Best practices for single-cell analysis across modalities

L Heumos, AC Schaar, C Lance, A Litinetskaya… - Nature Reviews …, 2023 - nature.com
Recent advances in single-cell technologies have enabled high-throughput molecular
profiling of cells across modalities and locations. Single-cell transcriptomics data can now …

Spatial components of molecular tissue biology

G Palla, DS Fischer, A Regev, FJ Theis - Nature Biotechnology, 2022 - nature.com
Methods for profiling RNA and protein expression in a spatially resolved manner are rapidly
evolving, making it possible to comprehensively characterize cells and tissues in health and …

Computational principles and challenges in single-cell data integration

R Argelaguet, ASE Cuomo, O Stegle… - Nature biotechnology, 2021 - nature.com
The development of single-cell multimodal assays provides a powerful tool for investigating
multiple dimensions of cellular heterogeneity, enabling new insights into development …

Statistical and machine learning methods for spatially resolved transcriptomics data analysis

Z Zeng, Y Li, Y Li, Y Luo - Genome biology, 2022 - Springer
The recent advancement in spatial transcriptomics technology has enabled multiplexed
profiling of cellular transcriptomes and spatial locations. As the capacity and efficiency of the …

Strategic vision for improving human health at The Forefront of Genomics

ED Green, C Gunter, LG Biesecker, V Di Francesco… - Nature, 2020 - nature.com
Starting with the launch of the Human Genome Project three decades ago, and continuing
after its completion in 2003, genomics has progressively come to have a central and …

Spatially resolved transcriptomes—next generation tools for tissue exploration

M Asp, J Bergenstråhle, J Lundeberg - Bioessays, 2020 - Wiley Online Library
Recent advances in spatially resolved transcriptomics have greatly expanded the
knowledge of complex multicellular biological systems. The field has quickly expanded in …

Spatially resolved transcriptomics adds a new dimension to genomics

L Larsson, J Frisén, J Lundeberg - Nature methods, 2021 - nature.com
As single-cell omics continue to advance, the field of spatially resolved transcriptomics has
emerged with a set of experimental and computational methods to map out the positions of …

A roadmap for the human developmental cell atlas

M Haniffa, D Taylor, S Linnarsson, BJ Aronow… - Nature, 2021 - nature.com
Abstract The Human Developmental Cell Atlas (HDCA) initiative, which is part of the Human
Cell Atlas, aims to create a comprehensive reference map of cells during development. This …

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 …

Principles and challenges of modeling temporal and spatial omics data

B Velten, O Stegle - Nature Methods, 2023 - nature.com
Studies with temporal or spatial resolution are crucial to understand the molecular dynamics
and spatial dependencies underlying a biological process or system. With advances in high …