Cell systems最新文献_第8页

Automated single-cell omics end-to-end framework with data-driven batch inference. 采用数据驱动批量推理的自动化单细胞全息端到端框架。

Cell systems Pub Date : 2024-10-16 Epub Date: 2024-10-03 DOI: 10.1016/j.cels.2024.09.003

Yuan Wang, William Thistlethwaite, Alicja Tadych, Frederique Ruf-Zamojski, Daniel J Bernard, Antonio Cappuccio, Elena Zaslavsky, Xi Chen, Stuart C Sealfon, Olga G Troyanskaya

{"title":"Automated single-cell omics end-to-end framework with data-driven batch inference.","authors":"Yuan Wang, William Thistlethwaite, Alicja Tadych, Frederique Ruf-Zamojski, Daniel J Bernard, Antonio Cappuccio, Elena Zaslavsky, Xi Chen, Stuart C Sealfon, Olga G Troyanskaya","doi":"10.1016/j.cels.2024.09.003","DOIUrl":"10.1016/j.cels.2024.09.003","url":null,"abstract":"To facilitate single-cell multi-omics analysis and improve reproducibility, we present single-cell pipeline for end-to-end data integration (SPEEDI), a fully automated end-to-end framework for batch inference, data integration, and cell-type labeling. SPEEDI introduces data-driven batch inference and transforms the often heterogeneous data matrices obtained from different samples into a uniformly annotated and integrated dataset. Without requiring user input, it automatically selects parameters and executes pre-processing, sample integration, and cell-type mapping. It can also perform downstream analyses of differential signals between treatment conditions and gene functional modules. SPEEDI's data-driven batch-inference method works with widely used integration and cell-typing tools. By developing data-driven batch inference, providing full end-to-end automation, and eliminating parameter selection, SPEEDI improves reproducibility and lowers the barrier to obtaining biological insight from these valuable single-cell datasets. The SPEEDI interactive web application can be accessed at https://speedi.princeton.edu/. A record of this paper's transparent peer review process is included in the supplemental information.","PeriodicalId":93929,"journal":{"name":"Cell systems","volume":" ","pages":"982-990.e5"},"PeriodicalIF":0.0,"publicationDate":"2024-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11491117/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142376460","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

Data-driven batch detection enhances single-cell omics data analysis. 数据驱动的批量检测增强了单细胞组学数据分析。

Cell systems Pub Date : 2024-10-16 DOI: 10.1016/j.cels.2024.09.011

Ziqi Zhang, Xiuwei Zhang

引用次数: 0

How can concepts from ecology enable insights about cellular communities? 生态学的概念如何帮助我们了解细胞群落？

Cell systems Pub Date : 2024-10-16 DOI: 10.1016/j.cels.2024.09.010

Anna Weiss, Matti Gralka, Karoline Faust, David Basanta Gutierrez, Kenneth Pienta, Xu Zhou, Ophelia S Venturelli, Sean Gibbons, Mo Ebrahimkhani, Nika Shakiba, Shaohua Ma

引用次数: 0

Protein turnover regulation is critical for influenza A virus infection. 蛋白质周转调节对甲型流感病毒感染至关重要。

Cell systems Pub Date : 2024-10-16 Epub Date: 2024-10-04 DOI: 10.1016/j.cels.2024.09.004

Yiqi Huang, Christian Urban, Philipp Hubel, Alexey Stukalov, Andreas Pichlmair

引用次数: 0

Entrainment and multi-stability of the p53 oscillator in human cells. 人体细胞中 p53 振荡器的协调性和多重稳定性。

Cell systems Pub Date : 2024-10-16 Epub Date: 2024-10-04 DOI: 10.1016/j.cels.2024.09.001

Alba Jiménez, Alessandra Lucchetti, Mathias S Heltberg, Liv Moretto, Carlos Sanchez, Ashwini Jambhekar, Mogens H Jensen, Galit Lahav

{"title":"Entrainment and multi-stability of the p53 oscillator in human cells.","authors":"Alba Jiménez, Alessandra Lucchetti, Mathias S Heltberg, Liv Moretto, Carlos Sanchez, Ashwini Jambhekar, Mogens H Jensen, Galit Lahav","doi":"10.1016/j.cels.2024.09.001","DOIUrl":"10.1016/j.cels.2024.09.001","url":null,"abstract":"The tumor suppressor p53 responds to cellular stress and activates transcription programs critical for regulating cell fate. DNA damage triggers oscillations in p53 levels with a robust period. Guided by the theory of synchronization and entrainment, we developed a mathematical model and experimental system to test the ability of the p53 oscillator to entrain to external drug pulses of various periods and strengths. We found that the p53 oscillator can be locked and entrained to a wide range of entrainment modes. External periods far from p53's natural oscillations increased the heterogeneity between individual cells whereas stronger inputs reduced it. Single-cell measurements allowed deriving the phase response curves (PRCs) and multiple Arnold tongues of p53. In addition, multi-stability and non-linear behaviors were mathematically predicted and experimentally detected, including mode hopping, period doubling, and chaos. Our work revealed critical dynamical properties of the p53 oscillator and provided insights into understanding and controlling it. A record of this paper's transparent peer review process is included in the supplemental information.","PeriodicalId":93929,"journal":{"name":"Cell systems","volume":" ","pages":"956-968.e3"},"PeriodicalIF":0.0,"publicationDate":"2024-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11894796/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142378730","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

Exploring "dark-matter" protein folds using deep learning. 利用深度学习探索 "暗物质 "蛋白质折叠。

Cell systems Pub Date : 2024-10-16 Epub Date: 2024-10-08 DOI: 10.1016/j.cels.2024.09.006

Zander Harteveld, Alexandra Van Hall-Beauvais, Irina Morozova, Joshua Southern, Casper Goverde, Sandrine Georgeon, Stéphane Rosset, Michëal Defferrard, Andreas Loukas, Pierre Vandergheynst, Michael M Bronstein, Bruno E Correia

{"title":"Exploring \"dark-matter\" protein folds using deep learning.","authors":"Zander Harteveld, Alexandra Van Hall-Beauvais, Irina Morozova, Joshua Southern, Casper Goverde, Sandrine Georgeon, Stéphane Rosset, Michëal Defferrard, Andreas Loukas, Pierre Vandergheynst, Michael M Bronstein, Bruno E Correia","doi":"10.1016/j.cels.2024.09.006","DOIUrl":"10.1016/j.cels.2024.09.006","url":null,"abstract":"De novo protein design explores uncharted sequence and structure space to generate novel proteins not sampled by evolution. A main challenge in de novo design involves crafting \"designable\" structural templates to guide the sequence searches toward adopting target structures. We present a convolutional variational autoencoder that learns patterns of protein structure, dubbed Genesis. We coupled Genesis with trRosetta to design sequences for a set of protein folds and found that Genesis is capable of reconstructing native-like distance and angle distributions for five native folds and three novel, the so-called \"dark-matter\" folds as a demonstration of generalizability. We used a high-throughput assay to characterize the stability of the designs through protease resistance, obtaining encouraging success rates for folded proteins. Genesis enables exploration of the protein fold space within minutes, unrestricted by protein topologies. Our approach addresses the backbone designability problem, showing that small neural networks can efficiently learn structural patterns in proteins. A record of this paper's transparent peer review process is included in the supplemental information.","PeriodicalId":93929,"journal":{"name":"Cell systems","volume":" ","pages":"898-910.e5"},"PeriodicalIF":0.0,"publicationDate":"2024-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142395960","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

An efficient, not-only-linear correlation coefficient based on clustering. 基于聚类的高效非线性相关系数

Cell systems Pub Date : 2024-09-18 Epub Date: 2024-09-06 DOI: 10.1016/j.cels.2024.08.005

Milton Pividori, Marylyn D Ritchie, Diego H Milone, Casey S Greene

{"title":"An efficient, not-only-linear correlation coefficient based on clustering.","authors":"Milton Pividori, Marylyn D Ritchie, Diego H Milone, Casey S Greene","doi":"10.1016/j.cels.2024.08.005","DOIUrl":"10.1016/j.cels.2024.08.005","url":null,"abstract":"Identifying meaningful patterns in data is crucial for understanding complex biological processes, particularly in transcriptomics, where genes with correlated expression often share functions or contribute to disease mechanisms. Traditional correlation coefficients, which primarily capture linear relationships, may overlook important nonlinear patterns. We introduce the clustermatch correlation coefficient (CCC), a not-only-linear coefficient that utilizes clustering to efficiently detect both linear and nonlinear associations. CCC outperforms standard methods by revealing biologically meaningful patterns that linear-only coefficients miss and is faster than state-of-the-art coefficients such as the maximal information coefficient. When applied to human gene expression data from genotype-tissue expression (GTEx), CCC identified robust linear relationships and nonlinear patterns, such as sex-specific differences, that are undetectable by standard methods. Highly ranked gene pairs were enriched for interactions in integrated networks built from protein-protein interactions, transcription factor regulation, and chemical and genetic perturbations, suggesting that CCC can detect functional relationships missed by linear-only approaches. CCC is a highly efficient, next-generation, not-only-linear correlation coefficient for genome-scale data. A record of this paper's transparent peer review process is included in the supplemental information.","PeriodicalId":93929,"journal":{"name":"Cell systems","volume":" ","pages":"854-868.e3"},"PeriodicalIF":0.0,"publicationDate":"2024-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11951854/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142147119","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

Discovery of therapeutic targets in cancer using chromatin accessibility and transcriptomic data. 利用染色质可及性和转录组数据发现癌症治疗靶点。

Cell systems Pub Date : 2024-09-18 Epub Date: 2024-09-04 DOI: 10.1016/j.cels.2024.08.004

Andre Neil Forbes, Duo Xu, Sandra Cohen, Priya Pancholi, Ekta Khurana

引用次数: 0

Promoter DNA methylation and transcription factor condensation are linked to transcriptional memory in mammalian cells. 启动子 DNA 甲基化和转录因子凝集与哺乳动物细胞的转录记忆有关。

Cell systems Pub Date : 2024-09-18 Epub Date: 2024-09-06 DOI: 10.1016/j.cels.2024.08.007

Shenqi Fan, Liang Ma, Chengzhi Song, Xu Han, Bijunyao Zhong, Yihan Lin

{"title":"Promoter DNA methylation and transcription factor condensation are linked to transcriptional memory in mammalian cells.","authors":"Shenqi Fan, Liang Ma, Chengzhi Song, Xu Han, Bijunyao Zhong, Yihan Lin","doi":"10.1016/j.cels.2024.08.007","DOIUrl":"10.1016/j.cels.2024.08.007","url":null,"abstract":"The regulation of genes can be mathematically described by input-output functions that are typically assumed to be time invariant. This fundamental assumption underpins the design of synthetic gene circuits and the quantitative understanding of natural gene regulatory networks. Here, we found that this assumption is challenged in mammalian cells. We observed that a synthetic reporter gene can exhibit unexpected transcriptional memory, leading to a shift in the dose-response curve upon a second induction. Mechanistically, we investigated the cis-dependency of transcriptional memory, revealing the necessity of promoter DNA methylation in establishing memory. Furthermore, we showed that the synthetic transcription factor's effective DNA binding affinity underlies trans-dependency, which is associated with its capacity to undergo biomolecular condensation. These principles enabled modulating memory by perturbing either cis- or trans-regulation of genes. Together, our findings suggest the potential pervasiveness of transcriptional memory and implicate the need to model mammalian gene regulation with time-varying input-output functions. A record of this paper's transparent peer review process is included in the supplemental information.","PeriodicalId":93929,"journal":{"name":"Cell systems","volume":" ","pages":"808-823.e6"},"PeriodicalIF":0.0,"publicationDate":"2024-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142147121","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Versatile system cores as a conceptual basis for generality in cell and developmental biology. 多功能系统核心是细胞和发育生物学通用性的概念基础。

Cell systems Pub Date : 2024-09-18 Epub Date: 2024-09-04 DOI: 10.1016/j.cels.2024.08.001

Elisa Gallo, Stefano De Renzis, James Sharpe, Roberto Mayor, Jonas Hartmann

{"title":"Versatile system cores as a conceptual basis for generality in cell and developmental biology.","authors":"Elisa Gallo, Stefano De Renzis, James Sharpe, Roberto Mayor, Jonas Hartmann","doi":"10.1016/j.cels.2024.08.001","DOIUrl":"10.1016/j.cels.2024.08.001","url":null,"abstract":"The discovery of general principles underlying the complexity and diversity of cellular and developmental systems is a central and long-standing aim of biology. While new technologies collect data at an ever-accelerating rate, there is growing concern that conceptual progress is not keeping pace. We contend that this is due to a paucity of conceptual frameworks that support meaningful generalizations. This led us to develop the core and periphery (C&P) hypothesis, which posits that many biological systems can be decomposed into a highly versatile core with a large behavioral repertoire and a specific periphery that configures said core to perform one particular function. Versatile cores tend to be widely reused across biology, which confers generality to theories describing them. Here, we introduce this concept and describe examples at multiple scales, including Turing patterning, actomyosin dynamics, multi-cellular morphogenesis, and vertebrate gastrulation. We also sketch its evolutionary basis and discuss key implications and open questions. We propose that the C&P hypothesis could unlock new avenues of conceptual progress in mesoscale biology.","PeriodicalId":93929,"journal":{"name":"Cell systems","volume":" ","pages":"790-807"},"PeriodicalIF":0.0,"publicationDate":"2024-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142142059","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0