Tree-structured topic modelling of single-cell gene expression data uncovers hierarchical relationships between immune cell types

PE Ye, Y Zhang, RI Klein Geltink, Y Park - bioRxiv, 2023 - biorxiv.org
Immune cells undergo a series of differentiation steps following a lineage-tree structure
stemming from hematopoietic stem cells. During differentiation of immune cells in both …

The Molecular Basis of Differentiation Wave Activity in Embryogenesis

BJ Alicea, S Bastani, NK Gordon, S Crawford-Young… - bioRxiv, 2024 - biorxiv.org
As development varies greatly across the tree of life, it may seem difficult to suggest a model
that proposes a single mechanism for understanding collective cell behaviors and the …

Hierarchical annotation of eQTLs enables identification of genes with cell-type divergent regulation

PF Przytycki, KS Pollard - bioRxiv, 2023 - biorxiv.org
While context-type-specific regulation of genes is largely determined by cis-regulatory
regions, attempts to identify cell-type specific eQTLs are complicated by the nested nature of …

Cell Population Identification and Benchmarking of Tools in Single-Cell Data Analysis

A Sonrel - 2024 - zora.uzh.ch
In an era of Biology where modern imaging and sequencing technologies allow to study
almost any biological process at molecular levels, it is now possible to study the content …

Disentangling protein metabolic costs in human cells and tissues.

M Chagoyen, JF Poyatos - bioRxiv, 2023 - biorxiv.org
Many intrinsic functional characteristics of cells and tissues shape their genome-wide
expression patterns. But what other factors might also modulate these patterns are not fully …

Community effort to unravel the complex human neuronal landscape exemplified for the striatum

J Schultze, S Agrawal, R Scholz, C Hartmann, L Hetzel… - 2024 - researchsquare.com
Precise determination of cellular identity and molecular phenotypes through advanced high-
throughput technologies is crucial for understanding intricate tissue functions, especially in …

Do Single-cell Experiments Challenge the Concept of Cell Type?

F Gross - Organisms. Journal of Biological Sciences, 2023 - rosa.uniroma1.it
Recent debates among biologists have highlighted problems with the traditional concept of
cell type, which is considered vague and subjective. Single-cell technologies reveal the …

A computational framework for large-scale cell lineage reconstruction

B Kiyota - 2024 - open.library.ubc.ca
The advent of CRISPR-Cas9 genome editing technologies has spurred the development of
large-scale cell lineage tracing systems. These techniques involve integrating synthetic DNA …

Genome instability and somatic retropositional mosaicism in the adult human brain

J Möhner - 2023 - openscience.ub.uni-mainz.de
Zellen des Somas, insbesondere des Gehirns, bilden regionenspezifisch unterschiedlich
häufig genomische Variationen aus, was zu einem somatischen Mosaizismus führt. Dieses …

Study of human and mouse dermal fibroblast heterogeneity by single-cell RNA sequencing.

A Martínez Ascensión - 2023 - addi.ehu.es
The skin is a complex vital organ composed of several layers. The middle layer, the dermis,
is mainly composed of fibroblasts that produce the extracellular matrix (ECM) providing …