#16 · Tools & infrastructure
Cell-, tissue- and spatially resolved omics atlases enable deconvolution, causal…
The dominant thread is packaging molecular context into queryable, harmonized resources. CellMethMarker curates 347,514 de novo and 2.2M literature-derived methylation markers for deconvolution; scMRdb pairs 5206 GWAS summary statistics with 585 sc-eQTL datasets for cell-type-resolved Mendelian randomization; XYcellAtlas spans 6764 samples across 18 cancers; mV2G integrates 24 evidence types across 50 tissues with a CRISPR-informed model. CNVSIM, DiseaseCIO and RNAactDrug 2.0 extend this to copy-number subtypes, intervention outcomes and drug sensitivity features. A related but distinct strand covers fusion and chimeric RNA: RIFTT reduces false positives by combining Arriba and FusionCatcher, and a 569,640-chimera atlas across 1019 cell lines links candidates to dependency. The novelty is mainly scale and interpretable access, not new assays.
Published papers
DiseaseCIO: a multi-omics atlas for characterizing clinical intervention outcomes across diverse diseases.
DiseaseCIO is a database integrating microbiome, transcriptome, and epigenome data with disease intervention outcomes across 94 disease states, with…
scMRdb: a comprehensive resource for cell-type-resolved Mendelian randomization of complex traits.
scMRdb is a web resource harmonizing 5206 GWAS summary statistics with 585 sc-eQTL datasets for cell-type-resolved Mendelian randomization, with Steiger and…
XYcellAtlas: a cell-type- and spatial-resolved pan-cancer atlas of sex-biased and Y chromosome loss-associated molecular signatures.
XYcellAtlas is a web database integrating single-cell, epigenomic and spatial transcriptomic data from 6764 samples across 18 cancers to catalog sex-biased and…
mV2G: a multiomic atlas for tissue-specific variant-to-gene prioritization.
mV2G is a searchable multiomic atlas integrating 24 functional genomic evidence types across 50 human tissues, with a CRISPR-informed model prioritizing…
RNAactDrug 2.0: an updated resource for systematically exploring molecular features associated with drug sensitivity across multi-omics datasets.
RNAactDrug 2.0 is an updated database and web resource linking RNA, CNV, mutation, methylation and enhancer features to drug sensitivity across…
Integrative discovery and functional dependency mapping uncover essential chimeric RNAs in the active transcriptome.
Integrative pipeline yields an atlas of 569,640 chimeric RNAs across 1019 cancer cell lines, with dependency screening linking candidates to cell fitness.
RIFTT: Robust Identification of Fusion genes in Tumor Transcriptomes.
RIFTT integrates Arriba and FusionCatcher with new scoring metrics to reduce fusion-gene false positives in tumor RNA-seq, benchmarked on TCGA-LAML, BeatAML,…
Preprints
CellMethMarker provides an integrated database of human cell- and tissue-type-specific DNA methylation markers
CellMethMarker is a curated database of 347,514 de novo and 2.2M literature-derived cell- and tissue-type DNA methylation markers, supporting deconvolution and…
CNVSIM: an interpretable copy-number reference atlas for cancer subtyping
CNVSIM builds an interpretable copy-number reference atlas of 112 CNV-defined cancer subtypes from Progenetix data, with calibrated projection and cell-line…
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