QUAST: quality assessment tool for genome assemblies
Gurevich, Alexey, Saveliev, Vladislav, Vyahhi, Nikolay, Tesler, Glenn
Published in Bioinformatics (15.04.2013)
Published in Bioinformatics (15.04.2013)
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Journal Article
MolDiscovery: learning mass spectrometry fragmentation of small molecules
Cao, Liu, Guler, Mustafa, Tagirdzhanov, Azat, Lee, Yi-Yuan, Gurevich, Alexey, Mohimani, Hosein
Published in Nature communications (17.06.2021)
Published in Nature communications (17.06.2021)
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Journal Article
metaFlye: scalable long-read metagenome assembly using repeat graphs
Kolmogorov, Mikhail, Bickhart, Derek M, Behsaz, Bahar, Gurevich, Alexey, Rayko, Mikhail, Shin, Sung Bong, Kuhn, Kristen, Yuan, Jeffrey, Polevikov, Evgeny, Smith, Timothy P L, Pevzner, Pavel A
Published in Nature methods (01.11.2020)
Published in Nature methods (01.11.2020)
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Journal Article
SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing
Bankevich, Anton, Nurk, Sergey, Antipov, Dmitry, Gurevich, Alexey A, Dvorkin, Mikhail, Kulikov, Alexander S, Lesin, Valery M, Nikolenko, Sergey I, Pham, Son, Prjibelski, Andrey D, Pyshkin, Alexey V, Sirotkin, Alexander V, Vyahhi, Nikolay, Tesler, Glenn, Alekseyev, Max A, Pevzner, Pavel A
Published in Journal of computational biology (01.05.2012)
Published in Journal of computational biology (01.05.2012)
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Journal Article
Dereplication of microbial metabolites through database search of mass spectra
Mohimani, Hosein, Gurevich, Alexey, Shlemov, Alexander, Mikheenko, Alla, Korobeynikov, Anton, Cao, Liu, Shcherbin, Egor, Nothias, Louis-Felix, Dorrestein, Pieter C, Pevzner, Pavel A
Published in Nature communications (02.10.2018)
Published in Nature communications (02.10.2018)
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Journal Article
Assembling single-cell genomes and mini-metagenomes from chimeric MDA products
Nurk, Sergey, Bankevich, Anton, Antipov, Dmitry, Gurevich, Alexey A, Korobeynikov, Anton, Lapidus, Alla, Prjibelski, Andrey D, Pyshkin, Alexey, Sirotkin, Alexander, Sirotkin, Yakov, Stepanauskas, Ramunas, Clingenpeel, Scott R, Woyke, Tanja, McLean, Jeffrey S, Lasken, Roger, Tesler, Glenn, Alekseyev, Max A, Pevzner, Pavel A
Published in Journal of computational biology (01.10.2013)
Published in Journal of computational biology (01.10.2013)
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Journal Article
Dereplication of peptidic natural products through database search of mass spectra
Mohimani, Hosein, Gurevich, Alexey, Mikheenko, Alla, Garg, Neha, Nothias, Louis-Felix, Ninomiya, Akihiro, Takada, Kentaro, Dorrestein, Pieter C, Pevzner, Pavel A
Published in Nature chemical biology (01.01.2017)
Published in Nature chemical biology (01.01.2017)
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Journal Article
Integrating genomics and metabolomics for scalable non-ribosomal peptide discovery
Behsaz, Bahar, Bode, Edna, Gurevich, Alexey, Shi, Yan-Ni, Grundmann, Florian, Acharya, Deepa, Caraballo-Rodríguez, Andrés Mauricio, Bouslimani, Amina, Panitchpakdi, Morgan, Linck, Annabell, Guan, Changhui, Oh, Julia, Dorrestein, Pieter C, Bode, Helge B, Pevzner, Pavel A, Mohimani, Hosein
Published in Nature communications (28.05.2021)
Published in Nature communications (28.05.2021)
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Journal Article
Tutorial: assessing metagenomics software with the CAMI benchmarking toolkit
Meyer, Fernando, Lesker, Till-Robin, Koslicki, David, Fritz, Adrian, Gurevich, Alexey, Darling, Aaron E, Sczyrba, Alexander, Bremges, Andreas, McHardy, Alice C
Published in Nature protocols (01.04.2021)
Published in Nature protocols (01.04.2021)
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Journal Article
Publisher Correction: Integrating genomics and metabolomics for scalable non-ribosomal peptide discovery
Behsaz, Bahar, Bode, Edna, Gurevich, Alexey, Shi, Yan-Ni, Grundmann, Florian, Acharya, Deepa, Caraballo-Rodríguez, Andrés Mauricio, Bouslimani, Amina, Panitchpakdi, Morgan, Linck, Annabell, Guan, Changhui, Oh, Julia, Dorrestein, Pieter C., Bode, Helge B., Pevzner, Pavel A., Mohimani, Hosein
Published in Nature communications (08.07.2021)
Published in Nature communications (08.07.2021)
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Journal Article
HypoRiPPAtlas as an Atlas of hypothetical natural products for mass spectrometry database search
Lee, Yi-Yuan, Guler, Mustafa, Chigumba, Desnor N, Wang, Shen, Mittal, Neel, Miller, Cameron, Krummenacher, Benjamin, Liu, Haodong, Cao, Liu, Kannan, Aditya, Narayan, Keshav, Slocum, Samuel T, Roth, Bryan L, Gurevich, Alexey, Behsaz, Bahar, Kersten, Roland D, Mohimani, Hosein
Published in Nature communications (14.07.2023)
Published in Nature communications (14.07.2023)
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Journal Article
Increased diversity of peptidic natural products revealed by modification-tolerant database search of mass spectra
Gurevich, Alexey, Mikheenko, Alla, Shlemov, Alexander, Korobeynikov, Anton, Mohimani, Hosein, Pevzner, Pavel A
Published in Nature microbiology (01.03.2018)
Published in Nature microbiology (01.03.2018)
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Journal Article
A Multi-Omics Characterization of the Natural Product Potential of Tropical Filamentous Marine Cyanobacteria
Leão, Tiago, Wang, Mingxun, Moss, Nathan, da Silva, Ricardo, Sanders, Jon, Nurk, Sergey, Gurevich, Alexey, Humphrey, Gregory, Reher, Raphael, Zhu, Qiyun, Belda-Ferre, Pedro, Glukhov, Evgenia, Whitner, Syrena, Alexander, Kelsey L, Rex, Robert, Pevzner, Pavel, Dorrestein, Pieter C, Knight, Rob, Bandeira, Nuno, Gerwick, William H, Gerwick, Lena
Published in Marine drugs (06.01.2021)
Published in Marine drugs (06.01.2021)
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Journal Article
Metabolic Fingerprints from the Human Oral Microbiome Reveal a Vast Knowledge Gap of Secreted Small Peptidic Molecules
Edlund, Anna, Garg, Neha, Mohimani, Hosein, Gurevich, Alexey, He, Xuesong, Shi, Wenyuan, Dorrestein, Pieter C, McLean, Jeffrey S
Published in mSystems (01.07.2017)
Published in mSystems (01.07.2017)
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Journal Article
Nerpa: A Tool for Discovering Biosynthetic Gene Clusters of Bacterial Nonribosomal Peptides
Kunyavskaya, Olga, Tagirdzhanov, Azat M., Caraballo-Rodríguez, Andrés Mauricio, Nothias, Louis-Félix, Dorrestein, Pieter C., Korobeynikov, Anton, Mohimani, Hosein, Gurevich, Alexey
Published in Metabolites (11.10.2021)
Published in Metabolites (11.10.2021)
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Journal Article
Spatial Molecular Architecture of the Microbial Community of a Peltigera Lichen
Garg, Neha, Zeng, Yi, Edlund, Anna, Melnik, Alexey V, Sanchez, Laura M, Mohimani, Hosein, Gurevich, Alexey, Miao, Vivian, Schiffler, Stefan, Lim, Yan Wei, Luzzatto-Knaan, Tal, Cai, Shengxin, Rohwer, Forest, Pevzner, Pavel A, Cichewicz, Robert H, Alexandrov, Theodore, Dorrestein, Pieter C
Published in mSystems (01.11.2016)
Published in mSystems (01.11.2016)
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Journal Article
Versatile genome assembly evaluation with QUAST-LG
Mikheenko, Alla, Prjibelski, Andrey, Saveliev, Vladislav, Antipov, Dmitry, Gurevich, Alexey
Published in Bioinformatics (01.07.2018)
Published in Bioinformatics (01.07.2018)
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Journal Article
Icarus: visualizer for de novo assembly evaluation
Mikheenko, Alla, Valin, Gleb, Prjibelski, Andrey, Saveliev, Vladislav, Gurevich, Alexey
Published in Bioinformatics (Oxford, England) (01.11.2016)
Published in Bioinformatics (Oxford, England) (01.11.2016)
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Journal Article