Sheng Liu

PARP1 catalytic domain mutations drive high-level resistance to saruparib while preserving DNA damage response vulnerabilities

This study identifies PARP1 catalytic domain mutations as a mechanism of high-level resistance to saruparib in BRCA1-deficient breast cancer cells, while retaining DDR vulnerabilities.

The Epigenetic Factor PHF13 Governs Trophoblast Stemness and Differentiation

This study identifies PHF13 as a chromatin regulator critical for trophoblast stemness and differentiation, showing its role in maintaining stemness and restricting differentiation through gene regulatory networks.

Identification and functional characterization of an AMD associated c-ABL binding SNP streak within the ARMS2 gene promoter region

The paper identifies a 5-SNP block in the ARMS2 promoter that binds c-ABL and is associated with AMD, showing reduced transcriptional activity in reporter assays.

DANCE 2.0: Transforming single-cell analysis from black box to transparent workflow

DANCE 2.0 automates and interprets single-cell preprocessing by recommending optimal pipelines for various tasks, improving performance across six major analyses.

DiCE: Differential Centrality-Ensemble Analysis Based on Gene Expression Profiles and Protein-Protein Interaction Network

DiCE identifies disease-associated genes by combining differential expression with network centrality analysis, validated on prostate cancer datasets to find genes correlated with disease-free survival.

RABEP1 amplifies front signaling in neutrophil migration

This study identifies RABEP1 as a key regulator of neutrophil migration by promoting endosomal recycling, Rac activation, and actin polymerization in zebrafish and human cells.

Chemical inhibition of RPA gap protection sensitizes BRCA1-deficient cancers to PARP inhibition

This study shows that inhibiting RPA gap protection enhances PARP inhibitor efficacy in BRCA1-deficient cancers by increasing genomic instability and reducing tumor growth.

ZNFX1 is a Novel Master Regulator in Epigenetically-induced Pathogen Mimicry and Inflammasome Signaling in Cancer

This study identifies ZNFX1 as a master regulator of epigenetically-induced pathogen mimicry and inflammasome signaling in ovarian cancer, linking its expression to disease progression and survival.

CDHu40: a novel marker gene set of neuroendocrine prostate cancer (NEPC)

The paper identifies a novel marker gene set, CDHu40, for neuroendocrine prostate cancer (NEPC) using gene expression and PPI network analysis, showing strong prognostic significance.

Dynamic Single Cell Transcriptomics Defines Kidney FGF23/KL Bioactivity and Novel Segment-Specific Inflammatory Targets

This study uses single-cell transcriptomics to analyze FGF23 bioactivity and identify novel inflammatory targets in the kidney, revealing interactions between FGF23 and TNF/NF-κB pathways.

The Prolonged Terminal Phase of Human Life Induces Survival Response in the Skin Transcriptome

The paper investigates how the duration of the terminal phase of human life affects postmortem gene expression in skin, finding prolonged terminal phases induce survival pathways and downregulate organ-specific functions.

SARS-CoV-2 Viral Genes Compromise Survival and Functions of Human Pluripotent Stem Cell-derived Cardiomyocytes via Reducing Cellular ATP Level

This study shows SARS-CoV-2 genes Nsp6, Nsp8, and M reduce ATP levels in hPSC-CMs, causing apoptosis and dysfunction, and identifies drugs that may counteract these effects.

PanoView: An iterative clustering for single-cell RNA sequencing data

PanoView is an iterative clustering method for scRNA-seq data that outperforms existing methods in detecting major and rare cell types without parameter tuning.

Decomposing cell identity for transfer learning across cellular measurements, platforms, tissues, and species.

The paper introduces scCoGAPS and projectR to decompose cell identity into shared and species-specific factors, enabling transfer learning across datasets and species.

Lhx2 regulates temporal changes in chromatin accessibility and transcription factor binding in retinal progenitor cells.

This study identifies Lhx2 as a key regulator of chromatin accessibility and transcription factor binding in retinal progenitor cells, showing its role in stage-specific gene regulation.