Cell genomics最新文献_第7页

Meet the author: Hector L. Franco. 来认识一下作者：赫克托·l·弗兰科。

IF 11.1

Cell genomics Pub Date : 2025-02-12 DOI: 10.1016/j.xgen.2025.100772

Hector L Franco

引用次数: 0

Characterization and bioinformatic filtering of ambient gRNAs in single-cell CRISPR screens using CLEANSER. 使用cleaner在单细胞CRISPR筛选中对环境grna进行表征和生物信息学过滤。

IF 11.1

Cell genomics Pub Date : 2025-02-12 Epub Date: 2025-02-05 DOI: 10.1016/j.xgen.2025.100766

Siyan Liu, Marisa C Hamilton, Thomas Cowart, Alejandro Barrera, Lexi R Bounds, Alexander C Nelson, Sophie F Dornbaum, Julia W Riley, Richard W Doty, Andrew S Allen, Gregory E Crawford, William H Majoros, Charles A Gersbach

{"title":"Characterization and bioinformatic filtering of ambient gRNAs in single-cell CRISPR screens using CLEANSER.","authors":"Siyan Liu, Marisa C Hamilton, Thomas Cowart, Alejandro Barrera, Lexi R Bounds, Alexander C Nelson, Sophie F Dornbaum, Julia W Riley, Richard W Doty, Andrew S Allen, Gregory E Crawford, William H Majoros, Charles A Gersbach","doi":"10.1016/j.xgen.2025.100766","DOIUrl":"10.1016/j.xgen.2025.100766","url":null,"abstract":"Single-cell RNA sequencing CRISPR (perturb-seq) screens enable high-throughput investigation of the genome, allowing for characterization of thousands of genomic perturbations on gene expression. Ambient gRNAs, which are contaminating gRNAs, are a major source of noise in perturb-seq experiments because they result in an excess of false-positive gRNA assignments. Here, we utilize CRISPR barnyard assays to characterize ambient gRNAs in perturb-seq screens. We use these datasets to develop CRISPR Library Evaluation and Ambient Noise Suppression for Enhanced single-cell RNA-seq (CLEANSER), a mixture model that filters ambient gRNAs. CLEANSER includes both gRNA and cell-specific normalization parameters, correcting for confounding technical factors that affect individual gRNAs and cells. The output of CLEANSER is the probability that a gRNA-cell assignment is in the native distribution over the ambient distribution. We find that ambient gRNA filtering methods impact differential gene expression analysis outcomes and that CLEANSER outperforms alternate approaches by increasing gRNA-cell assignment accuracy across multiple screen formats.","PeriodicalId":72539,"journal":{"name":"Cell genomics","volume":" ","pages":"100766"},"PeriodicalIF":11.1,"publicationDate":"2025-02-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11872138/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143366918","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Tracing human trait evolution through integrative genomics and temporal annotations. 通过整合基因组学和时间注释追踪人类特征进化。

IF 11.1

Cell genomics Pub Date : 2025-02-12 Epub Date: 2025-01-24 DOI: 10.1016/j.xgen.2025.100767

Jian Zeng

引用次数: 0

CRISPR-Cas spacer acquisition is a rare event in human gut microbiome. CRISPR-Cas间隔序列获取在人类肠道微生物组中是罕见的事件。

IF 11.1

Cell genomics Pub Date : 2025-01-08 Epub Date: 2024-12-23 DOI: 10.1016/j.xgen.2024.100725

An-Ni Zhang, Jeffry M Gaston, Pablo Cárdenas, Shijie Zhao, Xiaoqiong Gu, Eric J Alm

{"title":"CRISPR-Cas spacer acquisition is a rare event in human gut microbiome.","authors":"An-Ni Zhang, Jeffry M Gaston, Pablo Cárdenas, Shijie Zhao, Xiaoqiong Gu, Eric J Alm","doi":"10.1016/j.xgen.2024.100725","DOIUrl":"10.1016/j.xgen.2024.100725","url":null,"abstract":"Host-parasite relationships drive the evolution of both parties. In microbe-phage dynamics, CRISPR functions as an adaptive defense mechanism, updating immunity via spacer acquisition. Here, we investigated these interactions within the human gut microbiome, uncovering low frequencies of spacer acquisition at an average rate of one spacer every ∼2.9 point mutations using isolates' whole genomes and ∼2.7 years using metagenome time series. We identified a highly prevalent CRISPR array in Bifidobacterium longum spreading via horizontal gene transfer (HGT), with six spacers found in various genomic regions in 15 persons from the United States and Europe. These spacers, targeting two prominent Bifidobacterium phages, comprised 76% of spacer occurrence of all spacers targeting these phages in all B. longum populations. This result suggests that HGT of an entire CRISPR-Cas system introduced three times more spacers than local CRISPR-Cas acquisition in B. longum. Overall, our findings identified key ecological and evolutionary factors in prokaryote adaptive immunity.","PeriodicalId":72539,"journal":{"name":"Cell genomics","volume":" ","pages":"100725"},"PeriodicalIF":11.1,"publicationDate":"2025-01-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11770219/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142886552","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Single-cell and spatial transcriptomic profiling revealed niche interactions sustaining growth of endometriotic lesions. 单细胞和空间转录组分析揭示了维持子宫内膜异位症病变生长的生态位相互作用。

IF 11.1

Cell genomics Pub Date : 2025-01-08 DOI: 10.1016/j.xgen.2024.100737

Song Liu, Xiaoyan Li, Zhiyue Gu, Jiayu Wu, Shuangzheng Jia, Jinghua Shi, Yi Dai, Yushi Wu, Hailan Yan, Jing Zhang, Yan You, Xiaowei Xue, Lulu Liu, Jinghe Lang, Xiaoyue Wang, Jinhua Leng

{"title":"Single-cell and spatial transcriptomic profiling revealed niche interactions sustaining growth of endometriotic lesions.","authors":"Song Liu, Xiaoyan Li, Zhiyue Gu, Jiayu Wu, Shuangzheng Jia, Jinghua Shi, Yi Dai, Yushi Wu, Hailan Yan, Jing Zhang, Yan You, Xiaowei Xue, Lulu Liu, Jinghe Lang, Xiaoyue Wang, Jinhua Leng","doi":"10.1016/j.xgen.2024.100737","DOIUrl":"10.1016/j.xgen.2024.100737","url":null,"abstract":"Endometriosis is a chronic condition with limited therapeutic options. The molecular aberrations promoting ectopic attachment and interactions with the local microenvironment sustaining lesion growth have been unclear, prohibiting development of targeted therapies. Here, we performed single-cell and spatial transcriptomic profiling of ectopic lesions and eutopic endometrium in endometriosis. We found that ectopic endometrial stromal (EnS) cells retained cyclical gene expression patterns of their eutopic counterparts while exhibiting unique gene expression that contributes to the pathogenesis of endometriosis. We identified two distinct ovarian stromal cells (OSCs) localized at different zones of the lesion, showing differential gene expression profiles associated with fibrosis and inflammation, respectively. We also identified WNT5A upregulation and aberrant activation of non-canonical WNT signaling in endometrial stromal cells that may contribute to the lesion establishment, offering novel targets for therapeutic intervention. These data will enhance our understanding of the molecular mechanisms underlying endometriosis and paves the way for developing non-hormonal treatments.","PeriodicalId":72539,"journal":{"name":"Cell genomics","volume":"5 1","pages":"100737"},"PeriodicalIF":11.1,"publicationDate":"2025-01-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11770218/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142959859","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Atlas-scale single-cell DNA methylation profiling with sciMETv3. 使用sciMETv3进行atlas级单细胞DNA甲基化分析。

IF 11.1

Cell genomics Pub Date : 2025-01-08 Epub Date: 2024-12-23 DOI: 10.1016/j.xgen.2024.100726

Ruth V Nichols, Lauren E Rylaarsdam, Brendan L O'Connell, Zohar Shipony, Nika Iremadze, Sonia N Acharya, Andrew C Adey

引用次数: 0

Meet the authors: Xiaoyue Wang and Jinhua Leng. 认识一下作者：王晓月和冷金华。

IF 11.1

Cell genomics Pub Date : 2025-01-08 DOI: 10.1016/j.xgen.2024.100742

Xiaoyue Wang, Jinhua Leng

引用次数: 0

Bridging genomics' greatest challenge: The diversity gap. 弥合基因组学最大的挑战：多样性差距。

IF 11.1

Cell genomics Pub Date : 2025-01-08 Epub Date: 2024-12-17 DOI: 10.1016/j.xgen.2024.100724

Manuel Corpas, Mkpouto Pius, Marie Poburennaya, Heinner Guio, Miriam Dwek, Shivashankar Nagaraj, Catalina Lopez-Correa, Alice Popejoy, Segun Fatumo

引用次数: 0

CSI-GEP: A GPU-based unsupervised machine learning approach for recovering gene expression programs in atlas-scale single-cell RNA-seq data. CSI-GEP：一种基于gpu的无监督机器学习方法，用于恢复atlas级单细胞RNA-seq数据中的基因表达程序。

IF 11.1

Cell genomics Pub Date : 2025-01-08 DOI: 10.1016/j.xgen.2024.100739

Xueying Liu, Richard H Chapple, Declan Bennett, William C Wright, Ankita Sanjali, Erielle Culp, Yinwen Zhang, Min Pan, Paul Geeleher

{"title":"CSI-GEP: A GPU-based unsupervised machine learning approach for recovering gene expression programs in atlas-scale single-cell RNA-seq data.","authors":"Xueying Liu, Richard H Chapple, Declan Bennett, William C Wright, Ankita Sanjali, Erielle Culp, Yinwen Zhang, Min Pan, Paul Geeleher","doi":"10.1016/j.xgen.2024.100739","DOIUrl":"10.1016/j.xgen.2024.100739","url":null,"abstract":"Exploratory analysis of single-cell RNA sequencing (scRNA-seq) typically relies on hard clustering over two-dimensional projections like uniform manifold approximation and projection (UMAP). However, such methods can severely distort the data and have many arbitrary parameter choices. Methods that can model scRNA-seq data as non-discrete \"gene expression programs\" (GEPs) can better preserve the data's structure, but currently, they are often not scalable, not consistent across repeated runs, and lack an established method for choosing key parameters. Here, we developed a GPU-based unsupervised learning approach, \"consensus and scalable inference of gene expression programs\" (CSI-GEP). We show that CSI-GEP can recover ground truth GEPs in real and simulated atlas-scale scRNA-seq datasets, significantly outperforming cutting-edge methods, including GPT-based neural networks. We applied CSI-GEP to a whole mouse brain atlas of 2.2 million cells, disentangling endothelial cell types missed by other methods, and to an integrated scRNA-seq atlas of human tumors and cell lines, discovering mesenchymal-like GEPs unique to cancer cells growing in culture.","PeriodicalId":72539,"journal":{"name":"Cell genomics","volume":"5 1","pages":"100739"},"PeriodicalIF":11.1,"publicationDate":"2025-01-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11770216/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142959844","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Double or nothing: Ancient duplications in the amylase locus drove human adaptation. 要么加倍，要么一无所有：古代淀粉酶位点的复制驱动着人类的适应。

IF 11.1

Cell genomics Pub Date : 2025-01-08 DOI: 10.1016/j.xgen.2024.100741

Shahar Silverman, Diyendo Massilani

引用次数: 0