Searching journal content for articles similar to Qiao et al. 34 (1): 94.

Displaying results 1-8 of 8
For checked items
  1. Research: Long-read single-cell RNA sequencing enables the study of cancer subclone-specific genotypes and phenotypes in chronic lymphocytic leukemia
    • Gage S. Black,
    • Xiaomeng Huang,
    • Yi Qiao,
    • Philip Moos,
    • Deepa Sampath,
    • Deborah M. Stephens,
    • Jennifer A. Woyach,
    • and Gabor T. Marth
    Genome Res. April 2025 35: 686-697; Published in Advance February 18, 2025, doi:10.1101/gr.279049.124
    ...Bayes and assign each cell to a clone of origin (Supplemental Fig. 4). Briefly, scBayes genotypes each cell by examining the presence of subclone-defining somatic mutations (as discovered from bulk DNA sequencing data, Fig. 3B, y-axis) in the scRNA-seq reads of the cell (Fig. 3B, x-axis) and uses a Bayesian...
  2. Method: A statistical learning method for simultaneous copy number estimation and subclone clustering with single-cell sequencing data
    • Fei Qin,
    • Guoshuai Cai,
    • Christopher I. Amos,
    • and Feifei Xiao
    Genome Res. January 2024 34: 85-93; Published in Advance January 30, 2024, doi:10.1101/gr.278098.123
    ...the assessment of ITH on a single-cell basis (Navin et al. 2011; Wang et al. 2014) using either single-cell DNA or RNA sequencing (scDNA/RNA-seq) to reveal cellular evolutionary relationships (Tang et al. 2019). Subclonal populations can be identified within tumor tissues using SCS, allowing for the inference...
  3. Method: PhISCS: a combinatorial approach for subperfect tumor phylogeny reconstruction via integrative use of single-cell and bulk sequencing data
    • Salem Malikic,
    • Farid Rashidi Mehrabadi,
    • Simone Ciccolella,
    • Md. Khaledur Rahman,
    • Camir Ricketts,
    • Ehsan Haghshenas,
    • Daniel Seidman,
    • Faraz Hach,
    • Iman Hajirasouliha,
    • and S. Cenk Sahinalp
    Genome Res. November 2019 29: 1860-1877; Published in Advance October 18, 2019, doi:10.1101/gr.234435.118
    ...of copies of a variant allele, this can even be potentially beneficial and reduce allelic dropout (since such an event would provide more starting material for the PCR amplification step that is typically performed prior to DNA sequencing).We ran PhISCS using single-cell data, first without considering any...
    OPEN ACCESS ARTICLE
  4. Perspective: Applications of single-cell genomics and computational strategies to study common disease and population-level variation
    • Benjamin J. Auerbach,
    • Jian Hu,
    • Muredach P. Reilly,
    • and Mingyao Li
    Genome Res. October 2021 31: 1728-1741; doi:10.1101/gr.275430.121
    ...substantially reduce the number of needed subjects (Fig. 1A). Although DNA genotyping needs to be performed for a large number of individuals when studying rare variants, the cost of DNA genotyping is much lower than that of scRNA-seq. When genetic risk factors are unknown, an alternative design is the extreme...
    OPEN ACCESS ARTICLE
  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
    ...transcriptionally distinct subpopulations and genetic subclones. At the same time, simultaneous unbiased assessment of DNA and RNA from an individual cell remains challenging (Dey et al. 2015; Macaulay et al. 2015; Wang et al. 2017).Computational approaches for bulk sequencing data detect copy number variations...
  6. 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
    ...by bulk genomic sequencing using three experimental approaches: targeted DNA, whole transcriptome, and targeted RNA (Fig. 1A). Our targeted RNA-based approach reliably detects subclonalmutations and enables recapitulation of single-cell DNA information, including phylogenetic structure. Integrative...
  7. Method: Quantification of somatic mutation flow across individual cell division events by lineage sequencing
    • Yehuda Brody,
    • Robert J. Kimmerling,
    • Yosef E. Maruvka,
    • David Benjamin,
    • Juniper J. Elacqua,
    • Nicholas J. Haradhvala,
    • Jaegil Kim,
    • Kent W. Mouw,
    • Kristjana Frangaj,
    • Amnon Koren,
    • Gad Getz,
    • Scott R. Manalis,
    • and Paul C. Blainey
    Genome Res. December 2018 28: 1901-1918; Published in Advance November 20, 2018, doi:10.1101/gr.238543.118
    .... Lineage sequencing concept and implementation. Overview of the lineage sequencing concept. Numbering indicates key conceptual and implementation steps. Single cells are sampled from a clonal population and sequenced (steps 1–6; in this study, subclonal culture was used to produce enough genomic DNA...
    OPEN ACCESS ARTICLE
  8. Method: TITAN: inference of copy number architectures in clonal cell populations from tumor whole-genome sequence data
    • Gavin Ha,
    • Andrew Roth,
    • Jaswinder Khattra,
    • Julie Ho,
    • Damian Yap,
    • Leah M. Prentice,
    • Nataliya Melnyk,
    • Andrew McPherson,
    • Ali Bashashati,
    • Emma Laks,
    • Justina Biele,
    • Jiarui Ding,
    • Alan Le,
    • Jamie Rosner,
    • Karey Shumansky,
    • Marco A. Marra,
    • C. Blake Gilks,
    • David G. Huntsman,
    • Jessica N. McAlpine,
    • Samuel Aparicio,
    • and Sohrab P. Shah
    Genome Res. November 2014 24: 1881-1893; Published in Advance July 24, 2014, doi:10.1101/gr.180281.114
    ...allele read counts for segmentation of subFigure 6. Single-cell validation of subclonal deletions in DG1136g using deep DNA sequencing of individual nuclei. (A,B) The 28 nuclei for Set1 and 18 nuclei for Set2 were designated as tumor and normal cell type using the status of mutations. Themutant allele...
    OPEN ACCESS ARTICLE
For checked items

Search Results

New Search

Modify Results

Citation format:
Results / page:
Results order:

This search

  • Alert me when new articles matching this search are published
  • Download all citations on this page to my citation manager

Preprint Server



Current Issue

  1. March 2026, 36 (3)
  1. Current Issue
  1. Alert me to new issues of Genome Research