A computational framework to explore large-scale biosynthetic diversity
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Marnix H. Medema | Neil L. Kelleher | Satria A. Kautsar | Antonio Fernandez-Guerra | Jorge C. Navarro-Muñoz | Nelly Selem-Mojica | James H. Tryon | Elizabeth I. Parkinson | Arne Roeters | Wouter Lokhorst | Regan J. Thomson | William W. Metcalf | R. J. Thomson | Michael W. Mullowney | Emmanuel L. C. De Los Santos | Marley Yeong | Pablo Cruz-Morales | Sahar Abubucker | Luciana Teresa Dias Cappelini | Anthony W. Goering | Francisco Barona-Gomez | N. Kelleher | Sahar Abubucker | F. Barona-Gómez | M. Medema | W. Metcalf | A. Fernàndez-Guerra | Pablo Cruz-Morales | Nelly Sélem-Mojica | S. Kautsar | J. C. Navarro-Muñoz | E. D. L. de los Santos | A. Fernandez-Guerra | Luciana T. D. Cappelini | Marley Yeong | Arne Roeters | Wouter Lokhorst | E. L. C. de los Santos
[1] K. A. Short,et al. The complete genomic sequence of Streptomyces spectabilis NRRL-2792 and identification of secondary metabolite biosynthetic gene clusters , 2019, Journal of Industrial Microbiology & Biotechnology.
[2] Ajit Singh,et al. Machine Learning With Python , 2019 .
[3] Ryan A McClure,et al. Discovery of the Tyrobetaine Natural Products and Their Biosynthetic Gene Cluster via Metabologenomics. , 2018, ACS chemical biology.
[4] Elizabeth A. Shank,et al. Large-Scale Bioinformatics Analysis of Bacillus Genomes Uncovers Conserved Roles of Natural Products in Bacterial Physiology , 2017, mSystems.
[5] Oliver Kohlbacher,et al. SANDPUMA: ensemble predictions of nonribosomal peptide chemistry reveal biosynthetic diversity across Actinobacteria , 2017, Bioinform..
[6] I. Ebersberger,et al. Natural product diversity associated with the nematode symbionts Photorhabdus and Xenorhabdus , 2017, Nature Microbiology.
[7] Donovan H. Parks,et al. Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life , 2017, Nature Microbiology.
[8] William H. Gerwick,et al. Retrospective analysis of natural products provides insights for future discovery trends , 2017, Proceedings of the National Academy of Sciences.
[9] Michael A. Skinnider,et al. PRISM 3: expanded prediction of natural product chemical structures from microbial genomes , 2017, Nucleic Acids Res..
[10] Kai Blin,et al. antiSMASH 4.0—improvements in chemistry prediction and gene cluster boundary identification , 2017, Nucleic Acids Res..
[11] Kristian Fog Nielsen,et al. Global analysis of biosynthetic gene clusters reveals vast potential of secondary metabolite production in Penicillium species , 2017, Nature Microbiology.
[12] Lena Gerwick,et al. Comparative genomics uncovers the prolific and distinctive metabolic potential of the cyanobacterial genus Moorea , 2017, Proceedings of the National Academy of Sciences.
[13] Vinayak Agarwal,et al. Metagenomic discovery of polybrominated diphenyl ether biosynthesis by marine sponges , 2017, Nature chemical biology.
[14] Chad W. Johnston,et al. Polyketide and nonribosomal peptide retro-biosynthesis and global gene cluster matching. , 2016, Nature chemical biology.
[15] Ryan A McClure,et al. Elucidating the Rimosamide-Detoxin Natural Product Families and Their Biosynthesis Using Metabolite/Gene Cluster Correlations. , 2016, ACS chemical biology.
[16] Ryan A McClure,et al. New Aspercryptins, Lipopeptide Natural Products, Revealed by HDAC Inhibition in Aspergillus nidulans. , 2016, ACS chemical biology.
[17] F. Barona-Gómez,et al. Phylogenomic Analysis of Natural Products Biosynthetic Gene Clusters Allows Discovery of Arseno-Organic Metabolites in Model Streptomycetes , 2016, bioRxiv.
[18] Ryan A McClure,et al. Metabologenomics: Correlation of Microbial Gene Clusters with Metabolites Drives Discovery of a Nonribosomal Peptide with an Unusual Amino Acid Monomer , 2016, ACS central science.
[19] Richard H. Baltz,et al. Natural product discovery: past, present, and future , 2016, Journal of Industrial Microbiology & Biotechnology.
[20] Hadley Wickham,et al. An Implementation of the Grammar of Graphics , 2015 .
[21] Michael A. Skinnider,et al. Genomes to natural products PRediction Informatics for Secondary Metabolomes (PRISM) , 2015, Nucleic acids research.
[22] Michael A. Skinnider,et al. An automated Genomes-to-Natural Products platform (GNP) for the discovery of modular natural products , 2015, Nature Communications.
[23] Michael A Fischbach,et al. Computational approaches to natural product discovery. , 2015, Nature chemical biology.
[24] M. Smanski,et al. Minimum Information about a Biosynthetic Gene cluster. , 2015, Nature chemical biology.
[25] R. Kolter,et al. Natural products in soil microbe interactions and evolution. , 2015, Natural product reports.
[26] Kai Blin,et al. antiSMASH 3.0—a comprehensive resource for the genome mining of biosynthetic gene clusters , 2015, Nucleic Acids Res..
[27] Anna Lechner,et al. Molecular networking and pattern-based genome mining improves discovery of biosynthetic gene clusters and their products from Salinispora species. , 2015, Chemistry & biology.
[28] Paula Y. Calle,et al. Multiplexed metagenome mining using short DNA sequence tags facilitates targeted discovery of epoxyketone proteasome inhibitors , 2015, Proceedings of the National Academy of Sciences.
[29] Andrej Sali,et al. A Systematic Computational Analysis of Biosynthetic Gene Cluster Evolution: Lessons for Engineering Biosynthesis , 2014, PLoS Comput. Biol..
[30] Neil L Kelleher,et al. A Roadmap for Natural Product Discovery Based on Large-Scale Genomics and Metabolomics , 2014, Nature chemical biology.
[31] Rainer Breitling,et al. Pep2Path: Automated Mass Spectrometry-Guided Genome Mining of Peptidic Natural Products , 2014, PLoS Comput. Biol..
[32] Pavel A. Pevzner,et al. NRPquest: Coupling Mass Spectrometry and Genome Mining for Nonribosomal Peptide Discovery , 2014, Journal of natural products.
[33] Roger G. Linington,et al. Insights into Secondary Metabolism from a Global Analysis of Prokaryotic Biosynthetic Gene Clusters , 2014, Cell.
[34] Nuno Bandeira,et al. Automated Genome Mining of Ribosomal Peptide Natural Products , 2014, ACS chemical biology.
[35] Krystle L. Chavarria,et al. Diversity and evolution of secondary metabolism in the marine actinomycete genus Salinispora , 2014, Proceedings of the National Academy of Sciences.
[36] Nuno Bandeira,et al. MS/MS networking guided analysis of molecule and gene cluster families , 2013, Proceedings of the National Academy of Sciences.
[37] J. Davies,et al. Specialized microbial metabolites: functions and origins , 2013, The Journal of Antibiotics.
[38] Kai Blin,et al. antiSMASH 2.0—a versatile platform for genome mining of secondary metabolite producers , 2013, Nucleic Acids Res..
[39] K. Katoh,et al. MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability , 2013, Molecular biology and evolution.
[40] Jörn Piel,et al. Metagenome Mining Reveals Polytheonamides as Posttranslationally Modified Ribosomal Peptides , 2012, Science.
[41] Nuno Bandeira,et al. Mass spectral molecular networking of living microbial colonies , 2012, Proceedings of the National Academy of Sciences.
[42] Sergey I. Nikolenko,et al. SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing , 2012, J. Comput. Biol..
[43] L. Holm,et al. The Pfam protein families database , 2011, Nucleic Acids Res..
[44] Kai Blin,et al. antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences , 2011, Nucleic Acids Res..
[45] Gaël Varoquaux,et al. Scikit-learn: Machine Learning in Python , 2011, J. Mach. Learn. Res..
[46] Evgeny M. Zdobnov,et al. The Newick utilities: high-throughput phylogenetic tree processing in the Unix shell , 2010, Bioinform..
[47] Adam P. Arkin,et al. FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix , 2009, Molecular biology and evolution.
[48] J. Suh,et al. The Gene Cluster for Spectinomycin Biosynthesis and the Aminoglycoside-Resistance Function of spcM in Streptomycesspectabilis , 2008, Current Microbiology.
[49] M. Fischbach,et al. The evolution of gene collectives: How natural selection drives chemical innovation , 2008, Proceedings of the National Academy of Sciences.
[50] Roy D. Welch,et al. Complete genome sequence of the myxobacterium Sorangium cellulosum , 2007, Nature Biotechnology.
[51] Corinna Lange,et al. Genomics-driven discovery of PKS-NRPS hybrid metabolites from Aspergillus nidulans. , 2007, Nature chemical biology.
[52] Delbert Dueck,et al. Clustering by Passing Messages Between Data Points , 2007, Science.
[53] Lei Zhu,et al. An initial strategy for comparing proteins at the domain architecture level , 2006, Bioinform..
[54] Robert C. Edgar,et al. MUSCLE: multiple sequence alignment with high accuracy and high throughput. , 2004, Nucleic acids research.
[55] Robert P. Hausinger,et al. Fe(II)/α-Ketoglutarate-Dependent Hydroxylases and Related Enzymes , 2004 .
[56] B. Barrell,et al. Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2) , 2002, Nature.
[57] Wei Qian,et al. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. , 2000, Molecular biology and evolution.
[58] H. Seto,et al. The Structures of Minor Congeners of the Detoxin Complex , 1981 .
[59] H. Seto,et al. The detoxin complex, selective antagonists of blasticidin S. , 1968, The Journal of antibiotics.
[60] K. Katoh,et al. Improvements in Performance and Usability , 2013 .
[61] Hadley Wickham,et al. Mastering the grammar , 2009 .
[62] Gábor Csárdi,et al. The igraph software package for complex network research , 2006 .
[63] D. Holdstock. Past, present--and future? , 2005, Medicine, conflict, and survival.