ArticleNature communications2025
Phospho-seq: integrated, multi-modal profiling of intracellular protein dynamics in single cells.
Article in Nature communications, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Synthesizing Mechanistic Hypotheses from Single-Cell Omics via Discretized Feature Attribution and Empirical Language Model Grounding.bioRxiv : the preprint server for biology · 2026Article
- Comparison between a conventional tool and deep learning models for RNA velocity analysis of scRNA-Seq data.Molecular genetics and genomics : MGG · 2026Article
- Disordered protein LAT encodes relative levels of signaling pathways in T cell activation.Science (New York, N.Y.) · 2026Article
- Genome-wide single-cell perturbation screens with VIPerturb-seq.bioRxiv : the preprint server for biology · 2026Article
- An expanded role for single-cell chemical genomics profiling in drug discovery.The Biochemical journal · 2026Review
- Mapping transcriptional responses to cellular perturbation dictionaries with RNA fingerprinting.bioRxiv : the preprint server for biology · 2025Article
- Iterative, multimodal, and scalable single-cell profiling for discovery and characterization of signaling regulators.bioRxiv : the preprint server for biology · 2025Article
- Integration of phospho-signaling and transcriptomics in single cells reveals distinct Th17 cell fates.Cell reports · 2025Article
- Exploring the untapped potential of single-cell and spatial omics in plant biology.The New phytologist · 2025Review
- Systems Human Immunology and AI: Immune Setpoint and Immune Health.Annual review of immunology · 2025Review
- scTrends: A living review of commercial single-cell and spatial 'omic technologies.Cell genomics · 2024Review
- InTraSeq: A Multimodal Assay that Uncovers New Single-Cell Biology and Regulatory Mechanisms.Research square · 2024Article
- Inferring pattern-driving intercellular flows from single-cell and spatial transcriptomics.Nature methods · 2024Article
- Next-generation forward genetic screens: uniting high-throughput perturbations with single-cell analysis.Trends in genetics : TIG · 2024Review
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8 authors.
Funding
Abstract
Cell signaling plays a critical role in neurodevelopment, regulating cellular behavior and fate. While multimodal single-cell sequencing technologies are rapidly advancing, scalable and flexible profiling of cell signaling states alongside other molecular modalities remains challenging. Here we present Phospho-seq, an integrated approach that aims to quantify cytoplasmic and nuclear proteins, including those with post-translational modifications, and to connect their activity with cis-regulatory elements and transcriptional targets. We utilize a simplified benchtop antibody conjugation method to create large custom neuro-focused antibody panels for simultaneous protein and scATAC-seq profiling on whole cells, alongside both experimental and computational strategies to incorporate transcriptomic measurements. We apply our workflow to cell lines, induced pluripotent stem cells, and months-old retinal and brain organoids to demonstrate its broad applicability. We show that Phospho-seq can provide insights into cellular states and trajectories, shed light on gene regulatory relationships, and help explore the causes and effects of diverse cell signaling in neurodevelopment.
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