Cell-type deconvolution analysis identifies cancer-associated myofibroblast component as a poor prognostic factor in multiple cancer types
Cancer-associated fibroblasts (CAFs) constitute a prominent component of the tumor
microenvironment and play critical roles in cancer progression and drug resistance …
microenvironment and play critical roles in cancer progression and drug resistance …
Robust differences in cortical cell type proportions across healthy human aging inferred through cross-dataset transcriptome analyses
Y Chen, E Hunter, K Arbabi, A Guet-McCreight… - Neurobiology of …, 2023 - Elsevier
Age-related declines in cognitive function are driven by cell type-specific changes in the
brain. However, it remains challenging to study cellular differences associated with healthy …
brain. However, it remains challenging to study cellular differences associated with healthy …
DeepFun: a deep learning sequence-based model to decipher non-coding variant effect in a tissue-and cell type-specific manner
More than 90% of the genetic variants identified from genome-wide association studies
(GWAS) are located in non-coding regions of the human genome. Here, we present a user …
(GWAS) are located in non-coding regions of the human genome. Here, we present a user …
deCS: A Tool for Systematic Cell Type Annotations of Single-Cell RNA Sequencing Data Among Human Tissues
Single-cell RNA sequencing (scRNA-seq) is revolutionizing the study of complex and
dynamic cellular mechanisms. However, cell type annotation remains a main challenge as it …
dynamic cellular mechanisms. However, cell type annotation remains a main challenge as it …
Transcriptomic Analysis of the Amygdala in Subjects with Schizophrenia, Bipolar Disorder and Major Depressive Disorder Reveals Differentially Altered Metabolic …
Abstract Background and Hypothesis The amygdala, crucial for mood, anxiety, fear, and
reward regulation, shows neuroanatomical and molecular divergence in psychiatric …
reward regulation, shows neuroanatomical and molecular divergence in psychiatric …
Evaluating performance and applications of sample-wise cell deconvolution methods on human brain transcriptomic data
Sample-wise deconvolution methods estimate cell-type proportions and gene expressions
in bulk tissue samples, yet their performance and biological applications remain unexplored …
in bulk tissue samples, yet their performance and biological applications remain unexplored …
[HTML][HTML] lute: estimating the cell composition of heterogeneous tissue with varying cell sizes using gene expression
Relative cell type fraction estimates in bulk RNA-sequencing data are important to control for
cell composition differences across heterogenous tissue samples. Current computational …
cell composition differences across heterogenous tissue samples. Current computational …
Cell-type-specific profibrotic scores across multi-organ systems predict cancer prognosis
Simple Summary Fibrosis is a major player and contributor in the tumor microenvironment.
Profibrotic changes precede the early development and establishment of a variety of human …
Profibrotic changes precede the early development and establishment of a variety of human …
A single-cell atlas of the human brain in Alzheimer's disease and its implications for personalized drug repositioning
Alzheimer's disease (AD) is a neurodegenerative disease with complex pathophysiology,
and AD-dysregulated pathways are inconsistent across different brain regions and patients …
and AD-dysregulated pathways are inconsistent across different brain regions and patients …
[HTML][HTML] Differentially Altered Metabolic Pathways in the Amygdala of Subjects with Schizophrenia, Bipolar Disorder and Major Depressive Disorder
Study Design. We used a cohort of subjects diagnosed with SCZ, BPD or MDD, and non-
psychiatrically ill control subjects (n= 15/group), together with our bioinformatic 3-pod …
psychiatrically ill control subjects (n= 15/group), together with our bioinformatic 3-pod …