Literature DB >> 33589842

A community resource for paired genomic and metabolomic data mining.

Michelle A Schorn1,2, Stefan Verhoeven3, Lars Ridder3, Florian Huber3, Deepa D Acharya4, Alexander A Aksenov5, Gajender Aleti6, Jamshid Amiri Moghaddam7, Allegra T Aron5, Saefuddin Aziz8,9, Anelize Bauermeister5,10, Katherine D Bauman11, Martin Baunach12, Christine Beemelmanns7, J Michael Beman13,14, María Victoria Berlanga-Clavero15, Alex A Blacutt16, Helge B Bode17,18,19,20, Anne Boullie21, Asker Brejnrod5, Tim S Bugni22, Alexandra Calteau23, Liu Cao24, Víctor J Carrión25,26, Raquel Castelo-Branco27,28,29, Shaurya Chanana4, Alexander B Chase11, Marc G Chevrette4, Leticia V Costa-Lotufo10, Jason M Crawford30,31,32, Cameron R Currie33,34, Bart Cuypers35,36, Tam Dang37, Tristan de Rond11, Alyssa M Demko11, Elke Dittmann12, Chao Du25, Christopher Drozd16, Jean-Claude Dujardin36, Rachel J Dutton38,39, Anna Edlund40,41, David P Fewer29, Neha Garg42, Julia M Gauglitz5, Emily C Gentry5, Lena Gerwick11, Evgenia Glukhov11, Harald Gross8, Muriel Gugger21, Dulce G Guillén Matus11, Eric J N Helfrich17,19,43,44, Benjamin-Florian Hempel37,45, Jae-Seoun Hur46, Marianna Iorio47, Paul R Jensen11, Kyo Bin Kang48, Leonard Kaysser8,49, Neil L Kelleher50, Chung Sub Kim30,31,51, Ki Hyun Kim51, Irina Koester52, Gabriele M König53, Tiago Leao5,11, Seoung Rak Lee51,54, Yi-Yuan Lee24, Xuanji Li55, Jessica C Little56, Katherine N Maloney57, Daniel Männle8,49,58, Christian Martin H59, Andrew C McAvoy42, Willam W Metcalf60, Hosein Mohimani24, Carlos Molina-Santiago15, Bradley S Moore11,39,61, Michael W Mullowney50, Mitchell Muskat11, Louis-Félix Nothias5, Ellis C O'Neill62, Elizabeth I Parkinson63, Daniel Petras5,52, Jörn Piel43, Emily C Pierce38, Karine Pires64, Raphael Reher11, Diego Romero15, M Caroline Roper16, Michael Rust43, Hamada Saad8,65, Carmen Saenz66, Laura M Sanchez56, Søren Johannes Sørensen55, Margherita Sosio47, Roderich D Süssmuth37, Douglas Sweeney11, Kapil Tahlan67, Regan J Thomson50, Nicholas J Tobias19,68, Amaro E Trindade-Silva69, Gilles P van Wezel25, Mingxun Wang5, Kelly C Weldon5,39, Fan Zhang22, Nadine Ziemert49,58, Katherine R Duncan70, Max Crüsemann53, Simon Rogers71, Pieter C Dorrestein72,73,74,75, Marnix H Medema76, Justin J J van der Hooft77.   

Abstract

Entities:  

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Year:  2021        PMID: 33589842      PMCID: PMC7987574          DOI: 10.1038/s41589-020-00724-z

Source DB:  PubMed          Journal:  Nat Chem Biol        ISSN: 1552-4450            Impact factor:   15.040


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  3 in total

1.  IMG-ABC v.5.0: an update to the IMG/Atlas of Biosynthetic Gene Clusters Knowledgebase.

Authors:  Krishnaveni Palaniappan; I-Min A Chen; Ken Chu; Anna Ratner; Rekha Seshadri; Nikos C Kyrpides; Natalia N Ivanova; Nigel J Mouncey
Journal:  Nucleic Acids Res       Date:  2020-01-08       Impact factor: 16.971

2.  MIBiG 2.0: a repository for biosynthetic gene clusters of known function.

Authors:  Satria A Kautsar; Kai Blin; Simon Shaw; Jorge C Navarro-Muñoz; Barbara R Terlouw; Justin J J van der Hooft; Jeffrey A van Santen; Vittorio Tracanna; Hernando G Suarez Duran; Victòria Pascal Andreu; Nelly Selem-Mojica; Mohammad Alanjary; Serina L Robinson; George Lund; Samuel C Epstein; Ashley C Sisto; Louise K Charkoudian; Jérôme Collemare; Roger G Linington; Tilmann Weber; Marnix H Medema
Journal:  Nucleic Acids Res       Date:  2020-01-08       Impact factor: 16.971

3.  MetaboLights: a resource evolving in response to the needs of its scientific community.

Authors:  Kenneth Haug; Keeva Cochrane; Venkata Chandrasekhar Nainala; Mark Williams; Jiakang Chang; Kalai Vanii Jayaseelan; Claire O'Donovan
Journal:  Nucleic Acids Res       Date:  2020-01-08       Impact factor: 16.971

  3 in total
  27 in total

1.  MIMOSA2: A metabolic network-based tool for inferring mechanism-supported relationships in microbiome-metabolome data.

Authors:  Cecilia Noecker; Alexander Eng; Efrat Muller; Elhanan Borenstein
Journal:  Bioinformatics       Date:  2022-01-06       Impact factor: 6.937

Review 2.  Strategies to access biosynthetic novelty in bacterial genomes for drug discovery.

Authors:  Franziska Hemmerling; Jörn Piel
Journal:  Nat Rev Drug Discov       Date:  2022-03-16       Impact factor: 84.694

Review 3.  Metabolomics and genomics in natural products research: complementary tools for targeting new chemical entities.

Authors:  Lindsay K Caesar; Rana Montaser; Nancy P Keller; Neil L Kelleher
Journal:  Nat Prod Rep       Date:  2021-11-17       Impact factor: 13.423

Review 4.  Advancements in capturing and mining mass spectrometry data are transforming natural products research.

Authors:  Scott A Jarmusch; Justin J J van der Hooft; Pieter C Dorrestein; Alan K Jarmusch
Journal:  Nat Prod Rep       Date:  2021-11-17       Impact factor: 13.423

5.  ActinoBase: tools and protocols for researchers working on Streptomyces and other filamentous actinobacteria.

Authors:  Morgan Anne Feeney; Jake Terry Newitt; Emily Addington; Lis Algora-Gallardo; Craig Allan; Lucas Balis; Anna S Birke; Laia Castaño-Espriu; Louise K Charkoudian; Rebecca Devine; Damien Gayrard; Jacob Hamilton; Oliver Hennrich; Paul A Hoskisson; Molly Keith-Baker; Joshua G Klein; Worarat Kruasuwan; David R Mark; Yvonne Mast; Rebecca E McHugh; Thomas C McLean; Elmira Mohit; John T Munnoch; Jordan Murray; Katie Noble; Hiroshi Otani; Jonathan Parra; Camila F Pereira; Louisa Perry; Linamaria Pintor-Escobar; Leighton Pritchard; Samuel M M Prudence; Alicia H Russell; Jana K Schniete; Ryan F Seipke; Nelly Sélem-Mojica; Agustina Undabarrena; Kristiina Vind; Gilles P van Wezel; Barrie Wilkinson; Sarah F Worsley; Katherine R Duncan; Lorena T Fernández-Martínez; Matthew I Hutchings
Journal:  Microb Genom       Date:  2022-07

6.  The Natural Product Domain Seeker version 2 (NaPDoS2) webtool relates ketosynthase phylogeny to biosynthetic function.

Authors:  Leesa J Klau; Sheila Podell; Kaitlin E Creamer; Alyssa M Demko; Hans W Singh; Eric E Allen; Bradley S Moore; Nadine Ziemert; Anne Catrin Letzel; Paul R Jensen
Journal:  J Biol Chem       Date:  2022-09-12       Impact factor: 5.486

Review 7.  Mining genomes to illuminate the specialized chemistry of life.

Authors:  Marnix H Medema; Tristan de Rond; Bradley S Moore
Journal:  Nat Rev Genet       Date:  2021-06-03       Impact factor: 53.242

8.  Ranking microbial metabolomic and genomic links in the NPLinker framework using complementary scoring functions.

Authors:  Grímur Hjörleifsson Eldjárn; Andrew Ramsay; Justin J J van der Hooft; Katherine R Duncan; Sylvia Soldatou; Juho Rousu; Rónán Daly; Joe Wandy; Simon Rogers
Journal:  PLoS Comput Biol       Date:  2021-05-04       Impact factor: 4.475

Review 9.  The Chemistry of Stress: Understanding the 'Cry for Help' of Plant Roots.

Authors:  Muhammad Syamsu Rizaludin; Nejc Stopnisek; Jos M Raaijmakers; Paolina Garbeva
Journal:  Metabolites       Date:  2021-06-02

10.  MolDiscovery: learning mass spectrometry fragmentation of small molecules.

Authors:  Liu Cao; Mustafa Guler; Azat Tagirdzhanov; Yi-Yuan Lee; Alexey Gurevich; Hosein Mohimani
Journal:  Nat Commun       Date:  2021-06-17       Impact factor: 14.919

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