Yixin Chen

A Minimal Chemo-mechanical Markov Model for Rotary Catalysis of F1-ATPase

The paper develops a minimal chemo-mechanical Markov model for F1-ATPase rotary catalysis, showing that four beta-subunit conformations are required and reconciling the bi-site versus tri-site controversy.

EasyMultiProfiler: An Efficient Multi-Omics Data Integration and Analysis Workflow for Microbiome Research

EasyMultiProfiler provides a streamlined workflow for integrating and analyzing multi-omics microbiome data, addressing challenges in standardization and reproducibility.

GeST: Towards Building A Generative Pretrained Transformer for Learning Cellular Spatial Context

GeST is a generative transformer model pretrained on spatial transcriptomics data to learn spatial context, showing improved generation and zero-shot spatial niche embedding extraction.

Network for Knowledge Organization (NEKO): an AI knowledge mining workflow for synthetic biology research

NEKO is an AI workflow using LLMs to extract and organize scientific knowledge from literature, providing more specific and actionable insights than existing models.

PathFinder: a novel graph transformer model to infer multi-cell intra- and inter-cellular signaling pathways and communications

PathFinder infers multi-cell signaling pathways and communications using a graph transformer model, identifying novel interactions in AD mouse models.

Benchmarking multi-omics integration algorithms across single-cell RNA and ATAC data

This study benchmarks 12 multi-omics integration methods on scRNA-seq and scATAC-seq data across three tasks, identifying method-specific strengths and providing selection guidelines.

hECA: the cell-centric assembly of a cell atlas

The paper introduces hECA, a cell-centric human Ensemble Cell Atlas, which integrates scRNA-seq data from multiple studies to enable targeted data retrieval, multi-view presentations, and customizable reference creation for cell type annotations.

Characterization of the SARS-CoV-2 Spike in an Early Prefusion Conformation

The paper characterizes an early prefusion conformation of the SARS-CoV-2 Spike protein using cryo-EM and shows it forms a homotrimer with significant glycosylation.

Genetic and molecular mechanism for distinct clinical phenotypes conveyed by allelic truncating mutations implicated in FBN1

The paper investigates how different FBN1 truncating mutations cause distinct clinical phenotypes in Marfan syndrome and Marfanoid-progeroid-lipodystrophy syndrome through molecular and genetic analysis.

A new statistic for efficient detection of repetitive sequences

The paper introduces a new statistic for efficiently detecting repetitive sequences in genomic data and demonstrates its effectiveness across multiple scenarios.