Pseudotime analysis for time-series single-cell sequencing and imaging data

G Li, HJ Kim, S Pendyala, R Zhang, CM Disteche… - bioRxiv, 2023 - biorxiv.org
Many single-cell RNA-sequencing studies have collected time-series data to investigate
transcriptional changes with respect to various notions of biological time, such as cell …

The transcripts of a gastrula-premarked enhancer prime posterior tissue development through cross-talk with morphogen effector

Y Chen, F Tan, X Yang, Q Fang, L Zhang, J Liao… - bioRxiv, 2024 - biorxiv.org
The regulatory mechanisms governing cell fate determination, particularly lineage
diversification during mammalian embryonic development, remain poorly understood with in …

The transcriptional landscape of human liver endothelial cells

P Toledano-Sanz, P Reventun, M Viskadourou… - Blood …, 2023 - ashpublications.org
Human liver endothelial cells (HLEC) line the hepatic sinusoids and are reported to have
specialized functions, which underscores their importance in human physiology …

Decoding cell identity with multi-scale explainable deep learning

J Zhu, Z Zhang, Y Xiang, B Xie, X Dong, L Xie, P Zhou… - bioRxiv, 2024 - biorxiv.org
Cells are the fundamental structural and functional units of life. Studying the definition and
composition of different cell types can help us understand the complex mechanisms …

Chioso: Segmentation-free Annotation of Spatial Transcriptomics Data at Sub-cellular Resolution via Adversarial Learning

J Yu - bioRxiv, 2024 - biorxiv.org
Recent advances in spatial transcriptomics technology have produced full-transcriptomic
scale dataset with subcellular spatial resolutions. Here we present a new computational …

Charting the development of Drosophila leg sensory organs at single-cell resolution

BR Hopkins, O Barmina, A Kopp - bioRxiv, 2022 - biorxiv.org
To respond to the world around them, animals rely on the input of a network of sensory
organs distributed across the body. A single individual will generally express several distinct …

How does data structure impact cell-cell similarity? Evaluating the influence of structural properties on proximity metric performance in single cell RNA-seq data

ER Watson, A Mora, AT Fard, JC Mar - bioRxiv, 2022 - biorxiv.org
Accurately identifying cell populations is paramount to the quality of downstream analyses
and overall interpretations of single-cell RNA-seq (scRNA-seq) datasets but remains a …

Sagittarius: Extrapolating Heterogeneous Time-Series Gene Expression Data

A Woicik, M Zhang, J Chan, J Ma, S Wang - bioRxiv, 2022 - biorxiv.org
Understanding the temporal dynamics of gene expression is crucial for developmental
biology, tumor biology, and biogerontology. However, some time points remain challenging …

Genetic Subclones Identify Phenotypic Variation in Diffuse Large B-Cell Lymphoma

B Wang - 2023 - repository.cam.ac.uk
Diffuse large B cell lymphoma (DLBCL) is the most common form of non-Hodgkin's
lymphoma. Many efforts have characterised DLBCL subtypes that account for some of the …

[PDF][PDF] Stepwise emergence of the neuronal gene expression program in early animal evolution

A Sebé-Pedrós - 2023 - repositori.upf.edu
The assembly of the neuronal and other major cell type programs occurred early in animal
evolution. We can reconstruct this process by studying non-bilaterians like placozoans …