Deep learning and alignment of spatially resolved single-cell transcriptomes with Tangram

Expansion sequencing: Spatially precise in situ transcriptomics in intact biological systems

(2021) Shahar Alon et al.   SCIENCE

Spatially mapped single-cell chromatin accessibility

(2021) Casey A. Thornton et al.   Nature Communications

The Allen Mouse Brain Common Coordinate Framework: A 3D Reference Atlas

(2020) Quanxin Wang et al.   CELL

Systematic comparison of single-cell and single-nucleus RNA-sequencing methods

(2020) Jiarui Ding et al.   NATURE BIOTECHNOLOGY

nucleAIzer: A Parameter-free Deep Learning Framework for Nucleus Segmentation Using Image Style Transfer

(2020) Reka Hollandi et al.   Cell Systems

Chromatin Potential Identified by Shared Single-Cell Profiling of RNA and Chromatin

(2020) Sai Ma et al.   CELL

Single-cell and spatial transcriptomics enables probabilistic inference of cell type topography

(2020) Alma Andersson et al.   Communications Biology

Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution

(2019) Samuel G. Rodriques et al.   SCIENCE

Transcriptome-scale super-resolved imaging in tissues by RNA seqFISH+

(2019) Chee-Huat Linus Eng et al.   NATURE

The emergent landscape of the mouse gut endoderm at single-cell resolution

(2019) Sonja Nowotschin et al.   NATURE

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

Intra- and Inter-cellular Rewiring of the Human Colon during Ulcerative Colitis

(2019) Christopher S. Smillie et al.   CELL

Identifying gene expression programs of cell-type identity and cellular activity with single-cell RNA-Seq

(2019) Dylan Kotliar et al.   eLife

VoxelMorph: A Learning Framework for Deformable Medical Image Registration

(2019) Guha Balakrishnan et al.   IEEE TRANSACTIONS ON MEDICAL IMAGING

High-definition spatial transcriptomics for in situ tissue profiling

(2019) Sanja Vickovic et al.   NATURE METHODS

Spatiotemporal immune zonation of the human kidney

(2019) Benjamin J. Stewart et al.   SCIENCE

Gene expression cartography

(2019) Mor Nitzan et al.   NATURE

Probabilistic cell typing enables fine mapping of closely related cell types in situ

(2019) Xiaoyan Qian et al.   NATURE METHODS

Toward a Common Coordinate Framework for the Human Body

(2019) Jennifer E. Rood et al.   CELL

Three-dimensional intact-tissue sequencing of single-cell transcriptional states

(2018) Xiao Wang et al.   SCIENCE

RNA velocity of single cells

(2018) Gioele La Manno et al.   NATURE

Shared and distinct transcriptomic cell types across neocortical areas

(2018) Bosiljka Tasic et al.   NATURE

Spatial organization of the somatosensory cortex revealed by osmFISH

(2018) Simone Codeluppi et al.   NATURE METHODS

The Human Cell Atlas: from vision to reality

(2017) Orit Rozenblatt-Rosen et al.   NATURE

Simultaneous epitope and transcriptome measurement in single cells

(2017) Marlon Stoeckius et al.   NATURE METHODS

Single-Cell RNA-Seq Reveals Hypothalamic Cell Diversity

(2017) Renchao Chen et al.   Cell Reports

The Human Cell Atlas

(2017) Aviv Regev et al.   eLife

Diffusion pseudotime robustly reconstructs lineage branching

(2016) Laleh Haghverdi et al.   NATURE METHODS

Visualization and analysis of gene expression in tissue sections by spatial transcriptomics

(2016) P. L. Stahl et al.   SCIENCE

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

(2015) Evan Z. Macosko et al.   CELL

Single-cell chromatin accessibility reveals principles of regulatory variation

(2015) Jason D. Buenrostro et al.   NATURE

Electrophysiological, transcriptomic and morphologic profiling of single neurons using Patch-seq

(2015) Cathryn R Cadwell et al.   NATURE BIOTECHNOLOGY

Spatial reconstruction of single-cell gene expression data

(2015) Rahul Satija et al.   NATURE BIOTECHNOLOGY

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

(2015) Kaia Achim et al.   NATURE BIOTECHNOLOGY

Spatially resolved, highly multiplexed RNA profiling in single cells

(2015) K. H. Chen et al.   SCIENCE

Large-scale evaluation of ANTs and FreeSurfer cortical thickness measurements

(2014) Nicholas J. Tustison et al.   NEUROIMAGE

In situ sequencing for RNA analysis in preserved tissue and cells

(2013) Rongqin Ke et al.   NATURE METHODS