Yi Yang

Cell cycle-driven epigenetic resetting maintains stem cell fate for shoot branching

The paper shows that cell cycle progression in Arabidopsis stem cells maintains pluripotency by resetting epigenetic marks and silencing fate-determining genes through PRC2 recruitment.

Image-Derived 3D Blood-Brain Mechanics: Cerebral Haemodynamics, Brain Motion and In Vivo Benchmarking

This study develops a 3D computational framework to model cerebral haemodynamics, arterial wall deformation, and brain tissue motion, benchmarked against in vivo measurements.

Reconstructing clone-resolved transcriptional programs from bulk tumor sequencing

PICTographPlus infers clone-resolved transcriptional programs from bulk RNA-seq by integrating clonal phylogenies and proportions, achieving high accuracy in recovering clone-level expression and localizing pathway changes.

Differences in other-directed emotion regulation tracks connectivity between amygdala and prefrontal regions during fairness decisions

The paper examines how individual differences in other-directed emotion regulation relate to neural and behavioral responses during fairness decisions in social contexts.

Capturing Natural Evolution in Function-guided RNA Design via Genomic Foundation Models

The paper introduces a zero-shot RNA design method using genomic foundation models, achieving improved fluorescence and binding affinity in RNA aptamers.

Angular Deviation Diffuser: A Transformer-Based Diffusion Model for Efficient Protein Conformational Ensemble Generation

This paper introduces a transformer-based diffusion model that generates protein conformational ensembles efficiently, showing alignment with MD simulations and broader conformational coverage.

Longitudinal structural variant phylogenies define tumor evolution under therapeutic selection pressure in metastatic prostate cancer

SVCFit estimates SV cellular fractions from bulk sequencing to reconstruct clonal evolution in mCRPC under therapy, showing treatment-driven clonal reconfiguration.

scEccDNAdb: an integrated single-cell eccDNA resource for human and mouse

The paper introduces scEccDNAdb, a database of single-cell eccDNA data from human and mouse, providing annotations and tools for analysis.

MINE is a method for detecting spatial density of regulatory chromatin interactions based on a MultI-modal NEtwork

The paper introduces MINE, a toolkit to detect and analyze spatial density of regulatory chromatin interactions using Hi-C, ATAC-seq, and histone ChIP-seq data.