Searching journal content for articles similar to Erdmann-Pham et al. 31 (10): 1794.

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  1. Method: A deconvolution framework that uses single-cell sequencing plus a small benchmark data set for accurate analysis of cell type ratios in complex tissue samples
    • Shuai Guo,
    • Xiaoqian Liu,
    • Xuesen Cheng,
    • Yujie Jiang,
    • Shuangxi Ji,
    • Qingnan Liang,
    • Andrew Koval,
    • Yumei Li,
    • Leah A. Owen,
    • Ivana K. Kim,
    • Ana Aparicio,
    • Sanghoon Lee,
    • Anil K. Sood,
    • Scott Kopetz,
    • John Paul Shen,
    • John N. Weinstein,
    • Margaret M. DeAngelis,
    • Rui Chen,
    • and Wenyi Wang
    Genome Res. January 2025 35: 147-161; Published in Advance November 25, 2024, doi:10.1101/gr.278822.123
    ...Department of Statistics, University of California at Riverside, Riverside, CA 92521, USA; ↵16Division of Ophthalmology, Department of Surgery, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA Corresponding author: wwang7@mdanderson.orgAbstractBulk deconvolution with single-cell...
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  2. Editorial: New frontiers in single-cell genomics
    • Nicholas E. Navin,
    • Orit Rozenblatt-Rosen,
    • and Nancy R. Zhang
    Genome Res. October 2021 31: ix-x; doi:10.1101/gr.276129.121
    ...issue) 31: 1952–1969. doi:10.1101/gr.271791.120 ↵Erdmann-Pham DD, Fischer J, Hong J, Song YS. 2021. Likelihood-based deconvolution of bulk gene expression data using single-cell references. Genome Res (this issue) 31: 1794–1806. doi:10.1101/gr.272344.120 ↵Gao Y, Li L, Amos CI, Li W. 2021. Analysis...
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  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
    .... 2016), for example, is a Markov chain Monte Carlo (MCMC) search method that aims to infer the maximum-likelihood (ML) mutational history from a potentially incomplete and noisy matrix containing genotypes of single cells. OncoNEM (Ross and Markowetz 2016) is a maximum-likelihood-based search approach...
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  4. Method: SiCloneFit: Bayesian inference of population structure, genotype, and phylogeny of tumor clones from single-cell genome sequencing data
    • Hamim Zafar,
    • Nicholas Navin,
    • Ken Chen,
    • and Luay Nakhleh
    Genome Res. November 2019 29: 1847-1859; Published in Advance October 18, 2019, doi:10.1101/gr.243121.118
    ...). Such technologies provide sequencing data pertaining to single cells, thus allowing for direct measurement of genotypes and prevalences of tumor subclones without requiring deconvolution of aggregate signals (Zafar et al. 2018). At the same time, they offer the possibility of reconstructing the clonal lineage tree...
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