Leveraging spatial transcriptomics data to recover cell locations in single-cell RNA-seq with CeLEry

[1]  Milad R. Vahid,et al.  High-resolution alignment of single-cell and spatial transcriptomes with CytoSPACE , 2023, Nature Biotechnology.

[2]  Mingyao Li,et al.  Deciphering tumor ecosystems at super-resolution from spatial transcriptomics with TESLA , 2022, bioRxiv.

[3]  Zachary R. Lewis,et al.  High-plex imaging of RNA and proteins at subcellular resolution in fixed tissue by spatial molecular imaging. , 2022, Nature biotechnology.

[4]  Mingyao Li,et al.  SpaGCN: Integrating gene expression, spatial location and histology to identify spatial domains and spatially variable genes by graph convolutional network , 2021, Nature Methods.

[5]  Evan Z. Macosko,et al.  Deep learning and alignment of spatially resolved single-cell transcriptomes with Tangram , 2021, Nature Methods.

[6]  Huanming Yang,et al.  Spatiotemporal transcriptomic atlas of mouse organogenesis using DNA nanoball-patterned arrays , 2021, Cell.

[7]  Mingyao Li,et al.  Statistical and machine learning methods for spatially resolved transcriptomics with histology , 2021, Computational and structural biotechnology journal.

[8]  Q. Nie,et al.  The landscape of cell-cell communication through single-cell transcriptomics. , 2021, Current opinion in systems biology.

[9]  Evan Z. Macosko,et al.  Highly sensitive spatial transcriptomics at near-cellular resolution with Slide-seqV2 , 2020, Nature Biotechnology.

[10]  O. Harismendy,et al.  Deciphering cell–cell interactions and communication from gene expression , 2020, Nature reviews. Genetics.

[11]  M. Ramialison,et al.  From whole-mount to single-cell spatial assessment of gene expression in 3D , 2020, Communications Biology.

[12]  K. Roeder,et al.  APOE and TREM2 regulate amyloid responsive microglia in Alzheimer’s disease , 2020, Acta Neuropathologica.

[13]  Lihua Zhang,et al.  Inference and analysis of cell-cell communication using CellChat , 2020, Nature Communications.

[14]  Xin Shao,et al.  Uncovering an Organ's Molecular Architecture at Single-Cell Resolution by Spatially Resolved Transcriptomics. , 2020, Trends in biotechnology.

[15]  Joseph Bergenstråhle,et al.  Spatially Resolved Transcriptomes—Next Generation Tools for Tissue Exploration , 2020, BioEssays : news and reviews in molecular, cellular and developmental biology.

[16]  Q. Nie,et al.  Inferring spatial and signaling relationships between cells from single cell transcriptomic data , 2020, Nature Communications.

[17]  Hongkui Zeng,et al.  A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation , 2020, Cell.

[18]  J. Kleinman,et al.  Transcriptome-scale spatial gene expression in the human dorsolateral prefrontal cortex , 2020, Nature Neuroscience.

[19]  N. Friedman,et al.  Gene expression cartography , 2019, Nature.

[20]  Xiang Zhou,et al.  Statistical analysis of spatial expression patterns for spatially resolved transcriptomic studies , 2019, Nature Methods.

[21]  D. Burgess.  Spatial transcriptomics coming of age , 2019, Nature Reviews Genetics.

[22]  Shila Ghazanfar,et al.  The human body at cellular resolution: the NIH Human Biomolecular Atlas Program , 2019, Nature.

[23]  Jihwan Park,et al.  Deep learning enables accurate clustering and batch effect removal in single-cell RNA-seq analysis , 2019, bioRxiv.

[24]  Rickard Sandberg,et al.  Identification of spatial expression trends in single-cell gene expression data , 2018, Nature Methods.

[25]  S. Teichmann,et al.  SpatialDE: identification of spatially variable genes , 2018, Nature Methods.

[26]  Shalev Itzkovitz,et al.  Spatial transcriptomics: paving the way for tissue-level systems biology. , 2017, Current opinion in biotechnology.

[27]  A. Regev,et al.  Spatial reconstruction of single-cell gene expression , 2015, Nature Biotechnology.

[28]  Alexander van Oudenaarden,et al.  Spatially resolved transcriptomics and beyond , 2014, Nature Reviews Genetics.

[29]  J. Coyle,et al.  Alzheimer's disease and senile dementia: loss of neurons in the basal forebrain. , 1982, Science.