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Showing 1–15 of 15 results
Advanced filters: Author: Alexey Gurevich Clear advanced filters

  • Current genome mining methods predict many putative non-ribosomal peptides (NRPs) from their corresponding biosynthetic gene clusters, but it remains unclear which of those exist in nature and how to identify their post-assembly modifications. Here, the authors develop NRPminer, a modification-tolerant tool for the discovery of NRPs from large genomic and mass spectrometry datasets, and use it to find 180 NRPs from different environments.

    • Bahar Behsaz
    • Edna Bode
    • Hosein Mohimani
    ResearchOpen Access
    Nature Communications
    Volume: 12, P: 1-17

  • Long-read metagenomics offers a valuable approach for profiling bacterial communities. This work presents a long-read assembler, metaFlye, that specifically addresses the challenges of assembling metagenomes.

    • Mikhail Kolmogorov
    • Derek M. Bickhart
    • Pavel A. Pevzner
    Research
    Nature Methods
    Volume: 17, P: 1103-1110

  • New natural products can be identified via mass spectrometry by excluding all known ones from the analysis, a process called dereplication. Here, the authors extend a previously published dereplication algorithm to different classes of secondary metabolites.

    • Hosein Mohimani
    • Alexey Gurevich
    • Pavel A. Pevzner
    ResearchOpen Access
    Nature Communications
    Volume: 9, P: 1-12

  • A gap exists between large-scale genome mining and mass spectral datasets for natural product discovery. Here the authors bridge the gap by developing HypoRiPPAtlas, an Atlas of hypothetical natural product structures, which is ready-to-use for in silico database search of tandem mass spectra.

    • Yi-Yuan Lee
    • Mustafa Guler
    • Hosein Mohimani
    ResearchOpen Access
    Nature Communications
    Volume: 14, P: 1-17

  • A large number of mass spectra from different samples have been collected, and to identify small molecules from these spectra, database searches are needed, which is challenging. Here, the authors report molDiscovery, a mass spectral database search method that uses an algorithm to generate mass spectrometry fragmentations and learns a probabilistic model to match small molecules with their mass spectra.

    • Liu Cao
    • Mustafa Guler
    • Hosein Mohimani
    ResearchOpen Access
    Nature Communications
    Volume: 12, P: 1-13

  • Aggregated mass spectral data by consortia such as the Global Natural Products Social (GNPS) molecular networking infrastructure enable natural product discovery. DEREPLICATOR, validated on peptidic natural products, is a computational tool to identify known metabolites in complex samples.

    • Hosein Mohimani
    • Alexey Gurevich
    • Pavel A Pevzner
    Research
    Nature Chemical Biology
    Volume: 13, P: 30-37

  • This study presents the results of the second round of the Critical Assessment of Metagenome Interpretation challenges (CAMI II), which is a community-driven effort for comprehensively benchmarking tools for metagenomics data analysis.

    • Fernando Meyer
    • Adrian Fritz
    • Alice Carolyn McHardy
    ResearchOpen Access
    Nature Methods
    Volume: 19, P: 429-440

  • Feature-based molecular networking allows the generation of molecular networks for mass spectrometry data that can recognize isomers, incorporate relative quantification and integrate ion mobility data.

    • Louis-Félix Nothias
    • Daniel Petras
    • Pieter C. Dorrestein
    Research
    Nature Methods
    Volume: 17, P: 905-908