@CellRepMethods

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

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Joined November 2020
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Cell Reports Methods@CellRepMethods
2h
A single ROSA26 mouse line for robust tdTomato labeling with Cre, FLP, Dre, Vika, SCre, and VCre recombinases dlvr.it/TVhFZL

A single ROSA26 mouse line for robust tdTomato labeling with Cre, FLP, Dre, Vika, SCre, and VCre...

Nakashiba et al. engineer a multi-recombinase reporter mouse line, ROSA26-6R, consolidating responsiveness to six recombinases into a single locus. This platform minimizes colony management effort...

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Cell Reports Methods@CellRepMethods
6h
Self-supervised missing-wedge correction enables accurate cellular morphology and volume reconstruction in soft X-ray tomography dlvr.it/TVh8lh

Self-supervised missing-wedge correction enables accurate cellular morphology and volume reconstr...

Chueh et al. present a self-supervised sinogram inpainting framework to correct missing-wedge artifacts in soft X-ray tomography. By recovering unrecorded projection angles without ground-truth data,...

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Cell Reports Methods@CellRepMethods
Sep 25
Intravital 3-photon microscopy of leukocyte dynamics in the splenic white pulp dlvr.it/TVfHPL

Intravital 3-photon microscopy of leukocyte dynamics in the splenic white pulp

Schienstock et al. present a technical framework using surgical preparation of the mouse spleen, intravital 3-photon microscopy, and quantitative image analysis to interrogate in vivo leukocyte...

cell.com
158
Cell Reports Methods@CellRepMethods
Sep 24
A knockin Ntsr1Flp driver enables intersectional and systemic targeting of heterogeneous midbrain dopamine circuits dlvr.it/TVdYqV

A knockin Ntsr1Flp driver enables intersectional and systemic targeting of heterogeneous midbrain...

Garcia et al. develop intersectional viral-genetic approaches to access molecularly overlapping dopamine and non-dopaminergic neuron subtypes in the mouse midbrain. Their strategy enables selective...

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142
Cell Reports Methods@CellRepMethods
Sep 24
A single-cell spatiotemporal manifold of tissue morphology and dynamics dlvr.it/TVdSpG

A single-cell spatiotemporal manifold of tissue morphology and dynamics

Haus et al. create a learned, embedding-based representation of cell position in developing embryos. Embeddings describe dynamic morphology at the single-cell level, enabling applications in identi...

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141
Cell Reports Methods@CellRepMethods
Sep 18
HisTrader identifies nucleosome-free regions within ChIP-based profiling of histone post-translational modifications dlvr.it/TVY5Lx

HisTrader identifies nucleosome-free regions within ChIP-based profiling of histone post-translat...

Kirbizakis et al. develop HisTrader, a tool that pinpoints the short stretches of accessible DNA, where regulatory proteins bind, from widely available histone modification data. HisTrader enables...

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Cell Reports Methods@CellRepMethods
Sep 18
Revealing therapeutic single-cell transcriptomic signatures using a simple classifier dlvr.it/TVY0pm

Revealing therapeutic single-cell transcriptomic signatures using a simple classifier

Gene-expression-based drug screening usually requires at least 50–100 copies of the same clone or cells treated in the same way. Ma et al. describe a single-cell analysis platform that enables the...

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Cell Reports Methods@CellRepMethods
Sep 16
Self-amplifying RNA enables rapid, durable, integration-free programming of hiPSCs dlvr.it/TVWHCk

Self-amplifying RNA enables rapid, durable, integration-free programming of hiPSCs

Self-amplifying RNAs (saRNAs) have the potential for rapid, durable, non-integrating delivery of transgenes in human induced pluripotent stem cells. Della Santina et al. show that transcription...

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Cell Reports Methods@CellRepMethods
Sep 15
Parallelized bright-field and fluorescence imaging platform for organoids dlvr.it/TVVNYp

Parallelized bright-field and fluorescence imaging platform for organoids

Kim et al. present a multi-camera array scanner (MCAS) that uses 48 parallel lenses to image organoids. The MCAS reduces acquisition time by 98% compared to commercial systems. The platform enables...

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Cell Reports Methods@CellRepMethods
Sep 10
highSpaClone enables copy number alteration inference and tumor subclone analysis for high-resolution spatial transcriptomics dlvr.it/TVQXJW

highSpaClone enables copy number alteration inference and tumor subclone analysis for high-resolu...

Zang et al. present highSpaClone, a computational framework for inferring copy number alterations (CNAs) and tumor subclones from high-resolution spatially resolved transcriptomics (SRT) data. By...

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Cell Reports Methods@CellRepMethods
Sep 4
A deep learning framework for oligopeptide candidate discovery across metabolism-related contexts dlvr.it/TVKw8J

A deep learning framework for oligopeptide candidate discovery across metabolism-related contexts

Xiao et al. present Deepeptide, a deep learning-based pipeline for identifying oligopeptide leads without requiring indication-specific training data. By linking disease-related information, biolog...

cell.com
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Cell Reports Methods@CellRepMethods
Aug 20
Deep mapping of structural perturbations to energetics enables precise TCR design dlvr.it/TV61rc

Deep mapping of structural perturbations to energetics enables precise TCR design

Luo et al. present mpTCRai, a deep learning framework for predicting TCR-antigen specificity. By mapping sequence mutations to structural perturbations and energetic consequences, mpTCRai serves as a...

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Cell Reports Methods@CellRepMethods
Aug 17
Inference of lineage hierarchies, growth, and drug response mechanisms in cancer cell populations without tracking dlvr.it/TV3S7B

Inference of lineage hierarchies, growth, and drug response mechanisms in cancer cell populations...

Piras et al. present a statistical framework to infer lineage hierarchies and phenotypic transition probabilities in heterogeneous cell populations without tracking individual cells. Using multi-type...

cell.com
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Cell Reports Methods@CellRepMethods
Aug 15
A sensitive method for profiling cell-type-specific secretomes of rare cells from complex tissues dlvr.it/TV1y5K

A sensitive method for profiling cell-type-specific secretomes of rare cells from complex tissues

Shipkovenska et al. present an improved method for profiling cell-type-specific secretomes in complex tissues without the use of viral vectors. The authors perform proof-of-principle validation by...

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Cell Reports Methods@CellRepMethods
Aug 13
AAV-DJ enables efficient, function-preserving neuronal transduction for circuit interrogation in human cortical and thalamic organoids dlvr.it/TV0dQR

AAV-DJ enables efficient, function-preserving neuronal transduction for circuit interrogation in...

Adachi et al. systematically benchmark AAV capsids in human cortical and thalamic organoids by integrating gene delivery, cell type tropism, cytotoxicity, and neuronal function. By identifying AAV-DJ...

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Cell Reports Methods@CellRepMethods
Aug 12
SwitchClass distinguishes baseline- and perturbation-aligned features across intermediate molecular states dlvr.it/TTzlmh

SwitchClass distinguishes baseline- and perturbation-aligned features across intermediate molecular...

Xiao et al. present SwitchClass, a label-switch classification framework that scores whether molecular features in intermediate states align with baseline or perturbation. Across proteomic, phospho...

cell.com
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Cell Reports Methods@CellRepMethods
Aug 6
Strategic enhancement of Cas9 nickase-driven gene amplification dlvr.it/TTv24t

Strategic enhancement of Cas9 nickase-driven gene amplification

Takesue et al. enhance the nCas9-based gene amplification method BITREx through the development of (1) a plasmid reporter that predicts gRNA performance and (2) BITREx 2.0, a dual-nicking strategy...

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Cell Reports Methods@CellRepMethods
Aug 4
Volumetric denoising enables high-throughput volume electron microscopy and efficient downstream analysis dlvr.it/TTs9Nx

Volumetric denoising enables high-throughput volume electron microscopy and efficient downstream...

Chen et al. determined the pivotal role of sufficient axial resolution in maintaining data quality of volume electron microscopy despite varying image signal-to-noise ratios and developed a volumet...

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Cell Reports Methods@CellRepMethods
Jul 31
Targeting the peripheral nervous system in adipose tissue with engineered AAV vectors dlvr.it/TTp9TP

Targeting the peripheral nervous system in adipose tissue with engineered AAV vectors

Peripheral innervation of adipose tissue is essential for metabolic regulation, yet gene delivery tools remain underdeveloped. Willows et al. establish a framework for targeting AAV-mediated transg...

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Cell Reports Methods@CellRepMethods
Jul 31
AAV-delivered TurboRFP enables streamlined tracing and analysis of corticospinal tract sprouting dlvr.it/TTp4q6

AAV-delivered TurboRFP enables streamlined tracing and analysis of corticospinal tract sprouting

Hernaiz-Llorens et al. establish an AAV1-hSyn-TurboRFP workflow for streamlined corticospinal tract sprouting analysis. The method enables direct visualization of fine CST axons without secondary...

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