Cell Reports Methods最新文献_第2页

An improved FLARE system for recording and manipulating neuronal activity.

IF 4.3

Cell Reports Methods Pub Date : 2025-03-15 DOI: 10.1016/j.crmeth.2025.101012

Guanwei Zhou, Ruonan Li, Ola Bartolik, Yuqian Ma, Wei Wei Wan, Jennifer Meng, Yujia Hu, Bing Ye, Wenjing Wang

引用次数: 0

A real-time, multi-subject three-dimensional pose tracking system for the behavioral analysis of non-human primates.

IF 4.3

Cell Reports Methods Pub Date : 2025-02-24 Epub Date: 2025-02-17 DOI: 10.1016/j.crmeth.2025.100986

Chaoqun Cheng, Zijian Huang, Ruiming Zhang, Guozheng Huang, Han Wang, Likai Tang, Xiaoqin Wang

{"title":"A real-time, multi-subject three-dimensional pose tracking system for the behavioral analysis of non-human primates.","authors":"Chaoqun Cheng, Zijian Huang, Ruiming Zhang, Guozheng Huang, Han Wang, Likai Tang, Xiaoqin Wang","doi":"10.1016/j.crmeth.2025.100986","DOIUrl":"10.1016/j.crmeth.2025.100986","url":null,"abstract":"The ability to track the positions and poses of multiple animals in three-dimensional (3D) space in real time is highly desired by non-human primate (NHP) researchers in behavioral and systems neuroscience. This capability enables the analysis of social behaviors involving multiple NHPs and supports closed-loop experiments. Although several animal 3D pose tracking systems have been developed, most are difficult to deploy in new environments and lack real-time analysis capabilities. To address these limitations, we developed MarmoPose, a deep-learning-based, real-time 3D pose tracking system for multiple common marmosets, an increasingly critical NHP model in neuroscience research. This system can accurately track the 3D poses of multiple marmosets freely moving in their home cage with minimal hardware requirements. By employing a marmoset skeleton model, MarmoPose can further optimize 3D poses and estimate invisible body locations. Additionally, MarmoPose achieves high inference speeds and enables real-time closed-loop experimental control based on events detected from 3D poses.","PeriodicalId":29773,"journal":{"name":"Cell Reports Methods","volume":" ","pages":"100986"},"PeriodicalIF":4.3,"publicationDate":"2025-02-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11955267/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143450180","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 common mechanisms of adverse drug reactions and disease phenotypes through network-based analysis. 通过网络分析探索药物不良反应和疾病表型的共同机制。

IF 4.3

Cell Reports Methods Pub Date : 2025-02-24 Epub Date: 2025-02-14 DOI: 10.1016/j.crmeth.2025.100990

Farzaneh Firoozbakht, Maria Louise Elkjaer, Diane E Handy, Rui-Sheng Wang, Zoe Chervontseva, Matthias Rarey, Joseph Loscalzo, Jan Baumbach, Olga Tsoy

{"title":"Exploring common mechanisms of adverse drug reactions and disease phenotypes through network-based analysis.","authors":"Farzaneh Firoozbakht, Maria Louise Elkjaer, Diane E Handy, Rui-Sheng Wang, Zoe Chervontseva, Matthias Rarey, Joseph Loscalzo, Jan Baumbach, Olga Tsoy","doi":"10.1016/j.crmeth.2025.100990","DOIUrl":"10.1016/j.crmeth.2025.100990","url":null,"abstract":"The need for a deeper understanding of adverse drug reaction (ADR) mechanisms is vital for improving drug safety and repurposing. This study introduces Drug Adverse Reaction Mechanism Explainer (DREAMER), a network-based framework that uses a comprehensive knowledge graph to uncover molecular mechanisms underlying ADRs and disease phenotypes. By examining shared phenotypes of drugs and diseases and their effects on protein-protein interaction networks, DREAMER identifies proteins linked to ADR mechanisms. Applied to 649 ADRs, DREAMER identified molecular mechanisms for 67 ADRs, including ventricular arrhythmia and metabolic acidosis, and emphasized pathways like GABAergic signaling and coagulation proteins in personality disorders and intracranial hemorrhage. We further demonstrate the application of DREAMER in drug repurposing and propose sotalol, ranolazine, and diltiazem as candidate drugs to be repurposed for cardiac arrest. In summary, DREAMER effectively detects molecular mechanisms underlying phenotypes, emphasizing the importance of network-based analyses with integrative data for enhancing drug safety and accelerating the discovery of novel therapeutic strategies.","PeriodicalId":29773,"journal":{"name":"Cell Reports Methods","volume":" ","pages":"100990"},"PeriodicalIF":4.3,"publicationDate":"2025-02-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11955268/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143426269","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

Spatiotemporal analysis of ratiometric biosensors in live multicellular spheroids using SPoRTS.

IF 4.3

Cell Reports Methods Pub Date : 2025-02-24 Epub Date: 2025-02-17 DOI: 10.1016/j.crmeth.2025.100987

Matthew J Borrelli, Bart Kolendowski, Gabriel E DiMattia, Trevor G Shepherd

引用次数: 0

Efficient cell-wide mapping of mitochondria in electron microscopic volumes using webKnossos.

IF 4.3

Cell Reports Methods Pub Date : 2025-02-24 DOI: 10.1016/j.crmeth.2025.100989

Yi Jiang, Haoyu Wang, Kevin M Boergens, Norman Rzepka, Fangfang Wang, Yunfeng Hua

{"title":"Efficient cell-wide mapping of mitochondria in electron microscopic volumes using webKnossos.","authors":"Yi Jiang, Haoyu Wang, Kevin M Boergens, Norman Rzepka, Fangfang Wang, Yunfeng Hua","doi":"10.1016/j.crmeth.2025.100989","DOIUrl":"10.1016/j.crmeth.2025.100989","url":null,"abstract":"Recent technical advances in volume electron microscopy (vEM) and artificial-intelligence-assisted image processing have facilitated high-throughput quantifications of cellular structures, such as mitochondria, that are ubiquitous and morphologically diversified. A still often-overlooked computational challenge is to assign a cell identity to numerous mitochondrial instances, for which both mitochondrial and cell membrane contouring used to be required. Here, we present a vEM reconstruction procedure (called mito-SegEM) that utilizes virtual-path-based annotation to assign automatically segmented mitochondrial instances at the cellular scale, therefore bypassing the requirement of membrane contouring. The embedded toolset in webKnossos (an open-source online annotation platform) is optimized for fast annotation, visualization, and proofreading of cellular organelle networks. We demonstrate the broad applications of mito-SegEM on volumetric datasets from various tissues, including the brain, intestine, and testis, to achieve an accurate and efficient reconstruction of mitochondria in a use-dependent fashion.","PeriodicalId":29773,"journal":{"name":"Cell Reports Methods","volume":"5 2","pages":"100989"},"PeriodicalIF":4.3,"publicationDate":"2025-02-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11955265/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143504684","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

Non-invasive real-time pulsed Doppler assessment of blood flow in mouse ophthalmic artery.

IF 4.3

Cell Reports Methods Pub Date : 2025-02-24 Epub Date: 2025-02-14 DOI: 10.1016/j.crmeth.2025.100983

Iraida Sharina, Radwa Awad, Soren Cobb, Emil Martin, Sean P Marrelli, Anilkumar K Reddy

引用次数: 0

A probabilistic modeling framework for genomic networks incorporating sample heterogeneity.

IF 4.3

Cell Reports Methods Pub Date : 2025-02-24 Epub Date: 2025-02-14 DOI: 10.1016/j.crmeth.2025.100984

Liying Chen, Satwik Acharyya, Chunyu Luo, Yang Ni, Veerabhadran Baladandayuthapani

{"title":"A probabilistic modeling framework for genomic networks incorporating sample heterogeneity.","authors":"Liying Chen, Satwik Acharyya, Chunyu Luo, Yang Ni, Veerabhadran Baladandayuthapani","doi":"10.1016/j.crmeth.2025.100984","DOIUrl":"10.1016/j.crmeth.2025.100984","url":null,"abstract":"Probabilistic graphical models are powerful tools to quantify, visualize, and interpret network dependencies in complex biological systems such as high-throughput -omics. However, many graphical models assume sample homogeneity, limiting their effectiveness. We propose a flexible Bayesian approach called graphical regression (GraphR), which (1) incorporates sample heterogeneity at different scales through a regression-based formulation, (2) enables sparse sample-specific network estimation, (3) identifies and quantifies potential effects of heterogeneity on network structures, and (4) achieves computational efficiency via variational Bayes algorithms. We illustrate the comparative efficiency of GraphR against existing state-of-the-art methods in terms of network structure recovery and computational cost across multiple settings. We use GraphR to analyze three multi-omic and spatial transcriptomic datasets to investigate inter- and intra-sample molecular networks and delineate biological discoveries that otherwise cannot be revealed by existing approaches. We have developed a GraphR R package along with an accompanying Shiny App that provides comprehensive analysis and dynamic visualization functions.","PeriodicalId":29773,"journal":{"name":"Cell Reports Methods","volume":" ","pages":"100984"},"PeriodicalIF":4.3,"publicationDate":"2025-02-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11955270/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143426267","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

Mathematically mapping the network of cells in the tumor microenvironment.

IF 4.3

Cell Reports Methods Pub Date : 2025-02-24 Epub Date: 2025-02-14 DOI: 10.1016/j.crmeth.2025.100985

Mike van Santvoort, Óscar Lapuente-Santana, Maria Zopoglou, Constantin Zackl, Francesca Finotello, Pim van der Hoorn, Federica Eduati

{"title":"Mathematically mapping the network of cells in the tumor microenvironment.","authors":"Mike van Santvoort, Óscar Lapuente-Santana, Maria Zopoglou, Constantin Zackl, Francesca Finotello, Pim van der Hoorn, Federica Eduati","doi":"10.1016/j.crmeth.2025.100985","DOIUrl":"10.1016/j.crmeth.2025.100985","url":null,"abstract":"Cell-cell interaction (CCI) networks are key to understanding disease progression and treatment response. However, existing methods for inferring these networks often aggregate data across patients or focus on cell-type level interactions, providing a generalized overview but overlooking patient heterogeneity and local network structures. To address this, we introduce \"random cell-cell interaction generator\" (RaCInG), a model based on random graphs to derive personalized networks leveraging prior knowledge on ligand-receptor interactions and bulk RNA sequencing data. We applied RaCInG to 8,683 cancer patients to extract 643 network features related to the tumor microenvironment and unveiled associations with immune response and subtypes, enabling prediction and explanation of immunotherapy responses. RaCInG demonstrated robustness and showed consistencies with state-of-the-art methods. Our findings highlight RaCInG's potential to elucidate patient-specific network dynamics, offering insights into cancer biology and treatment responses. RaCInG is poised to advance our understanding of complex CCI s in cancer and other biomedical domains.","PeriodicalId":29773,"journal":{"name":"Cell Reports Methods","volume":" ","pages":"100985"},"PeriodicalIF":4.3,"publicationDate":"2025-02-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11955271/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143426272","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

Refined culture conditions with increased physiological relevance uncover oncogene-dependent metabolic signatures in Ewing sarcoma spheroids.

IF 4.3

Cell Reports Methods Pub Date : 2025-02-24 Epub Date: 2025-02-07 DOI: 10.1016/j.crmeth.2025.100966

A Katharina Ceranski, Martha J Carreño-Gonzalez, Anna C Ehlers, Kimberley M Hanssen, Nadine Gmelin, Florian H Geyer, Zuzanna Kolodynska, Endrit Vinca, Tobias Faehling, Philipp Poeller, Shunya Ohmura, Florencia Cidre-Aranaz, Almut Schulze, Thomas G P Grünewald

{"title":"Refined culture conditions with increased physiological relevance uncover oncogene-dependent metabolic signatures in Ewing sarcoma spheroids.","authors":"A Katharina Ceranski, Martha J Carreño-Gonzalez, Anna C Ehlers, Kimberley M Hanssen, Nadine Gmelin, Florian H Geyer, Zuzanna Kolodynska, Endrit Vinca, Tobias Faehling, Philipp Poeller, Shunya Ohmura, Florencia Cidre-Aranaz, Almut Schulze, Thomas G P Grünewald","doi":"10.1016/j.crmeth.2025.100966","DOIUrl":"10.1016/j.crmeth.2025.100966","url":null,"abstract":"Ewing sarcoma (EwS) cell line culture largely relies on standard techniques, which do not recapitulate physiological conditions. Here, we report on a feasible and cost-efficient EwS cell culture technique with increased physiological relevance employing an advanced medium composition, reduced fetal calf serum, and spheroidal growth. Improved reflection of the transcriptional activity related to proliferation, hypoxia, and differentiation in EwS patient tumors was detected in EwS cells grown in this refined in vitro condition. Moreover, transcriptional signatures associated with the oncogenic activity of the EwS-specific FET::ETS fusion transcription factors in the refined culture condition were shifted from proliferative toward metabolic gene signatures. The herein-presented EwS cell culture technique with increased physiological relevance provides a broadly applicable approach for enhanced in vitro modeling relevant to advancing EwS research and the validity of experimental results.","PeriodicalId":29773,"journal":{"name":"Cell Reports Methods","volume":" ","pages":"100966"},"PeriodicalIF":4.3,"publicationDate":"2025-02-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11955266/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143374773","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

Comparative prospects of imaging methods for whole-brain mammalian connectomics.

IF 4.3

Cell Reports Methods Pub Date : 2025-02-24 Epub Date: 2025-02-18 DOI: 10.1016/j.crmeth.2025.100988

Logan Thrasher Collins, Todd Huffman, Randal Koene

{"title":"Comparative prospects of imaging methods for whole-brain mammalian connectomics.","authors":"Logan Thrasher Collins, Todd Huffman, Randal Koene","doi":"10.1016/j.crmeth.2025.100988","DOIUrl":"10.1016/j.crmeth.2025.100988","url":null,"abstract":"Mammalian whole-brain connectomes are a foundational ingredient for a holistic understanding of brains. Indeed, imaging connectomes at sufficient resolution to densely reconstruct cellular morphology and synapses represents a long-standing goal in neuroscience. Mouse connectomes could soon come within reach, while human connectomes remain a more distant yet still worthy goal. Though the technologies needed to reconstruct whole-brain connectomes have not yet reached full maturity, they are advancing rapidly. Close examination of these technologies may help plan connectomics projects. Here, we quantitatively compare imaging technologies that have the potential to enable whole-brain mammalian connectomics. We perform calculations on electron microscopy (EM) techniques and expansion light-sheet fluorescence microscopy (ExLSFM) methods. We consider techniques that have sufficient resolution to identify all synapses and sufficient speed to be relevant for whole mammalian brains. We offer this analysis as a resource for those considering how to organize efforts toward imaging whole-brain mammalian connectomes.","PeriodicalId":29773,"journal":{"name":"Cell Reports Methods","volume":" ","pages":"100988"},"PeriodicalIF":4.3,"publicationDate":"2025-02-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11955263/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143459778","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