Xiaoqi Zheng

Benchmarking the translational potential of AI-based drug-resistance prediction from Mycobacterium tuberculosis whole-genome sequencing data

This paper benchmarks AI-based drug-resistance prediction models for Mycobacterium tuberculosis using a large unified dataset, finding XGBoost performs best in precision-recall and F1 metrics, while neural models excel in AUROC.

Castl: Robust Identification of Spatially Variable Genes in Spatial Transcriptomics via an Ensemble-based Framework

Castl identifies spatially variable genes by integrating multiple methods to reduce variability and control false discovery rates across datasets.

Harmonizing single cell 3D genome data with STARK and scNucleome

The paper introduces STARK, a toolkit for processing sc3DG-seq data, benchmarks 11 technologies, and establishes scNucleome as a resource for 3D genome research.

Spider: a flexible and unified framework for simulating spatial transcriptomics data

Spider generates synthetic spatial transcriptomics data by simulating cell type proportions and transitions, enabling benchmarking of analysis tools.

CellPatch: a Highly Efficient Foundation Model for Single-Cell Transcriptomics with Heuristic Patching

CellPatch is a lightweight foundation model for single-cell transcriptomics that achieves state-of-the-art performance with low computational costs.

STCC: consensus clustering enhances spatial domain detection for spatial transcriptomics data

STCC improves spatial domain detection in spatial transcriptomics by combining multiple clustering tools through consensus strategies, enhancing accuracy and stability across different data types.

Assessing base-resolution DNA mechanics on the genome scale

The paper introduces BendNet, a neural network that predicts DNA bending at base-resolution from sequences, revealing stiffness patterns and TF binding preferences in the human genome.

Tertiary Lymphoid Structure and CD8 T Cell Exclusion in Minimally Invasive Adenocarcinoma

The paper characterizes the tumor microenvironment of early-stage lung adenocarcinoma, identifying tertiary lymphoid structures and CD8 T cell exclusion mediated by follicular regulatory T cells.