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List of works by Alexey A. Gurevich

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SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing

scientific article
QUAST: quality assessment tool for genome assemblies

scientific article
Assembling single-cell genomes and mini-metagenomes from chimeric MDA products

scientific article
Feature-based molecular networking in the GNPS analysis environment

scientific article published on 24 August 2020
Critical Assessment of Metagenome Interpretation-a benchmark of metagenomics software.

scientific article published on 2 October 2017
MetaQUAST: evaluation of metagenome assemblies

scientific article published on 26 November 2015
Dereplication of microbial metabolites through database search of mass spectra

scientific article published in Nature Communications
Assembling Genomes and Mini-metagenomes from Highly Chimeric Reads

Dereplication of peptidic natural products through database search of mass spectra

scientific article
Versatile genome assembly evaluation with QUAST-LG.

scientific article published in July 2018
ExSPAnder: a universal repeat resolver for DNA fragment assembly

scientific article
Increased diversity of peptidic natural products revealed by modification-tolerant database search of mass spectra.

scientific article published on 22 January 2018
Assembling short reads from jumping libraries with large insert sizes

scientific article published on 3 June 2015
Icarus: visualizer for de novo assembly evaluation

scientific article published on 4 July 2016
Metabolic Fingerprints from the Human Oral Microbiome Reveal a Vast Knowledge Gap of Secreted Small Peptidic Molecules

scientific article
MetaMiner: A Scalable Peptidogenomics Approach for Discovery of Ribosomal Peptide Natural Products with Blind Modifications from Microbial Communities

scientific article published on 16 October 2019
Critical Assessment of Metagenome Interpretation − a benchmark of computational metagenomics software

article
Spatial Molecular Architecture of the Microbial Community of a Peltigera Lichen

scientific article (publication date: 20 December 2016)
De Novo Peptide Sequencing Reveals Many Cyclopeptides in the Human Gut and Other Environments

scientific article published on 18 December 2019
TandemTools: mapping long reads and assessing/improving assembly quality in extra-long tandem repeats

scientific article published on 01 July 2020
MolDiscovery: learning mass spectrometry fragmentation of small molecules

scientific article published on 17 June 2021
A Multi-Omics Characterization of the Natural Product Potential of Tropical Filamentous Marine Cyanobacteria

scientific article published on 06 January 2021
Integrating genomics and metabolomics for scalable non-ribosomal peptide discovery

scientific article published on 28 May 2021
metaFlye: scalable long-read metagenome assembly using repeat graphs

scientific article published on 05 October 2020
NPS: scoring and evaluating the statistical significance of peptidic natural product-spectrum matches

scientific article published on 01 July 2019
Nerpa: A Tool for Discovering Biosynthetic Gene Clusters of Bacterial Nonribosomal Peptides

scientific article published on 11 October 2021
MIBiG 4.0: advancing biosynthetic gene cluster curation through global collaboration

scientific article published on 9 December 2024
HypoRiPPAtlas as an Atlas of hypothetical natural products for mass spectrometry database search

scientific article published in 2023
MetaRiPPquest: A Peptidogenomics Approach for the Discovery of Ribosomally Synthesized and Post-translationally Modified Peptides

scientific article published on 3 December 2017
NPOmix: A machine learning classifier to connect mass spectrometry fragmentation data to biosynthetic gene clusters

Critical Assessment of Metagenome Interpretation: the second round of challenges

scientific article published in April 2022
CAMI Benchmarking Portal: online evaluation and ranking of metagenomic software

scientific article published on 7 May 2025
NPOmix: a machine learning classifier to connect mass spectrometry fragmentation data to biosynthetic gene clusters

scientific article published on 6 October 2021

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