ArticleNature biotechnology2017
Discovering and linking public omics data sets using the Omics Discovery Index.
Abstract readLetter
In one paragraph
Article in Nature biotechnology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 117 papers, 2 of them syntheses that pooled it.
0numbers the graph read from it
0cells of the map it votes in
117citing papers in PubMed, 2 pooled it
–field-weighted citation impact
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
117 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Pooled it
- Systematic Review of Multi-Omics Approaches to Investigate Toxicological Effects in Macrophages.International journal of molecular sciences · 2020Pooled it
- AI-based multimodal integration of genomics and electronic health records.Nature reviews. Genetics · 2026Review
- Integrating multi-omics technologies to decipher microbiome functions.Nature communications · 2026Review
- VITAGRAPH: building a knowledge graph for biologically relevant learning tasks.Scientific data · 2026Article
- Review
- OrchidMD: An Integrated and User-Interactive Orchid Multi-Omics Database for Mining Genes and Biological Research.Plant biotechnology journal · 2026Article
- The ProteomeXchange consortium in 2026: making proteomics data FAIR.Nucleic acids research · 2026Article
- Leveraging artificial intelligence for efficient microbial production.Bioresource technology · 2026Review
- HIFU-Driven Targeted Pyroptosis Therapy in Basal-Like Breast Cancer.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Gut microbiota and tuberculosis.iMeta · 2025Review
- How to use learning curves to evaluate the sample size for malaria prediction models developed using machine learning algorithms.Malaria journal · 2025Article
- Omics Sciences in Regular Physical Activity.International journal of molecular sciences · 2025Review
- Improving plant breeding through AI-supported data integration.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2025Review
- Advancing Gut Microbiome Research: The Shift from Metagenomics to Multi-Omics and Future Perspectives.Journal of microbiology and biotechnology · 2025Review
- Datagraphy: toward a systematic approach to dataset discovery.GigaScience · 2025Article
- The PRIDE database at 20 years: 2025 update.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
- Drug Repurposing: Insights into Current Advances and Future Applications.Current medicinal chemistry · 2025Review
- FAIR Data Cube, a FAIR data infrastructure for integrated multi-omics data analysis.Journal of biomedical semantics · 2024Article
57 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
34 authors.
Yasset Perez-RiverolEuropean Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, United Kingdom.ORCID 0000-0001-6579-6941
Mingze BaiEuropean Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, United Kingdom.ORCID 0000-0002-9782-2056
Felipe da Veiga LeprevostDepartment of Pathology, University of Michigan, Ann Arbor, Michigan, USA.ORCID 0000-0002-8228-5374
Silvano SquizzatoEuropean Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, United Kingdom.ORCID 0000-0001-7433-0991
Young Mi ParkEuropean Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, United Kingdom.ORCID 0000-0001-6587-6562
Kenneth HaugEuropean Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, United Kingdom.ORCID 0000-0003-3168-4145
Adam J CarrollResearch School of Biology, Australian National University, Canberra, Australian Capital Territory, Australia.
Dylan SpaldingEuropean Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, United Kingdom.ORCID 0000-0002-4285-2493
Justin PaschallEuropean Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, United Kingdom.
Mingxun WangDepartment of Computer Science and Engineering, University of California, San Diego, La Jolla, California, USA.
Noemi Del-ToroEuropean Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, United Kingdom.
Tobias TernentEuropean Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, United Kingdom.
Peng ZhangDepartment of Pathology, University of Michigan, Ann Arbor, Michigan, USA.
Nicola BusoEuropean Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, United Kingdom.ORCID 0000-0002-0555-0226
Nuno BandeiraDepartment of Computer Science and Engineering, University of California, San Diego, La Jolla, California, USA.
Eric W DeutschInstitute for Systems Biology, Seattle, Washington, USA.
David S CampbellInstitute for Systems Biology, Seattle, Washington, USA.
Ronald C BeavisBiochemistry &Medical Genetics, University of Manitoba, Winnipeg, Manitoba, Canada.
Reza M SalekEuropean Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, United Kingdom.ORCID 0000-0001-8604-1732
Ugis SarkansEuropean Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, United Kingdom.ORCID 0000-0001-9227-8488
Robert PetryszakEuropean Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, United Kingdom.
Maria KeaysEuropean Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, United Kingdom.
Eoin FahyDepartment of Bioengineering, University of California, San Diego, La Jolla, California, USA.
Manish SudDepartment of Bioengineering, University of California, San Diego, La Jolla, California, USA.
Shankar SubramaniamDepartment of Bioengineering, University of California, San Diego, La Jolla, California, USA.
Ariana BarberaDepartment of Medicine, University of Cambridge, Cambridge, United Kingdom.
Rafael C JiménezELIXIR Hub, Wellcome Genome Campus, Hinxton, United Kingdom.
Alexey I NesvizhskiiDepartment of Pathology, University of Michigan, Ann Arbor, Michigan, USA.ORCID 0000-0002-2806-7819
Susanna-Assunta SansoneOxford e-Research Centre, University of Oxford, Oxford, United Kingdom.
Christoph SteinbeckEuropean Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, United Kingdom.ORCID 0000-0001-6966-0814
Rodrigo LopezEuropean Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, United Kingdom.ORCID 0000-0003-1256-7306
Juan A VizcaínoEuropean Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, United Kingdom.ORCID 0000-0002-3905-4335
Peipei PingDepartment of Physiology and Department of Medicine, Division of Cardiology, David Geffen School of Medicine at UCLA, University of California, Los Angeles, Los Angeles, California, USA.
Henning HermjakobEuropean Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, United Kingdom.ORCID 0000-0001-8479-0262
Funding
TRAININGU54GM114833 · NIGMS · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI LINDSEY, MERRY L., PING, PEIPEI · 2014 to 2017
$13.8MBioCADDIE: Biomedical and healthCAre Data Discovery and Indexing Engine centerU24AI117966 · NIAID · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI OHNO-MACHADO, LUCILA · 2014 to 2016
$10.9MTrainingP41GM103484 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI PEVZNER, PAVEL A · 2012 to 2018
$8.7MThe Metabolomics Data Center and Workbench (MDCW)U01DK097430 · NIDDK · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI SUBRAMANIAM, SHANKAR · 2012 to 2017
$7.4MCOMPUTATIONAL TOOLS FOR MASS SPECTROMETRY-BASED INTERACTOME DATAR01GM094231 · NIGMS · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI Alexey I Nesvizhskii · 2010 to 2026
$5.4MUniversity of Michigan Proteogenomics Data Analysis CenterU24CA210967 · NCI · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI CHINNAIYAN, ARUL M, DHANASEKARAN, SARAVANA M · 2016 to 2020
$4.1MTheoretical Foundations and Software Infrastructure for Biological Network DatabasesU01CA198941 · NCI · CASE WESTERN RESERVE UNIVERSITY · PI KOYUTURK, MEHMET · 2015 to 2017
$1.4MBiotechnology and Biological Sciences Research Council BB/E025080/1Biotechnology and Biological Sciences Research Council BB/I000771/1Biotechnology and Biological Sciences Research Council BB/K01997X/1Biotechnology and Biological Sciences Research Council BB/L024225/1NCI NIH HHS U01 CA198941NCI NIH HHS U24 CA210967NIAID NIH HHS U24 AI117966NIDDK NIH HHS U01 DK097430NIGMS NIH HHS P41 GM103484NIGMS NIH HHS R01 GM094231NIGMS NIH HHS U54 GM114833Wellcome TrustWellcome Trust WT101477MA
Abstract
PubMed holds no abstract for this paper.
Indexed as
GenomicsProteomicsComputational BiologyData MiningHumansInformation Storage and Retrieval
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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.