This study integrates proteogenomic analyses of esophageal squamous cell carcinoma to identify molecular subtypes and potential therapeutic strategies.

bioRxiv · Apr 22, 2026 · PreprintCancer Biology

Single-Cell Genomics Elucidates Molecular Variations and Regulatory Mechanisms in Circulating Immune Cells

Jianhua Yin, Yuhui Zheng, Zhuoli Huang, Wenwen Zhou, Yue Yuan, Pengfei Cai, Yong Bai, Shichen Yang, Yue Gao, Shanshan Duan, Yang Wang, Zekai Xu, W H Zhang, Xinyu Zhang, Yilin Wei, , Chuanyu Liu

The paper introduces CIMA, a multi-omics atlas of human immune cells, identifying regulatory mechanisms and genetic associations across sex, age, and genetic factors.

Science · Jan 8, 2026Peer-reviewedImmunology

Multi-omics Reveals Immune Response and Metabolic Profiles during High-Altitude Mountaineering

Jianhua Yin, Jingzhi Lv, Shichen Yang, Yang Wang, Zhuoli Huang, Xue Bing Wang, Guixue Hou, Wenwen Zhou, Ying Liu, Weikai Wang, Xiumei Lin, Yunting Huang, Yuhui Zheng, Chen Wei, Yue Yuan, , Jian Wang

This study uses multi-omics data to analyze immune and metabolic changes in mountain climbers during acclimatization and extreme altitude exposure.

Cell Reports · Dec 31, 2024Peer-reviewedBioinformatics

Multi-trait genome-wide association study in 34,394 Chinese women reveals the genetic architecture of plasma metabolites during pregnancy

SiYang Maggie Liu, Jilong Yao, Liang Lin, Xianmei Lan, Linlin Wu, Xuelian He, Nannan Kong, Yan Li, Yuqing Deng, Jiansheng Xie, Huanhuan Zhu, Xiaoxia Wu, Zilong Li, Likuan Xiong, Yuan Wang, , Siqi Liu

This study identifies 30 novel metabolite-gene associations in 34,394 Chinese pregnant women and finds pleiotropy and causal relationships between metabolites and diseases.

Cell Genomics · Oct 1, 2024Peer-reviewedGenetic & Genomic Medicine

IntroSpect: motif-guided immunopeptidome database building tool to improve the sensitivity of HLA binding peptide identification

Le Zhang, Geng Liu, Guixue Hou, Haitao Xiang, Xi Zhang, Ying Huang, Xiuqing Zhang, Bo Li, Leo J. Lee

IntroSpect improves HLA binding peptide identification sensitivity by 80% using motif-guided database building, while maintaining high accuracy and FDR control.

bioRxiv · Aug 2, 2021 · PreprintBioinformatics

Standardization and Harmonization of Distributed Multi-National Proteotype Analysis supporting Precision Medicine Studies

Yue Xuan, Nicholas W. Bateman, Sébastien Gallien, Sandra Götze, Yue Zhou, Pedro Navarro, Mo Hu, Niyati Parikh, Brian L. Hood, Kelly A. Conrads, Christina Looße, Reta Birhanu Kitata, Sander R. Piersma, Davide Chiasserini, Hongwen Zhu, , Thomas P. Conrads

This paper standardizes a proteotype analysis workflow across multiple international sites to enable distributed, reproducible proteomic data generation for precision medicine.

Nature Communications · Oct 16, 2020Peer-reviewedMolecular Biology

EPIP: MHC-I epitope prediction integrating mass spectrometry derived motifs and tissue-specific expression profiles

Weipeng Hu, Si Qiu, Youping Li, Xinxin Lin, Le Zhang, Haitao Xiang, Xing Han, Sitao Zhu, Lei Chen, Sha Li, Wenhui Li, Zhe Ren, Guixue Hou, Zhilong Lin, Jianliang Lu, , Leo J. Lee

EPIP predicts MHC-I epitope presentation by integrating mass spectrometry-derived motifs and tissue-specific RNA-seq data, outperforming existing methods in independent validation.

bioRxiv · Aug 24, 2020 · PreprintBioinformatics

Multi-laboratory assessment of reproducibility, qualitative and quantitative performance of SWATH-mass spectrometry

Ben C Collins, Christie L Hunter, Yansheng Liu, Birgit Schilling, George Rosenberger Rosenberger, Samuel L Bader, Daniel W Chan, Bradford W Gibson, Anne-Claude Gingras, Jason M Held, Mio Hirayama-Kurogi, Guixue Hou, Christoph Krisp Krisp, Brett Larsen, Liang Lin, , Ruedi Aebersold

This study evaluates SWATH-MS across 11 labs, showing consistent detection and quantification of over 4,000 proteins with reproducible quantitative data.

bioRxiv · Sep 14, 2016Biochemistry