@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
4h
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
7h
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...

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160
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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143
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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142
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 17
Development and application of nbLIBRA-seq for high-throughput discovery of antigen-specific nanobodies dlvr.it/TVXFNM

Development and application of nbLIBRA-seq for high-throughput discovery of antigen-specific...

Leonard et al. present LIBRA-seq for nanobody discovery (nbLIBRA-seq), a method for rapidly screening and discovering antigen-specific nanobodies in alpaca. The approach increases the throughput and...

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Cell Reports Methods@CellRepMethods
Sep 17
Moving beyond linear summation to infer interaction order from neural and biological dynamics dlvr.it/TVX84q

Moving beyond linear summation to infer interaction order from neural and biological dynamics

Biological networks can involve interactions among more than two components, but detecting them from dynamics is difficult. Altshuler et al. introduce a recurrent network framework that compares...

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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 10
Cryoprotectants-assisted plunge freezing of thick brain tissue specimens for targeted physiologically relevant cryo-imaging in situ dlvr.it/TVQBgW

Cryoprotectants-assisted plunge freezing of thick brain tissue specimens for targeted physiologic...

Weier et al. demonstrate applicability of plunge-freezing for mammalian brain tissue vitrification in the presence of physiologically appropriate cryoprotectant-containing solutions. Subsequent...

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Cell Reports Methods@CellRepMethods
Sep 9
A morphology-driven workflow to decipher 3D electron microscopy segmentation in diatoms dlvr.it/TVPkqj

A morphology-driven workflow to decipher 3D electron microscopy segmentation in diatoms

Uwizeye et al. present an AI framework that segments whole-cell 3D electron microscopy volumes accurately using little training data and ordinary computers. By replacing laborious manual tracing, it...

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157
Cell Reports Methods@CellRepMethods
Sep 9
Causal assessment of Bayesian gene regulatory networks from single-cell transcriptomics dlvr.it/TVPdBJ

Causal assessment of Bayesian gene regulatory networks from single-cell transcriptomics

Sato et al. present scstruc, an R package for learning and evaluating directed gene regulatory networks from single-cell transcriptomic data. By combining Bayesian network structure learning,...

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Cell Reports Methods@CellRepMethods
Sep 8
Multimodal alignment improves generalizability of genomic biomarker prediction in computational pathology dlvr.it/TVNk6C

Multimodal alignment improves generalizability of genomic biomarker prediction in computational...

Redekop et al. present MARBLE, a multimodal contrastive pretraining approach for histology and genetic biomarker alignment. Fine-tuning the image-only module, using a real-world cohort of MSK-IMPACT...

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Cell Reports Methods@CellRepMethods
Sep 7
ON-Time enables rapid microbiome sequencing and analysis for precision medicine dlvr.it/TVMs24

ON-Time enables rapid microbiome sequencing and analysis for precision medicine

MacKenzie et al. present ON-Time, a rapid metagenomic sequencing and analysis workflow that characterizes microbial composition of individual patient fecal samples in <5 h. Validated against mock...

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143
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...

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Cell Reports Methods@CellRepMethods
Sep 4
Engineering lymphatic collecting vessel phenotypes through combined hyaluronic acid cues and oscillatory shear stress dlvr.it/TVKq1Y

Engineering lymphatic collecting vessel phenotypes through combined hyaluronic acid cues and...

To advance lymphatic vessel engineering, Lightsey at el. develop a microfluidic device-based approach that integrates physiologically relevant extracellular matrix cues with oscillatory shear stress....

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Cell Reports Methods@CellRepMethods
Sep 3
Spatially resolved synaptic connectome mapping with FISH-decodable CASS barcodes dlvr.it/TVK1JB

Spatially resolved synaptic connectome mapping with FISH-decodable CASS barcodes

Dissociation-based viral tracing loses neuronal spatial data, while EM and in situ sequencing are costly. Zhu et al. present FISH-detectable CASS barcodes with rabies monosynaptic tracing to capture...

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