Silvia Liu

The SET1/COMPASS subunit RBBP5 orchestrates epigenetic control of global proteostasis and the 12h oscillator to safeguard metabolic and cellular homeostasis

This study identifies RBBP5 as an essential epigenetic regulator of the 12h oscillator and proteostasis, linking it to metabolic and cellular homeostasis in mammals.

Fibulin-2 transduces a matrix-to-metabolism signal in kidney fibrosis

This study identifies Fibulin-2 as a matrix cue that transduces fibrotic ECM remodeling into mitochondrial metabolic reprogramming in kidney fibrosis.

Profilin-1 Deficiency Activates STING to Drive T Cell-Mediated Anti-Tumor Immunity in Breast Cancer

This paper shows that reducing Profilin-1 in breast cancer cells triggers genomic instability and activates the cGAS-STING pathway, enhancing T cell-mediated anti-tumor immunity and leading to tumor regression.

AI-guided analysis of human pancreatic islet sociology reveals distinct cell compositional changes in type 1 diabetes

The paper uses AI to analyze pancreatic islet composition in type 1 diabetes, finding age, sex, and region-dependent changes and beta-cell loss with reciprocal cell expansion.

Molecular insights into Profilin1-dependent regulation of cellular phosphatidylinositol-(4,5)-bisphosphate

This study shows that loss of Profilin1 reduces plasma membrane PIP2 levels, linking actin regulation to PIP2 homeostasis and revealing Pfn1's broader role in lipid metabolism.

Co-repression of Yap1 and Sox9 Abrogates Established Cholangiocarcinoma by Eliminating Transcriptional Compensation

This study shows that deleting both Sox9 and Yap1 eliminates cholangiocarcinoma by blocking transcriptional compensation, suggesting co-targeting as a therapeutic strategy.

Diploid Hepatocytes Resist Acetaminophen-Induced Liver Injury Through Suppressed JNK Signaling

The paper shows diploid hepatocytes are more resistant to acetaminophen-induced liver injury due to reduced JNK signaling and mitochondrial damage.

Stiffness sensing fuels matrix-driven metabolic reboot for kidney repair and regeneration

This study identifies Mfap2 as a key ECM component that regulates kidney repair by linking mechanical cues to metabolic reprogramming through Esr2-mediated transcriptional control.

Calpain-4 Knockdown Modulates Cholesterol Metabolism and LXRα Nuclear Localization in Alcohol-Related Liver Disease

This study shows that Calpain-4 knockdown reduces cholesterol levels and relocalizes LXRα to the nucleus in alcohol-related liver disease.

Alpha diversity analysis of hepatic transcriptome reveals novel pathways inalcohol-related hepatitis

The paper analyzes transcriptome diversity in alcohol-related liver disease to identify novel pathways and genes not detected by differential expression analysis.

SALL4 is required for YAP1-dependent malignant and regenerative hepatocyte reprogramming into cholangiocyte lineage

This study identifies SALL4 as a regulator of YAP1-driven hepatocyte-to-cholangiocyte reprogramming, showing its role in both malignant and regenerative liver processes.

SON-dependent nuclear speckle rejuvenation alleviates proteinopathies

This study identifies pyrvinium pamoate as a compound that rejuvenates nuclear speckles, improving protein quality control and reducing YAP1 activity, thereby alleviating proteinopathies in pre-clinical models.

Integrating Artificial Intelligence-Driven Digital Pathology and Genomics to Establish Patient-Derived Organoids as a Novel Alternative Model for Drug Response in Head and Neck Cancer

This study establishes patient-derived organoids (PDOs) for HNSCC drug response testing, integrating AI-driven histopathology and multi-omics analysis to create a scalable preclinical model.

SOX2-VSX2 Co-Occupancy Shapes Retinal Neurogenesis Through Dynamic Chromatin Regulation

This study identifies SOX2 and VSX2 co-occupancy in retinal progenitor cells and shows how their cooperative binding regulates chromatin accessibility and neurogenesis.

Aicardi-Goutieres Syndrome Associated ADAR G1007R mutation dominantly induces neuroinflammation in mouse brain

This paper describes a mouse model with a human ADAR G1007R mutation that causes neuroinflammation and shows that deleting MDA5 can reverse brain inflammation.

Comprehensive evaluation and practical guideline of gating methods for high-dimensional cytometry data: manual gating, unsupervised clustering, and auto-gating

This study evaluates manual gating, unsupervised clustering, and auto-gating methods for high-dimensional cytometry data using six datasets and provides practical guidelines for selecting appropriate methods.

Therapeutic potential of SOX9 dysruption in Combined Hepatocellular Carcinoma-Cholangiocarcinoma

This study contrasts the effects of developmental and acute Sox9 deletion in cHCC-CCA models, showing that Sox9 elimination can reduce tumor burden and highlights therapeutic potential.

IFDlong: an isoform and fusion detector for accurate annotation and quantification of long-read RNA-seq data

IFDlong is a tool for detecting and quantifying isoform and fusion transcripts in long-read RNA-seq data, showing high accuracy and performance in simulations and real datasets.

Utility Analyses of AVITI Sequencing Chemistry

This study compares the AVITI and Illumina sequencing chemistries for DNA and RNA short-read and long-read sequencing, finding AVITI has higher quality scores and lower error rates in short-read applications.

Long-read single-cell sequencing reveals expressions of hypermutation clusters of isoforms in human liver cancer cells

The paper uses long-read single-cell sequencing to identify mutation-specific mRNA isoforms and fusion transcripts in liver cancer cells, improving classification of cancer versus benign cells.

Single-nucleus chromatin accessibility identifies a critical role for TWIST1 in idiopathic pulmonary fibrosis myofibroblast activity

The paper identifies TWIST1 as a critical regulator of myofibroblast activity in IPF using single-nucleus ATAC-seq and scRNA-seq integration.

Evidence for conservation of primordial 12-hour ultradian gene program in humans under free-living conditions.

The paper identifies robust ~12h transcriptional rhythms in human peripheral white blood cells under free-living conditions, showing homology to circatidal gene programs in marine species.

JAX-CNV: A whole genome sequencing-based algorithm for copy number detection at clinical grade level

JAX-CNV is a whole genome sequencing-based algorithm for copy number variant detection, achieving 100% recall and 4% false discovery rate in clinical validation.

Targeted Transcriptome Analysis using Synthetic Long Read Sequencing Uncovers Isoform Reprograming in the Progression of Colon Cancer

This study uses LoopSeq, a synthetic long read sequencing method, to analyze isoform changes in colon cancer and identifies novel gene fusions and isoform-specific SNVs.