Best practices for single-cell analysis across modalities
Recent advances in single-cell technologies have enabled high-throughput molecular
profiling of cells across modalities and locations. Single-cell transcriptomics data can now …
profiling of cells across modalities and locations. Single-cell transcriptomics data can now …
Applications of single-cell RNA sequencing in drug discovery and development
B Van de Sande, JS Lee, E Mutasa-Gottgens… - Nature Reviews Drug …, 2023 - nature.com
Single-cell technologies, particularly single-cell RNA sequencing (scRNA-seq) methods,
together with associated computational tools and the growing availability of public data …
together with associated computational tools and the growing availability of public data …
scGPT: toward building a foundation model for single-cell multi-omics using generative AI
Generative pretrained models have achieved remarkable success in various domains such
as language and computer vision. Specifically, the combination of large-scale diverse …
as language and computer vision. Specifically, the combination of large-scale diverse …
Impact of the Human Cell Atlas on medicine
Single-cell atlases promise to provide a 'missing link'between genes, diseases and
therapies. By identifying the specific cell types, states, programs and contexts where disease …
therapies. By identifying the specific cell types, states, programs and contexts where disease …
Transformers in single-cell omics: a review and new perspectives
Recent efforts to construct reference maps of cellular phenotypes have expanded the
volume and diversity of single-cell omics data, providing an unprecedented resource for …
volume and diversity of single-cell omics data, providing an unprecedented resource for …
Protein design with guided discrete diffusion
A popular approach to protein design is to combine a generative model with a discriminative
model for conditional sampling. The generative model samples plausible sequences while …
model for conditional sampling. The generative model samples plausible sequences while …
Optimal transport for single-cell and spatial omics
High-throughput single-cell profiling provides an unprecedented ability to uncover the
molecular states of millions of cells. These technologies are, however, destructive to cells …
molecular states of millions of cells. These technologies are, however, destructive to cells …
Toward a foundation model of causal cell and tissue biology with a Perturbation Cell and Tissue Atlas
JE Rood, A Hupalowska, A Regev - Cell, 2024 - cell.com
Comprehensively charting the biologically causal circuits that govern the phenotypic space
of human cells has often been viewed as an insurmountable challenge. However, in the last …
of human cells has often been viewed as an insurmountable challenge. However, in the last …
Single-cell profiling to explore pancreatic cancer heterogeneity, plasticity and response to therapy
Pancreatic ductal adenocarcinoma (PDAC) is a highly lethal cancer entity characterized by a
heterogeneous genetic landscape and an immunosuppressive tumor microenvironment …
heterogeneous genetic landscape and an immunosuppressive tumor microenvironment …
DIALOGUE maps multicellular programs in tissue from single-cell or spatial transcriptomics data
L Jerby-Arnon, A Regev - Nature biotechnology, 2022 - nature.com
Deciphering the functional interactions of cells in tissues remains a major challenge. Here
we describe DIALOGUE, a method to systematically uncover multicellular programs (MCPs) …
we describe DIALOGUE, a method to systematically uncover multicellular programs (MCPs) …