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Cell Reports Methods @CellRepMethods

A new multi-disciplinary, gold #OA journal from @CellPressNews publishing cutting-edge methodological advances.

Joined November 2020
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130 Photos and videos
Systematic benchmarking of CUT&Tag improves the reliability and reproducibility of chromatin analysis dlvr.it/TT1Mx7

Systematic benchmarking of CUT&Tag improves the reliability and reproducibility of chromatin...

Murray et al. identify key experimental factors that strongly influence CUT&Tag performance across chromatin targets. By optimizing cell input, peak calling, duplicate handling, and crosslinking...

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Φ-Space ST: A platform-agnostic method to identify cell states in spatial transcriptomics studies dlvr.it/TT1GnV

Φ-Space ST: A platform-agnostic method to identify cell states in spatial transcriptomics studies

Mao et al. present Φ-Space ST, a platform-agnostic method for annotating continuous cell states in spatial transcriptomics using multiple scRNA-seq references. Validated across Visium, CosMx, Xenium,...

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A hybrid micro-ECoG for functionally targeted multi-site and multi-scale investigation dlvr.it/TT0L0l

A hybrid micro-ECoG for functionally targeted multi-site and multi-scale investigation

Jendritza et al. introduce a μECoG that enables high-resolution functional mapping of brain regions in rats, cats, and marmosets. The μECoG can be repeatedly penetrated with intracortical arrays for...

cell.com
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FLIM Playground: An interactive, end-to-end graphical user interface for analyzing single cells with fluorescence lifetime imaging microscopy dlvr.it/TSzNBd

FLIM Playground: An interactive, end-to-end graphical user interface for analyzing single cells...

Analysis of cellular-resolution fluorescence lifetime imaging microscopy (FLIM) remains fragmented across siloed tools requiring custom code. Zhao et al. present FLIM Playground for unified feature...

cell.com
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OrgLine: A versatile pipeline for organoid morphometry using detector-guided prompts dlvr.it/TSxYhP

OrgLine: A versatile pipeline for organoid morphometry using detector-guided prompts

Deng et al. present OrgLine, a bright-field organoid analysis pipeline that combines pre-trained detection with prompt-guided segmentation. Using a curated benchmark, they evaluate transfer across...

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DeepFaceMouse enables scalable prediction of large-scale brain activity from facial dynamics in mice dlvr.it/TSxS4c

DeepFaceMouse enables scalable prediction of large-scale brain activity from facial dynamics in mice

Ozdemirli et al. introduce DeepFaceMouse, a deep learning framework that decodes cortex-wide brain activity from facial dynamics in mice. The method achieves high precision and robust generalization...

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Unsupervised deep learning enables blur-free resolution enhancement in two-photon microscopy dlvr.it/TSvGSx

Unsupervised deep learning enables blur-free resolution enhancement in two-photon microscopy

Two-photon microscopy reveals deep-tissue biology but produces blurry, hard-to-analyze 3D images. Morita et al. develop TENET, a physics-informed unsupervised deep learning framework that deblurs,...

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A DirectView focus reduction assay for high-throughput quantification of neutralizing antibodies against influenza A and B viruses dlvr.it/TStvfc

A DirectView focus reduction assay for high-throughput quantification of neutralizing antibodies...

Feng et al. establish DirectView FRA, a high-throughput focus reduction assay that rapidly quantifies influenza-neutralizing antibodies by visualizing viral foci using a fluorogenic neuraminidase...

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Uncertainty-aware graph structure optimization with ensemble learning for enhanced cancer gene identification dlvr.it/TStQRM

Uncertainty-aware graph structure optimization with ensemble learning for enhanced cancer gene...

Hu et al. develop NexusGene, a method that integrates uncertainty-aware graph structure learning with clustering-enhanced ensemble learning to improve cancer driver gene identification. By refining...

cell.com
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Precision tumor-on-chip for personalized assessment of drug efficacy and immune cell delivery dlvr.it/TStJpx

Precision tumor-on-chip for personalized assessment of drug efficacy and immune cell delivery

Kremneva et al. present a microfluidic tumor-on-chip platform integrating patient-derived organoids with vascular flow to simulate physiological drug delivery. This model captures treatment resista...

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Optimizing microhomology-based genome editing by engineering DNA polymerase θ for improved efficiency and reduced on-target indels dlvr.it/TSsS05

Optimizing microhomology-based genome editing by engineering DNA polymerase θ for improved effici...

Wang et al. present engineered polymerase θ functional domains that enable efficient and precise microhomology-mediated genome editing. The resulting pPET and hPET systems outperform existing...

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Cross-species integration of single-cell data reveals conserved pathology-associated cell populations across animal models and human samples dlvr.it/TSsKln

Cross-species integration of single-cell data reveals conserved pathology-associated cell populat...

Li et al. present TACMAN, a framework for integrating cross-species single-cell RNA-seq data. TACMAN aligns conserved cell types and reveals shared disease-associated populations across species,...

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AmygdalaGo-BOLT for boundary-aware segmentation of the human amygdala dlvr.it/TSrRZX

AmygdalaGo-BOLT for boundary-aware segmentation of the human amygdala

Zhou et al. present AmygdalaGo-BOLT, a deep learning tool for precise amygdala segmentation from brain MRI. By improving accuracy, robustness, and cross-dataset generalizability, the approach enables...

cell.com
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Ordering molecular diversity in untargeted metabolomics via molecular community networking dlvr.it/TSrKNR

Ordering molecular diversity in untargeted metabolomics via molecular community networking

Coler et al. introduce molecular community networking (MCN), a new approach for mass spectrometry data organization by identifying natural molecular clusters and pruning them to their strongest...

cell.com
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Rapid neuronal labeling and functional imaging in the developing mouse brain with AAV-PHP.eB dlvr.it/TSqS8Z

Rapid neuronal labeling and functional imaging in the developing mouse brain with AAV-PHP.eB

Ye et al. show that AAV-PHP.eB enables robust neuronal expression within 3 days after neonatal injection, allowing rapid access to early postnatal brain development. Combined with simple delivery...

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Temporal control of sgRNA library activation unlocks large-scale in vivo CRISPR screens dlvr.it/TSqL1m

Temporal control of sgRNA library activation unlocks large-scale in vivo CRISPR screens

Fenoglio et al. demonstrate the application of CRISPR-StAR, an inducible in vivo screening platform with internal intra-tumor normalization, and developed a Bayesian bioinformatics pipeline to...

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Development of far-red fluorescent proteins for temporal domain multiplexing and super-resolution imaging dlvr.it/TSnFsP

Development of far-red fluorescent proteins for temporal domain multiplexing and super-resolution...

Fakorede et al. engineered three far-red fluorescent proteins with matched spectra but distinct photobleaching rates, enabling temporal domain multiplexing to resolve multiple labels within a single...

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Detecting protein higher-order structural changes using kinase as a phospho-labeler dlvr.it/TSlb9s

Detecting protein higher-order structural changes using kinase as a phospho-labeler

Maeda et al. present a labeling-based approach for detecting protein higher-order structural changes using in vitro kinase reactions. By combining residue-specific labeling through kinase substrate...

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Real-time cell viability monitoring for high-throughput drug screening using tumor xenograft-derived cells dlvr.it/TSlTZw

Real-time cell viability monitoring for high-throughput drug screening using tumor xenograft-deri...

Esmaeilishirazifard et al. present a high-throughput drug screening platform that uses real-time bioluminescent monitoring to measure the viability of PDTX-derived tumor cells during drug treatment....

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Parallel gene amplification by Cas9 nickase for generating functionally heterogeneous cell populations dlvr.it/TSjnh2

Parallel gene amplification by Cas9 nickase for generating functionally heterogeneous cell popula...

Takesue et al. present parallel BITREx to randomize the copy numbers and stoichiometry of cooperating genes in yeast. This platform generates cell populations with diverse functional performances by...

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