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Gene regulatory network inference in the era of single-cell multi-omics
The interplay between chromatin, transcription factors and genes generates complex
regulatory circuits that can be represented as gene regulatory networks (GRNs). The study …
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
Single-cell transcriptomics has broadened our understanding of cellular diversity and gene
expression dynamics in healthy and diseased tissues. Recently, spatial transcriptomics has …
expression dynamics in healthy and diseased tissues. Recently, spatial transcriptomics has …
hdWGCNA identifies co-expression networks in high-dimensional transcriptomics data
Biological systems are immensely complex, organized into a multi-scale hierarchy of
functional units based on tightly regulated interactions between distinct molecules, cells …
functional units based on tightly regulated interactions between distinct molecules, cells …
Dictionary learning for integrative, multimodal and scalable single-cell analysis
Map** single-cell sequencing profiles to comprehensive reference datasets provides a
powerful alternative to unsupervised analysis. However, most reference datasets are …
powerful alternative to unsupervised analysis. However, most reference datasets are …
[HTML][HTML] Automatic cell-type harmonization and integration across Human Cell Atlas datasets
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 …
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 …
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
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 …
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
The tumour evolution model posits that malignant transformation is preceded by randomly
distributed driver mutations in cancer genes, which cause clonal expansions in …
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
Although multiple pancreatic islet single-cell RNA-sequencing (scRNA-seq) datasets have
been generated, a consensus on pancreatic cell states in development, homeostasis and …
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
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 …
extended charging time of electric vehicles. However, fast charging exacerbates battery …