Inferring cells differentiation processes from single-cell Multiome ATACseq+RNAseq data.
Inferring cells differentiation processes from single-cell Multiome ATACseq+RNAseq data.
批准号:
22K21301
负责人:
Loza Lopez.Martin.de.Jesus
金额:
$1.83万
依托单位:
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
项目状态:
已结题
起止时间:
2022-08-31 至 2024-03-31
中文摘要
我根据最近发表在一份高影响因子杂志上的一种方法确认了这个项目的意义。我建立了计算环境,并致力于估计集群内细胞的基因表达水平。我测试了不同的线性方法,包括正则化项和不带正则项。得出正则化估计,尤其是岭回归估计更适合于单细胞RNA-SEQ数据,因为它们减少了数据高度稀疏性的影响。我对估计的特定于簇的基因动力学进行了不同的内插测试,结果令人满意。通过这些测试,我能够在电子计算机上模拟细胞从一个集群分化到另一个集群。
英文摘要
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.
期刊论文(7)
专著(0)
科研奖励(0)
会议论文
DOI:
--
发表时间:
2022
期刊:
影响因子:
--
作者:
[K. Kawaharazuka, K. Okada, M. Inaba, Loza Martin]
通讯作者:
Loza Martin
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]
通讯作者:
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
DOI:
--
发表时间:
2022
期刊:
影响因子:
--
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
Identification and characterization of ubiquitously active cis-regulatory elements in mouse and their implications in tumor suppression
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批准号:24K18097
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项目类别:Grant-in-Aid for Early-Career Scientists
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资助金额:$3.0万
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财政年份:2024
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负责人:Loza Lopez.Martin.de.Jesus
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依托单位:
海外基金