Journal Date Title Code Data Citation BioAge Nature Medicine 2023 BioAge: predicting human chronological age from multi-organ transcriptomes Nature Neuroscience 2019 Common brain disorders are associated with heritable patterns of apparent aging of the brain Boolean network Bioinformatics 2010 BoolNet—an R package for generation, reconstruction and analysis of Boolean networks Cell-cell communication Nature Communications 2022 Knowledge-graph-based cell-cell communication inference for spatially resolved transcriptomic data with SpaTalk Celltype Enrichment Frontiers in Neuroscience 2016 Identification of Vulnerable Cell Types in Major Brain Disorders Using Single Cell Transcriptomes and Expression Weighted Cell Type Enrichment Data integration Nature Communications 2022 Elucidating tumor heterogeneity from spatially resolved transcriptomics data by multi-view graph collaborative learning Genome Biology 2022 Evaluation of cell-cell interaction methods by integrating single-cell RNA sequencing data with spatial information Differential expression Genome Biology 2024 Powerful and accurate detection of temporal gene expression patterns from multi-sample multi-stage single-cell transcriptomics data with TDEseq Enrichment analysis Nature Communications 2015 Biological interpretation of genome-wide association studies using predicted gene functions Nature Communications 2022 Multi-modal quantification of pathway activity with MAYA Computational and Structural Biotechnology Journal 2021 UCell: Robust and scalable single-cell gene signature scoring Feature selection BMC Biology 2024 COMSE: analysis of single-cell RNA-seq data using community detection-based feature selection Gene regulatory network Bioinformatics 2023 STGRNS: an interpretable transformer-based method for inferring gene regulatory networks from single-cell transcriptomic data Medicine Genome Research 2024 Diffusion-based generation of gene regulatory networks from scRNA-seq data with DigNet
