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The Drosophila embryo at single-cell transcriptome resolution

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Comparison of the gap segmentation gene hunchback between Drosophila melanogaster and Drosophila virilis reveals novel modes of evolutionary change.

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Fate-mapping in wild-typeDrosophila melanogaster

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Fate-mapping in wild-typeDrosophila melanogaster

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Multiobjective evolutionary algorithms to identify highly autocorrelated areas: the case of spatial distribution in financially compromised farms

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Developmental fate of pole cells in Drosophila melanogaster

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The “Regulatory Genome” for Animal Development

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The Hippo Signaling Pathway Coordinately Regulates Cell Proliferation and Apoptosis by Inactivating Yorkie, the Drosophila Homolog of YAP

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High-Resolution Profiling of Histone Methylations in the Human Genome

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Global Analysis of mRNA Localization Reveals a Prominent Role in Organizing Cellular Architecture and Function

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A Quantitative Spatiotemporal Atlas of Gene Expression in the Drosophila Blastoderm

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Disruptions of Topological Chromatin Domains Cause Pathogenic Rewiring of Gene-Enhancer Interactions

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Droplet Barcoding for Single-Cell Transcriptomics Applied to Embryonic Stem Cells

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Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets

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Comprehensive Classification of Retinal Bipolar Neurons by Single-Cell Transcriptomics

inferredcites →https://doi.org/10.1016/j.celrep.2013.09.001openalex-snapshot

CAST-ChIP Maps Cell-Type-Specific Chromatin States in the Drosophila Central Nervous System

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Evolution of the Ventral Midline in Insect Embryos

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Promiscuity and specificity in BMP receptor activation

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Designing Cell-Type-Specific Genome-wide Experiments

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De Novo Prediction of Stem Cell Identity using Single-Cell Transcriptome Data

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Chapter 3 Evolution of Cis‐Regulatory Sequences in Drosophila

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Whole-Genome Analysis of Dorsal-Ventral Patterning in the Drosophila Embryo

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Assembly of yolk spindles in the early Drosophila embryo

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Whole-Genome Expression Profiles Identify Gene Batteries in Drosophila

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Evidence for stabilizing selection in a eukaryotic enhancer element

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Genome-wide maps of chromatin state in pluripotent and lineage-committed cells

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Histone modifications at human enhancers reflect global cell-type-specific gene expression

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The developmental transcriptome of Drosophila melanogaster

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Single-cell messenger RNA sequencing reveals rare intestinal cell types

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Spatial reconstruction of single-cell gene expression data

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High-throughput spatial mapping of single-cell RNA-seq data to tissue of origin

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Fiji: an open-source platform for biological-image analysis

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Cell type–specific chromatin immunoprecipitation from multicellular complex samples using BiTS-ChIP

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Gene regulatory networks for development

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Histone H3K27ac separates active from poised enhancers and predicts developmental state

inferredcites →https://doi.org/10.1083/jcb.201302049openalex-snapshot

Injury-induced BMP signaling negatively regulates Drosophila midgut homeostasis

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Interplay of Signal Mediators of Decapentaplegic (Dpp): Molecular Characterization of Mothers against dpp, Medea, and Daughters against dpp

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STAR: ultrafast universal RNA-seq aligner

inferredcites →https://doi.org/10.1093/molbev/msu071openalex-snapshot

Molecular Evolution of the Yap/Yorkie Proto-Oncogene and Elucidation of Its Core Transcriptional Program

inferredcites →https://doi.org/10.1093/nar/gkw1016openalex-snapshot

FlyBase at 25: looking to the future

inferredcites →https://doi.org/10.1101/099473openalex-snapshot

Cell fixation and preservation for droplet-based single-cell transcriptomics

inferredcites →https://doi.org/10.1101/gad.1166404openalex-snapshot

pyramus and thisbe: FGF genes that pattern the mesoderm of Drosophila embryos

inferredcites →https://doi.org/10.1101/gad.2046211openalex-snapshot

Post-transcription initiation function of the ubiquitous SAGA complex in tissue-specific gene activation

inferredcites →https://doi.org/10.1101/gr.110098.110openalex-snapshot

Plasticity in patterns of histone modifications and chromosomal proteins in Drosophila heterochromatin

inferredcites →https://doi.org/10.1101/gr.112961.110openalex-snapshot

The transcriptional diversity of 25 Drosophila cell lines

inferredcites →https://doi.org/10.1101/gr.114611.110openalex-snapshot

Developmental control of the DNA replication and transcription programs

inferredcites →https://doi.org/10.1101/gr.131748.111openalex-snapshot

Cell-type-specific nuclei purification from whole animals for genome-wide expression and chromatin profiling

inferredcites →https://doi.org/10.1101/gr.191122.115openalex-snapshot

Linking RNA biology to lncRNAs

inferredcites →https://doi.org/10.1126/science.1099247openalex-snapshot

Multiplex Detection of RNA Expression in Drosophila Embryos

inferredcites →https://doi.org/10.1126/science.1158170openalex-snapshot

The Transcription/Migration Interface in Heart Precursors of Ciona intestinalis

inferredcites →https://doi.org/10.1126/science.1171468openalex-snapshot

Epigenetic Temporal Control of Mouse Hox Genes in Vivo

inferredcites →https://doi.org/10.1126/science.1247651openalex-snapshot

Massively Parallel Single-Cell RNA-Seq for Marker-Free Decomposition of Tissues into Cell Types

inferredcites →https://doi.org/10.1126/science.6289436openalex-snapshot

Genetic Transformation of Drosophila with Transposable Element Vectors

inferredcites →https://doi.org/10.1128/mcb.24.2.912-923.2004openalex-snapshot

Template Requirements for Telomerase Translocation in Kluyveromyces lactis

inferredcites →https://doi.org/10.1186/1471-2105-4-57openalex-snapshot

Conservation of regulatory elements between two species of Drosophila

inferredcites →https://doi.org/10.1186/gb-2002-3-12-research0088openalex-snapshot

Systematic determination of patterns of gene expression during Drosophila embryogenesis

inferredcites →https://doi.org/10.1186/gb-2007-8-7-r145openalex-snapshot

Global analysis of patterns of gene expression during Drosophilaembryogenesis

inferredcites →https://doi.org/10.1186/s12915-017-0383-5openalex-snapshot

Cell fixation and preservation for droplet-based single-cell transcriptomics

inferredcites →https://doi.org/10.1242/dev.01124openalex-snapshot

A regulatory code for neurogenic gene expression in theDrosophilaembryo

inferredcites →https://doi.org/10.1242/dev.015255openalex-snapshot

In vivo regulation of Yorkie phosphorylation and localization

inferredcites →https://doi.org/10.1371/journal.pgen.1004625openalex-snapshot

BMPs Regulate msx Gene Expression in the Dorsal Neuroectoderm of Drosophila and Vertebrates by Distinct Mechanisms

inferredcites →https://doi.org/10.1371/journal.pone.0071820openalex-snapshot

Sequencing mRNA from Cryo-Sliced Drosophila Embryos to Determine Genome-Wide Spatial Patterns of Gene Expression

inferredcites →https://doi.org/10.15252/embj.201488117openalex-snapshot

Paternal RNA contributions in the Caenorhabditis elegans zygote

inferredcites →https://doi.org/10.15252/embj.201488769openalex-snapshot

Global characterization of the oocyte‐to‐embryo transition in Caenorhabditis elegans uncovers a novel mRNA clearance mechanism

inferredcites →https://doi.org/10.15252/embj.201489293openalex-snapshot

Chronic exposure to TGFβ1 regulates myeloid cell inflammatory response in an IRF7‐dependent manner

inferredcites →https://doi.org/10.1534/genetics.116.186783openalex-snapshot

Quantitative Single-Embryo Profile ofDrosophilaGenome Activation and the Dorsal–Ventral Patterning Network

inferredcites →https://doi.org/10.2144/04363st03openalex-snapshot

New Drosophila transgenic reporters: insulated P-element vectors expressing fast-maturing RFP

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H3K27 modifications define segmental regulatory domains in the Drosophila bithorax complex

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inferred← citeshttps://doi.org/10.1016/j.ydbio.2019.11.008openalex-snapshot

A single-cell transcriptome atlas for zebrafish development

inferred← citeshttps://doi.org/10.1016/j.ydbio.2020.04.009openalex-snapshot

The tissues and regulatory pattern of limb chondrogenesis

inferred← citeshttps://doi.org/10.1016/j.ydbio.2020.12.015openalex-snapshot

Modeling mammalian trunk development in a dish

inferred← citeshttps://doi.org/10.1016/j.ydbio.2022.05.018openalex-snapshot

Transcriptional profiling from whole embryos to single neuroblast lineages in Drosophila

inferred← citeshttps://doi.org/10.1016/j.yjmcc.2021.09.011openalex-snapshot

3D-cardiomics: A spatial transcriptional atlas of the mammalian heart

inferred← citeshttps://doi.org/10.1017/s0960258518000156openalex-snapshot

Interpreting biological variation: seeds, populations and sensitivity thresholds

inferred← citeshttps://doi.org/10.1021/acs.analchem.0c02499openalex-snapshot

Double Emulsion Picoreactors for High-Throughput Single-Cell Encapsulation and Phenotyping via FACS

inferred← citeshttps://doi.org/10.1021/acs.est.2c01098openalex-snapshot

Advances in Single-Cell Toxicogenomics in Environmental Toxicology

inferred← citeshttps://doi.org/10.1021/acschemneuro.8b00100openalex-snapshot

NeuroSystematics and Periodic System of Neurons: Model vs Reference Species at Single-Cell Resolution

inferred← citeshttps://doi.org/10.1038/nature25981openalex-snapshot

The cis-regulatory dynamics of embryonic development at single-cell resolution

inferred← citeshttps://doi.org/10.1038/nbt.4103openalex-snapshot

Simultaneous single-cell profiling of lineages and cell types in the vertebrate brain

inferred← citeshttps://doi.org/10.1038/nbt.4231openalex-snapshot

Paired-cell sequencing enables spatial gene expression mapping of liver endothelial cells

inferred← citeshttps://doi.org/10.1038/nbt.4260openalex-snapshot

Identification of spatially associated subpopulations by combining scRNAseq and sequential fluorescence in situ hybridization data

inferred← citeshttps://doi.org/10.1038/nrg.2017.77openalex-snapshot

Transcriptomic blueprints

inferred← citeshttps://doi.org/10.1038/s41467-018-07540-zopenalex-snapshot

Single cell RNA-sequencing identifies a metabolic aspect of apoptosis in Rbf mutant

inferred← citeshttps://doi.org/10.1038/s41467-020-15189-wopenalex-snapshot

Cell lineage-specific transcriptome analysis for interpreting cell fate specification of proembryos

inferred← citeshttps://doi.org/10.1038/s41467-020-15968-5openalex-snapshot

Inferring spatial and signaling relationships between cells from single cell transcriptomic data

inferred← citeshttps://doi.org/10.1038/s41467-020-20092-5openalex-snapshot

Single-cell atlas of the first intra-mammalian developmental stage of the human parasite Schistosoma mansoni

inferred← citeshttps://doi.org/10.1038/s41467-021-22117-zopenalex-snapshot

Defective metabolic programming impairs early neuronal morphogenesis in neural cultures and an organoid model of Leigh syndrome

inferred← citeshttps://doi.org/10.1038/s41467-021-24014-xopenalex-snapshot

Model-based prediction of spatial gene expression via generative linear mapping

inferred← citeshttps://doi.org/10.1038/s41467-022-30177-yopenalex-snapshot

A 3D gene expression atlas of the floral meristem based on spatial reconstruction of single nucleus RNA sequencing data

inferred← citeshttps://doi.org/10.1038/s41467-023-41408-1openalex-snapshot

Lola-I is a promoter pioneer factor that establishes de novo Pol II pausing during development

inferred← citeshttps://doi.org/10.1038/s41467-023-43037-0openalex-snapshot

A single cell genomics atlas of the Drosophila larval eye reveals distinct photoreceptor developmental timelines

inferred← citeshttps://doi.org/10.1038/s41467-024-48960-4openalex-snapshot

Rapid response of fly populations to gene dosage across development and generations

inferred← citeshttps://doi.org/10.1038/s41467-025-57719-4openalex-snapshot

Chromatin landscape at cis-regulatory elements orchestrates cell fate decisions in early embryogenesis

inferred← citeshttps://doi.org/10.1038/s41576-019-0093-7openalex-snapshot

Integrative single-cell analysis

inferred← citeshttps://doi.org/10.1038/s41576-020-0223-2openalex-snapshot

Lineage tracing meets single-cell omics: opportunities and challenges

inferred← citeshttps://doi.org/10.1038/s41576-021-00370-8openalex-snapshot

Integrating single-cell and spatial transcriptomics to elucidate intercellular tissue dynamics

inferred← citeshttps://doi.org/10.1038/s41581-018-0021-7openalex-snapshot

Single-cell RNA sequencing for the study of development, physiology and disease

inferred← citeshttps://doi.org/10.1038/s41586-019-1210-7openalex-snapshot

Transcriptional cofactors display specificity for distinct types of core promoters

inferred← citeshttps://doi.org/10.1038/s41586-019-1773-3openalex-snapshot

Gene expression cartography

inferred← citeshttps://doi.org/10.1038/s41586-020-2941-1openalex-snapshot

Decoding myofibroblast origins in human kidney fibrosis

inferred← citeshttps://doi.org/10.1038/s41586-021-03634-9openalex-snapshot

Exploring tissue architecture using spatial transcriptomics

inferred← citeshttps://doi.org/10.1038/s41587-020-0469-4openalex-snapshot

Benchmarking single-cell RNA-sequencing protocols for cell atlas projects

inferred← citeshttps://doi.org/10.1038/s41587-021-01182-1openalex-snapshot

Spatial components of molecular tissue biology

inferred← citeshttps://doi.org/10.1038/s41587-023-01697-9openalex-snapshot

High-resolution alignment of single-cell and spatial transcriptomes with CytoSPACE

inferred← citeshttps://doi.org/10.1038/s41588-021-00799-xopenalex-snapshot

Independence of chromatin conformation and gene regulation during Drosophila dorsoventral patterning

inferred← citeshttps://doi.org/10.1038/s41588-022-01018-xopenalex-snapshot

Systematic reconstruction of cellular trajectories across mouse embryogenesis

inferred← citeshttps://doi.org/10.1038/s41592-019-0492-xopenalex-snapshot

Gene expression atlas of a developing tissue by single cell expression correlation analysis

inferred← citeshttps://doi.org/10.1038/s41592-019-0692-4openalex-snapshot

Computational methods for single-cell omics across modalities

inferred← citeshttps://doi.org/10.1038/s41592-022-01409-2openalex-snapshot

Museum of spatial transcriptomics

inferred← citeshttps://doi.org/10.1038/s41592-022-01480-9openalex-snapshot

Benchmarking spatial and single-cell transcriptomics integration methods for transcript distribution prediction and cell type deconvolution

inferred← citeshttps://doi.org/10.1038/s41592-022-01728-4openalex-snapshot

Screening cell–cell communication in spatial transcriptomics via collective optimal transport

inferred← citeshttps://doi.org/10.1038/s41592-024-02184-yopenalex-snapshot

TISSUE: uncertainty-calibrated prediction of single-cell spatial transcriptomics improves downstream analyses

inferred← citeshttps://doi.org/10.1038/s41592-025-02897-8openalex-snapshot

DynamicAtlas: a morphodynamic atlas for Drosophila development

inferred← citeshttps://doi.org/10.1038/s41596-018-0046-1openalex-snapshot

Preparation of plant tissue to enable Spatial Transcriptomics profiling using barcoded microarrays

inferred← citeshttps://doi.org/10.1038/s41596-018-0073-yopenalex-snapshot

Tutorial: guidelines for the experimental design of single-cell RNA sequencing studies

inferred← citeshttps://doi.org/10.1038/s41596-021-00573-7openalex-snapshot

NovoSpaRc: flexible spatial reconstruction of single-cell gene expression with optimal transport

inferred← citeshttps://doi.org/10.1038/s41598-020-58327-6openalex-snapshot

Systematic Comparison of High-throughput Single-Cell and Single-Nucleus Transcriptomes during Cardiomyocyte Differentiation

inferred← citeshttps://doi.org/10.1038/s41598-020-61591-1openalex-snapshot

Finding cell-specific expression patterns in the early Ciona embryo with single-cell RNA-seq

inferred← citeshttps://doi.org/10.1038/s42003-020-01341-1openalex-snapshot

From whole-mount to single-cell spatial assessment of gene expression in 3D

inferred← citeshttps://doi.org/10.1038/s42003-021-01803-0openalex-snapshot

smiFISH and embryo segmentation for single-cell multi-gene RNA quantification in arthropods

inferred← citeshttps://doi.org/10.1038/s42003-022-03175-5openalex-snapshot

Deciphering tissue structure and function using spatial transcriptomics

inferred← citeshttps://doi.org/10.1038/s42003-023-04834-xopenalex-snapshot

Methanol fixation is the method of choice for droplet-based single-cell transcriptomics of neural cells

inferred← citeshttps://doi.org/10.1038/s42003-025-08335-xopenalex-snapshot

Genome-wide quantitative dissection of an arthropod segmented body plan at single-cell resolution

inferred← citeshttps://doi.org/10.1038/s43588-021-00110-2openalex-snapshot

From complex datasets to predictive models of embryonic development

inferred← citeshttps://doi.org/10.1038/s44222-023-00084-yopenalex-snapshot

Microtechnologies for single-cell and spatial multi-omics

inferred← citeshttps://doi.org/10.1039/d2lc00514jopenalex-snapshot

An integrated microfluidic device for multiplexed imaging of spatial gene expression patterns of Drosophila embryos

inferred← citeshttps://doi.org/10.1039/d2nr05435copenalex-snapshot

Image recovery from unknown network mechanisms for DNA sequencing-based microscopy

inferred← citeshttps://doi.org/10.1063/5.0091135openalex-snapshot

Deep learning in spatial transcriptomics: Learning from the next next-generation sequencing

inferred← citeshttps://doi.org/10.1073/pnas.1821178116openalex-snapshot

A computational framework for DNA sequencing microscopy

inferred← citeshttps://doi.org/10.1073/pnas.1913931118openalex-snapshot

Revealing lineage-related signals in single-cell gene expression using random matrix theory

inferred← citeshttps://doi.org/10.1073/pnas.1921625117openalex-snapshot

Behavior-related gene regulatory networks: A new level of organization in the brain

inferred← citeshttps://doi.org/10.1073/pnas.2112892119openalex-snapshot

Dynamics of Drosophila endoderm specification

inferred← citeshttps://doi.org/10.1080/03008207.2025.2501703openalex-snapshot

Spatial transcriptomic applications in orthopedics

inferred← citeshttps://doi.org/10.1080/19420889.2020.1838809openalex-snapshot

Why isn’t sex optional? Stem-cell competition, loss of regenerative capacity, and cancer in metazoan evolution

inferred← citeshttps://doi.org/10.1083/jcb.202104107openalex-snapshot

Mechanical competition alters the cellular interpretation of an endogenous genetic program

inferred← citeshttps://doi.org/10.1088/1478-3975/abba85openalex-snapshot

Heterogeneity and ‘memory’ in stem cell populations

inferred← citeshttps://doi.org/10.1093/9780197846032.001.0001openalex-snapshot

Populations of Individuals

inferred← citeshttps://doi.org/10.1093/9780197846032.002.0004openalex-snapshot

Foreword

inferred← citeshttps://doi.org/10.1093/9780197846032.002.0005openalex-snapshot

Preface

inferred← citeshttps://doi.org/10.1093/9780197846032.002.0006openalex-snapshot

Epigraph

inferred← citeshttps://doi.org/10.1093/9780197846032.003.0001openalex-snapshot

Populations of Individuals

inferred← citeshttps://doi.org/10.1093/9780197846032.003.0002openalex-snapshot

Population-based Threshold Models

inferred← citeshttps://doi.org/10.1093/9780197846032.003.0003openalex-snapshot

Origin and Integration of Biological Processes

inferred← citeshttps://doi.org/10.1093/9780197846032.003.0004openalex-snapshot

Microorganisms

inferred← citeshttps://doi.org/10.1093/9780197846032.003.0005openalex-snapshot

Plants

inferred← citeshttps://doi.org/10.1093/9780197846032.003.0006openalex-snapshot

Animals

inferred← citeshttps://doi.org/10.1093/9780197846032.003.0007openalex-snapshot

Developmental Plasticity, Ecology and Evolution

inferred← citeshttps://doi.org/10.1093/9780197846032.003.0008openalex-snapshot

Implications and Anticipations

inferred← citeshttps://doi.org/10.1093/9780197846032.005.0001openalex-snapshot

Methods

inferred← citeshttps://doi.org/10.1093/bib/bbaa042openalex-snapshot

Computational methods for the integrative analysis of single-cell data

inferred← citeshttps://doi.org/10.1093/bib/bbaa181openalex-snapshot

The winning methods for predicting cellular position in the DREAM single-cell transcriptomics challenge

inferred← citeshttps://doi.org/10.1093/bib/bbab148openalex-snapshot

Anti-bias training for (sc)RNA-seq: experimental and computational approaches to improve precision

inferred← citeshttps://doi.org/10.1093/bib/bbac297openalex-snapshot

Spatial transcriptomics prediction from histology jointly through Transformer and graph neural networks

inferred← citeshttps://doi.org/10.1093/bib/bbac412openalex-snapshot

Decoding brain memory formation by single-cell RNA sequencing

inferred← citeshttps://doi.org/10.1093/bib/bbae171openalex-snapshot

stDiff: a diffusion model for imputing spatial transcriptomics through single-cell transcriptomics

inferred← citeshttps://doi.org/10.1093/bib/bbae523openalex-snapshot

SELF-Former: multi-scale gene filtration transformer for single-cell spatial reconstruction

inferred← citeshttps://doi.org/10.1093/bib/bbaf537openalex-snapshot

Network based simultaneous embedding of cells and marker genes from scRNA-seq studies

inferred← citeshttps://doi.org/10.1093/bib/bbag122openalex-snapshot

STGNET: extending panel coverage in imaging-based spatial transcriptomics using deep generative adversarial networks

inferred← citeshttps://doi.org/10.1093/bib/bbz096openalex-snapshot

Evaluation of single-cell classifiers for single-cell RNA sequencing data sets

inferred← citeshttps://doi.org/10.1093/bioinformatics/btaa139openalex-snapshot

scRMD: imputation for single cell RNA-seq data via robust matrix decomposition

inferred← citeshttps://doi.org/10.1093/bioinformatics/btaa183openalex-snapshot

projectR: an R/Bioconductor package for transfer learning via PCA, NMF, correlation and clustering

inferred← citeshttps://doi.org/10.1093/bioinformatics/btae253openalex-snapshot

SPRITE: improving spatial gene expression imputation with gene and cell networks

inferred← citeshttps://doi.org/10.1093/bioinformatics/btaf083openalex-snapshot

COME: contrastive mapping learning for spatial reconstruction of single-cell RNA sequencing data

inferred← citeshttps://doi.org/10.1093/bioinformatics/btag324openalex-snapshot

CeSpGRN: inferring cell-specific gene regulatory networks from single-cell multi-omics and spatial data

inferred← citeshttps://doi.org/10.1093/bioinformatics/btz240openalex-snapshot

scRNAss: a single-cell RNA-seq assembler via imputing dropouts and combing junctions

inferred← citeshttps://doi.org/10.1093/biomtc/ujag046openalex-snapshot

LLOT: application of Laplacian Linear Optimal Transport in spatial transcriptome reconstruction

inferred← citeshttps://doi.org/10.1093/g3journal/jkad160openalex-snapshot

Glyoxal as an alternative fixative for single-cell RNA sequencing

inferred← citeshttps://doi.org/10.1093/g3journal/jkad178openalex-snapshot

Cellular heterogeneity of the developing worker honey bee (Apis mellifera) pupa: a single cell transcriptomics analysis

inferred← citeshttps://doi.org/10.1093/g3journal/jkae032openalex-snapshot

Embryonic spatiotemporal expression pattern of Folded gastrulation suggests roles in multiple morphogenetic events and regulation by AbdA

inferred← citeshttps://doi.org/10.1093/genetics/iyab019openalex-snapshot

Methods and tools for spatial mapping of single-cell RNAseq clusters inDrosophila

inferred← citeshttps://doi.org/10.1093/genetics/iyac035openalex-snapshot

FlyBase: a guided tour of highlighted features

inferred← citeshttps://doi.org/10.1093/genetics/iyae176openalex-snapshot

Two coacting shadow enhancers regulate twin of eyeless expression during early Drosophila development

inferred← citeshttps://doi.org/10.1093/genetics/iyaf214openalex-snapshot

CrebA regulation of secretory capacity: genome-wide transcription profiling coupled with in vivo DNA binding studies

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