Xin Lü

Identifying phenotype-genotype-function coupling in 3D organoid imaging using Shape, Appearance and Motion Phenotype Observation Tool (SPOT)

The paper develops SPOT, a tool for analyzing 3D morpho-dynamics from 2D live-cell imaging, and applies it to organoids to identify phenotype-genotype-function relationships.

Quantitative multi-scale morphodynamic analysis reveals ratchet-like collective DVE migration and epiblast retrograde cell flow during anterior patterning in the mouse embryo

Development of a universal imaging "phenome" using Shape, Appearance and Motion (SAM) features and the SAM Observation Tool (SPOT)

The paper develops a universal imaging phenome using SAM features and SPOT tool, showing it outperforms deep learning models in capturing dynamic cell behaviors.

Calcium signalling is required for anterior patterning in the mouse embryo

The paper investigates the role of calcium signaling in anterior-posterior axis formation in the mouse embryo, finding that SERCA inhibition disrupts DVE migration and axial patterning.

Absolute quantitative and base-resolution sequencing reveals comprehensive landscape of pseudouridine across the human transcriptome

This paper introduces BACS, a method for single-base resolution pseudouridine quantification, and identifies {Psi} sites in human RNA and viral transcripts.

Single-cell phenomics reveals behavioural and mechanical heterogeneities underpinning collective migration during mouse anterior patterning

The paper uses single-cell phenomics to study DVE cell migration in mouse embryos, revealing mechanical heterogeneities and how surrounding cells facilitate collective migration.

ASPP2/PP1 complexes maintain the integrity of pseudostratified epithelia undergoing remodelling during morphogenesis

This study identifies the ASPP2/PP1 complex as critical for maintaining pseudostratified epithelial integrity during morphogenesis by preventing apical delamination and supporting F-actin organization.

Motion Sensing Superpixels (MOSES): A systematic framework to quantify and discover cellular motion phenotypes

MOSES quantifies cellular motion phenotypes across different epithelial cell types and identifies boundary formation changes in response to external stimuli.

Single cell RNA-seq reveals profound transcriptional similarity between Barretts esophagus and esophageal glands

The paper uses single-cell RNA-seq to compare Barretts esophagus with normal esophageal tissues, finding transcriptional similarities with esophageal cells but not with gastric or duodenal cells.

BEARscc determines robustness of single-cell clusters using simulated technical replicates

BEARscc improves single-cell RNA-seq clustering by simulating technical replicates using RNA spike-ins to reduce technical variance.