Mapping cells through time and space with moscot

D Klein, G Palla, M Lange, M Klein, Z Piran, M Gander… - bioRxiv, 2023 - biorxiv.org
Single-cell genomics technologies enable multimodal profiling of millions of cells across
temporal and spatial dimensions. Experimental limitations prevent the measurement of all …

Embryo-scale, single-cell spatial transcriptomics

SR Srivatsan, MC Regier, E Barkan, JM Franks… - Science, 2021 - science.org
Spatial patterns of gene expression manifest at scales ranging from local (eg, cell-cell
interactions) to global (eg, body axis patterning). However, current spatial transcriptomics …

Reconstruction of developmental landscapes by optimal-transport analysis of single-cell gene expression sheds light on cellular reprogramming

G Schiebinger, J Shu, M Tabaka, B Cleary… - BioRxiv, 2017 - biorxiv.org
Understanding the molecular programs that guide cellular differentiation during
development is a major goal of modern biology. Here, we introduce an approach …

Highly multiplexed spatially resolved gene expression profiling of mouse organogenesis

T Lohoff, S Ghazanfar, A Missarova, N Koulena… - BioRxiv, 2020 - biorxiv.org
Transcriptional and epigenetic profiling of single-cells has advanced our knowledge of the
molecular bases of gastrulation and early organogenesis. However, current approaches rely …

Spateo: multidimensional spatiotemporal modeling of single-cell spatial transcriptomics

X Qiu, DY Zhu, J Yao, Z Jing, L Zuo, M Wang, KH Min… - BioRxiv, 2022 - biorxiv.org
Cells do not live in a vacuum, but in a milieu defined by cell–cell communication that can be
measured via emerging high-resolution spatial transcriptomics approaches. However …

SpiceMix enables integrative single-cell spatial modeling of cell identity

B Chidester, T Zhou, S Alam, J Ma - Nature genetics, 2023 - nature.com
Spatial transcriptomics can reveal spatially resolved gene expression of diverse cells in
complex tissues. However, the development of computational methods that can use the …

Integrating spatial and single-cell transcriptomics data using deep generative models with SpatialScope

X Wan, J Xiao, SST Tam, M Cai, R Sugimura… - Nature …, 2023 - nature.com
The rapid emergence of spatial transcriptomics (ST) technologies is revolutionizing our
understanding of tissue spatial architecture and biology. Although current ST methods …

Cell2location maps fine-grained cell types in spatial transcriptomics

V Kleshchevnikov, A Shmatko, E Dann… - Nature …, 2022 - nature.com
Spatial transcriptomic technologies promise to resolve cellular wiring diagrams of tissues in
health and disease, but comprehensive mapping of cell types in situ remains a challenge …

Revealing spatial multimodal heterogeneity in tissues with SpaTrio

P Yang, L Jin, J Liao, K Jin, X Shao, C Li, J Qian… - Cell Genomics, 2023 - cell.com
Capturing and depicting the multimodal tissue information of tissues at the spatial scale
remains a significant challenge owing to technical limitations in single-cell multi-omics and …

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

T Biancalani, G Scalia, L Buffoni, R Avasthi, Z Lu… - Nature …, 2021 - nature.com
Charting an organs' biological atlas requires us to spatially resolve the entire single-cell
transcriptome, and to relate such cellular features to the anatomical scale. Single-cell and …