NiCo identifies extrinsic drivers of cell state modulation by niche covariation analysis
Cell states are modulated by intrinsic driving forces such as gene expression noise and
extrinsic signals from the tissue microenvironment. The distinction between intrinsic and …
extrinsic signals from the tissue microenvironment. The distinction between intrinsic and …
Living in a noisy world—origins of gene expression noise and its impact on cellular decision‐making
The expression level of a gene can vary between genetically identical cells under the same
environmental condition—a phenomenon referred to as gene expression noise. Several …
environmental condition—a phenomenon referred to as gene expression noise. Several …
Scalable identification of lineage-specific gene regulatory networks from metacells with NetID
The identification of gene regulatory networks (GRNs) is crucial for understanding cellular
differentiation. Single-cell RNA sequencing data encode gene-level covariations at high …
differentiation. Single-cell RNA sequencing data encode gene-level covariations at high …
Multimodal screen identifies noise-regulatory proteins
Ó García-Blay, X Hu, CL Wassermann… - Developmental Cell, 2024 - cell.com
Gene-expression noise can influence cell-fate choices across pathology and physiology.
However, a crucial question persists: do regulatory proteins or pathways exist that control …
However, a crucial question persists: do regulatory proteins or pathways exist that control …
Optimal distance metrics for single-cell RNA-seq populations
In single-cell data workflows and modeling, distance metrics are commonly used in loss
functions, model evaluation, and subpopulation analysis. However, these metrics behave …
functions, model evaluation, and subpopulation analysis. However, these metrics behave …
Piezo1 stretch‐activated channel activity differs between murine bone marrow‐derived and cardiac tissue‐resident macrophages
A Simon‐Chica, A Klesen, R Emig… - The Journal of …, 2024 - Wiley Online Library
Macrophages (MΦ) play pivotal roles in tissue homeostasis and repair. Their mechanical
environment has been identified as a key modulator of various cell functions, and MΦ …
environment has been identified as a key modulator of various cell functions, and MΦ …
[HTML][HTML] Compound models and Pearson residuals for normalization of single-cell RNA-seq data without UMIs
Before downstream analysis can reveal biological signals in single-cell RNA sequencing
data, normalization and variance stabilization are required to remove technical noise …
data, normalization and variance stabilization are required to remove technical noise …
Med12 cooperates with multiple differentiation signals to enhance embryonic stem cell plasticity
M Fernkorn, C Schröter - bioRxiv, 2024 - biorxiv.org
Cell differentiation results from coordinated changes in gene transcription in response to
combinations of signals. FGF, Wnt, and mTOR signals regulate the differentiation of …
combinations of signals. FGF, Wnt, and mTOR signals regulate the differentiation of …
Spatio-temporal dynamics of the fibrotic niche in cardiac repair
The heart is one of the least regenerative organs in humans, and ischemic heart disease is
the leading cause of death worldwide. Understanding the cellular and molecular processes …
the leading cause of death worldwide. Understanding the cellular and molecular processes …
Multimodal screen reveals noise regulatory proteins
O Garcia-Blay, X Hu, CL Wassermann, T van Bokhoven… - bioRxiv, 2024 - biorxiv.org
Gene-expression noise can influence cell-fate choices across pathology and physiology.
However, a crucial question persists: do regulatory proteins or pathways exist that control …
However, a crucial question persists: do regulatory proteins or pathways exist that control …