Research graph
References from Improving cell-type composition inference in spatial transcriptomics with SpaDAMA. Local targets link to admitted publications; unresolved targets remain external evidence.
Multimodal contrastive learning for spatial gene expression prediction using histology images
2024 · External reference
Exploring tissue architecture using spatial transcriptomics
10.1038/s41586-021-03634-9 · 2021 · External reference
Spatially resolved transcriptomics technology facilitates cancer research
2023 · External reference
SpaMask: Dual masking graph autoencoder with contrastive learning for spatial transcriptomics
2025 · External reference
Inferring single-cell resolution spatial gene expression via fusing spot-based spatial transcriptomics, location, and histology using GCN
2024 · External reference
The dawn of spatial omics
10.1126/science.abq4964 · 2023 · External reference
Transcriptome-scale super-resolved imaging in tissues by RNA seqFISH
10.1038/s41586-019-1049-y · 2019 · External reference
RNA imaging. Spatially resolved, highly multiplexed RNA profiling in single cells
2015 · External reference
SpaDiT: diffusion transformer for spatial gene expression prediction using scRNA-seq
2024 · External reference
Spatial transcriptomics: molecular maps of the mammalian brain
10.1146/annurev-neuro-100520-082639 · 2021 · External reference
Transcriptional landscape of the prenatal human brain
10.1038/nature13185 · 2014 · External reference
Slide-seq: a scalable technology for measuring genome-wide expression at high spatial resolution
10.1126/science.aaw1219 · 2019 · External reference
Spatiotemporal transcriptomic atlas of mouse organogenesis using DNA nanoball-patterned arrays
10.1016/j.cell.2022.04.003 · 2022 · External reference
Multiscale dissection of spatial heterogeneity by integrating multi-slice spatial and single-cell transcriptomics
2025 · External reference
Dual decoding of cell types and gene expression in spatial transcriptomics with PANDA
10.1093/nar/gkae876 · 2024 · External reference
SPOTlight: seeded NMF regression to deconvolute spatial transcriptomics spots with single-cell transcriptomes
10.1093/nar/gkab043 · 2021 · External reference
Robust enumeration of cell subsets from tissue expression profiles
10.1038/nmeth.3337 · 2015 · External reference
Advances in spatial transcriptomics and related data analysis strategies
10.1186/s12967-023-04150-2 · 2023 · External reference
DestVI identifies continuums of cell types in spatial transcriptomics data
10.1038/s41587-022-01272-8 · 2022 · External reference
SPACEL: deep learning-based characterization of spatial transcriptome architectures
10.1038/s41467-023-43220-3 · 2023 · External reference
10.1109/cvpr52688.2022.01553
10.1109/cvpr52688.2022.01553 · External reference
10.1145/3583780.3614894
10.1145/3583780.3614894 · External reference
Unresolved reference
External reference
10.1109/cvpr.2017.316
10.1109/cvpr.2017.316 · External reference
Adjustment of scRNA-seq data to improve cell-type decomposition of spatial transcriptomics
10.1093/bib/bbae063 · 2024 · External reference
SPIRAL: integrating and aligning spatially resolved transcriptomics data across different experiments, conditions, and technologies
10.1186/s13059-023-03078-6 · 2023 · External reference
Benchmarking spatial and single-cell transcriptomics integration methods for transcript distribution prediction and cell type deconvolution
10.1038/s41592-022-01480-9 · 2022 · External reference
A spatiotemporal organ-wide gene expression and cell atlas of the developing human heart
2019 · External reference
Establishment of a human MYH6 compound heterozygous knockout hESC line to model cardiomyopathy and congenital heart defects by CRISPR/Cas9 system
10.1016/j.scr.2020.102128 · 2020 · External reference
Multiplexed functional assessments of MYH7 variants in human cardiomyocytes
10.1161/circgen.123.004377 · 2024 · External reference
SCANPY: large-scale single-cell gene expression data analysis
10.1186/s13059-017-1382-0 · 2018 · External reference
Transcriptional profiling of mouse B cell terminal differentiation defines a signature for antibody-secreting plasma cells
10.1038/ni.3154 · 2015 · External reference
Single-cell transcriptome profiling reveals neutrophil heterogeneity in homeostasis and infection
10.1038/s41590-020-0736-z · 2020 · External reference
A comprehensive benchmarking with practical guidelines for cellular deconvolution of spatial transcriptomics
10.1038/s41467-023-37168-7 · 2023 · External reference
blf and the drl cluster synergistically regulate cell fate commitment during zebrafish primitive hematopoiesis
10.1242/dev.200919 · 2022 · External reference
Analysis of zebrafish periderm enhancers facilitates identification of a regulatory variant near human KRT8/18
2020 · External reference
Spatially informed cell-type deconvolution for spatial transcriptomics
10.1038/s41587-022-01273-7 · 2022 · External reference
Integrating microarray-based spatial transcriptomics and single-cell RNA-seq reveals tissue architecture in pancreatic ductal adenocarcinomas
10.1038/s41587-019-0392-8 · 2020 · External reference
Probabilistic cell-type assignment of single-cell RNA-seq for tumor microenvironment profiling
10.1038/s41592-019-0529-1 · 2019 · External reference
A single-cell transcriptome atlas of the human pancreas
2016 · External reference
SMART: spatial transcriptomics deconvolution using marker-gene-assisted topic model
10.1186/s13059-024-03441-1 · 2024 · External reference
Deconvolution and inference of spatial communication through optimization algorithm for spatial transcriptomics
10.1038/s42003-025-07625-8 · 2025 · External reference
Stages of embryonic development of the zebrafish
10.1002/aja.1002030302 · 1995 · External reference
The zebrafish pronephros: a model to study nephron segmentation
10.1038/ki.2008.37 · 2008 · External reference
High-resolution in situ hybridization to whole-mount zebrafish embryos
10.1038/nprot.2007.514 · 2008 · External reference
The Kunitz-type serine protease inhibitor Spint2 is required for cellular cohesion, coordinated cell migration and cell survival during zebrafish hatching gland development
10.1016/j.ydbio.2021.03.017 · 2021 · External reference
Spatiotemporal mapping of gene expression landscapes and developmental trajectories during zebrafish embryogenesis
2022 · External reference
Crosstalk between dendritic cells and regulatory T cells: protective effect and therapeutic potential in multiple sclerosis
10.3389/fimmu.2022.970508 · 2022 · External reference
Pattern of human monocyte subpopulations in health and disease
10.1111/sji.12883 · 2020 · External reference
Regulation of human NK-cell cytokine and chemokine production by target cell recognition
10.1182/blood-2009-08-238469 · 2010 · External reference
Regulatory T cells and immune tolerance
10.1016/j.cell.2008.05.009 · 2008 · External reference
Role of the microbiota in immunity and inflammation
10.1016/j.cell.2014.03.011 · 2014 · External reference
Epicardial progenitors contribute to the cardiomyocyte lineage in the developing heart
10.1038/nature07060 · 2008 · External reference
Epicardial EMT and cardiac repair: an update
10.1186/s13287-024-03823-z · 2024 · External reference
Endothelial-pericyte interactions in angiogenesis
10.1007/s00441-003-0745-x · 2003 · External reference
The bHLH transcription factor Tcf21 is required for lineage-specific EMT of cardiac fibroblast progenitors
10.1242/dev.079970 · 2012 · External reference
Fibroblast growth factor signals regulate a wave of Hedgehog activation that is essential for coronary vascular development
10.1101/gad.1411406 · 2006 · External reference
Cardiac fibroblast: the renaissance cell
10.1161/circresaha.109.209809 · 2009 · External reference
Modeling primitive and definitive erythropoiesis with induced pluripotent stem cells
10.1182/bloodadvances.2023011708 · 2024 · External reference
Primitive and definitive erythropoiesis in mammals
10.3389/fphys.2014.00003 · 2014 · External reference
Acinar-to-Ductal Metaplasia (ADM): on the road to Pancreatic Intraepithelial Neoplasia (PanIN) and pancreatic cancer
10.3390/ijms24129946 · 2023 · External reference
Acinar cell plasticity and development of pancreatic ductal adenocarcinoma
10.1038/nrgastro.2017.12 · 2017 · External reference
The role of dendritic cells in cancer and anti-tumor immunity
10.1016/j.smim.2021.101481 · 2021 · External reference
Targeting VEGF/VEGFR to modulate antitumor immunity
10.3389/fimmu.2018.00978 · 2018 · External reference
Integrated analysis of multimodal single-cell data
2021 · External reference
SpaGE: spatial gene enhancement using scRNA-seq
10.1093/nar/gkaa740 · 2020 · External reference
SMaSH: a scalable, general marker gene identification framework for single-cell RNA-sequencing
10.1186/s12859-022-04860-2 · 2022 · External reference
scMEB: a fast and clustering-independent method for detecting differentially expressed genes in single-cell RNA-seq data
10.1186/s12864-023-09374-6 · 2023 · External reference
Deep domain adversarial neural network for the deconvolution of cell type mixtures in tissue proteome profiling
10.1038/s42256-023-00737-y · 2023 · External reference
Deep learning and alignment of spatially resolved single-cell transcriptomes with Tangram
10.1038/s41592-021-01264-7 · 2021 · External reference
Single-cell and spatial transcriptomics enables probabilistic inference of cell type topography
10.1038/s42003-020-01247-y · 2020 · External reference
Inferring spatial and signaling relationships between cells from single-cell transcriptomic data
10.1038/s41467-020-15968-5 · 2020 · External reference
NovoSpaRc: flexible spatial reconstruction of single-cell gene expression with optimal transport
10.1038/s41596-021-00573-7 · 2021 · External reference
Cell2location maps fine-grained cell types in spatial transcriptomics
10.1038/s41587-021-01139-4 · 2022 · External reference
Robust decomposition of cell type mixtures in spatial transcriptomics
10.1038/s41587-021-00830-w · 2022 · External reference
