Single-cell omics: experimental workflow, data analyses and applications

F Sun, H Li, D Sun, S Fu, L Gu, X Shao, Q Wang… - Science China Life …, 2024 - Springer
Cells are the fundamental units of biological systems and exhibit unique development
trajectories and molecular features. Our exploration of how the genomes orchestrate the …

A cell atlas foundation model for scalable search of similar human cells

G Heimberg, T Kuo, DJ DePianto, O Salem, T Heigl… - Nature, 2024 - nature.com
Single-cell RNA-seq (scRNA-seq) has profiled hundreds of millions of human cells across
organs, diseases, development, and perturbations to date. Mining these growing atlases …

Graph-based autoencoder integrates spatial transcriptomics with chromatin images and identifies joint biomarkers for Alzheimer's disease

X Zhang, X Wang, GV Shivashankar, C Uhler - Nature Communications, 2022 - nature.com
Tissue development and disease lead to changes in cellular organization, nuclear
morphology, and gene expression, which can be jointly measured by spatial transcriptomic …

Integrating spatial transcriptomics data across different conditions, technologies and developmental stages

X Zhou, K Dong, S Zhang - Nature Computational Science, 2023 - nature.com
With the rapid generation of spatial transcriptomics (ST) data, integrative analysis of multiple
ST datasets from different conditions, technologies and developmental stages is becoming …

Scalable querying of human cell atlases via a foundational model reveals commonalities across fibrosis-associated macrophages

G Heimberg, T Kuo, D DePianto, T Heigl, N Diamant… - BioRxiv, 2023 - biorxiv.org
Single-cell RNA-seq (scRNA-seq) studies have profiled over 100 million human cells across
diseases, developmental stages, and perturbations to date. A singular view of this vast and …

Batch alignment of single-cell transcriptomics data using deep metric learning

X Yu, X Xu, J Zhang, X Li - Nature communications, 2023 - nature.com
Abstract scRNA-seq has uncovered previously unappreciated levels of heterogeneity. With
the increasing scale of scRNA-seq studies, the major challenge is correcting batch effect …

Quantitative analysis of high‐throughput biological data

HF Juan, HC Huang - Wiley Interdisciplinary Reviews …, 2023 - Wiley Online Library
The study of multiple “omes,” such as the genome, transcriptome, proteome, and
metabolome has become widespread in biomedical research. High‐throughput techniques …

Generative pretraining from large-scale transcriptomes for single-cell deciphering

H Shen, J Liu, J Hu, X Shen, C Zhang, D Wu, M Feng… - Iscience, 2023 - cell.com
Exponential accumulation of single-cell transcriptomes poses great challenge for efficient
assimilation. Here, we present an approach entitled generative pretraining from …

CeDR Atlas: a knowledgebase of cellular drug response

YY Wang, H Kang, T Xu, L Hao, Y Bao… - Nucleic acids …, 2022 - academic.oup.com
Drug response to many diseases varies dramatically due to the complex genomics and
functional features and contexts. Cellular diversity of human tissues, especially tumors, is …

CellDeathPred: a deep learning framework for ferroptosis and apoptosis prediction based on cell painting

K Schorpp, A Bessadok, A Biibosunov… - Cell Death …, 2023 - nature.com
Cell death, such as apoptosis and ferroptosis, play essential roles in the process of
development, homeostasis, and pathogenesis of acute and chronic diseases. The …