ArticleNature2023
Unraveling the functional dark matter through global metagenomics.
Open access · hybridAbstract read
In one paragraph
Article in Nature, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 126 papers.
0numbers the graph read from it
0cells of the map it votes in
126citing papers in PubMed
48.4field-weighted citation impact, top 1% of its field
What it found
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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.
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Who cites it
126 citing papers in PubMed, 179 citations in OpenAlex.
- Resistant starch types 2 and 4 induce distinct and reversible changes in the human gut microbiome.Microbiology spectrum · 2026Trial
- UniProt data pruning and the growing invisibility of the dark proteome.NAR genomics and bioinformatics · 2026Article
- The protein-water H-bond network for bacterial response regulator REC domain activation.Journal of structural biology: X · 2026Article
- In silico structural and functional characterisation of two hypothetical proteins from the plant‑associated bacterium Kosakonia cowanii F52.Genomics & informatics · 2026Article
- "Quadrupling" the protein family space with global metagenomics.Nucleic acids research · 2026Article
- Resilience of blue carbon microbiomes in response to ecological and anthropogenic filtering.Nature communications · 2026Article
- Methods for the establishment of enzymatic mechanisms - from QM to ML.Chemical science · 2026Review
- Identifying fundamental gaps in functional metagenomics: a step towards unlocking microbiome research potential.NAR genomics and bioinformatics · 2026Article
- Obligate cross-feeding of metabolites is common in soil microbial communities.Nature microbiology · 2026Article
- Comparative metagenomic assessment of Illumina-compatible library preparation methods, short-read lengths, and PacBio HiFi sequencing reveals differences in microbial and functional diversity recovery from a complex environmental sample.Microbiology spectrum · 2026Article
- A genomic catalog of Earth's bacterial and archaeal symbionts.Nature biotechnology · 2026Article
- Large language models enhance annotation of enzymes in metagenomes.Science advances · 2026Article
- Siwa spring microbiomes as reservoirs of biosynthetic gene clusters: Unlocking natural product potential.World journal of microbiology & biotechnology · 2026Article
- Characterization of microbial dark matter at scale with MetaSBT and taxonomy-aware Sequence Bloom Trees.Nature biotechnology · 2026Article
- HaloTag-Based FACS-Compatible Assay for Intracellular Haloalkane Detection with a Potential Application to Halogenase Screening.Analytical chemistry · 2026Article
- The microbial unknome, a repertoire for microbial chatting?Heredity · 2026Review
- Predicting functions of uncharacterized gene products from microbial communities.Nature biotechnology · 2026Article
- Integrating host-microbiome multi-omics with machine learning: methods, benchmarks, and translational applications.Science China. Life sciences · 2026Review
- Linear-time prediction of proteome-scale microbial protein interactions.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- AI-empowered human microbiome research.Gut · 2026Review
66 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
24 authors at 20 institutions in 13 countries.
Georgios A PavlopoulosInstitute for Fundamental Biomedical Research, Biomedical Science Research Center Alexander Fleming, Vari, Greece. pavlopoulos@fleming.gr.
Fotis A BaltoumasInstitute for Fundamental Biomedical Research, Biomedical Science Research Center Alexander Fleming, Vari, Greece.ORCID 0000-0002-2870-2931
Sirui LiuJohn Harvard Distinguished Science Fellowship Program, Harvard University, Cambridge, MA, USA.
Oguz SelvitopiComputational Research Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
Antonio Pedro CamargoDOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.ORCID 0000-0003-3913-2484
Stephen NayfachDOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.ORCID 0000-0003-4625-4164
Ariful AzadLuddy School of Informatics, Computing and Engineering, Indiana University Bloomington, Bloomington, IN, USA.
Simon RouxDOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
Lee CallDOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
Natalia N IvanovaDOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.ORCID 0000-0002-5802-9485
I Min ChenDOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
David Paez-EspinoDOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.ORCID 0000-0002-2939-5398
Evangelos KaratzasInstitute for Fundamental Biomedical Research, Biomedical Science Research Center Alexander Fleming, Vari, Greece.
Novel Metagenome Protein Families Consortium
Ioannis IliopoulosDepartment of Basic Sciences, School of Medicine, University of Crete, Heraklion, Greece.
Konstantinos KonstantinidisSchool of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, USA.ORCID 0000-0002-0954-4755
James M TiedjeCenter for Microbial Ecology, Michigan State University, East Lansing, MI, USA.ORCID 0000-0002-8992-6218
Jennifer Pett-RidgePhysical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA.ORCID 0000-0002-4439-2398
David BakerDepartment of Biochemistry, University of Washington, Seattle, WA, USA.ORCID 0000-0001-7896-6217
Axel ViselDOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.ORCID 0000-0002-4130-7784
Christos A OuzounisDOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.ORCID 0000-0002-0086-8657
Sergey OvchinnikovJohn Harvard Distinguished Science Fellowship Program, Harvard University, Cambridge, MA, USA.ORCID 0000-0003-2774-2744
Aydin BuluçComputational Research Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.ORCID 0000-0001-7253-9038
Nikos C KyrpidesDOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA. nckyrpides@lbl.gov.ORCID 0000-0002-6131-0462
Lawrence Berkeley National Laboratory · USMontana State University · USMichigan State University · USUniversity of British Columbia · CAUniversity of Wisconsin–Madison · USUniversity of California, Davis · USUniversity of Michigan · USAlexander Fleming Biomedical Sciences Research Center · GRColorado State University · USGeorgia Institute of Technology · USHarvard University Press · USNortheastern University · USNorthern Arizona University · USOak Ridge National Laboratory · USPacific Northwest National Laboratory · USPennsylvania State University · USRutgers, The State University of New Jersey · USSan Diego State University · USScripps Institution of Oceanography · USUniversity of Georgia · US
Funding
SCIENCE AND TECHNOLOGY COMPETENCY & EDUCATION CORE (STCE)P20GM103475 · NIGMS · UNIVERSITY OF PUERTO RICO MED SCIENCES · PI SURANGANIE DHARMAWARDHANE · 2012 to 2026
$52.9MExploring the unknown protein universe using evolutionary informationDP5OD026389 · OD · HARVARD UNIVERSITY · PI OVCHINNIKOV, SERGEY L. · 2018 to 2022
$2.0MNIGMS NIH HHS P20 GM103475NIH HHS DP5 OD026389
Abstract
Metagenomes encode an enormous diversity of proteins, reflecting a multiplicity of functions and activities
Indexed as
MetagenomeMetagenomicsMicrobiologyProteinsCluster AnalysisDatabases, ProteinProtein ConformationProteins
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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.