ArticleNucleic acids research2020
LINCS Data Portal 2.0: next generation access point for perturbation-response signatures.
Article in Nucleic acids research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 108 papers.
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Who cites it
108 citing papers in PubMed.
- VCCV: conservative transcriptomic corroboration for measurement prioritization of computational drug-target hypotheses.Bioinformatics (Oxford, England) · 2026Article
- GeneInsight: Condensing gene set knowledge via language models.PLoS computational biology · 2026Article
- ExPO: an exposure-conditioned neural operator for L1000 signature prediction.Journal of cheminformatics · 2026Article
- xNNPCD identifies regulators of programmed cell death by integrating perturbation transcriptomes with cancer dependency profiles.bioRxiv : the preprint server for biology · 2026Article
- DrugPlayGround: Benchmarking Large Language Models and Embeddings for Drug Discovery.bioRxiv : the preprint server for biology · 2026Article
- Molecular Design with Artificial Intelligence: Progress and Perspectives for Small Molecules.Chemical reviews · 2026Review
- Cellular Context Influences Kinase Inhibitor Selectivity.Journal of medicinal chemistry · 2026Article
- Integrating artificial intelligence and manual curation to enhance bioassay annotations in ChEMBL.Journal of cheminformatics · 2026Article
- From Regeneration Failure to Functional Restoration: Unlocking the Neuronal-Intrinsic Regenerative Capacity as a Therapeutic Frontier for Optic Neuropathy and Glaucoma.CNS neuroscience & therapeutics · 2026Review
- NCES: A Cell-Specific Network-Augmented Essentiality Framework for Cancer Therapeutic Target Discovery.Computational and structural biotechnology journal · 2026Article
- Cellular Selectivity Analyses Reveal Distinguishing Profiles for Type II Kinase Inhibitors.bioRxiv : the preprint server for biology · 2025Article
- L2S2: chemical perturbation and CRISPR KO LINCS L1000 signature search engine.Nucleic acids research · 2025Article
- The Role of ETS2 in Macrophage Inflammation.DNA and cell biology · 2025Review
- Comprehensive Proteomics Metadata and Integrative Web Portals Facilitate Sharing and Integration of LINCS Multiomics Data.Molecular & cellular proteomics : MCP · 2025Article
- Transcriptome Complexity Disentangled: A Regulatory Molecules Approach.International journal of molecular sciences · 2025Article
- A multiplex single-cell RNA-Seq pharmacotranscriptomics pipeline for drug discovery.Nature chemical biology · 2025Article
- Progress in toxicogenomics to protect human health.Nature reviews. Genetics · 2025Review
- Reversal gene expression assessment for drug repurposing, a case study of glioblastoma.Journal of translational medicine · 2025Article
- PerturBase: a comprehensive database for single-cell perturbation data analysis and visualization.Nucleic acids research · 2025Article
- Public Omics Explorer (POE): Enabling integrative semantic search across GEO omics datasets based on PubMed publications.Computational and structural biotechnology journal · 2025Article
48 more citing papers are in PubMed but not listed here.
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Authors and funding
16 authors.
Funding
Abstract
The Library of Integrated Network-Based Cellular Signatures (LINCS) is an NIH Common Fund program with the goal of generating a large-scale and comprehensive catalogue of perturbation-response signatures by utilizing a diverse collection of perturbations across many model systems and assay types. The LINCS Data Portal (LDP) has been the primary access point for the compendium of LINCS data and has been widely utilized. Here, we report the first major update of LDP (http://lincsportal.ccs.miami.edu/signatures) with substantial changes in the data architecture and APIs, a completely redesigned user interface, and enhanced curated metadata annotations to support more advanced, intuitive and deeper querying, exploration and analysis capabilities. The cornerstone of this update has been the decision to reprocess all high-level LINCS datasets and make them accessible at the data point level enabling users to directly access and download any subset of signatures across the entire library independent from the originating source, project or assay. Access to the individual signatures also enables the newly implemented signature search functionality, which utilizes the iLINCS platform to identify conditions that mimic or reverse gene set queries. A newly designed query interface enables global metadata search with autosuggest across all annotations associated with perturbations, model systems, and signatures.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.