Cell Reports Methods

Efficient global accuracy estimation for protein complex structural models using multi-view representation learning Liu et al. present MViewEMA, a multi-view learning framework that integrates structural features across multiple scales to assess the accuracy of protein complex models, enabling faster model selection and improving the accuracy of deep learning-based structure predictions.

Efficient global accuracy estimation for protein complex structural models using multi-view representation learning

A 3D multi-compartment assembloid to study combined immune cell infiltration and cytotoxicity Hanna et al. develop a 3D model of the tumor microenvironment to study how immune cells migrate and infiltrate solid tumors. This approach allows researchers to evaluate how the movement of cell therapies through extracellular matrices influences their efficacy, particularly in challenging tumors like pancreatic cancer, thereby advancing treatment strategies.

A 3D multi-compartment assembloid to study combined immune cell infiltration and cytotoxicity

2P-FENDO-II: A fiber bundle microscope for all-optical, large field-of-view brain studies in freely moving mice Studying the brain’s natural mechanisms requires tools to precisely manipulate widespread neuronal circuits in freely moving animals. Blot et al. present a new microscope that allows the recording and control of neural activity with high precision, down to the level of individual cells, across large brain areas during naturalistic behavior.

2P-FENDO-II: A fiber bundle microscope for all-optical, large field-of-view brain studies in freely moving mice

HazardPyMatch: A tool for identifying reproductive and other hazards in scientific laboratories Parker et al. present HazardPyMatch, an automated tool that identifies hazardous chemicals such as reproductive hazards using standardized classifications and adaptable search criteria. This workflow improves laboratory safety and supports researchers with exposure sensitivities by making chemical hazard information more transparent and easier to evaluate.

HazardPyMatch: A tool for identifying reproductive and other hazards in scientific laboratories

An integrative spatial multi-omic workflow for unified analysis of tumor tissue Kriel et al. introduce SMINT, a scalable method that aligns maps of gene expression with metabolite imaging in the same tissue to build single-cell multi-omic maps. SMINT integrates metabolite activity with cell neighborhoods, helping generate new ideas about tumor spatial architecture.

An integrative spatial multi-omic workflow for unified analysis of tumor tissue

A unified framework combining linear and 3D molecular features for robust drug-protein interaction prediction Sun et al. develop PointDPI to predict drug-protein interactions (DPIs) by integrating linear and 3D molecular structures. PointDPI preserves inter-molecular relationships and predicts key regulatory sites, outperforming several state-of-the-art methods.

A unified framework combining linear and 3D molecular features for robust drug-protein interaction prediction

Dynamic estimation of metabolic state during CAR T cell production In this work, Jagannathan et al. use computational modeling to estimate metabolic dynamics of healthy-donor and patient-derived CAR T cells during ex vivo culture in a bioreactor and use it to show that early metabolism could correlate with cellular attributes of the harvested cell therapy product.

Dynamic estimation of metabolic state during CAR T cell production

An orthogonal CRISPR/Cpf1 platform for precise spatiotemporal gene regulation and osteoporotic fracture repair Zhao et al. developed OREC, an orthogonal CRISPR/Cpf1 platform combining chemical and light control for simultaneous regulation of multiple genes with spatiotemporal precision. The system successfully enhanced osteoporotic fracture repair in mice by activating bone formation while suppressing inhibitory signals, demonstrating therapeutic potential for complex gene therapy applications.

An orthogonal CRISPR/Cpf1 platform for precise spatiotemporal gene regulation and osteoporotic fracture repair

Predictive modeling of molecular activity underlying physical cell-cell interactions Azad et al. introduce Gloss, a computational framework that links intracellular gene programs measured with scRNA-seq to physical cell-cell interactions measured by LIPSTIC. Using a group lasso approach, Gloss robustly identifies the molecular drivers of immune communication in models of cancer and viral infection.

Predictive modeling of molecular activity underlying physical cell-cell interactions

DMC-BrainMap is an open-source, end-to-end tool for multi-feature brain mapping in different species In this study, Jung et al. present DMC-BrainMap, a software for performing mapping of anatomical data (e.g., cell bodies, axonal densities, injection sites, and optic fiber/Neuropixels probe tracts) from different species including mice, rats, and zebrafish into reference spaces.

DMC-BrainMap is an open-source, end-to-end tool for multi-feature brain mapping in different species

AxoMetric platform facilitates rapid and unbiased automated quantification of axon regeneration in tissue sections Finneran et al. develop a platform called AxoMetric that enables rapid and unbiased quantification of axon regeneration in tissue sections. They demonstrate that the platform is accurate and quicker than conventional manual quantification methods, providing research groups with a standardized tool to measure axon regeneration.

AxoMetric platform facilitates rapid and unbiased automated quantification of axon regeneration in tissue sections

Using DIPA-CRISPR for simple and efficient endogenous protein tagging in insects Ferrández-Roldán and Piulachs report a successful fluorescent knockin in cockroaches using DIPA-CRISPR and HDR. By inserting mCherry in-frame at the endogenous dll locus, they achieve robust in vivo visualization of protein localization in live embryos. This method enables accessible, precise genome editing in hemimetabolous insects without egg microinjection.

Using DIPA-CRISPR for simple and efficient endogenous protein tagging in insects

Multi-omic analysis of guided and unguided forebrain organoids reveals differences in cellular composition and metabolic profiles Øhlenschlæger et al. perform a multi-omic analysis of forebrain organoids generated by two key methods, guided and unguided differentiation. They document significant differences in the cell type composition and metabolic profiles of the two forebrain organoid types, providing a resource and methodological guide for the neural organoid field.

Multi-omic analysis of guided and unguided forebrain organoids reveals differences in cellular composition and metabolic profiles

Neural barcoding representing cortical spatiotemporal dynamics based on continuous-time Markov chains Culp et al. develop the Markovian neural barcode technique, a formal computational model of cortical brain dynamics that compactly encodes normative brain function and subsequent deviations due to experimental manipulations. The neural barcoding technique is designed as a contemporary lens to study the spatiotemporal statistics of cortical imaging data.

Neural barcoding representing cortical spatiotemporal dynamics based on continuous-time Markov chains

A multicellular analysis calcium imaging toolbox for ImageJ Hageter et al. developed an open-source toolkit (MCA) that works within the widely used imaging software, ImageJ. They provide an overview of the main functions MCA uses to analyze data from imaging datasets. They apply their software to a variety of model organisms and stimulus types to highlight the versatility of their software.

A multicellular analysis calcium imaging toolbox for ImageJ

African pygmy mouse iPSCs as a model for in vitro embryogenesis, interspecies chimerism, and blastocyst complementation Gjonlleshaj et al. report chimera-competent induced pluripotent stem cells from the African pygmy mouse, a rodent with distinctive genetics and exceptionally small size. These iPSCs reveal principles of differentiation in non-laboratory rodents and enable interspecies chimerism and blastocyst complementation with the house mouse, thereby expanding models for developmental and regenerative research.

African pygmy mouse iPSCs as a model for in vitro embryogenesis, interspecies chimerism, and blastocyst complementation

Fluorescent indicators for visualizing dynamic contact between cells and between processes originating from a single cell Kanadome et al. develop Gachapin and Gachapin-C, two reversible indicators for cell-cell contact dynamics. Gachapin enables multiplexed imaging of intercellular contacts alongside cytoskeletal and signaling activities. Gachapin-C provides more specific visualization of self-contacts within a single cell. These tools reveal contact assembly and disassembly in real time.

Fluorescent indicators for visualizing dynamic contact between cells and between processes originating from a single cell

Evaluation of statistical differential analysis methods for identification of senescent cells using single-cell transcriptomics In a benchmarking study with both simulated and real single-cell RNA sequencing datasets, Li et al. evaluate 10 differential gene expression (DGE) methods implemented in the Seurat package. The DESeq2 method outperforms the others, leading the authors to recommend it for DGE analyses in the Seurat package.

Evaluation of statistical differential analysis methods for identification of senescent cells using single-cell transcriptomics

High-efficiency transfection of Acanthamoeba castellanii using a cationic polymer Moreno et al. present a robust, cost-effective transfection method for Acanthamoeba castellanii employing the common polymer polyethylenimine, yielding up to 100-fold improvement in genetic delivery efficiency. By overcoming a major technical limitation, this advance facilitates molecular genetic manipulation of an evolutionarily, ecologically, and clinically significant amoeba.

High-efficiency transfection of Acanthamoeba castellanii using a cationic polymer

Simultaneous determination of free and total metabolite concentrations in proteinaceous specimens by 1D 1H CPMG NMR

HT SpaceM enables high-throughput mapping of metabolic diversity at the single-cell level

Dissecting novel object exploration in a fully automated homecage-based novel object recognition test Ho et al. develop homecage-based fully automated novel object recognition test to measure object memory in mice. The test is consistent across laboratories and removes human error, helping scientists study memory and brain function more accurately and reliably.

Dissecting novel object exploration in a fully automated homecage-based novel object recognition test

Epigenomic, transcriptomic, and proteomic characterization of breast cancer cell line reference samples Nepal et al. establish comprehensive genomic, epigenomic, transcriptomic, and proteomic reference data from paired breast cancer and B cell lines. These datasets provide benchmarks for multi-omics assay validation and cross-platform reproducibility.

Epigenomic, transcriptomic, and proteomic characterization of breast cancer cell line reference samples

Improved flux profiling in genome-scale modeling of human cell metabolism Huijer et al. present a regression-based method to accurately determine metabolic exchange fluxes in human cells. These fluxes provide reliable constraints for metabolic model simulations to study human metabolism and disease.

Improved flux profiling in genome-scale modeling of human cell metabolism

Evaluation of the effects of a new standard equation for doubly labeled water studies Falkenhain et al. show that a standardized equation for calculating energy expenditure from doubly labeled water provides more accurate results than a historically employed equation. Their work also offers a simple correction approach to align historic and future measurements, helping researchers compare studies and build clearer insights into human metabolism.

Evaluation of the effects of a new standard equation for doubly labeled water studies

Generation of thymus-reconstituting T cell progenitors from human pluripotent stem cells Philonenko et al. report generation of T cell progenitors from human pluripotent stem cells (hPSCs). These hPSC-pro-T cells demonstrate the single-cell transcription profile of early thymic progenitors from the human fetus. The T cell progenitors reconstitute the thymus over the long term and develop into mature T cells in vivo.

Generation of thymus-reconstituting T cell progenitors from human pluripotent stem cells

Homomorphic encryption enables privacy preserving polygenic risk scores Knight et al. present HEPRS, a fully homomorphic encryption pipeline that computes polygenic risk scores directly on encrypted genotypes. Using a 110k SNP schizophrenia model, encrypted and plaintext PRSs closely match while preserving privacy, enabling practical and secure PRS inference for clinical genomics.

Homomorphic encryption enables privacy preserving polygenic risk scores

Efficient CRISPR-Cas genome editing in brown algae Brown algae, a key yet understudied lineage of multicellular eukaryotes, have long lacked tools for functional genomics. Martinho et al. introduce a high-efficiency, transgene-free CRISPR platform enabling precise genome editing across multiple brown algal species, unlocking new possibilities for studying their development, evolution, and biotechnological potential.

Efficient CRISPR-Cas genome editing in brown algae

Assessing PARP trapping dynamics in ovarian cancer using a CRISPR-engineered FRET biosensor Marks et al. develop a CRISPR-engineered intramolecular FRET biosensor that enables high-content, single-cell quantification of PARP1 trapping via fluorescence lifetime imaging microscopy. This live-cell platform reveals how reduced PARP1 trapping may contribute to PARP inhibitor resistance, advancing dynamic analyses of DNA repair responses in ovarian cancer.

Assessing PARP trapping dynamics in ovarian cancer using a CRISPR-engineered FRET biosensor

In vivo AGO-APP for cell-type- and compartment-specific miRNA profiling in the mouse brain Kapoor et al. present two transgenic mouse lines enabling in vivo AGO affinity purification (AGO-APP) through expression of the T6B peptide. These models allow cell-type-specific and postsynapse-associated miRNA profiling, revealing distinct miRNA populations and synaptic enrichment patterns across olfactory bulb interneurons and cortical excitatory neurons.

In vivo AGO-APP for cell-type- and compartment-specific miRNA profiling in the mouse brain