivers in CLL Genome Research 1301 www..org inferred from bulk WES (r2 = 0.937) (Fig. 1C; Supplemental Table S3) using ABSOLUTE (Carter et al. 2012...
  4. Method: Copolymerization of single-cell nucleic acids into balls of acrylamide gel
    • Siran Li,
    • Jude Kendall,
    • Sarah Park,
    • Zihua Wang,
    • Joan Alexander,
    • Andrea Moffitt,
    • Nissim Ranade,
    • Cassidy Danyko,
    • Bruno Gegenhuber,
    • Stephan Fischer,
    • Brian D. Robinson,
    • Herbert Lepor,
    • Jessica Tollkuhn,
    • Jesse Gillis,
    • Eric Brouzes,
    • Alex Krasnitz,
    • Dan Levy,
    • and Michael Wigler
    Genome Res. January 2020 30: 49-61; Published in Advance November 14, 2019, doi:10.1101/gr.253047.119
    ...of cells and tissues (Navin et al. 2011; Patel et al. 2014; Tirosh et al. 2016; Villani et al. 2017). Many droplet-based technologies have emerged as high-throughput ways to study DNA (Lan et al. 2017; Pellegrino et al. 2018) or RNA (Klein et al. 2015; Macosko et al. 2015) of single cells. However...
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  5. Method: A plug and play microfluidic platform for standardized sensitive low-input chromatin immunoprecipitation
    • René A.M. Dirks,
    • Peter C. Thomas,
    • Haoyu Wu,
    • Robert C. Jones,
    • Hendrik G. Stunnenberg,
    • and Hendrik Marks
    Genome Res. May 2021 31: 919-933; Published in Advance March 11, 2021, doi:10.1101/gr.260745.120
    ...2010; Furey 2012). The ChIP-seq protocol relies on the affinity purification of a DNA-binding protein by the use of antibodies. Characterization of the DNA associated with the protein of interest by high-throughput sequencing allows for identification of the protein binding sites at a -wide scale...
  6. Method: Single molecule molecular inversion probes for targeted, high-accuracy detection of low-frequency variation
    • Joseph B. Hiatt,
    • Colin C. Pritchard,
    • Stephen J. Salipante,
    • Brian J. O'Roak,
    • and Jay Shendure
    Genome Res. May 2013 23: 843-854; Published in Advance February 4, 2013, doi:10.1101/gr.147686.112
    ...microbial evolution to human cancer genetics. However, despite the cost and throughput advances associated with massively parallel sequencing, it remains challenging to reliably detect mutations that are present at a low relative abundance in a given DNA sample. Here we describe smMIP, an assay...
  7. Method: A generic, cost-effective, and scalable cell lineage analysis platform
    • Tamir Biezuner,
    • Adam Spiro,
    • Ofir Raz,
    • Shiran Amir,
    • Lilach Milo,
    • Rivka Adar,
    • Noa Chapal-Ilani,
    • Veronika Berman,
    • Yael Fried,
    • Elena Ainbinder,
    • Galit Cohen,
    • Haim M. Barr,
    • Ruth Halaban,
    • and Ehud Shapiro
    Genome Res. November 2016 26: 1588-1599; Published in Advance August 24, 2016, doi:10.1101/gr.202903.115
    ...platform. (A) Tumor andmetastases are given as an example for the utilization of the platform to study cancer dynamics (red, yellow, and blue cell populations). (Top left box) Single cells are extracted from an individual, and DNA is extracted and amplified using whole- amplification (WGA). (Bottom box...
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