ArticleNature2025
Whole-cortex in situ sequencing reveals input-dependent area identity.
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Article in Nature, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers, 1 of them a synthesis that pooled it.
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40citing papers in PubMed, 1 pooled it
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Who cites it
40 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Cross-expression meta-analysis of mouse brain slices reveals coordinated gene expression across spatially adjacent cells.Genome biology · 2025Pooled it
- Selective collateralization of transcriptomically distinct neurons organizes visual-stream output from the primary visual cortex.bioRxiv : the preprint server for biology · 2026Article
- The default mode network exhibits circuit-specific selective vulnerability despite widespread amyloid burden in an animal model of Alzheimer's disease.Nature communications · 2026Article
- Tumor-distal mediastinal lymph nodes harbor tumor-related progenitor exhausted T cells in lung cancer after neoadjuvant chemoimmunotherapy.Cell reports. Medicine · 2026Article
- NicheTrans: spatial-aware cross-omics translation.Nature methods · 2026Article
- Conserved and specialized features of thalamocortical wiring revealed by single-cell projection mapping in mouse and marmoset.bioRxiv : the preprint server for biology · 2026Article
- Cluster replicability in single-cell and single-nucleus atlases of the mouse brain.Nature communications · 2026Article
- Tissueformer: extending single-cell foundation models to predict population-level phenotypes.BMC bioinformatics · 2026Article
- Review
- Spatially tunable multiomic sequencing using light-driven combinatorial barcoding of molecules in tissues.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- BARseq3: a modular system for integrating spatial multi-omics and cellular barcoding in single cells.bioRxiv : the preprint server for biology · 2026Article
- Dietary dimethylglycine sodium salt improves growth performance, liver function, and meat quality of broilers exposed to heat stress.Poultry science · 2026Article
- Connectome-seq: high-throughput mapping of neuronal connectivity at single-synapse resolution via barcode sequencing.Nature methods · 2026Article
- Developing a Robust Multiround HCR-FISH Method Modified for Caenorhabditis elegans.Genes to cells : devoted to molecular & cellular mechanisms · 2026Article
- Post-Critical Period Transcriptional and Physiological Adaptations of Primary Sensory Cortex after Sensory Loss.The Journal of neuroscience : the official journal of the Society for Neuroscience · 2026Article
- Antibody screening for tumor and immune hotspot targets: The frontier of new methods and technologies.Journal of pharmaceutical analysis · 2026Review
- High-parameter spatial multi-omics through histology-anchored integration.Nature methods · 2026Article
- Biophysical simulation enables segmentation and nervous system atlas mapping for image first spatial omics.NPJ systems biology and applications · 2025Article
- Review
- Data-driven fine-grained region discovery in the mouse brain with transformers.Nature communications · 2025Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors.
Xiaoyin Chen *Allen Institute for Brain Science, Seattle, WA, USA. xiaoyin.chen@alleninstitute.org.ORCID 0000-0002-2807-6125
Stephan Fischer *Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, Paris, France.ORCID 0000-0002-7034-4103
Mara C P Rue *Allen Institute for Brain Science, Seattle, WA, USA.
Aixin ZhangAllen Institute for Brain Science, Seattle, WA, USA.
Didhiti MukherjeeDepartment of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA.
Patrick O KanoldDepartment of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA.ORCID 0000-0002-7529-5435
Jesse GillisDepartment of Physiology, University of Toronto, Toronto, Ontario, Canada. jesse.gillis@utoronto.ca.ORCID 0000-0002-0936-9774
Anthony M ZadorCold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA. zador@cshl.edu.ORCID 0000-0002-8431-9136
Funding
Tool and Technology Development CoreU19MH114821 · NIMH · COLD SPRING HARBOR LABORATORY · PI MITRA, PARTHA PRATIM · 2017 to 2021
$64.5MNEURONAL CIRCUITS AND PLASTICITY OF NEONATAL AUDITORY CORTEXR01DC009607 · NIDCD · UNIV OF MARYLAND, COLLEGE PARK · PI PATRICK O KANOLD · 2009 to 2026
$7.8MSYNPLA: A scaleable method for monitoring circuit-specific learning-induced changes in synaptic strengthU01MH109113 · NIMH · COLD SPRING HARBOR LABORATORY · PI MALINOW, ROBERTO, ZADOR, ANTHONY M · 2015 to 2017
$2.9MHigh throughput mapping of neuronal circuitry using DNA sequencingRF1MH114132 · NIMH · COLD SPRING HARBOR LABORATORY · PI ZADOR, ANTHONY M · 2017 to 2017
$2.7MUnraveling the developmental logic of cortical long-range projections using in situ sequencing-based neuroanatomyDP2MH132940 · NIMH · ALLEN INSTITUTE · PI CHEN, XIAOYIN · 2022 to 2025
$2.6MRevealing the transcriptomic basis of neuronal identity through functional meta-analysisR01MH113005 · NIMH · COLD SPRING HARBOR LABORATORY · PI GILLIS, JESSE · 2017 to 2021
$2.4MHigh-throughput DNA sequencing method for probing the connectivity of neural circR01NS073129 · NINDS · COLD SPRING HARBOR LABORATORY · PI ZADOR, ANTHONY M · 2010 to 2014
$2.3MCRCNS: Theory and experiment of neural circuit mapping by DNA sequencingR01DA036913 · NIDA · COLD SPRING HARBOR LABORATORY · PI KOULAKOV, ALEXEI, ZADOR, ANTHONY M · 2013 to 2017
$2.1MHeuristics to evaluate biomedical and genomic knowledge bases for validityR01LM012736 · NLM · COLD SPRING HARBOR LABORATORY · PI GILLIS, JESSE · 2017 to 2020
$1.9MRevealing the transcriptional basis of corticothalamic projections using in situ sequence-based neuroanatomyR01MH133181 · NIMH · ALLEN INSTITUTE · PI XIAOYIN CHEN · 2024 to 2026
$1.8MCrossmodal plasticity in the auditory cortex in the precritical periodR21DC020560 · NIDCD · JOHNS HOPKINS UNIVERSITY · PI Didhiti Mukherjee · 2024 to 2026
$491kNIDA NIH HHS R01 DA036913NIDCD NIH HHS R01 DC009607NIMH NIH HHS DP2 MH132940NIMH NIH HHS R01 MH113005NIMH NIH HHS R01 MH133181NIMH NIH HHS RF1 MH114132NIMH NIH HHS U01 MH109113NIMH NIH HHS U19 MH114821NINDS NIH HHS R01 NS073129NLM NIH HHS R01 LM012736
Abstract
The cerebral cortex is composed of neuronal types with diverse gene expression that are organized into specialized cortical areas. These areas, each with characteristic cytoarchitecture
Indexed as
Cerebral CortexNeuronsTranscriptomeAnimalsAnimals, NewbornCluster AnalysisFemaleGene Expression ProfilingMaleMiceMice, Inbred C57BLProsencephalonSingle-Cell Analysis
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Read underepoch 390
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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.