Gene regulatory network inference in the era of single-cell multi-omics

P Badia-i-Mompel, L Wessels, S Müller-Dott… - Nature Reviews …, 2023 - nature.com
The interplay between chromatin, transcription factors and genes generates complex
regulatory circuits that can be represented as gene regulatory networks (GRNs). The study …

Profiling cell identity and tissue architecture with single-cell and spatial transcriptomics

GS Gulati, JP D'Silva, Y Liu, L Wang… - … Reviews Molecular Cell …, 2024 - nature.com
Single-cell transcriptomics has broadened our understanding of cellular diversity and gene
expression dynamics in healthy and diseased tissues. Recently, spatial transcriptomics has …

hdWGCNA identifies co-expression networks in high-dimensional transcriptomics data

S Morabito, F Reese, N Rahimzadeh, E Miyoshi… - Cell reports …, 2023 - cell.com
Biological systems are immensely complex, organized into a multi-scale hierarchy of
functional units based on tightly regulated interactions between distinct molecules, cells …

Dictionary learning for integrative, multimodal and scalable single-cell analysis

Y Hao, T Stuart, MH Kowalski, S Choudhary… - Nature …, 2024 - nature.com
Map** single-cell sequencing profiles to comprehensive reference datasets provides a
powerful alternative to unsupervised analysis. However, most reference datasets are …

[HTML][HTML] Automatic cell-type harmonization and integration across Human Cell Atlas datasets

C Xu, M Prete, S Webb, L Jardine, BJ Stewart, R Hoo… - Cell, 2023 - cell.com
Harmonizing cell types across the single-cell community and assembling them into a
common framework is central to building a standardized Human Cell Atlas. Here, we present …

Establishing a conceptual framework for holistic cell states and state transitions

SM Rafelski, JA Theriot - Cell, 2024 - cell.com
Cell states were traditionally defined by how they looked, where they were located, and what
functions they performed. In this post-genomic era, the field is largely focused on a …

Supervised discovery of interpretable gene programs from single-cell data

RZ Kunes, T Walle, M Land, T Nawy, D Pe'er - Nature Biotechnology, 2024 - nature.com
Factor analysis decomposes single-cell gene expression data into a minimal set of gene
programs that correspond to processes executed by cells in a sample. However, matrix …

In vivo single-cell CRISPR uncovers distinct TNF programmes in tumour evolution

PF Renz, U Ghoshdastider, S Baghai Sain… - Nature, 2024 - nature.com
The tumour evolution model posits that malignant transformation is preceded by randomly
distributed driver mutations in cancer genes, which cause clonal expansions in …

Delineating mouse β-cell identity during lifetime and in diabetes with a single cell atlas

K Hrovatin, A Bastidas-Ponce, M Bakhti, L Zappia… - Nature …, 2023 - nature.com
Although multiple pancreatic islet single-cell RNA-sequencing (scRNA-seq) datasets have
been generated, a consensus on pancreatic cell states in development, homeostasis and …

State-of-health estimation for fast-charging lithium-ion batteries based on a short charge curve using graph convolutional and long short-term memory networks

Y He, Z Deng, J Chen, W Li, J Zhou, F **ang… - Journal of Energy …, 2024 - Elsevier
A fast-charging policy is widely employed to alleviate the inconvenience caused by the
extended charging time of electric vehicles. However, fast charging exacerbates battery …