MetaRiPPquest: A Peptidogenomics Approach for the Discovery of Ribosomally Synthesized and Post-translationally Modified Peptides
暂无分享,去创建一个
Pavel A. Pevzner | Rob Knight | Pieter C. Dorrestein | Hosein Mohimani | Iddo Friedberg | Anton Korobeynikov | Alexey Gurevich | Kelsey L. Alexander | C. Benjamin Naman | Tiago Leão | Evgenia Glukhov | Nathan A. Moss | Tal Luzzatto-Knaan | Fernando Vargas | Louis-Felix Nothias | Nitin K. Singh | Jon G. Sanders | Rodolfo A. S. Benitez | Luke R. Thompson | Md-Nafiz Hamid | James T. Morton | Alla Mikheenko | Alexander Shlemov | Kasthuri Venkateswaran | William Gerwick | Lena Gerwick | Kelsey L Alexander | P. Pevzner | R. Knight | P. Dorrestein | I. Friedberg | A. Gurevich | W. Gerwick | J. Sanders | N. Singh | K. Venkateswaran | A. Korobeynikov | L. Gerwick | H. Mohimani | Tal Luzzatto-Knaan | Alexander Shlemov | L. Nothias | Fernando Vargas | E. Glukhov | N. Moss | Md-Nafiz Hamid | C. B. Naman | Tiago F. Leão | R. S. Benitez | P. Dorrestein | Alla Mikheenko | R. Knight | Louis-Félix Nothias | Iddo Friedberg | Nitin K. Singh | Jon G. Sanders | Luke R. Thompson | James T. Morton
[1] A. Rincé,et al. Characterization of the lacticin 481 operon: the Lactococcus lactis genes lctF, lctE, and lctG encode a putative ABC transporter involved in bacteriocin immunity , 1997, Applied and environmental microbiology.
[2] Katherine H. Huang,et al. Structure, Function and Diversity of the Healthy Human Microbiome , 2012, Nature.
[3] Justine W. Debelius,et al. Towards large-cohort comparative studies to define the factors influencing the gut microbial community structure of ASD patients , 2015, Microbial ecology in health and disease.
[4] Teruhiko Beppu,et al. AmfS, an Extracellular Peptidic Morphogen in Streptomyces griseus , 2002, Journal of bacteriology.
[5] M. Hudson,et al. The SapB morphogen is a lantibiotic-like peptide derived from the product of the developmental gene ramS in Streptomyces coelicolor. , 2004, Proceedings of the National Academy of Sciences of the United States of America.
[6] Kai Blin,et al. Improved Lanthipeptide Detection and Prediction for antiSMASH , 2014, PloS one.
[7] Neha Garg,et al. Dereplication of peptidic natural products through database search of mass spectra , 2016, Nature chemical biology.
[8] G. G. Stokes. "J." , 1890, The New Yale Book of Quotations.
[9] Wilfred A van der Donk,et al. Structural Characterization and Bioactivity Analysis of the Two-Component Lantibiotic Flv System from a Ruminant Bacterium. , 2016, Cell chemical biology.
[10] Weixin Tang,et al. Structural Characterization of Four Prochlorosins: A Novel Class of Lantipeptides Produced by Planktonic Marine Cyanobacteria , 2012, Biochemistry.
[11] P. Cochat,et al. Et al , 2008, Archives de pediatrie : organe officiel de la Societe francaise de pediatrie.
[12] 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 and Biology.
[13] Dmitry Antipov,et al. Assembling Single-Cell Genomes and Mini-Metagenomes From Chimeric MDA Products , 2013, J. Comput. Biol..
[14] Katherine H. Huang,et al. A framework for human microbiome research , 2012, Nature.
[15] Shigeki Matsunaga,et al. Polytheonamides A and B, highly cytotoxic, linear polypeptides with unprecedented structural features, from the marine sponge, Theonella swinhoei. , 2005, Journal of the American Chemical Society.
[16] Victor M. Markowitz,et al. IMG-ABC: A Knowledge Base To Fuel Discovery of Biosynthetic Gene Clusters and Novel Secondary Metabolites , 2015, mBio.
[17] Dekel Tsur,et al. Identification of post-translational modifications by blind search of mass spectra , 2005, Nature Biotechnology.
[18] Kai Blin,et al. antiSMASH 3.0—a comprehensive resource for the genome mining of biosynthetic gene clusters , 2015, Nucleic Acids Res..
[19] Christian Rinke,et al. An environmental bacterial taxon with a large and distinct metabolic repertoire , 2014, Nature.
[20] Sergey I. Nikolenko,et al. SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing , 2012, J. Comput. Biol..
[21] P. G. Arnison,et al. Ribosomally synthesized and post-translationally modified peptide natural products: overview and recommendations for a universal nomenclature. , 2013, Natural product reports.
[22] J. Vederas,et al. [Drug discovery and natural products: end of era or an endless frontier?]. , 2011, Biomeditsinskaia khimiia.
[23] Harald Gross,et al. The genomisotopic approach: a systematic method to isolate products of orphan biosynthetic gene clusters. , 2007, Chemistry & biology.
[24] Rekha Seshadri,et al. Complete genome sequence of the plant commensal Pseudomonas fluorescens Pf-5 , 2005, Nature Biotechnology.
[25] P ? ? ? ? ? ? ? % ? ? ? ? , 1991 .
[26] Peter Cimermancic,et al. A Systematic Analysis of Biosynthetic Gene Clusters in the Human Microbiome Reveals a Common Family of Antibiotics , 2014, Cell.
[27] Yasuyuki Nogata,et al. Wewakazole B, a Cytotoxic Cyanobactin from the Cyanobacterium Moorea producens Collected in the Red Sea. , 2016, Journal of natural products.
[28] Kristian Fog Nielsen,et al. Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking , 2016, Nature Biotechnology.
[29] Jörn Piel,et al. Metagenome Mining Reveals Polytheonamides as Posttranslationally Modified Ribosomal Peptides , 2012, Science.
[30] Pavel A. Pevzner,et al. NRPquest: Coupling Mass Spectrometry and Genome Mining for Nonribosomal Peptide Discovery , 2014, Journal of natural products.
[31] Neil L Kelleher,et al. Structure determination and interception of biosynthetic intermediates for the plantazolicin class of highly discriminating antibiotics. , 2011, ACS chemical biology.
[32] Kasthuri Venkateswaran,et al. Draft Genome Sequences of Two Aspergillus fumigatus Strains, Isolated from the International Space Station , 2016, Genome Announcements.
[33] J. Hansen,et al. Identification and Characterization of the Structural and Transporter Genes for, and the Chemical and Biological Properties of, Sublancin 168, a Novel Lantibiotic Produced by Bacillus subtilis 168* , 1998, The Journal of Biological Chemistry.
[34] Neha Garg,et al. Lantibiotics from Geobacillus thermodenitrificans , 2012, Proceedings of the National Academy of Sciences.
[35] H Kubota,et al. Molecular structure of the toxin domain of heat-stable enterotoxin produced by a pathogenic strain of Escherichia coli. A putative binding site for a binding protein on rat intestinal epithelial cell membranes. , 1996, The Journal of biological chemistry.
[36] O. Fiehn,et al. Using fragmentation trees and mass spectral trees for identifying unknown compounds in metabolomics. , 2015, Trends in analytical chemistry : TRAC.
[37] Christopher T. Walsh,et al. Antibiotics for Emerging Pathogens , 2009, Science.
[38] Sylvie Lautru,et al. Discovery of a new peptide natural product by Streptomyces coelicolor genome mining , 2005, Nature chemical biology.
[39] 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..
[40] A. Rincé,et al. Cloning, expression, and nucleotide sequence of genes involved in production of lactococcin DR, a bacteriocin from lactococcus lactis subsp. lactis , 1994, Applied and environmental microbiology.
[41] Pavel A. Pevzner,et al. Mutation-Tolerant Protein Identification by Mass Spectrometry , 2000, J. Comput. Biol..
[42] Pavel A. Pevzner,et al. A new approach to evaluating statistical significance of spectral identifications. , 2013, Journal of proteome research.
[43] Nuno Bandeira,et al. Mass spectral molecular networking of living microbial colonies , 2012, Proceedings of the National Academy of Sciences.
[44] Rick L. Stevens,et al. A communal catalogue reveals Earth’s multiscale microbial diversity , 2017, Nature.
[45] Steven P Gygi,et al. Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry , 2007, Nature Methods.
[46] Liujie Huo,et al. Discovery and Characterization of Bicereucin, an Unusual d-Amino Acid-Containing Mixed Two-Component Lantibiotic , 2016, Journal of the American Chemical Society.
[47] P. Pevzner,et al. metaSPAdes: a new versatile metagenomic assembler. , 2017, Genome research.
[48] Nuno Bandeira,et al. MS/MS networking guided analysis of molecule and gene cluster families , 2013, Proceedings of the National Academy of Sciences.
[49] M. Fischbach,et al. Small molecules from the human microbiota , 2015, Science.
[50] Neil L. Kelleher,et al. Discovery and in vitro biosynthesis of haloduracin, a two-component lantibiotic , 2006, Proceedings of the National Academy of Sciences.
[51] G. Challis,et al. Coelichelin, a new peptide siderophore encoded by the Streptomyces coelicolor genome: structure prediction from the sequence of its non-ribosomal peptide synthetase. , 2000, FEMS microbiology letters.
[52] Hosein Mohimani,et al. Dereplication, sequencing and identification of peptidic natural products: from genome mining to peptidogenomics to spectral networks. , 2016, Natural product reports.
[53] Sergey Koren,et al. Draft Genome Sequences from a Novel Clade of Bacillus cereus Sensu Lato Strains, Isolated from the International Space Station , 2017, Genome Announcements.
[54] M. Bibb,et al. Biosynthesis and Regulation of Grisemycin, a New Member of the Linaridin Family of Ribosomally Synthesized Peptides Produced by Streptomyces griseus IFO 13350 , 2011, Journal of bacteriology.
[55] Chris L. Tang,et al. Efficiency of database search for identification of mutated and modified proteins via mass spectrometry. , 2001, Genome research.
[56] Dekel Tsur,et al. Identification of post-translational modifications via blind search of mass-spectra , 2005, 2005 IEEE Computational Systems Bioinformatics Conference (CSB'05).
[57] Nuno Bandeira,et al. Automated Genome Mining of Ribosomal Peptide Natural Products , 2014, ACS chemical biology.
[58] Carla S. Jones,et al. Minimum Information about a Biosynthetic Gene cluster. , 2015, Nature chemical biology.
[59] William H Gerwick,et al. Wewakazole, a novel cyclic dodecapeptide from a Papua New Guinea Lyngbya majuscula. , 2003, Organic letters.
[60] K. Lewis,et al. A new antibiotic kills pathogens without detectable resistance , 2015, Nature.
[61] Pieter C. Dorrestein,et al. A mass spectrometry-guided genome mining approach for natural product peptidogenomics , 2011, Nature chemical biology.
[62] Christopher T Walsh,et al. A chemocentric view of the natural product inventory. , 2015, Nature chemical biology.
[63] Douglas A. Mitchell,et al. Plantazolicin, a Novel Microcin B17/Streptolysin S-Like Natural Product from Bacillus amyloliquefaciens FZB42 , 2010, Journal of bacteriology.
[64] Michael A Fischbach,et al. Computational approaches to natural product discovery. , 2015, Nature chemical biology.
[65] Rob Knight,et al. The Earth Microbiome project: successes and aspirations , 2014, BMC Biology.
[66] Nuno Bandeira,et al. Digitizing mass spectrometry data to explore the chemical diversity and distribution of marine cyanobacteria and algae , 2017, eLife.
[67] Iddo Friedberg,et al. A large scale prediction of bacteriocin gene blocks suggests a wide functional spectrum for bacteriocins , 2015, BMC Bioinformatics.
[68] A. Harvey,et al. The re-emergence of natural products for drug discovery in the genomics era , 2015, Nature Reviews Drug Discovery.
[69] Paul D. Cotter,et al. Identification of a Novel Two-Peptide Lantibiotic, Lichenicidin, following Rational Genome Mining for LanM Proteins , 2009, Applied and Environmental Microbiology.
[70] Nuno Bandeira,et al. Protein identification by spectral networks analysis. , 2011, Methods in molecular biology.
[71] Arthur Brady,et al. Strains, functions and dynamics in the expanded Human Microbiome Project , 2017, Nature.