MARD: a new method to detect differential gene expression in treatment-control time courses. - Chao Cheng; Xiaotu Ma; Xiting Yan; Fengzhu Sun; Lei M. Li (Bioinform., 2006)

Inferring activity changes of transcription factors by binding association with sorted expression profiles. - Chao Cheng; Xiting Yan; Fengzhu Sun; Lei M. Li (BMC Bioinform., 2007)

Testing gene set enrichment for subset of genes: Sub-GSE. - Xiting Yan; Fengzhu Sun (BMC Bioinform., 2008)

A novel pathway-based distance score enhances assessment of disease heterogeneity in gene expression. - Xiting Yan; Anqi Liang; Jose Gomez; Lauren Cohn; Hongyu Zhao; Geoffrey Lowell Chupp (BMC Bioinform., 2017)

Latent-space embedding of expression data identifies gene signatures from sputum samples of asthmatic patients. - Shaoke Lou; Tianxiao Li; Daniel Spakowicz; Xiting Yan; Geoffrey Lowell Chupp; Mark Gerstein (BMC Bioinform., 2020)

Openness weighted association studies: leveraging personal genome information to prioritize non-coding variants. - Shuang Song 006; Nayang Shan; Geng Wang; Xiting Yan; Jun S. Liu; Lin Hou (Bioinform., 2021)

G2S3: A gene graph-based imputation method for single-cell RNA sequencing data. - Weimiao Wu; Yunqing Liu; Qile Dai; Xiting Yan; Zuoheng Wang (PLoS Comput. Biol., 2021)

A novel Bayesian framework for harmonizing information across tissues and studies to increase cell type deconvolution accuracy. - Wenxuan Deng; Bolun Li; Jiawei Wang; Wei Jiang 019; Xiting Yan; Ningshan Li; Milica Vukmirovic; Naftali Kaminski; Jing Wang 003; Hongyu Zhao 003 (Briefings Bioinform., 2023)

iDESC: identifying differential expression in single-cell RNA sequencing data with multiple subjects. - Yunqing Liu; Jiayi Zhao; Taylor Sterling Adams; Ningya Wang; Jonas Schupp; Weimiao Wu; John E. McDonough; Geoffrey Lowell Chupp; Naftali Kaminski; Zuoheng Wang; Xiting Yan (BMC Bioinform., 2023)

Correction: iDESC: identifying differential expression in single-cell RNA sequencing data with multiple subjects. - Yunqing Liu; Jiayi Zhao; Taylor Sterling Adams; Ningya Wang; Jonas Schupp; Weimiao Wu; John E. McDonough; Geoffrey Lowell Chupp; Naftali Kaminski; Zuoheng Wang; Xiting Yan (BMC Bioinform., 2023)

COOL: A Conjoint Perspective on Spatio-Temporal Graph Neural Network for Traffic Forecasting. - Wei Ju 001; Yusheng Zhao; Yifang Qin; Siyu Yi; Jingyang Yuan; Zhiping Xiao 001; Xiao Luo 001; Xiting Yan; Ming Zhang 004 (Inf. Fusion, 2024)

Predicting lung aging using scRNA-Seq data. - Qi Song; Alex Singh; John E. McDonough; Taylor Sterling Adams; Robin Vos; Ruben De Man; Greg Myers; Laurens J. Ceulemans; Bart M. Vanaudenaerde; Wim A. Wuyts; Xiting Yan; Jonas Schupp; et al. (PLoS Comput. Biol., 2024)

Identifying Cellular Niches in Spatial Transcriptomics: An Investigation into the Capabilities of Large Language Models. - Huanhuan Wei; Xiao Luo 001; Hongyi Yu; Jinping Liang; Luning Yang; Lixing Lin; Alexandra Popa; Xiting Yan (ACL (1), 2025)