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BACKGROUND: Population phenotypic variation can arise from genetic differences between individuals, or from cellular heterogeneity in an isogenic group of cells or organisms. The emergence of gene expression differences between...

Gene expression noise Promoter response single cell Animals Cell Lineage CpG Islands Gene Expression genetic variation Mammals Mice Promoter Regions Genetic

Technological advances have enabled the profiling of multiple molecular layers at single-cell resolution, assaying cells from multiple samples or conditions. Consequently, there is a growing need for computational strategies to...

Data integration Factor Analysis multi-omics single cell Animals DNA Methylation Embryonic Development Factor Analysis Statistical Frontal Lobe Mice Sequence Analysis RNA Single-Cell Analysis

Recent technological developments allow us to measure the status of dozens of proteins in individual cells. This opens the way to understand the heterogeneity of complex multi-signaling networks across cells and cell types, with...

Cell Signaling Crowdsourcing mass cytometry predictive modeling single cell

Abstract: Technological advances have enabled the profiling of multiple molecular layers at single-cell resolution, assaying cells from multiple samples or conditions. Consequently, there is a growing need for computational...

method single cell multi-omics Data integration Factor Analysis

As our understanding of the importance of the human microbiota in health and disease grows, so does our need to carefully resolve and delineate its genomic content. 16S rRNA gene-based analyses yield important insights into...

single cell genomic assembly mobile genetic elements prophage single-amplified genome Bacteria Feces Flow Cytometry Gastrointestinal Microbiome Genome Bacterial Genomics High-Throughput Nucleotide Sequencing Humans Interspersed Repetitive Sequences Phylogeny Single-Cell Analysis

The recent development of single cell gene expression technologies, and especially single cell transcriptomics, have revolutionized the way biologists and clinicians investigate organs and organisms, allowing an unprecedented...

RNA-seq cellular landscape Gene Expression Heart qRT-PCR single cell transcriptomics

Abstract: Background: Early single-cell RNA-seq (scRNA-seq) studies suggested that it was unusual to see more than one isoform being produced from a gene in a single cell, even when multiple isoforms were detected in matched...

Research scRNA-seq single cell Alternative Splicing Isoform GENE Isoform Choice Dropouts

Abstract: Technological advances have enabled the profiling of multiple molecular layers at single-cell resolution, assaying cells from multiple samples or conditions. Consequently, there is a growing need for computational...

method single cell multi-omics Data integration Factor Analysis

Single-cell RNA-seq has the potential to facilitate isoform quantification as the confounding factor of a mixed population of cells is eliminated. However, best practice for using existing quantification methods has not been...

Benchmark Bulk RNA-seq Isoform quantification single cell scRNA-seq Animals B-Lymphocytes Benchmarking Cells Cultured Computer Simulation Gene Expression Profiling High-Throughput Nucleotide Sequencing Mice Protein Isoforms RNA Sequence Analysis RNA Single-Cell Analysis Software

Boolean network Gene Regulatory Networks Hematopoiesis single cell stem progenitor cells Algorithms Animals Cell Differentiation Gene Regulatory Networks Hematopoiesis Hematopoietic Stem Cells Mice Inbred C57BL Transcription Factors

Embryo human Pluripotency RNA-seq single cell Animals Blastocyst Blastocyst Inner Cell Mass Cell Line Cell Lineage Chromosome Mapping Embryo Culture Techniques Embryonic Development Gene Expression Profiling Genetic Markers Germ Layers Humans Pluripotent Stem Cells Primates Single-Cell Analysis

UNLABELLED: Extrusion-based cell deposition has become a prominent technique for expanding bioprinting applications. However, the associated print resolution in the order of nanolitre or above has been a limiting factor. The...

Cell sedimentation Microcapillary cell printing Resolution dispensing single cell

Carboplatin resistance Immune tumor microenvironment Mass cytometry/CyTOF Multimodal biomarkers Multiplex cellular imaging ovarian cancer single cell Female Humans Carboplatin Proteomics Ovarian Neoplasms Tumor Microenvironment

Single-cell RNA sequencing (scRNA-seq) is widely used to profile the transcriptome of individual cells. This provides biological resolution that cannot be matched by bulk RNA sequencing, at the cost of increased technical noise...

Bioconductor RNA-seq single cell Bioinformatics Workflow

Abstract: Background: Early single-cell RNA-seq (scRNA-seq) studies suggested that it was unusual to see more than one isoform being produced from a gene in a single cell, even when multiple isoforms were detected in matched...

Research scRNA-seq single cell Alternative Splicing Isoform GENE Isoform Choice Dropouts

Boolean network gene regulatory network Hematopoiesis Hematopoietic stem/progenitor cell Pseudotime single cell Transcriptional regulation Cell Differentiation Cell Lineage Computational Biology Gene Regulatory Networks Hematopoiesis Hematopoietic Stem Cells Humans Transcriptome

BACKGROUND:Early single-cell RNA-seq (scRNA-seq) studies suggested that it was unusual to see more than one isoform being produced from a gene in a single cell, even when multiple isoforms were detected in matched bulk RNA-seq...

GENE single cell Isoform Alternative Splicing Dropouts scRNA-seq Isoform Choice

Chromosomes Computational Biology Genes MOUSE regulatory network single cell Stem Cells Systems Biology Animals Cell Line Chromatin Immunoprecipitation Computer Simulation Gene Expression Profiling Gene Regulatory Networks Hematopoiesis Hematopoietic Stem Cells Mice Models Theoretical Sequence Analysis DNA Transcription Factors

The Arabidopsis circadian clock orchestrates gene regulation across the day/night cycle. Although a multiple feedback loop circuit has been shown to generate the 24-hr rhythm, it remains unclear how robust the clock is in...

A. thaliana cell-to-cell coupling circadian clock Computational Biology plant biology single cell Systems Biology Time-lapse microscopy Arabidopsis Cells Circadian Clocks Gene Expression Regulation Plant Gene Regulatory Networks Seedlings