Cell Reports Methods

DVOUG enables robust DNA sequence assembly and reconstruction with a dynamic, variable-order graph

A signature-protein-based approach for accurate and efficient profiling of the human gut virome Gut virome analysis is limited by tools that struggle with viral diversity and novelty. Yang et al. present SinProVirP, a signature-protein-based profiler that accurately quantifies known and novel viruses with high efficiency, enabling large-scale, cross-cohort studies of the virome’s role in health and disease.

A signature-protein-based approach for accurate and efficient profiling of the human gut virome

Spatial ploidy inference using quantitative imaging Russell et al. construct a high-throughput experimental and computational pipeline that calculates nuclear ploidy from microscopy images and outputs a representative ploidy map showing the spatial arrangement of the nuclear ploidies. They demonstrate and validate their pipeline using Arabidopsis, Drosophila, and human tissue.

Spatial ploidy inference using quantitative imaging

FAME-CRISPR improves CRISPR-Cas9 genome editing via HDAC inhibition and engineered virus-like particle delivery Djamshidi et al. describe a strategy that they call fast, accurate and more efficient (FAME)-CRISPR utilizing pan-histone deacetylase inhibitors and engineered virus-like particles to improve the efficiency and speed of genome-editing experiments.

FAME-CRISPR improves CRISPR-Cas9 genome editing via HDAC inhibition and engineered virus-like particle delivery

Approaches for identification of 5′ UTR mutations impacting translation and protein production from neurodevelopmental disorder genes 5′ UTRs regulate the translation of the coding sequences and are often mutated in patients with autism and other diagnoses. However, their functional impacts are unclear, especially in the brain. Here, Plassmeyer et al. benchmarked approaches for functionally characterizing hundreds of UTR variants, including high-throughput assays in the living brain.

Approaches for identification of 5′ UTR mutations impacting translation and protein production from neurodevelopmental disorder genes

OSCAR is an online ML-powered tool for organoid cell counting using bright-field images Burnell et al. develop a computer-based method to count the number of cells in a well of organoids from a regular microscope image. They compare its use to standard counting techniques and test it in experiments where organoids are cultured with immune cells.

OSCAR is an online ML-powered tool for organoid cell counting using bright-field images

Computational modeling reveals cognitive processes in simple rodent depression tests Li et al. present a framework integrating automated behavioral tracking and computational modeling to dissect mouse depression tests. They reveal that the forced swim and tail suspension tests engage overlapping but partially distinct cognitive processes and that the dominant cognitive components shift across different stages of the tests.

Computational modeling reveals cognitive processes in simple rodent depression tests

One-step approach producing barcoded rabies virus with optimized diversity Tan et al. introduce a one-step method to produce barcoded rabies viruses that shortens timelines, boosts rescue efficiency, and eliminates background contamination. The approach yields barcode libraries with higher diversity and uniformity while maintaining conventional tracing performance, enabling more reliable and scalable connectomic mapping.

One-step approach producing barcoded rabies virus with optimized diversity

Development and application of a barcoded rabies viral tracing method for mapping brain-wide inputs to single neurons Tan et al. combine barcoded rabies tracing with single-cell RNA-seq to map local and long-range inputs to single mPFC neurons, revealing cells with high local innervation and a positive link between local input size and distant input diversity.

Development and application of a barcoded rabies viral tracing method for mapping brain-wide inputs to single neurons

Visual detection of seizures in mice using supervised machine learning Sabnis et al. use non-invasive video recordings of mice to develop a method using supervised machine learning to automatically quantify seizure severity. This approach provides a scalable and objective tool for seizure assessment, augmenting manual scoring and offering a more precise method for drug discovery and disease modeling in preclinical research.

Visual detection of seizures in mice using supervised machine learning

Real-time 4D MRI reconstruction using DVR-NeMF, a framework for dynamic volumetric reconstruction Wang et al. introduce DVR-NeMF, a neural magnetic field framework that reconstructs dynamic 4D MRI in real-time level with high fidelity. By leveraging spatiotemporal priors, the method enables reliable heart-function assessment, offering a step toward broader clinical use of MRI for dynamic imaging.

Real-time 4D MRI reconstruction using DVR-NeMF, a framework for dynamic volumetric reconstruction

Vector-guided graph learning for spatial multi-slice multi-omics alignment Lou et al. present stLVG, a lightweight vector-guided graph model for spatial multi-slice and multi-omics data integration. stLVG incorporates distance- and angle-based weights to capture spatial geometry, enabling robust alignment, cross-omics label transfer, and identification of tumor boundary regions across diverse spatial transcriptomics datasets.

Vector-guided graph learning for spatial multi-slice multi-omics alignment

Fast and sensitive detection of targeted gene fusions using frequency minimizers and fuzzy pattern matching with Fuzzion2 Rice et al. report Fuzzion2, a high-performance program for targeted gene fusion detection in unmapped read pairs. Sensitivity meets or exceeds that of de novo callers, making Fuzzion2 well suited for clinical testing and large-scale research investigations such as the mapping of distinct fusion landscapes between pediatric and adult cancers.

Fast and sensitive detection of targeted gene fusions using frequency minimizers and fuzzy pattern matching with Fuzzion2

Temporal reassignment and correspondence evaluation with quality control for time-course imaging of 3D cell culture Cramer et al. present TRACE-QC, a method for quality control of time-course imaging in 3D cell cultures. Using iterative Procrustes analysis, it reorders and aligns spheroid positions, corrects mislabeled images, and improves data integrity. TRACE-QC enhances assay reliability and interpretability without experimental modifications or parameter tuning.

Temporal reassignment and correspondence evaluation with quality control for time-course imaging of 3D cell culture

Cortical organoid-derived models of the melanoma brain metastatic niche enable prioritization of cancer-targeting drugs Krieg et al. develop melanoma brain metastasis models based on cortical brain organoids. They demonstrate the potential for therapeutic applications, screening a library of anti-cancer compounds and identifying the XPO1 inhibitor selinexor as a promising candidate that demonstrates effectiveness against cancer cells while maintaining low toxicity.

Cortical organoid-derived models of the melanoma brain metastatic niche enable prioritization of cancer-targeting drugs

Non-invasive measurement of biomolecular condensate interfacial tension and bending rigidity Williamson et al. present FlickerPrint, an open-source computational analysis tool for measuring the interfacial tension and bending rigidity of soft bodies from their shape fluctuations in time-series confocal microscopy videos. The package allows for thousands of biomolecular condensates, vesicles, and other soft bodies to be analyzed.

Non-invasive measurement of biomolecular condensate interfacial tension and bending rigidity

Simultaneous capture of single cell RNA-seq, ATAC-seq, and CRISPR perturbation enables multiomic screens to identify gene regulatory relationships Shevade et al. present CAT-ATAC (CRISPR and transcriptomics-assay for transposase-accessible chromatin), a single-cell sequencing assay that profiles gene expression, chromatin accessibility, and CRISPR perturbation from the same cells by modifying the commercially available 10× Multiome assay, and demonstrate its utility in multiple biological and therapeutically relevant applications.

Simultaneous capture of single cell RNA-seq, ATAC-seq, and CRISPR perturbation enables multiomic screens to identify gene regulatory relationships

High-speed neural imaging with multiplexed miniaturized two-photon microscopy Zhang et al. develop two types of multiplexed miniaturized two-photon microscopes (M-MINI2Ps) that increase imaging speed via beam multiplexing while preserving spatial resolution and demonstrate their utility in large-scale calcium imaging and voltage imaging of brain activity in freely moving mice.

High-speed neural imaging with multiplexed miniaturized two-photon microscopy

Benchmarking of human read removal strategies for viral and microbial metagenomics Forbes et al. benchmark human read removal methods for viral and microbial metagenomics. Using synthetic and microbiome datasets, along with a set of benchmark methods, they demonstrate that a custom Bowtie2 configuration (“very-sensitive-local” mode with single end) with the T2T-CHM13 reference best balances host read removal and microbial integrity.

Benchmarking of human read removal strategies for viral and microbial metagenomics

EyaHOST, a modular genetic system for investigation of intercellular and tumor-host interactions in Drosophila melanogaster Teles-Reis et al. present EyaHOST, a modular Drosophila system that enables clone generation in the eye disc with independent genetic manipulation of other tissues. EyaHOST uses an Eya-KD “kick-out” system for clonal QF2-driven tumor initiation and GAL4 for organ-specific host perturbation, providing a scalable platform for dissecting tumor-host interactions.

EyaHOST, a modular genetic system for investigation of intercellular and tumor-host interactions in Drosophila melanogaster

Imaging the time course of DNA damage response at a nonrepetitive endogenous locus

Combinatorial responsiveness of chemosensory neurons in mouse explants revealed by DynamicNeuroTracker Noh et al. present DynamicNeuronTracker, which segments single neurons despite positional jitter from tissue deformation in 3D calcium imaging. Analyzing the imaging of pheromone-sensing neurons under controlled stimulation, they identify 15 neuronal subpopulations with distinct responses to eight bile acids and steroids, revealing a pronounced bias toward estrogen and pregnanolone.

Combinatorial responsiveness of chemosensory neurons in mouse explants revealed by DynamicNeuroTracker

Targeted long-read methylation analysis using hybridization capture suitable for clinical specimens Kunigo et al. introduce t-nanoEM, a practical method that enables high-depth, target-specific long-read methylation analysis with as little as 8 ng of DNA. They develop a pipeline for haplotype-resolved and mutated allele-specific methylation analysis and demonstrate its utility by successfully applying it to clinical breast and lung cancer samples.

Targeted long-read methylation analysis using hybridization capture suitable for clinical specimens

DiffHiChIP: Identifying differential chromatin contacts from HiChIP data

A tabletop blast device for the study of the long-term consequences of traumatic brain injury on brain organoids

MetaLigand provides a prior-knowledge-guided framework for predicting non-peptide ligand mediated cell-cell communication Xin et al. present MetaLigand, a computational tool that infers cellular communication involving non-peptide molecules in health and disease. We apply this tool to analyze complex cellular interactions and identify molecular changes relevant to age-related macular degeneration.

MetaLigand provides a prior-knowledge-guided framework for predicting non-peptide ligand mediated cell-cell communication

SICyLIA-cTMT dissects redox proteome dynamics with high accuracy and depth at microgram scale Cysteine oxidation controls diverse signaling pathways but remains difficult to study at scale. Lilla et al. present SICyLIA-cTMT, a quantitative mass spectrometry workflow that simultaneously measures cysteine redox dynamics and protein abundance with high accuracy from minimal input. The method enhances coverage, reduces instrument time, and enables comprehensive analysis of oxidative signaling in cells and tissues.

SICyLIA-cTMT dissects redox proteome dynamics with high accuracy and depth at microgram scale

A transmission electron microscopy platform for assessing mitochondrial and nuclear architecture in cardiomyocytes Kiessling et al. introduce a TEM platform and analysis workflow that consistently images the nuclear center and perinuclear mitochondria in adult cardiomyocytes, enabling automated quantification and discovery of spatially resolved remodeling. Using Drp1-deficient mice, they demonstrate the ability to detect stress-induced anomalies in nanoscale organellar architecture.

A transmission electron microscopy platform for assessing mitochondrial and nuclear architecture in cardiomyocytes

Single-cell multiomics data integration and generation with scPairing Niu et al. present scPairing, a deep learning tool facilitating the integration and generation of single-cell multiomics data through cell pairing. Pairing produces realistic multiomics data that can be used in downstream analyses to uncover relationships between cellular modalities. scPairing also extends to trimodal data generation.

Single-cell multiomics data integration and generation with scPairing

Real-time pH imaging of macrophage lysosomes using the pH-sensitive probe ApHID