Jie Liu

Identification of co-expressed gene sets for major molecular initiating events in rodent liver carcinogenesis using wild type and knock out rats

The paper identifies co-expressed gene sets linked to molecular initiating events in rodent liver carcinogenesis by comparing wild-type and knockout rats exposed to chemical activators.

PanKbase Integrated Single-Cell Map: A Comprehensive Atlas of Human Pancreatic Islets

The paper integrates multiple scRNA-seq datasets to create a comprehensive atlas of human pancreatic islets, identifying 13 cell populations and providing a resource for diabetes research.

IgG4⁺ plasma cell enrichment and {lambda}-chain-biased BCR remodeling drive low-grade autoimmunity in chronic obstructive pulmonary disease

This study identifies IgG4⁺ plasma cell enrichment and λ-chain-biased BCR remodeling in COPD, linking them to low-grade autoimmunity and chronic inflammation.

Computational reconstruction of hierarchical cis-regulatory networks reveals synergistic transcription control and disease-associated rewiring

ORIGAMI reconstructs cis-regulatory networks using multi-omics data and deep learning, revealing synergistic transcription control and disease-associated rewiring.

The Human Pancreas Cell Atlas defines a healthy reference framework for disease contextualization and translational benchmarking

The paper constructs a healthy human pancreas reference atlas to contextualize disease states and benchmark models.

Engineering a pacemaker-driven human mini-heart guided by spatial multi-omics of sinoatrial node development

This paper develops a pacemaker-driven human mini-heart using spatial multi-omics and stem-cell engineering to study cardiac conduction and drug discovery.

Tripeptidyl peptidase II is essential for maintaining cerebrovascular homeostasis of female mice and represents a novel therapeutic target for vascular dementia

This study identifies TPP2 as essential for cerebrovascular homeostasis in female mice, linking its deficiency to vascular degeneration and cognitive impairment, and suggests Far1 as a therapeutic target.

CHORD: a framework for cross-species single-cell integration across gene, cell and cell-type levels

CHORD integrates cross-species single-cell transcriptomic data to learn gene, cell, and cell-type representations, enabling cell-type annotation and cross-species comparison of developmental and phenotypic patterns.

A TROP2/Claudin Program Mediates Immune Exclusion to Impede Checkpoint Blockade in Breast Cancer

This study identifies TROP2 as a regulator of tight junction-mediated immune exclusion in TNBC, showing that targeting TROP2 enhances anti-PD1 therapy response.

Synthetic Immunological Niche Reveals Early Immune Dysregulationand Stratifies Therapeutic Response in Type 1 Diabetes

The paper develops a synthetic immunological niche to identify early immune dysregulation and stratify therapeutic response in Type 1 Diabetes.

The Drosophila wing is a high-throughput and versatile screening tool for Tau-mediated disease mechanisms and drug discovery.

This paper describes using Drosophila wing discs to study Tau-mediated disease mechanisms and screen for neuroprotective drugs, showing that human Tau causes cell death and that NAP reduces toxicity.

METTL3-mediated SOCS3 m6A Modification in Preserving CD4+ T Cell Homeostasis in HIV Infected Long-term Non-progressors

This study identifies a novel m6A-METTL3-SOCS3 regulatory axis that preserves CD4+ T cell homeostasis in HIV-infected long-term non-progressors by modulating JAK2/STAT4 signaling.

3'HS1 CTCF binding site in human β-globin locus regulates fetal hemoglobin expression

The paper shows that deleting the 3HS1 CTCF binding site increases fetal hemoglobin expression in hematopoietic stem cells and erythroid progenitor cells, suggesting therapeutic potential for hemoglobinopathies.

Cancer-associated fibroblasts in pancreatic ductal adenocarcinoma determine response to SLC7A11 inhibition

This study shows that SLC7A11 in pancreatic ductal adenocarcinoma stroma, not tumor cells, predicts poor survival and that inhibiting it reduces CAF activity and tumor growth.

Jointly embedding multiple single-cell omics measurements

MMD-MA embeds cells measured by different single-cell assays into a shared latent space without cell or feature correspondence, recovering true pairings in simulations and a 61-cell expression/methylation co-assay.

A draft reference genome sequence for Scutellaria baicalensis Georgi

The paper reports a draft reference genome sequence for Scutellaria baicalensis using Illumina and PacBio sequencing, providing a foundation for studying its bioactive compound biosynthesis.

Unsupervised embedding of single-cell Hi-C data

This paper applies bulk Hi-C analysis methods to scHi-C data with unsupervised embedding, finding HiCRep with MDS outperforms other methods and is robust to low sequencing depth.

Genome-wide identification of CDC34 that stabilizes EGFR and promotes lung carcinogenesis

This study identifies CDC34 as a critical E2 ubiquitin conjugase that stabilizes EGFR and promotes lung carcinogenesis by inhibiting its degradation.

Genomic, transcriptomic and phenomic variation reveals the complex adaptation of modern maize breeding

This study analyzes genomic, transcriptomic, and phenomic variation in 368 maize inbred lines to uncover adaptation mechanisms during maize's temperate-tropical divergence.