Shenzhen Bay Laboratory
MAAS (Genome Medicine, 2025): Multimodal-based analysis of single-cell ATAC-seq data enables highly accurate delineation of clinically relevant tumor cell subpopulations.
SCALPEL (Nature Communications, 2025): Quantification of transcript isoforms at the single-cell level using SCALPEL.
rareAPA (Nature Communications, 2025): Impact of Rare Non-coding Variants on Human Diseases through Alternative Polyadenylation Outliers.
DATTSS (Science Advances, 2024): Dynamic analyses of Alternative Tandem TSS events from standard RNA-seq data.
CancerAPA (Nature Communications, 2024): A distinct class of pan-cancer susceptibility genes revealed by alternative polyadenylation transcriptome-wide association study.
xQTLbiolinks (Briefings in Bioinformatics, 2023): A user-friendly R package, as the first end-to-end bioinformatics tool for efficient mining and analyzing public and user-customized xQTLs data for the discovery of disease susceptibility genes.
DaPars2 (Nature Genetics, 2021): A tool that directly infers the dynamic alternative polyadenylation (APA) usage by comparing standard RNA-seq from multiple samples.
scDaPars (Genome Research, 2021): A bioinformatics algorithm to accurately quantify Alternative Polyadenylation (APA) events at both single-cell and single-gene resolution using standard scRNA-seq data.
MAT3UTR (Nature Genetics, 2018): A mathematical model to quantify the trans effect of 3ʹ-UTR shortening to their affected ceRNA partner.
eRNA-QTL-atlas (Advanced Science, 2025): The eRNA-QTL atlas is a better indicator of enhancer activity termed enhancer RNAs (eRNAs), broadly transcribed bidirectional or unidirectional non-coding RNAs (ncRNAs) across numerous cell types and tissues.
rareAPA (Nature Communications, 2025): The rareAPA is a comprehensive database exploring rare APA events (APA outliers/ aOutliers) and the functional rare variants (RVs) leading to aOutliers.
eRNA_IDO (Genomics, Proteomics & Bioinformatics, 2024): eRNA-IDO is an integrative platform for identification, interactome discovery, and functional annotation of enhancer RNAs (eRNAs).which comprises two modules: eRNA-ID and eRNA-Anno.
TCGD (Nature Communications, 2024): TCGD is a database of publicly available Cancer GWAS summary statistics. Each GWAS can be browsed with the manhattan plot, risk loci, SNP heritability and genetic correlations with other GWAS in the database.
immune-3′aQTL (Nature Communications, 2023): This immune-3′aQTL a database provides 3' untranslated region (3'UTR) alternative polyadenylation (APA) quantitative trait loci (3'aQTLs) across in 18 human immune baseline cell types and 8 stimulation conditions.
scQTLbase (Nucleic Acids Research, 2023): The scQTLbase is an integrated human single-cell eQTL portal, which features 304 datasets across 57 cell types and 95 cell states and contains ~16 million SNPs significantly associated with gene expression in a certain cell type or status
ipaQTL-atlas (Nucleic Acids Research, 2022): The ipaQTL-atlas is a database for intronic polyadenylation based on 15,170 RNA-seq samples across 49 human Genotype-Tissue Expression (GTEx) project (version 8) tissues from 838 individuals.
3′aQTL-atlas (Nature Genetics, 2021): The 3′aQTL-atlas is a comprehensive list of 3′aQTLs, containing approximately 1.49 million SNPs associated with the APA of target genes, based on 15,201 RNA-seq samples across 49 human normal tissues isolated from 838 individuals
TC3A (Nucleic Acids Research, 2018): The Cancer 3′UTR Atlas (TC3A) is a repository to host a comprehensive compilation of APA events for more than ∼10,537 tumors across 32 cancer types (Note: The data can be accessed using doi:0.7303/syn24982198 or directly access synapse)