Xin Liu

OTTER: Orchestrated Transcriptomic, Tumor-xenograft (PDX/CDX), and Epigenomic Reporting Workflow

OTTER improves bisulfite deconvolution in tumor xenograft sequencing by restoring recall to 52%-54% while preserving transcriptomic accuracy.

An FEV-Associated Metastasis-Initiating-Like State Linked to Tumor Cell Plasticity and Immune Niche Remodeling in Prostate Cancer

The paper identifies a metastasis-initiating-like state in prostate cancer linked to FEV, tumor plasticity, and immune niche remodeling through integrated multi-omics analysis.

Spatial Transcriptomics Reveal Developmental Dynamics of the Human Cerebral Cortex and Striatum

This study uses spatial transcriptomics and snRNA-seq to identify 25 forebrain regions and characterize dynamic changes in the human fetal cortex and striatum during late first and early second trimesters.

Single-Cell Multi-Omics Dissects Transcript Isoform and Immune Repertoire Dynamics in Human Immunosenescence

This study uses single-cell multi-omics to analyze transcript isoform and immune repertoire changes in aging human immune cells, identifying age-related molecular features in T cells and B cells.

Context-dependent variant interpretation from Mendelian disease to genetic predisposition: a proof-of-concept using LPL

This paper proposes a context-dependent framework for variant interpretation by analyzing LPL loss-of-function variants, showing how residual activity levels influence clinical outcomes.

Persistent Post-Inflammatory Matrix Stiffening Defines a Premalignant Mechanical Niche in Ulcerative Colitis-Associated Neoplasia

This study identifies persistent post-inflammatory matrix stiffening as a premalignant mechanical niche in UC-associated neoplasia, showing its role in epithelial remodeling and potential therapeutic targeting.

The genetic repertoire of the deep sea: from sequence to structure and function

This study analyzes the genetic diversity of the deep sea, linking protein structures to genetic variants and identifying biotechnologically relevant features.

Decoding Immune Reconstitution Failure in People Living with HIV through Single-cell Genomics

This study uses single-cell multi-omics to analyze immune reconstitution failure in HIV patients, identifying genetic and epigenetic factors and developing a predictive model.

Identification and Characterization of Metastasis-initiating cells

This paper introduces scMIC, a computational framework for identifying metastasis-initiating cells from single-cell data, validated across multiple cancer types and datasets.

Quantitative Multicolored Deep Imaging of Human Bones Reveals a Composite Osteo-Sinusoidal Niche for Mesenchymal Stromal Cells.

The paper uses a tissue-clearing protocol to spatially map BM-MSCs in human bones, revealing distinct microenvironment features in young and aged bones.

Learning universal knowledge graph embedding for predicting biomedical pairwise interactions

This paper introduces LukePi, a self-supervised pre-training framework for GNNs on biomedical knowledge graphs, which improves link prediction in low-data and distribution-shift scenarios.

A novel vimentin variant from tumor-associated macrophages directs cancer metastasis by engaging IGF-1R

This study identifies a novel vimentin variant secreted by tumor-associated macrophages that promotes cancer metastasis by activating IGF-1R and increasing integrin expression.

Machine Learning to Identify Molecular Markers for Metabolic Disease Development Using Mouse Models

This study uses machine learning to identify molecular markers for metabolic disease development by analyzing mouse models of diet, aging, and FXR inactivation.

B7-H1(PD-L1) confers chemoresistance through ERK and p38 MAPK pathway in tumor cells

This study shows B7-H1(PD-L1) promotes chemoresistance in tumor cells via ERK pathway activation and reduces it via p38 MAPK pathway activation when B7-H1 is deficient.

Genome‑wide Identification and Characterization of Transcription Factors of Basic Leucine Zipper Family in Malus domestica

This study identifies and characterizes 116 bZIP transcription factors in the apple genome, analyzing their phylogeny, gene structure, protein motifs, dimerization potential, expression patterns, and stress responses.