ArticleNature biotechnology2024
Prediction of single-cell RNA expression profiles in live cells by Raman microscopy with Raman2RNA.
Article in Nature biotechnology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 49 papers, 1 of them a synthesis that pooled it.
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Who cites it
49 citing papers in PubMed, 1 synthesis or guideline pooled it, 69 citations in OpenAlex.
- Metabolomics and metabolites in cancer diagnosis and treatment.Molecular biomedicine · 2025Pooled it
- RamanOmics decodes the spatial vibrational-molecular architecture of senescence in aging and repair.Nature aging · 2026Article
- Article
- CardamomOT: A mechanistic optimal transport-based framework for gene regulatory network inference, trajectory reconstruction and generative modeling.PLoS computational biology · 2026Article
- All-optical multimodal mapping of single-cell-type-specific metabolic activities via REDCAT.Nature methods · 2026Article
- PLANCK: super-multiplex optical imaging without labeling.bioRxiv : the preprint server for biology · 2026Article
- Nascent extracellular matrix: the missing piece in hydrogel design.Cell biomaterials · 2026Article
- The Next Frontier in Vibrational Imaging: Chemically Designed Raman Probes Pass the Spectral Barrier.JACS Au · 2026Review
- Single-cell morphodynamical trajectories enable prediction of gene expression accompanying cell state change.Cell systems · 2026Article
- Interpretation, extrapolation and perturbation of single cells.Nature reviews. Genetics · 2026Review
- Deep Learning-Guided Holotomography Reveals Early Structural Remodelling During Pluripotency Exit.bioRxiv : the preprint server for biology · 2026Article
- Revealing global stoichiometry conservation architecture in cells from Raman spectral patterns.eLife · 2026Article
- Redefining cellular reprogramming with advanced genomic technologies.Nature reviews. Genetics · 2026Review
- Advances in predicting omics profiles from imaging data.Briefings in bioinformatics · 2026Review
- Dynamic, single-cell monitoring of CAR T cell identity and activation with Raman spectroscopy.bioRxiv : the preprint server for biology · 2026Article
- RamEx: an R package for high-throughput microbial ramanome analyses with accurate quality assessment.Microbiome · 2026Article
- Challenges and Opportunities in Multi-Omics Data Acquisition and Analysis: Toward Integrative Solutions.Biomolecules · 2026Review
- AI-Based Prediction of Gene Expression in Single-Cell and Multiscale Genomics and Transcriptomics.International journal of molecular sciences · 2026Review
- Single-cell Raman profiling of B cell differentiation and leukemic transformation with transcriptome inference.Frontiers in immunology · 2026Article
- Vibrational Probes in Bioimaging and Chemical Biology.Chemical & biomedical imaging · 2025Article
Corrections and comments
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Authors and funding
14 authors at 2 institutions in 1 country.
Funding
Abstract
Single-cell RNA sequencing and other profiling assays have helped interrogate cells at unprecedented resolution and scale, but are inherently destructive. Raman microscopy reports on the vibrational energy levels of proteins and metabolites in a label-free and nondestructive manner at subcellular spatial resolution, but it lacks genetic and molecular interpretability. Here we present Raman2RNA (R2R), a method to infer single-cell expression profiles in live cells through label-free hyperspectral Raman microscopy images and domain translation. We predict single-cell RNA sequencing profiles nondestructively from Raman images using either anchor-based integration with single molecule fluorescence in situ hybridization, or anchor-free generation with adversarial autoencoders. R2R outperformed inference from brightfield images (cosine similarities: R2R >0.85 and brightfield <0.15). In reprogramming of mouse fibroblasts into induced pluripotent stem cells, R2R inferred the expression profiles of various cell states. With live-cell tracking of mouse embryonic stem cell differentiation, R2R traced the early emergence of lineage divergence and differentiation trajectories, overcoming discontinuities in expression space. R2R lays a foundation for future exploration of live genomic dynamics.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.