Literature DB >> 26284661

Minimum Information about a Biosynthetic Gene cluster.

Marnix H Medema1, Renzo Kottmann1, Pelin Yilmaz1, Matthew Cummings2, John B Biggins3, Kai Blin4, Irene de Bruijn5, Yit Heng Chooi6, Jan Claesen7, R Cameron Coates8, Pablo Cruz-Morales9, Srikanth Duddela10, Stephanie Düsterhus11, Daniel J Edwards12, David P Fewer13, Neha Garg14, Christoph Geiger11, Juan Pablo Gomez-Escribano15, Anja Greule16, Michalis Hadjithomas8, Anthony S Haines17, Eric J N Helfrich18, Matthew L Hillwig19, Keishi Ishida20, Adam C Jones21, Carla S Jones22, Katrin Jungmann10, Carsten Kegler23, Hyun Uk Kim24, Peter Kötter11, Daniel Krug10, Joleen Masschelein25, Alexey V Melnik14, Simone M Mantovani26, Emily A Monroe27, Marcus Moore28, Nathan Moss26, Hans-Wilhelm Nützmann29, Guohui Pan30, Amrita Pati8, Daniel Petras31, F Jerry Reen32, Federico Rosconi33, Zhe Rui34, Zhenhua Tian35, Nicholas J Tobias23, Yuta Tsunematsu36, Philipp Wiemann37, Elizabeth Wyckoff38, Xiaohui Yan30, Grace Yim39, Fengan Yu40, Yunchang Xie41, Bertrand Aigle42, Alexander K Apel43, Carl J Balibar44, Emily P Balskus45, Francisco Barona-Gómez9, Andreas Bechthold16, Helge B Bode46, Rainer Borriss47, Sean F Brady3, Axel A Brakhage20, Patrick Caffrey48, Yi-Qiang Cheng49, Jon Clardy50, Russell J Cox51, René De Mot52, Stefano Donadio53, Mohamed S Donia54, Wilfred A van der Donk55, Pieter C Dorrestein56, Sean Doyle57, Arnold J M Driessen58, Monika Ehling-Schulz59, Karl-Dieter Entian11, Michael A Fischbach7, Lena Gerwick26, William H Gerwick60, Harald Gross43, Bertolt Gust43, Christian Hertweck61, Monica Höfte62, Susan E Jensen63, Jianhua Ju41, Leonard Katz64, Leonard Kaysser43, Jonathan L Klassen65, Nancy P Keller66, Jan Kormanec67, Oscar P Kuipers68, Tomohisa Kuzuyama69, Nikos C Kyrpides70, Hyung-Jin Kwon71, Sylvie Lautru72, Rob Lavigne73, Chia Y Lee74, Bai Linquan75, Xinyu Liu19, Wen Liu35, Andriy Luzhetskyy10, Taifo Mahmud76, Yvonne Mast77, Carmen Méndez78, Mikko Metsä-Ketelä79, Jason Micklefield80, Douglas A Mitchell81, Bradley S Moore60, Leonilde M Moreira82, Rolf Müller10, Brett A Neilan83, Markus Nett20, Jens Nielsen84, Fergal O'Gara85, Hideaki Oikawa86, Anne Osbourn29, Marcia S Osburne87, Bohdan Ostash88, Shelley M Payne38, Jean-Luc Pernodet72, Miroslav Petricek89, Jörn Piel18, Olivier Ploux90, Jos M Raaijmakers5, José A Salas91, Esther K Schmitt92, Barry Scott93, Ryan F Seipke94, Ben Shen95, David H Sherman40, Kaarina Sivonen13, Michael J Smanski96, Margherita Sosio53, Evi Stegmann97, Roderich D Süssmuth31, Kapil Tahlan28, Christopher M Thomas17, Yi Tang98, Andrew W Truman15, Muriel Viaud99, Jonathan D Walton100, Christopher T Walsh101, Tilmann Weber4, Gilles P van Wezel102, Barrie Wilkinson15, Joanne M Willey103, Wolfgang Wohlleben97, Gerard D Wright39, Nadine Ziemert97, Changsheng Zhang41, Sergey B Zotchev104, Rainer Breitling2, Eriko Takano2, Frank Oliver Glöckner105.   

Abstract

Entities:  

Mesh:

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Year:  2015        PMID: 26284661      PMCID: PMC5714517          DOI: 10.1038/nchembio.1890

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


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  29 in total

1.  Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications.

Authors:  Pelin Yilmaz; Renzo Kottmann; Dawn Field; Rob Knight; James R Cole; Linda Amaral-Zettler; Jack A Gilbert; Ilene Karsch-Mizrachi; Anjanette Johnston; Guy Cochrane; Robert Vaughan; Christopher Hunter; Joonhong Park; Norman Morrison; Philippe Rocca-Serra; Peter Sterk; Manimozhiyan Arumugam; Mark Bailey; Laura Baumgartner; Bruce W Birren; Martin J Blaser; Vivien Bonazzi; Tim Booth; Peer Bork; Frederic D Bushman; Pier Luigi Buttigieg; Patrick S G Chain; Emily Charlson; Elizabeth K Costello; Heather Huot-Creasy; Peter Dawyndt; Todd DeSantis; Noah Fierer; Jed A Fuhrman; Rachel E Gallery; Dirk Gevers; Richard A Gibbs; Inigo San Gil; Antonio Gonzalez; Jeffrey I Gordon; Robert Guralnick; Wolfgang Hankeln; Sarah Highlander; Philip Hugenholtz; Janet Jansson; Andrew L Kau; Scott T Kelley; Jerry Kennedy; Dan Knights; Omry Koren; Justin Kuczynski; Nikos Kyrpides; Robert Larsen; Christian L Lauber; Teresa Legg; Ruth E Ley; Catherine A Lozupone; Wolfgang Ludwig; Donna Lyons; Eamonn Maguire; Barbara A Methé; Folker Meyer; Brian Muegge; Sara Nakielny; Karen E Nelson; Diana Nemergut; Josh D Neufeld; Lindsay K Newbold; Anna E Oliver; Norman R Pace; Giriprakash Palanisamy; Jörg Peplies; Joseph Petrosino; Lita Proctor; Elmar Pruesse; Christian Quast; Jeroen Raes; Sujeevan Ratnasingham; Jacques Ravel; David A Relman; Susanna Assunta-Sansone; Patrick D Schloss; Lynn Schriml; Rohini Sinha; Michelle I Smith; Erica Sodergren; Aymé Spo; Jesse Stombaugh; James M Tiedje; Doyle V Ward; George M Weinstock; Doug Wendel; Owen White; Andrew Whiteley; Andreas Wilke; Jennifer R Wortman; Tanya Yatsunenko; Frank Oliver Glöckner
Journal:  Nat Biotechnol       Date:  2011-05       Impact factor: 54.908

2.  SBSPKS: structure based sequence analysis of polyketide synthases.

Authors:  Swadha Anand; M V R Prasad; Gitanjali Yadav; Narendra Kumar; Jyoti Shehara; Md Zeeshan Ansari; Debasisa Mohanty
Journal:  Nucleic Acids Res       Date:  2010-05-05       Impact factor: 16.971

3.  Glycogenomics as a mass spectrometry-guided genome-mining method for microbial glycosylated molecules.

Authors:  Roland D Kersten; Nadine Ziemert; David J Gonzalez; Brendan M Duggan; Victor Nizet; Pieter C Dorrestein; Bradley S Moore
Journal:  Proc Natl Acad Sci U S A       Date:  2013-11-04       Impact factor: 11.205

4.  The minimum information about a genome sequence (MIGS) specification.

Authors:  Dawn Field; George Garrity; Tanya Gray; Norman Morrison; Jeremy Selengut; Peter Sterk; Tatiana Tatusova; Nicholas Thomson; Michael J Allen; Samuel V Angiuoli; Michael Ashburner; Nelson Axelrod; Sandra Baldauf; Stuart Ballard; Jeffrey Boore; Guy Cochrane; James Cole; Peter Dawyndt; Paul De Vos; Claude DePamphilis; Robert Edwards; Nadeem Faruque; Robert Feldman; Jack Gilbert; Paul Gilna; Frank Oliver Glöckner; Philip Goldstein; Robert Guralnick; Dan Haft; David Hancock; Henning Hermjakob; Christiane Hertz-Fowler; Phil Hugenholtz; Ian Joint; Leonid Kagan; Matthew Kane; Jessie Kennedy; George Kowalchuk; Renzo Kottmann; Eugene Kolker; Saul Kravitz; Nikos Kyrpides; Jim Leebens-Mack; Suzanna E Lewis; Kelvin Li; Allyson L Lister; Phillip Lord; Natalia Maltsev; Victor Markowitz; Jennifer Martiny; Barbara Methe; Ilene Mizrachi; Richard Moxon; Karen Nelson; Julian Parkhill; Lita Proctor; Owen White; Susanna-Assunta Sansone; Andrew Spiers; Robert Stevens; Paul Swift; Chris Taylor; Yoshio Tateno; Adrian Tett; Sarah Turner; David Ussery; Bob Vaughan; Naomi Ward; Trish Whetzel; Ingio San Gil; Gareth Wilson; Anil Wipat
Journal:  Nat Biotechnol       Date:  2008-05       Impact factor: 54.908

Review 5.  Ribosomally synthesized and post-translationally modified peptide natural products: overview and recommendations for a universal nomenclature.

Authors:  Paul G Arnison; Mervyn J Bibb; Gabriele Bierbaum; Albert A Bowers; Tim S Bugni; Grzegorz Bulaj; Julio A Camarero; Dominic J Campopiano; Gregory L Challis; Jon Clardy; Paul D Cotter; David J Craik; Michael Dawson; Elke Dittmann; Stefano Donadio; Pieter C Dorrestein; Karl-Dieter Entian; Michael A Fischbach; John S Garavelli; Ulf Göransson; Christian W Gruber; Daniel H Haft; Thomas K Hemscheidt; Christian Hertweck; Colin Hill; Alexander R Horswill; Marcel Jaspars; Wendy L Kelly; Judith P Klinman; Oscar P Kuipers; A James Link; Wen Liu; Mohamed A Marahiel; Douglas A Mitchell; Gert N Moll; Bradley S Moore; Rolf Müller; Satish K Nair; Ingolf F Nes; Gillian E Norris; Baldomero M Olivera; Hiroyasu Onaka; Mark L Patchett; Joern Piel; Martin J T Reaney; Sylvie Rebuffat; R Paul Ross; Hans-Georg Sahl; Eric W Schmidt; Michael E Selsted; Konstantin Severinov; Ben Shen; Kaarina Sivonen; Leif Smith; Torsten Stein; Roderich D Süssmuth; John R Tagg; Gong-Li Tang; Andrew W Truman; John C Vederas; Christopher T Walsh; Jonathan D Walton; Silke C Wenzel; Joanne M Willey; Wilfred A van der Donk
Journal:  Nat Prod Rep       Date:  2013-01       Impact factor: 13.423

6.  The Genomic Standards Consortium.

Authors:  Dawn Field; Linda Amaral-Zettler; Guy Cochrane; James R Cole; Peter Dawyndt; George M Garrity; Jack Gilbert; Frank Oliver Glöckner; Lynette Hirschman; Ilene Karsch-Mizrachi; Hans-Peter Klenk; Rob Knight; Renzo Kottmann; Nikos Kyrpides; Folker Meyer; Inigo San Gil; Susanna-Assunta Sansone; Lynn M Schriml; Peter Sterk; Tatiana Tatusova; David W Ussery; Owen White; John Wooley
Journal:  PLoS Biol       Date:  2011-06-21       Impact factor: 8.029

7.  NRPSpredictor2--a web server for predicting NRPS adenylation domain specificity.

Authors:  Marc Röttig; Marnix H Medema; Kai Blin; Tilmann Weber; Christian Rausch; Oliver Kohlbacher
Journal:  Nucleic Acids Res       Date:  2011-05-09       Impact factor: 16.971

8.  A mass spectrometry-guided genome mining approach for natural product peptidogenomics.

Authors:  Roland D Kersten; Yu-Liang Yang; Yuquan Xu; Peter Cimermancic; Sang-Jip Nam; William Fenical; Michael A Fischbach; Bradley S Moore; Pieter C Dorrestein
Journal:  Nat Chem Biol       Date:  2011-10-09       Impact factor: 15.040

9.  A roadmap for natural product discovery based on large-scale genomics and metabolomics.

Authors:  James R Doroghazi; Jessica C Albright; Anthony W Goering; Kou-San Ju; Robert R Haines; Konstantin A Tchalukov; David P Labeda; Neil L Kelleher; William W Metcalf
Journal:  Nat Chem Biol       Date:  2014-09-28       Impact factor: 15.040

10.  ClusterMine360: a database of microbial PKS/NRPS biosynthesis.

Authors:  Kyle R Conway; Christopher N Boddy
Journal:  Nucleic Acids Res       Date:  2012-10-26       Impact factor: 16.971

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  281 in total

Review 1.  Ribosomally synthesized and post-translationally modified peptide natural product discovery in the genomic era.

Authors:  Kenton J Hetrick; Wilfred A van der Donk
Journal:  Curr Opin Chem Biol       Date:  2017-03-02       Impact factor: 8.822

2.  Assembly and clustering of natural antibiotics guides target identification.

Authors:  Chad W Johnston; Michael A Skinnider; Chris A Dejong; Philip N Rees; Gregory M Chen; Chelsea G Walker; Shawn French; Eric D Brown; János Bérdy; Dennis Y Liu; Nathan A Magarvey
Journal:  Nat Chem Biol       Date:  2016-02-01       Impact factor: 15.040

3.  Linking secondary metabolites to gene clusters through genome sequencing of six diverse Aspergillus species.

Authors:  Inge Kjærbølling; Tammi C Vesth; Jens C Frisvad; Jane L Nybo; Sebastian Theobald; Alan Kuo; Paul Bowyer; Yudai Matsuda; Stephen Mondo; Ellen K Lyhne; Martin E Kogle; Alicia Clum; Anna Lipzen; Asaf Salamov; Chew Yee Ngan; Chris Daum; Jennifer Chiniquy; Kerrie Barry; Kurt LaButti; Sajeet Haridas; Blake A Simmons; Jon K Magnuson; Uffe H Mortensen; Thomas O Larsen; Igor V Grigoriev; Scott E Baker; Mikael R Andersen
Journal:  Proc Natl Acad Sci U S A       Date:  2018-01-09       Impact factor: 11.205

4.  Competition among Nasal Bacteria Suggests a Role for Siderophore-Mediated Interactions in Shaping the Human Nasal Microbiota.

Authors:  Reed M Stubbendieck; Daniel S May; Marc G Chevrette; Mia I Temkin; Evelyn Wendt-Pienkowski; Julian Cagnazzo; Caitlin M Carlson; James E Gern; Cameron R Currie
Journal:  Appl Environ Microbiol       Date:  2019-05-02       Impact factor: 4.792

Review 5.  Fungal secondary metabolism: regulation, function and drug discovery.

Authors:  Nancy P Keller
Journal:  Nat Rev Microbiol       Date:  2019-03       Impact factor: 60.633

6.  Phenetic Comparison of Prokaryotic Genomes Using k-mers.

Authors:  Maxime Déraspe; Frédéric Raymond; Sébastien Boisvert; Alexander Culley; Paul H Roy; François Laviolette; Jacques Corbeil
Journal:  Mol Biol Evol       Date:  2017-10-01       Impact factor: 16.240

7.  Inter-Modular Linkers play a crucial role in governing the biosynthesis of non-ribosomal peptides.

Authors:  Sherif Farag; Rachel M Bleich; Elizabeth A Shank; Olexandr Isayev; Albert A Bowers; Alexander Tropsha
Journal:  Bioinformatics       Date:  2019-10-01       Impact factor: 6.937

8.  Bipartite interactions, antibiotic production and biosynthetic potential of the Arabidopsis leaf microbiome.

Authors:  Eric J N Helfrich; Christine M Vogel; Reiko Ueoka; Martin Schäfer; Florian Ryffel; Daniel B Müller; Silke Probst; Markus Kreuzer; Jörn Piel; Julia A Vorholt
Journal:  Nat Microbiol       Date:  2018-07-23       Impact factor: 17.745

9.  Analysis of the Pseudouridimycin Biosynthetic Pathway Provides Insights into the Formation of C-nucleoside Antibiotics.

Authors:  Margherita Sosio; Eleonora Gaspari; Marianna Iorio; Silvia Pessina; Marnix H Medema; Alice Bernasconi; Matteo Simone; Sonia I Maffioli; Richard H Ebright; Stefano Donadio
Journal:  Cell Chem Biol       Date:  2018-03-15       Impact factor: 8.116

Review 10.  Symbiosis-inspired approaches to antibiotic discovery.

Authors:  Navid Adnani; Scott R Rajski; Tim S Bugni
Journal:  Nat Prod Rep       Date:  2017-07-06       Impact factor: 13.423

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