ArticleMolecular bioSystems2015
Compound signature detection on LINCS L1000 big data.
Article in Molecular bioSystems, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers.
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Who cites it
40 citing papers in PubMed.
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- Recent Advances and Emerging Directions in Machine Learning-Based Breast Cancer Drug Discovery: A Comprehensive Review.Breast cancer (Dove Medical Press) · 2026Review
- CDCM: a correlation-dependent connectivity map approach to rapidly screen drugs during outbreaks of infectious diseases.Briefings in bioinformatics · 2024Article
- Combination of antidepressants and antipsychotics as a novel treatment option for psychosis in Alzheimer's disease.CPT: pharmacometrics & systems pharmacology · 2023Article
- Multivariate genome-wide association meta-analysis of over 1 million subjects identifies loci underlying multiple substance use disorders.Nature. Mental health · 2023Article
- Chemical-induced gene expression ranking and its application to pancreatic cancer drug repurposing.Patterns (New York, N.Y.) · 2022Article
- Oklahoma Nathan Shock Aging Center - assessing the basic biology of aging from genetics to protein and function.GeroScience · 2021Article
- Precision omics data integration and analysis with interoperable ontologies and their application for COVID-19 research.Briefings in functional genomics · 2021Article
- A deep learning framework for high-throughput mechanism-driven phenotype compound screening and its application to COVID-19 drug repurposing.Nature machine intelligence · 2021Article
- Drug-induced cell viability prediction from LINCS-L1000 through WRFEN-XGBoost algorithm.BMC bioinformatics · 2021Article
- Crinet: A computational tool to infer genome-wide competing endogenous RNA (ceRNA) interactions.PloS one · 2021Article
- Applications of Genome-Wide Screening and Systems Biology Approaches in Drug Repositioning.Cancers · 2020Review
- A deep learning framework for high-throughput mechanism-driven phenotype compound screening.bioRxiv : the preprint server for biology · 2020Article
- Prognostic Molecular Classification of Appendiceal Mucinous Neoplasms Treated with Cytoreductive Surgery and Hyperthermic Intraperitoneal Chemotherapy.Annals of surgical oncology · 2020Article
- A Bayesian approach to accurate and robust signature detection on LINCS L1000 data.Bioinformatics (Oxford, England) · 2020Article
- Multi-Omics Analysis of Brain Metastasis Outcomes Following Craniotomy.Frontiers in oncology · 2020Article
- Predicting drug-induced transcriptome responses of a wide range of human cell lines by a novel tensor-train decomposition algorithm.Bioinformatics (Oxford, England) · 2019Article
- Article
- Drug candidate identification based on gene expression of treated cells using tensor decomposition-based unsupervised feature extraction for large-scale data.BMC bioinformatics · 2019Article
- Article
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
The Library of Integrated Network-based Cellular Signatures (LINCS) L1000 big data provide gene expression profiles induced by over 10 000 compounds, shRNAs, and kinase inhibitors using the L1000 platform. We developed csNMF, a systematic compound signature discovery pipeline covering from raw L1000 data processing to drug screening and mechanism generation. The csNMF pipeline demonstrated better performance than the original L1000 pipeline. The discovered compound signatures of breast cancer were consistent with the LINCS KINOMEscan data and were clinically relevant. The csNMF pipeline provided a novel and complete tool to expedite signature-based drug discovery leveraging the LINCS L1000 resources.
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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.