Inferring cells differentiation processes from single-cell Multiome ATACseq+RNAseq data.

从单细胞 Multiome ATACseq RNAseq 数据推断细胞分化过程。

• 批准号: 22K21301
• 负责人: Loza Lopez.Martin.de.Jesus
• 金额: $ 1.83万
• 依托单位: The University of Tokyo
• 依托单位国家: 日本
• 项目类别: Grant-in-Aid for Research Activity Start-up
• 财政年份: 2022
• 资助国家: 日本
• 起止时间: 2022-08-31 至 2024-03-31
• 项目状态: 已结题
• 来源: https://kaken.nii.ac.jp/en/grant/KAKENHI-PROJECT-22K21301/
• 关键词: Bioinformatics; Cells-reprogramming; Multiomics; RNA-velocity; Single-cell; Cell-fate

I confirmed the significance of this project in terms of a recent method published in a high-impact factor journal.I set up the computational environment and worked on the estimation of gene expression levels of cells within clusters.I tested different linear methods with and without regularization terms. I conclude that estimation with regularization, especially the ridge regressor, was more appropriate for single-cell RNA-seq data as they reduce the impact of the high sparsity of the data.I set up the fuzzy logic interpolation. I performed different tests on the interpolation of the estimated cluster-specific gene dynamics with satisfactory results. With these tests, I was able to perform in-silico simulations of a cell differentiating from one cluster to another.

我根据最近在高影响因子期刊上发表的方法证实了该项目的重要性。我建立了计算环境并致力于估计簇内细胞的基因表达水平。我测试了有或没有的不同线性方法正则化项。我的结论是，正则化估计，尤其是岭回归器，更适合单细胞 RNA-seq 数据，因为它们减少了数据高稀疏性的影响。我设置了模糊逻辑插值。我对估计的簇特定基因动态的插值进行了不同的测试，得到了令人满意的结果。通过这些测试，我能够对细胞从一个簇区分到另一个簇进行计算机模拟。

项目成果

Characterization of housekeeping enhancers and their targets in the human genome

人类基因组中管家增强子及其靶标的表征

• 发表时间: 2022
• 作者: K. Kawaharazuka;K. Okada;M. Inaba;Loza Martin
• 通讯作者: Loza Martin

Unbiased integration of single cell transcriptome replicates

• DOI: 10.1101/2021.05.05.442380
• 发表时间: 2021-05
• 期刊: NAR Genomics and Bioinformatics
• 影响因子: 4.6
• 作者: Martin Loza Lopez;Shunsuke Teraguchi;D. Standley;Diego Diez

Housekeeping enhancers in the human genome

人类基因组中的管家增强子

• 发表时间: 2022
• 作者: Y. Ribayashi;K. Kawaharazuka;Y. Toshimitsu;D. Kusuyama;A. Miki;K. Shinjo;M. Bando;T. Suzuki;Y. Kojio;K. Okada;M. Inaba;Loza Martin
• 通讯作者: Loza Martin