ArticleCell systems2019
MetaMiner: A Scalable Peptidogenomics Approach for Discovery of Ribosomal Peptide Natural Products with Blind Modifications from Microbial Communities.
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Article in Cell systems, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 42 papers.
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42citing papers in PubMed
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Who cites it
42 citing papers in PubMed.
- Large-scale discovery platform enables identification of peptides targeting drug-resistant candidiasis.Cell reports methods · 2026Article
- Resilience of recombinant antibiotic resistance gene-containing plasmids against common cell culture disposal methods.Cell reports methods · 2026Article
- Advances in natural product discovery: strategies, technologies, and insights.Natural products and bioprospecting · 2026Review
- Mangrove cyanobacterial diversity as a source of bioactive natural products.Current research in microbial sciences · 2026Article
- Seq2Saccharide: Discovering Oligosaccharides and Aminoglycosides Natural Products by Integrating Computational Mass Spectrometry and Genome Mining.Journal of the American Chemical Society · 2025Article
- Sequence modeling tools to decode the biosynthetic diversity of the human microbiome.mSystems · 2025Review
- Last Decade Insights in Exploiting Marine Microorganisms as Sources of New Bioactive Natural Products.Marine drugs · 2025Review
- Advances in lasso peptide discovery, biosynthesis, and function.Trends in genetics : TIG · 2024Review
- A Chronicle Review ofIndian journal of microbiology · 2024Review
- Bacteriocin diversity, function, discovery and application as antimicrobials.Nature reviews. Microbiology · 2024Review
- Discovering type I cis-AT polyketides through computational mass spectrometry and genome mining with Seq2PKS.Nature communications · 2024Article
- Learning sequence, structure, and function representations of proteins with language models.bioRxiv : the preprint server for biology · 2023Article
- Identification of peptides from honeybee gut symbionts as potential antimicrobial agents against Melissococcus plutonius.Nature communications · 2023Article
- HypoRiPPAtlas as an Atlas of hypothetical natural products for mass spectrometry database search.Nature communications · 2023Article
- Correlative metabologenomics of 110 fungi reveals metabolite-gene cluster pairs.Nature chemical biology · 2023Article
- Review
- Microbial Metabolites Annotation by Mass Spectrometry-Based Metabolomics.Advances in experimental medicine and biology · 2023Article
- NPOmix: A machine learning classifier to connect mass spectrometry fragmentation data to biosynthetic gene clusters.PNAS nexus · 2022Article
- Integrated Metabolomic-Genomic Workflows Accelerate Microbial Natural Product Discovery.Analytical chemistry · 2022Review
- Review
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Authors and funding
28 authors.
Liu CaoComputational Biology Department, Carnegie Mellon University, Pittsburgh, PA, USA.
Alexey GurevichCenter for Algorithmic Biotechnology, Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia.
Kelsey L AlexanderCenter for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, San Diego, CA, USA; Department of Chemistry and Biochemistry, University of California, San Diego, San Diego, CA, USA.
C Benjamin NamanCenter for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, San Diego, CA, USA; Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, Department of Marine Pharmacy, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, Zhejiang, China.
Tiago LeãoCenter for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, San Diego, CA, USA.
Evgenia GlukhovCenter for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, San Diego, CA, USA.
Tal Luzzatto-KnaanCollaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, San Diego, CA, USA.
Fernando VargasCollaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, San Diego, CA, USA.
Robby QuinnCollaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, San Diego, CA, USA.
Amina BouslimaniCollaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, San Diego, CA, USA.
Louis Felix NothiasCollaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, San Diego, CA, USA.
Nitin K SinghJet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, USA.
Jon G SandersDepartment of Pediatrics, University of California, San Diego School of Medicine, San Diego, CA, USA.
Rodolfo A S BenitezDepartment of Pediatrics, University of California, San Diego School of Medicine, San Diego, CA, USA.
Luke R ThompsonDepartment of Biological Sciences and Northern Gulf Institute, University of Southern Mississippi, Hattiesburg, MS, USA; Ocean Chemistry and Ecosystems Division, Atlantic Oceanographic and Meteorological Laboratory, National Oceanic and Atmospheric Administration, stationed at Southwest Fisheries Science Center, La Jolla, CA, USA.
Md-Nafiz HamidDepartment of Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames, IA, USA; Interdepartmental program in Bioinformatics and Computational Biology, Iowa State University, Ames, IA, USA.
James T MortonDepartment of Pediatrics, University of California, San Diego School of Medicine, San Diego, CA, USA; Department of Computer Science and Engineering, University of California, San Diego, San Diego, CA, USA.
Alla MikheenkoCenter for Algorithmic Biotechnology, Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia.
Alexander ShlemovCenter for Algorithmic Biotechnology, Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia.
Anton KorobeynikovCenter for Algorithmic Biotechnology, Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia; Department of Mathematics and Mechanics, St. Petersburg State University, St. Petersburg, Russia.
Iddo FriedbergDepartment of Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames, IA, USA; Interdepartmental program in Bioinformatics and Computational Biology, Iowa State University, Ames, IA, USA.
Rob KnightDepartment of Pediatrics, University of California, San Diego School of Medicine, San Diego, CA, USA; Department of Computer Science and Engineering, University of California, San Diego, San Diego, CA, USA; Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, San Diego, CA, USA; Department of Bioengineering, University of California, San Diego, San Diego, CA, USA.
Kasthuri VenkateswaranJet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, USA.
William H GerwickCenter for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, San Diego, CA, USA.
Lena GerwickCenter for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, San Diego, CA, USA.
Pieter C DorresteinCollaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, San Diego, CA, USA; Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, San Diego, CA, USA.
Pavel A PevznerDepartment of Computer Science and Engineering, University of California, San Diego, San Diego, CA, USA; Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, San Diego, CA, USA.
Hosein MohimaniComputational Biology Department, Carnegie Mellon University, Pittsburgh, PA, USA; Department of Computer Science and Engineering, University of California, San Diego, San Diego, CA, USA. Electronic address: hoseinm@andrew.cmu.edu.
Funding
Contemporary Approaches to Cancer Cell Signaling and CommunicationT32CA009523 · NCI · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI DONOGHUE, DANIEL J, YANG, JING · 1985 to 2025
$12.1MTrainingP41GM103484 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI PEVZNER, PAVEL A · 2012 to 2018
$8.7MUnified Computation Tools for Natural Products ResearchR01GM107550 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI COTTRELL, GARRISON W, GERWICK, WILLIAM HENRY · 2013 to 2025
$8.2MDiscovering novel small molecule antibiotics from complex microbial communities by integrating computational mass spectrometry and metagenome miningDP2GM137413 · NIGMS · CARNEGIE-MELLON UNIVERSITY · PI MOHIMANI, HOSEIN · 2019 to 2019
$2.2MExperiment based genome mining of ribosomal natural productsR01GM097509 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI DORRESTEIN, PIETER C, MOORE, BRADLEY S · 2012 to 2015
$1.9MDevelopment of an efficient cyanobacterial platform for heterologous expression and biosynthetic interrogations of natural products.R01GM118815 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI GERWICK, LENA, GERWICK, WILLIAM HENRY · 2017 to 2020
$1.2MRegulation of Receptor Tyrosine KinasesR01GM065490 · NIGMS · UNIVERSITY OF CALIFORNIA SAN DIEGO · PI DONOGHUE, DANIEL J · 2002 to 2005
$1.0MNCI NIH HHS T32 CA009523NIGMS NIH HHS DP2 GM137413NIGMS NIH HHS P41 GM103484NIGMS NIH HHS R01 GM065490NIGMS NIH HHS R01 GM097509NIGMS NIH HHS R01 GM107550NIGMS NIH HHS R01 GM118815
Abstract
Ribosomally synthesized and post-translationally modified peptides (RiPPs) are an important class of natural products that contain antibiotics and a variety of other bioactive compounds. The existing methods for discovery of RiPPs by combining genome mining and computational mass spectrometry are limited to discovering specific classes of RiPPs from small datasets, and these methods fail to handle unknown post-translational modifications. Here, we present MetaMiner, a software tool for addressing these challenges that is compatible with large-scale screening platforms for natural product discovery. After searching millions of spectra in the Global Natural Products Social (GNPS) molecular networking infrastructure against just eight genomic and metagenomic datasets, MetaMiner discovered 31 known and seven unknown RiPPs from diverse microbial communities, including human microbiome and lichen microbiome, and microorganisms isolated from the International Space Station.
Indexed as
Computational BiologyGenomicsHumansMicrobiotaPeptidesProtein Processing, Post-TranslationalRibosomesSoftwarePeptidescomputational mass spectrometrymetagenomicsmicrobial metabolitesnatural products discoveryribosomally synthesized and post-translationally modified peptides
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