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Patch-seq: Multimodal Profiling of Single-Cell Morphology, Electrophysiology, and Gene Expression
Cells exhibit diverse morphologic phenotypes, biophysical and functional properties, and gene expression patterns. Understanding how these features...
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Single-Copy Gene Editing of a Cell Wall-Anchored Pilin in Actinomyces oris
The Gram-positive bacterium Actinomyces oris expresses a unique cell wall-anchored fimbria comprised of the fimbrial shaft FimA and the tip...
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Tumor cell type and gene marker identification by single layer perceptron neural network on single-cell RNA sequence data
Tumors have drawn increasing attention recently because of their heterogeneous interior structures. Particularly, single-cell RNA (scRNA) mechanics...
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scCompressSA: dual-channel self-attention based deep autoencoder model for single-cell clustering by compressing gene–gene interactions
BackgroundSingle-cell clustering has played an important role in exploring the molecular mechanisms about cell differentiation and human diseases....
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Gene Regulatory Network Modeling Using Single-Cell Multi-Omics in Plants
Single-cell multi-omics technology can be applied to plant cells to characterize gene expression and open chromatin regions in individual cells. In...
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Guidance on Processing the 10x Genomics Single Cell Gene Expression Assay
The demand for technologies that allow the study of gene expression at single cell resolution continues to increase. One such assay was launched in...
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Gene trajectory inference for single-cell data by optimal transport metrics
Single-cell RNA sequencing has been widely used to investigate cell state transitions and gene dynamics of biological processes. Current strategies...
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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...
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Inferring gene regulatory networks from single-cell multiome data using atlas-scale external data
Existing methods for gene regulatory network (GRN) inference rely on gene expression data alone or on lower resolution bulk data. Despite the recent...
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scCDC: a computational method for gene-specific contamination detection and correction in single-cell and single-nucleus RNA-seq data
In droplet-based single-cell and single-nucleus RNA-seq assays, systematic contamination of ambient RNA molecules biases the quantification of gene...
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IntroGRN: Gene Regulatory Network Inference from Single-Cell RNA Data Based on Introspective VAE
The inference of gene regulatory networks (GRNs) from single-cell RNA sequencing (scRNA-seq) data enables describing the regulatory relationships...
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Cell Features Reconstruction from Gene Association Network of Single Cell
Gene expression as an unstable form of cell characterization has been widely used for single-cell analyses. Although there are cell-specific networks...
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RENGE infers gene regulatory networks using time-series single-cell RNA-seq data with CRISPR perturbations
Single-cell RNA-seq analysis coupled with CRISPR-based perturbation has enabled the inference of gene regulatory networks with causal relationships....
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Ocean to Tree: Leveraging Single-Molecule RNA-Seq to Repair Genome Gene Models and Improve Phylogenomic Analysis of Gene and Species Evolution
Understanding gene evolution across genomes and organisms, including ctenophores, can provide unexpected biological insights. It enables powerful...
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Gene regulatory network reconstruction: harnessing the power of single-cell multi-omic data
Inferring gene regulatory networks (GRNs) is a fundamental challenge in biology that aims to unravel the complex relationships between genes and...
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Dictys: dynamic gene regulatory network dissects developmental continuum with single-cell multiomics
Gene regulatory networks (GRNs) are key determinants of cell function and identity and are dynamically rewired during development and disease....
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Single Crossover to Inactivate Target Gene in Cyanobacteria
Anabaena sp. PCC 7120 (hereafter Anabaena 7120) is a model cyanobacterium for studying pathways such as photosynthesis and nitrogen fixation along...
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Assessing transcriptomic heterogeneity of single-cell RNASeq data by bulk-level gene expression data
BackgroundSingle-cell RNA sequencing (sc-RNASeq) data illuminate transcriptomic heterogeneity but also possess a high level of noise, abundant...
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Multiplexed single-cell 3D spatial gene expression analysis in plant tissue using PHYTOMap
Retrieving the complex responses of individual cells in the native three-dimensional tissue context is crucial for a complete understanding of tissue...
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Single-cell lineage capture across genomic modalities with CellTag-multi reveals fate-specific gene regulatory changes
Complex gene regulatory mechanisms underlie differentiation and reprogramming. Contemporary single-cell lineage-tracing (scLT) methods use expressed,...
