Research graph
References from StrokeCell-Reg: a computational tool for decoding cell-type-specific gene regulatory signatures in stroke using single-cell transcriptomics. Local targets link to admitted publications; unresolved targets remain external evidence.
Ischaemic stroke
10.1038/s41572-019-0118-8 · 2019 · External reference
The immunology of stroke: from mechanisms to translation
10.1038/nm.2399 · 2011 · External reference
Neurotoxic reactive astrocytes are induced by activated microglia
10.1038/nature21029 · 2017 · External reference
Single-cell RNA-seq reveals the transcriptional landscape in ischemic stroke
10.1177/0271678x211026770 · 2022 · External reference
Comprehensive integration of single-cell data
10.1016/j.cell.2019.05.031 · 2019 · External reference
SCANPY: large-scale single-cell gene expression data analysis
10.1186/s13059-017-1382-0 · 2018 · External reference
SCENIC: single-cell regulatory network inference and clustering
10.1038/nmeth.4463 · 2017 · External reference
A scalable SCENIC workflow for single-cell gene regulatory network analysis
10.1038/s41596-020-0336-2 · 2020 · External reference
Inference and analysis of cell-cell communication using CellChat
10.1038/s41467-021-21246-9 · 2021 · External reference
CellPhoneDB: inferring cell-cell communication from combined expression of multi-subunit ligand-receptor complexes
10.1038/s41596-020-0292-x · 2020 · External reference
Benchmark and integration of resources for the estimation of human transcription factor activities
10.1101/gr.240663.118 · 2019 · External reference
TRRUST v2: an expanded reference database of human and mouse transcriptional regulatory interactions
10.1093/nar/gkx1013 · 2018 · External reference
RegNetwork: an integrated database of transcriptional and post-transcriptional regulatory networks in human and mouse
10.1093/database/bav095 · 2015 · External reference
Fast, sensitive and accurate integration of single-cell data with Harmony
10.1038/s41592-019-0619-0 · 2019 · External reference
Molecular architecture of the mouse nervous system
10.1016/j.cell.2018.06.021 · 2018 · External reference
Reversible middle cerebral artery occlusion without craniectomy in rats
10.1161/01.str.20.1.84 · 1989 · External reference
Comprehensive insight on immune landscape in intracerebral hemorrhage patients with single-cell RNA sequencing: from blood to hematoma
10.1186/s12974-025-03518-z · 2025 · External reference
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
10.1186/s13059-014-0550-8 · 2014 · External reference
Enrichr: a comprehensive gene set enrichment analysis web server 2016 update
10.1093/nar/gkw377 · 2016 · External reference
GRNBoost2 and Arboreto: efficient and scalable inference of gene regulatory networks
10.1093/bioinformatics/bty916 · 2019 · External reference
i-cisTarget 2015 update: generalized cis-regulatory enrichment analysis in human, mouse and fly
10.1093/nar/gkv395 · 2015 · External reference
Integrated analysis of chromatin and transcriptomic profiling identifies PU.1 as a core regulatory factor in microglial activation induced by chronic cerebral hypoperfusion
10.1007/s12035-023-03734-9 · 2024 · External reference
Neuroinflammation after ischemic stroke involves INPP5D expression mediated by the TMPO-AS1-PU.1 complex
10.1080/01616412.2022.2143615 · 2023 · External reference
Arresting the bad seed: HDAC3 regulates proliferation of different microglia after ischemic stroke
10.1126/sciadv.ade6900 · 2024 · External reference
10.1002/glia.24377
10.1002/glia.24377 · 2023 · External reference
10.1016/j.nbd.2020.105217
10.1016/j.nbd.2020.105217 · 2021 · External reference
The nuclear factor NF-kappaB pathway in inflammation
10.1101/cshperspect.a001651 · 2009 · External reference
Stats: transcriptional control and biological impact
10.1038/nrm909 · 2002 · External reference
Regulation of mammalian O2 homeostasis by hypoxia-inducible factor 1
10.1146/annurev.cellbio.15.1.551 · 1999 · External reference
Microglia emerge from erythromyeloid precursors via Pu.1- and Irf8-dependent pathways
10.1038/nn.3318 · 2013 · External reference
chromVAR: inferring transcription-factor-associated accessibility from single-cell epigenomic data
10.1038/nmeth.4401 · 2017 · External reference
ArchR is a scalable software package for integrative single-cell chromatin accessibility analysis
10.1038/s41588-021-00790-6 · 2021 · External reference
Single-cell chromatin state analysis with Signac
10.1038/s41592-021-01282-5 · 2021 · External reference
Unresolved reference
2013 · External reference
g:Profiler: a web server for functional enrichment analysis and conversions of gene lists. 2019 update
10.1093/nar/gkz369 · 2019 · External reference
Microglial and macrophage polarization-new prospects for brain repair
10.1038/nrneurol.2014.207 · 2015 · External reference
A unique microglia type associated with restricting development of Alzheimer's disease
10.1016/j.cell.2017.05.018 · 2017 · External reference
Single-cell RNA sequencing of microglia throughout the mouse lifespan and in the injured brain reveals complex cell-state changes
10.1016/j.immuni.2018.11.004 · 2019 · External reference
The TREM2-APOE pathway drives the transcriptional phenotype of dysfunctional microglia in neurodegenerative diseases
10.1016/j.immuni.2017.08.008 · 2017 · External reference
10.7554/elife.89507
10.7554/elife.89507 · 2024 · External reference
10.1016/j.expneurol.2025.115550
10.1016/j.expneurol.2025.115550 · 2026 · External reference
