Yeqing Chen

CellPilot: an agentic framework that pilots small language models through autonomous single-cell annotation

CellPilot improves single-cell annotation accuracy by integrating small language models into a structured workflow, achieving performance close to larger models while maintaining transparency.

TFAP2A links drug resistance to antitumor immunity

This study identifies TFAP2A as a driver of BRAF/MEK inhibitor resistance and immunosuppression, showing its disruption enhances antitumor immunity and overcomes drug resistance.

CoLa-VAE: A Cell-Cell Communication-Aware Variational Autoencoder for Representation Learning and Expression Denoising

CoLa-VAE improves denoising and representation learning in single-cell data by integrating cell-cell communication information, enhancing downstream analyses like differential communication detection and spatial deconvolution.

Single-cell lineage tracing maps clonal and transcriptional dynamics in melanoma metastasis

This study uses single-cell lineage tracing to map clonal and transcriptional dynamics in melanoma metastasis, identifying distinct transcriptional programs and spatial organization patterns.

Clonal dynamics shaped by diverse drug-tolerant persister states in melanoma resistance

This study identifies drug-tolerant persister states in melanoma using MeRLin, showing their role in resistance and tumor recurrence.

MYC-ATF4-ASS1 axis governs intracellular arginine synthesis and dictates the immune microenvironment in melanoma

The paper identifies the MYC-ATF4-ASS1 axis in melanoma that controls arginine synthesis and modulates immune responses, showing therapeutic potential with arginine depletors and BRAF/MEK inhibitors.

Mechanistic insights and in vivo HIV suppression by the BRD4-targeting small molecule ZL0580

This study identifies ZL0580 as a BRD4-targeting small molecule that suppresses HIV in vivo through epigenetic mechanisms, showing potent antiviral effects in a humanized mouse model.

Dissecting Opioid Effects in Cell-Cell Communication Within the Ventral Tegmental Area

This study examines how opioid abuse affects cell-cell communication in the ventral tegmental area using snRNA-seq data, finding reduced overall communication but enhanced NRXN signaling in specific pathways.

Dysregulated Gene Regulatory Networks in Substance Use Disorder and HIV Infection: Insights from Single-Cell Genomics

This study identifies dysregulated gene regulatory networks in opioid use disorder and HIV using snRNA-seq data from brain samples, revealing altered FOS-centered networks and potential therapeutic targets.

A Comprehensive Proteogenomic and Spatial Analysis of Innate and Acquired Resistance of Metastatic Melanoma to Immune Checkpoint Blockade Therapies

This study identifies molecular mechanisms of resistance to immune checkpoint blockade in metastatic melanoma using proteogenomic and spatial analyses of tumor and immune microenvironment data.

A pan-cancer PDX histology image repository with genomic and pathological annotations for deep learning analysis

The paper presents a pan-cancer PDX histology image repository with genomic and pathological annotations for deep learning analysis of tumor regions and xenograft-transplant lymphoproliferative disorder prediction.