Cell Reports Methods最新文献_第2页

Comparative analysis of gene regulation in single cells using Compass. Compass在单细胞中基因调控的比较分析。

IF 4.3

Cell Reports Methods Pub Date : 2025-05-19 Epub Date: 2025-05-08 DOI: 10.1016/j.crmeth.2025.101035

Changxin Wan, Yilong Qu, Zhiyou Ye, Tianbei Zhang, Huifang Ma, Ming Chen, Wenpin Hou, Zhicheng Ji

引用次数: 0

IGLoo enables comprehensive analysis and assembly of immunoglobulin heavy-chain loci in lymphoblastoid cell lines using PacBio high-fidelity reads. 使用PacBio高保真读数，IGLoo能够全面分析和组装淋巴母细胞样细胞系中的免疫球蛋白重链位点。

IF 4.3

Cell Reports Methods Pub Date : 2025-05-19 Epub Date: 2025-05-01 DOI: 10.1016/j.crmeth.2025.101033

Mao-Jan Lin, Ben Langmead, Yana Safonova

{"title":"IGLoo enables comprehensive analysis and assembly of immunoglobulin heavy-chain loci in lymphoblastoid cell lines using PacBio high-fidelity reads.","authors":"Mao-Jan Lin, Ben Langmead, Yana Safonova","doi":"10.1016/j.crmeth.2025.101033","DOIUrl":"10.1016/j.crmeth.2025.101033","url":null,"abstract":"High-quality human genome assemblies derived from lymphoblastoid cell lines (LCLs) provide reference genomes and pangenomes for genomics studies. However, LCLs pose technical challenges for profiling immunoglobulin (IG) genes, as their IG loci contain a mixture of germline and somatically recombined haplotypes, making genotyping and assembly difficult with widely used frameworks. To address this, we introduce IGLoo, a software tool that analyzes sequence data and assemblies derived from LCLs, characterizing somatic V(D)J recombination events and identifying breakpoints and missing IG genes in the assemblies. Furthermore, IGLoo implements a reassembly framework to improve germline assembly quality by integrating information on somatic events and population structural variations in IG loci. Applying IGLoo to the assemblies from the Human Pangenome Reference Consortium, we gained valuable insights into the mechanisms, gene usage, and patterns of V(D)J recombination and the causes of assembly artifacts in the IG heavy-chain (IGH) locus, and we improved the representation of IGH assemblies.","PeriodicalId":29773,"journal":{"name":"Cell Reports Methods","volume":" ","pages":"101033"},"PeriodicalIF":4.3,"publicationDate":"2025-05-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144050631","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

A circadian behavioral analysis suite for real-time classification of daily rhythms in complex behaviors. 一个昼夜行为分析套件，用于复杂行为的日常节奏的实时分类。

IF 4.3

Cell Reports Methods Pub Date : 2025-05-19 DOI: 10.1016/j.crmeth.2025.101050

Logan J Perry, Gavin E Ratcliff, Arthur Mayo, Blanca E Perez, Larissa Rays Wahba, K L Nikhil, William C Lenzen, Yangyuan Li, Jordan Mar, Isabella Farhy-Tselnicker, Wanhe Li, Jeff R Jones

{"title":"A circadian behavioral analysis suite for real-time classification of daily rhythms in complex behaviors.","authors":"Logan J Perry, Gavin E Ratcliff, Arthur Mayo, Blanca E Perez, Larissa Rays Wahba, K L Nikhil, William C Lenzen, Yangyuan Li, Jordan Mar, Isabella Farhy-Tselnicker, Wanhe Li, Jeff R Jones","doi":"10.1016/j.crmeth.2025.101050","DOIUrl":"10.1016/j.crmeth.2025.101050","url":null,"abstract":"Long-term analysis of animal behavior has been limited by reliance on real-time sensors or manual scoring. Existing machine learning tools can automate analysis but often fail under variable conditions or ignore temporal dynamics. We developed a scalable pipeline for continuous, real-time acquisition and classification of behavior across multiple animals and conditions. At its core is a self-supervised vision model paired with a lightweight classifier that enables robust performance with minimal manual labeling. Our system achieves expert-level performance and can operate indefinitely across diverse recording environments. As a proof-of-concept, we recorded 97 mice over 2 weeks to test whether sex hormones influence circadian behaviors. We discovered sex- and estrogen-dependent rhythms in behaviors such as digging and nesting. We introduce the Circadian Behavioral Analysis Suite (CBAS), a modular toolkit that supports high-throughput, long-timescale behavioral phenotyping, allowing for the temporal analysis of behaviors that were previously difficult or impossible to observe.","PeriodicalId":29773,"journal":{"name":"Cell Reports Methods","volume":"5 5","pages":"101050"},"PeriodicalIF":4.3,"publicationDate":"2025-05-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144112033","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

CalliCog is an open-source cognitive neuroscience toolkit for freely behaving nonhuman primates. CalliCog是一个开源的认知神经科学工具包，用于自由行为的非人类灵长类动物。

IF 4.3

Cell Reports Methods Pub Date : 2025-05-19 Epub Date: 2025-05-07 DOI: 10.1016/j.crmeth.2025.101034

Jack T Scott, Bruno L Mendivez Vasquez, Brian J Stewart, Dylan D Panacheril, Darren K J Rajit, Angela Y Fan, James A Bourne

{"title":"CalliCog is an open-source cognitive neuroscience toolkit for freely behaving nonhuman primates.","authors":"Jack T Scott, Bruno L Mendivez Vasquez, Brian J Stewart, Dylan D Panacheril, Darren K J Rajit, Angela Y Fan, James A Bourne","doi":"10.1016/j.crmeth.2025.101034","DOIUrl":"10.1016/j.crmeth.2025.101034","url":null,"abstract":"Nonhuman primates (NHPs) are pivotal for unlocking the complexities of human cognition, yet traditional cognitive studies remain constrained to specialized laboratories. To address this gap, we present CalliCog: an open-source, scalable in-cage platform tailored for experiments in small freely behaving primate species such as the common marmoset (Callithrix jacchus). CalliCog includes modular operant chambers that operate autonomously and integrate seamlessly with home cages, eliminating human intervention. Our results showcase the power of CalliCog to train experimentally naive marmosets in touchscreen-based cognitive tasks. Across two independent facilities, marmosets achieved touchscreen proficiency within 2 weeks and successfully completed tasks probing behavioral flexibility and working memory. Moreover, CalliCog enabled precise synchronization of behavioral data with electrocorticography (ECoG) recordings from freely moving animals, opening new frontiers for neurobehavioral research. By making CalliCog openly accessible, we aim to democratize cognitive experimentation with small NHPs, narrowing the translational gap between preclinical models and human cognition.","PeriodicalId":29773,"journal":{"name":"Cell Reports Methods","volume":" ","pages":"101034"},"PeriodicalIF":4.3,"publicationDate":"2025-05-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144052843","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

Highly quantitative measurement of differential protein-genome binding with PerCell chromatin sequencing. 利用PerCell染色质测序对差异蛋白-基因组结合进行高度定量测量。

IF 4.3

Cell Reports Methods Pub Date : 2025-05-15 DOI: 10.1016/j.crmeth.2025.101052

Alexi Tallan, Jack Kucinski, Benjamin Sunkel, Cenny Taslim, Stephanie LaHaye, Qi Liu, Jun Qi, Meng Wang, Genevieve C Kendall, Benjamin Z Stanton

引用次数: 0

An AAV capsid proposed as microglia-targeting directs genetic expression in forebrain excitatory neurons. 一种AAV衣壳被提出作为小胶质细胞靶向指导前脑兴奋性神经元的基因表达。

IF 4.3

Cell Reports Methods Pub Date : 2025-05-13 DOI: 10.1016/j.crmeth.2025.101054

Wenhao Cao, Zhiqun Tan, Bereket T Berackey, Jason K Nguyen, Sara R Brown, Shiyang Du, Bin Lin, Qiao Ye, Magdalene Seiler, Todd C Holmes, Xiangmin Xu

引用次数: 0

An improved FLARE system for recording and manipulating neuronal activity. 用于记录和操纵神经元活动的改进的FLARE系统。

IF 4.3

Cell Reports Methods Pub Date : 2025-04-21 Epub Date: 2025-03-21 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

Minimally invasive, wide-field two-photon imaging of the brainstem at cellular resolution. 脑干细胞分辨率的微创、宽视场双光子成像。

IF 4.3

Cell Reports Methods Pub Date : 2025-04-21 Epub Date: 2025-04-04 DOI: 10.1016/j.crmeth.2025.101010

Masakazu Agetsuma, Azumi Hatakeyama, Daisuke Yamada, Hiroshi Kuniishi, Chihiro Ito, Eri Takeuchi, Shinji Tsuji, Motosuke Tsutsumi, Takako Ichiki, Kohei Otomo, Toshinori Yoshioka, Tomoko Kobayashi, Atsushi Noritake, Yoshitsugu Aoki, Tomomi Nemoto, Hiroshi Yukawa, Akiyoshi Saitoh, Junichi Nabekura, Masayuki Sekiguchi

{"title":"Minimally invasive, wide-field two-photon imaging of the brainstem at cellular resolution.","authors":"Masakazu Agetsuma, Azumi Hatakeyama, Daisuke Yamada, Hiroshi Kuniishi, Chihiro Ito, Eri Takeuchi, Shinji Tsuji, Motosuke Tsutsumi, Takako Ichiki, Kohei Otomo, Toshinori Yoshioka, Tomoko Kobayashi, Atsushi Noritake, Yoshitsugu Aoki, Tomomi Nemoto, Hiroshi Yukawa, Akiyoshi Saitoh, Junichi Nabekura, Masayuki Sekiguchi","doi":"10.1016/j.crmeth.2025.101010","DOIUrl":"10.1016/j.crmeth.2025.101010","url":null,"abstract":"Brain-viscera communication is crucial for regulating mental health, with the vagus nerve being a key structure mediating this interaction. Clinically, artificial vagus nerve stimulation (VNS) is used to treat various neuropsychiatric disorders, highlighting the importance of vagal afferent fibers in emotion regulation. The nucleus tractus solitarii (NTS) is a brainstem structure proposed to receive signals from vagal afferents and relay them to brain networks for emotion regulation. However, due to the anatomical complexity and difficulty in accessing the deep-brain NTS region in vivo, its underlying mechanisms remain unclear. Here, we developed a wide-field and deep-brain two-photon imaging method using a double-prism optical interface. This approach enables cellular-resolution imaging to specifically detect NTS neural activity while largely preserving the overlying cerebellum, a region also implicated in emotion regulation. We evaluated NTS neuronal responses to VNS and a gastrointestinal hormone, demonstrating the method's utility for investigating the vagus-NTS pathway in vivo.","PeriodicalId":29773,"journal":{"name":"Cell Reports Methods","volume":" ","pages":"101010"},"PeriodicalIF":4.3,"publicationDate":"2025-04-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143789245","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

Differential performance of strategies for single-cell whole-genome amplification. 单细胞全基因组扩增策略的差异表现。

IF 4.3

Cell Reports Methods Pub Date : 2025-04-21 DOI: 10.1016/j.crmeth.2025.101025

Nuria Estévez-Gómez, Tamara Prieto, Laura Tomás, Pilar Alvariño, Amy Guillaumet-Adkins, Holger Heyn, Sonia Prado-López, David Posada

{"title":"Differential performance of strategies for single-cell whole-genome amplification.","authors":"Nuria Estévez-Gómez, Tamara Prieto, Laura Tomás, Pilar Alvariño, Amy Guillaumet-Adkins, Holger Heyn, Sonia Prado-López, David Posada","doi":"10.1016/j.crmeth.2025.101025","DOIUrl":"https://doi.org/10.1016/j.crmeth.2025.101025","url":null,"abstract":"Single-cell genomics enables studying tissues and organisms at the highest resolution. However, since a cell contains a small amount of DNA, single-cell DNA sequencing (scDNA-seq) typically requires single-cell whole-genome amplification (scWGA). Unfortunately, scWGA methods introduce technical biases that complicate the interpretation of scDNA-seq data. We compared six scWGA methods, three MDA (multiple displacement amplification; GenomiPhi, REPLI-g, and TruePrime) and three non-MDA (Ampli1, MALBAC, and PicoPLEX), on 206 tumoral and 24 healthy human cells. scWGA methods performed differently depending on the parameter of interest. REPLI-g minimized regional amplification bias, while non-MDA methods showed a more uniform and reproducible amplification. Ampli1 exhibited the lowest allelic imbalance and dropout, the most accurate insertion or deletion (indel) and copy-number detection, and a low polymerase error rate. However, REPLI-g yielded higher DNA quantities, longer amplicons, and greater genome coverage. We offer a comprehensive guide for selecting a scWGA approach, outlining trade-offs that influence the interpretation of scDNA-seq data.","PeriodicalId":29773,"journal":{"name":"Cell Reports Methods","volume":"5 4","pages":"101025"},"PeriodicalIF":4.3,"publicationDate":"2025-04-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144031525","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

Human MAPT knockin mouse models of frontotemporal dementia for the neurodegenerative research community. 人类MAPT敲入额颞叶痴呆小鼠模型的神经退行性研究社区。

IF 4.3

Cell Reports Methods Pub Date : 2025-04-21 Epub Date: 2025-04-11 DOI: 10.1016/j.crmeth.2025.101024

Takahiro Morito, Mohan Qi, Naoko Kamano, Hiroki Sasaguri, Sumi Bez, Martha Foiani, Karen Duff, Seico Benner, Toshihiro Endo, Hiroshi Hama, Hiroshi Kurokawa, Atushi Miyawaki, Hiroshi Mizuma, Naruhiko Sahara, Masafumi Shimojo, Makoto Higuchi, Takaomi C Saido, Naoto Watamura

{"title":"Human MAPT knockin mouse models of frontotemporal dementia for the neurodegenerative research community.","authors":"Takahiro Morito, Mohan Qi, Naoko Kamano, Hiroki Sasaguri, Sumi Bez, Martha Foiani, Karen Duff, Seico Benner, Toshihiro Endo, Hiroshi Hama, Hiroshi Kurokawa, Atushi Miyawaki, Hiroshi Mizuma, Naruhiko Sahara, Masafumi Shimojo, Makoto Higuchi, Takaomi C Saido, Naoto Watamura","doi":"10.1016/j.crmeth.2025.101024","DOIUrl":"https://doi.org/10.1016/j.crmeth.2025.101024","url":null,"abstract":"Existing models of frontotemporal dementia (FTD) may not fully recapitulate the pathophysiology of the disease. To generate more pathophysiologically relevant FTD models, we engineered MAPT knockin mouse lines carrying triple mutations, among which the MAPTP301S;Int10+3;S320F line exhibited robust tau pathology starting before 6 months of age. Severe tau accumulation was predominantly observed in the thalamus, hypothalamus, and amygdala with milder involvement of the cortex and hippocampus, leading to synaptic loss, brain atrophy, and FTD-like behavioral abnormalities. Crossbreeding MAPTP301S;Int10+3;S320F mice with App knockin, AppNL-G-F, mice markedly enhanced tau pathology in the cortex and hippocampus, highlighting the interplay between β-amyloid and tau. These findings establish the mutant mice as valuable models for investigating the mechanisms underlying FTD and other tauopathies, providing a relevant platform for in vivo drug screening.","PeriodicalId":29773,"journal":{"name":"Cell Reports Methods","volume":"5 4","pages":"101024"},"PeriodicalIF":4.3,"publicationDate":"2025-04-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144018913","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