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CeDAR: incorporating cell type hierarchy improves cell type-specific differential analyses in bulk omics data
Bulk high-throughput omics data contain signals from a mixture of cell types. Recent developments of deconvolution methods facilitate cell...
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Stem cell homeostasis regulated by hierarchy and neutral competition
Tissue stem cells maintain themselves through self-renewal while constantly supplying differentiating cells. Two distinct models have been proposed...
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Exploring Hierarchical Structures of Cell Types in scRNA-seq Data
The development of single-cell transcriptome sequencing technology has provided a deeper understanding of cell types. Cell types consist of...
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Atypical functional connectivity hierarchy in Rolandic epilepsy
Functional connectivity hierarchy is an important principle in the process of brain functional organization and an important feature reflecting brain...
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Analysis of Energy-Driven Leader-Follower Hierarchy During Collective Cancer Cell Invasion
Many solid tumors can invade the surrounding three-dimensional (3D) tissue in a collective manner, and increasing evidence suggests that collective...
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Single-cell Mayo Map (scMayoMap): an easy-to-use tool for cell type annotation in single-cell RNA-sequencing data analysis
BackgroundSingle-cell RNA-sequencing (scRNA-seq) has become a widely used tool for both basic and translational biomedical research. In scRNA-seq...
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From Cell States to Cell Fates: Control of Cell State Transitions
We examine the coordinated behavior of thousands of genes in cell fate transitions through genome expression as an integrated dynamical system using...
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Hierarchy of Ecological Homeostasis as a Principle of Systemology
Abstract —The broad concept of “homeostasis” in relation not only to organisms, but also to populations, ecosystems, and socio–ecological and economic...
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Improving replicability in single-cell RNA-Seq cell type discovery with
Dune BackgroundSingle-cell transcriptome sequencing (scRNA-Seq) has allowed new types of investigations at unprecedented levels of resolution. Among the...
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Application of Single-Cell Sequencing on Stem Cell Research
The variation and heterogeneity within cells are the fundamental features of stem cells. Each tissue has a resident stem cell niche compartmentalized...
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Spontaneous quorum-sensing hierarchy reprogramming in Pseudomonas aeruginosa laboratory strain PAO1
Pseudomonas aeruginosa strain PAO1 has been commonly used in the laboratory, with frequent genome variations reported. Quorum sensing (QS), a...
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EGG CELL 1 contributes to egg-cell-dependent preferential fertilization in Arabidopsis
During double fertilization in angiosperms, the pollen tube delivers two sperm cells into an embryo sac; one sperm cell fuses with an egg cell, and...
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PD-1 signalling defines and protects leukaemic stem cells from T cell receptor-induced cell death in T cell acute lymphoblastic leukaemia
T cell acute lymphoblastic leukaemia (T-ALL) is an aggressive malignancy with poor prognosis, but a decisive marker and effective treatment for...
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A small bacteriophage protein determines the hierarchy over co-residential jumbo phage in Bacillus thuringiensis serovar israelensis
Bacillus thuringiensis serovar israelensis is the most widely used biopesticide against insects, including vectors of animal and human diseases....
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Single-cell gene and isoform expression analysis reveals signatures of ageing in haematopoietic stem and progenitor cells
Single-cell approaches have revealed that the haematopoietic hierarchy is a continuum of differentiation, from stem cell to committed progenitor,...
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Application of Single-Cell Sequencing on Stem Cell Research
The variation and heterogeneity within cells are the fundamental features of stem cells. Each tissue has a resident stem cell niche compartmentalized...
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GTM-decon: guided-topic modeling of single-cell transcriptomes enables sub-cell-type and disease-subtype deconvolution of bulk transcriptomes
Cell-type composition is an important indicator of health. We present Guided Topic Model for deconvolution (GTM-decon) to automatically infer...
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Single-Cell RNAseq Clustering
Single-cell RNA sequencing (scRNA-seq) allows the creation of large collections of individual cells transcriptome. Unsupervised clustering is an...
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Accounting for cell type hierarchy in evaluating single cell RNA-seq clustering
Cell clustering is one of the most common routines in single cell RNA-seq data analyses, for which a number of specialized methods are available. The...
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Cell Migration in Three Dimensions
Cell migration plays an essential role in many pathophysiological processes, including embryonic development, wound healing, immunity, and cancer...