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Briefings in Bioinformatics|December 10, 2025
STIFT: spatiotemporal transcriptomics integration through spatially informed multi-timepoint bridgingJi Qi, Muyang Ge, Jishuai Miao, et al.Nature Communications|July 7, 2025
TIVelo: RNA velocity estimation leveraging cluster-level trajectory inferenceMuyang Ge, Jishuai Miao, Ji Qi, et al.NAR Genomics and Bioinformatics|February 12, 2021
Dimensionality reduction for single cell RNA sequencing data using constrained robust non-negative matrix factorizationShuqin Zhang, Liu Yang, Jinwen Yang, et al.Nucleic Acids Research|May 5, 2017
Predicting transcription factor binding motifs from DNA-binding domains, chromatin accessibility and gene expression dataMahdi Zamanighomi, Zhixiang Lin, Yong Wang, et al.Plos One|November 29, 2017
Semi-automatic tracking, smoothing and segmentation of hyoid bone motion from videofluoroscopic swallowing studyWon-Seok Kim, Pengcheng Zeng, Jian Qing Shi, et al.Computer Methods and Programs in Biomedicine|June 16, 2018
Improved lung nodule diagnosis accuracy using lung CT images with uncertain classZhiqiong Wang, Junchang Xin, Peishun Sun, et al.Nature Communications|April 13, 2021
RA3 is a reference-guided approach for epigenetic characterization of single cellsShengquan Chen, Guanao Yan, Wenyu Zhang, et al.Genome Biology|July 27, 2026
Comprehensive benchmarking of RNA velocity methods across single-cell datasetsYida Wu, Chuihan Kong, Xu Liao, et al.Journal of Molecular Cell Biology|January 5, 2018
Simultaneous inference of phenotype-associated genes and relevant tissues from GWAS data via Bayesian integration of multiple tissue-specific gene networksMengmeng Wu, Zhixiang Lin, Shining Ma, et al.Briefings in Bioinformatics|May 13, 2022
FIRM: Flexible integration of single-cell RNA-sequencing data for large-scale multi-tissue cell atlas datasetsJingsi Ming, Zhixiang Lin, Jia Zhao, et al.Pageof 6