#13 · Tools & infrastructure
Curated databases catalog cell markers, enhancers, tRNA modifications and lncRNAs across…
The dominant thread is curated, evidence-linked reference resources that organize experimentally supported or literature-derived biological elements for expert query. ENdb 2.0 adds 4831 evidence records and TF-target links across five species, while tModBase v2.0 expands to 528 datasets across 23 species with an AI-powered assistant. EVLncRNAs 4.0 pairs curated functional lncRNAs with RAG-based search and PMID-linked citations. CellMarker 3.0 and CellMethMarker supply cell- and tissue-type markers for single-cell and deconvolution workflows, the latter comprising 347,514 de novo and 2.2M literature-derived methylation markers. RED 2.0 rebases rice expression onto the T2T Nipponbare reference. What is new is explicit treatment of gene redundancy: LoGIC catalogs local gene clusters whose homologs may compensate, and tWhEEL infers redundancy from transcripts to score CRISPR knockout feasibility.
Published papers
LoGIC: a cross-species local gene-cluster integrative catalog.
Homologous genes, especially those sharing close genomic locations and forming gene clusters, often have compensatory roles, therefore pose remarkable challenge
ENdb 2.0: an updated database of experimentally supported enhancers.
ENdb 2.0 is an updated, manually curated database of experimentally supported enhancers across five species, adding 4831 evidence records, TF-target links, and…
EVLncRNAs 4.0: an updated database of experimentally validated functional long non-coding RNAs with evidence-grounded AI access.
EVLncRNAs 4.0 updates a curated database of experimentally validated functional lncRNAs, adding RAG-based AI search with PMID-linked citations across 199…
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