Qi Liu

LineageFlow: Growth-Corrected State Dynamics for Probabilistic Cell-Fate Prediction

LineageFlow predicts clonal fate and transcriptional profiles by integrating growth dynamics and state transitions in single-cell lineage data.

Facilitating Valid Statistical Inference in Biomedical Image Synthesis

This paper evaluates the statistical validity of synthetic biomedical images and introduces PAMS to improve biological inference.

AbRefine: Framework-Conditioned Refinement for Structure-Guided Antibody CDR Design

AbRefine improves antibody CDR design by fusing structural and sequence predictions using framework context, achieving better recovery and lower log-likelihood than static fusion.

Senescence-associated KRAS upregulation in peripheral T cells links to premature coronary artery disease

The paper identifies KRAS upregulation in senescent CD8+ T cells as linked to premature coronary artery disease through single-cell and bulk transcriptomic analyses.

Maleic acid adjuvates BCG to induce CD4+CD8+ T cells and sterilize tuberculosis

This study shows that maleic acid enhances BCG vaccination to induce CD4+CD8+ T cells that sterilize Mtb infection in mice.

Chemically induced USP21-KLHL12 association recruits USP21 to COPII assembly

The paper shows that BAY-805 induces USP21-KLHL12 association, recruiting USP21 to COPII vesicles and impairing large cargo transport.

Tensor-based representation learning for multi-omics integrative clustering and feature discovery

MIA is a tensor-based framework for multi-omics data integration that improves clustering and feature discovery, showing effectiveness in cancer subtype identification.

Enhancing Pan-cancer Spatial Transcriptomics atSingle-cell Resolution with stPainter

STPAINTER enhances spatial transcriptomics data using a pre-trained scRNA-seq atlas, enabling high-fidelity downstream analysis across cancer types.

Diabetes-associated MYT1 and MYT3 regulate human beta-cell insulin secretion and survival via other diabetes-risk genes

This study shows MYT1 and ST18 regulate human beta-cell survival and insulin secretion under normal and stress conditions, with their genes enriched for T2D-risk loci.

Reconstructing True 3D Spatial Omics at Single-Cell Resolution

This paper introduces a computational framework for true 3D spatial reconstruction of tissues, demonstrating improved fidelity over 2D methods across multiple spatial omics modalities.

BioClaw: Human-Bot Research Collaboration Ecosystems in Group Chats

BioClaw enables human-bot collaboration in group chats to execute biomedical analyses using containerized tools and workflows across multiple domains and data types.

Molecular architecture of the tumor microenvironment caused by BRCA1 and BRCA2 somatic mutations in lung adenocarcinoma

This study examines BRCA1/2 mutations in lung adenocarcinoma, finding distinct immune and transcriptional patterns linked to different clinical outcomes and potential therapeutic targets.

Hierarchical Assembly of Native Cytoplasmic Lattices Revealed by Cryo-EM

The paper uses cryo-EM to reveal the high-resolution structure of mouse oocyte cytoplasmic lattices, identifying their components and hierarchical assembly mechanism.

Systematic characterization of existing and novel inducible transgenic systems in human pluripotent stem cells after prolonged differentiation

This study evaluates inducible transgenic systems in human pluripotent stem cells and differentiated cells, identifying a small molecule-mediated splicing switch that enables tunable transgene expression without protein tags.

Multi-ancestry genome-wide and transcriptome-wide association analyses identify new risk loci and genes for inflammatory bowel disease

This study identifies 60 new susceptibility loci and 441 candidate risk genes for inflammatory bowel disease through multi-ancestry GWAS and TWAS, with implications for precision medicine.

Inter-brain similarity and connectivity based on EEG hyperscanning during patient-acupuncturist interactions

This study uses EEG hyperscanning to examine inter-brain similarity and connectivity during patient-acupuncturist interactions, finding that acupuncture affects both spatial correlation and specific frequency band connectivity.

Rapid identification of key genes for the rod-shaped morphology in bacteria using multi-species genomes

The paper uses machine learning to predict bacterial shape from genomic data and identifies key genes involved in rod-shaped morphology through experimental validation.