Xiaojing Yang

Reconstructing lineage-constrained gene-program dynamics with PhyloFM

PhyloFM reconstructs continuous cell-fate dynamics using lineage constraints from single-cell data, improving accuracy in multiple biological systems.

Benchmarking Static Gene Regulatory Network Reconstruction and Dynamic Transition Probing in Single-Cell Foundation Models.

This study benchmarks static gene regulatory network reconstruction and dynamic transition probing in single-cell foundation models across multiple datasets and reference networks.

δ-α cell-to-cell interactions modulate pancreatic islet Ca2+ oscillation modes

The paper shows that δ-cell interactions modulate pancreatic islet Ca2+ oscillation patterns through somatostatin secretion and pharmacological/optogenetic perturbations, revealing a Hopf bifurcation mechanism.

Detecting Special Genes in Marine Symbionts: A Phylogeny-Deviation Approach Identifies Recombination-Enhancing Variants

The paper identifies recombination-enhancing variants in marine symbionts using a phylogeny-deviation approach, finding genes that improve recombination efficiency in Escherichia coli.

Glial ferritin maintains neural stem cells via transporting iron required for self-renewal in Drosophila

This study shows glial ferritin transports iron to Drosophila neural stem cells, supporting their self-renewal and proliferation by maintaining energy production.

Transcription-independent hold of the G1/S transition is exploited to cope with DNA replication stress

The paper shows that overexpression of WHI7 bypasses the need for Mec1 and Rad53 in Saccharomyces cerevisiae, revealing a transcription-independent role in delaying G1/S transition during replication stress.

Inflammaging in human photoexposed skin: Early onset of senescence and imbalanced epidermal homeostasis across the decades.

The paper investigates inflammaging in human photoexposed skin, identifying early senescence and imbalanced epidermal homeostasis across age groups.

Pancreatic α and β cells are globally phase-locked

The paper shows that pancreatic α and β cells exhibit globally phase-locked Ca2+ oscillations with tunable phase shifts that set islet oscillation patterns.

Non-epigenetic mechanisms enable short memories of the environment for cell cycle commitment

The paper shows yeast cells use phosphorylation of Whi5 to temporarily remember environmental signals and decide to enter the cell cycle.

DNA Break-Induced Epigenetic Drift as a Cause of Mammalian Aging

The paper shows that DNA double-strand breaks induce epigenomic changes that accelerate the aging clock in mammals.

Cell cycle inhibitor Whi5 records environmental information to coordinate growth and division in yeast

This study shows that Whi5 in yeast acts as an environmental indicator that coordinates cell growth and division by adjusting cell cycle entry based on environmental conditions.