Expansion of RiPP biosynthetic space through integration of pan-genomics and machine learning uncovers a novel class of lanthipeptides

Cacaoidin, first member of the new lanthidin RiPP family

(2020) Francisco Javier Ortiz-López et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Precursor peptide-targeted mining of more than one hundred thousand genomes expands the lanthipeptide natural product family

(2020) Mark C. Walker et al.   BMC GENOMICS

Polyphasic classification of the gifted natural product producer Streptomyces roseifaciens sp. nov.

(2019) Lizah T. van der Aart et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Uncovering the unexplored diversity of thioamidated ribosomal peptides in Actinobacteria using the RiPPER genome mining tool

(2019) Javier Santos-Aberturas et al.   NUCLEIC ACIDS RESEARCH

antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline

(2019) Kai Blin et al.   NUCLEIC ACIDS RESEARCH

A computational framework to explore large-scale biosynthetic diversity

(2019) Jorge C. Navarro-Muñoz et al.   Nature Chemical Biology

NeuRiPP: Neural network identification of RiPP precursor peptides

(2019) Emmanuel L. C. de los Santos   Scientific Reports

DeepRiPP integrates multiomics data to automate discovery of novel ribosomally synthesized natural products

(2019) Nishanth J. Merwin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Discovery and biosynthesis of thioviridamide-like compounds

(2018) Jian Tang et al.   CHINESE CHEMICAL LETTERS

Identification of essential biosynthetic genes and a true biosynthetic product for thioviridamide

(2018) Masumi Izawa et al.   JOURNAL OF GENERAL AND APPLIED MICROBIOLOGY

Bioinformatic Expansion and Discovery of Thiopeptide Antibiotics

(2018) Christopher J. Schwalen et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Mapping in vivo target interaction profiles of covalent inhibitors using chemical proteomics with label-free quantification

(2018) Eva J van Rooden et al.   Nature Protocols

BAGEL4: a user-friendly web server to thoroughly mine RiPPs and bacteriocins

(2018) Auke J van Heel et al.   NUCLEIC ACIDS RESEARCH

Natural noncanonical protein splicing yields products with diverse β-amino acid residues

(2018) Brandon I. Morinaka et al.   SCIENCE

A standardized workflow for submitting data to the Minimum Information about a Biosynthetic Gene cluster (MIBiG) repository: prospects for research-based educational experiences

(2018) Samuel C. Epstein et al.   Standards in Genomic Sciences

Dynamics of Pellet Fragmentation and Aggregation in Liquid-Grown Cultures of Streptomyces lividans

(2018) Boris Zacchetti et al.   Frontiers in Microbiology

A topologically distinct modified peptide with multiple bicyclic core motifs expands the diversity of microviridin-like peptides

(2018) Heejin Roh et al.   CHEMBIOCHEM

Enzymatic Reconstitution and Biosynthetic Investigation of the Lasso Peptide Fusilassin

(2018) Adam J. DiCaprio et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Radical Approach to Enzymatic β-Thioether Bond Formation

(2018) Alessio Caruso et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Database resources of the National Center for Biotechnology Information

(2018) Eric W Sayers et al.   NUCLEIC ACIDS RESEARCH

OrthoDB v10: sampling the diversity of animal, plant, fungal, protist, bacterial and viral genomes for evolutionary and functional annotations of orthologs

(2018) Evgenia V Kriventseva et al.   NUCLEIC ACIDS RESEARCH

The Pfam protein families database in 2019

(2018) Sara El-Gebali et al.   NUCLEIC ACIDS RESEARCH

BUSCO Applications from Quality Assessments to Gene Prediction and Phylogenomics

(2017) Robert M Waterhouse et al.   MOLECULAR BIOLOGY AND EVOLUTION

A new genome-mining tool redefines the lasso peptide biosynthetic landscape

(2017) Jonathan I Tietz et al.   Nature Chemical Biology

PRISM 3: expanded prediction of natural product chemical structures from microbial genomes

(2017) Michael A. Skinnider et al.   NUCLEIC ACIDS RESEARCH

antiSMASH 4.0—improvements in chemistry prediction and gene cluster boundary identification

(2017) Kai Blin et al.   NUCLEIC ACIDS RESEARCH

Comparative transcriptomics as a guide to natural product discovery and biosynthetic gene cluster functionality

(2017) Gregory C. A. Amos et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Exploring Peptide Ligase Orthologs in Actinobacteria—Discovery of Pseudopeptide Natural Products, Ketomemicins

(2016) Yasushi Ogasawara et al.   ACS Chemical Biology

Phylogenomic Analysis of Natural Products Biosynthetic Gene Clusters Allows Discovery of Arseno-Organic Metabolites in Model Streptomycetes

(2016) Pablo Cruz-Morales et al.   Genome Biology and Evolution

Aggregation of germlings is a major contributing factor towards mycelial heterogeneity of Streptomyces

(2016) Boris Zacchetti et al.   Scientific Reports

Goodbye to brute force in antibiotic discovery?

(2016) Roberto Kolter et al.   Nature Microbiology

Expanded Natural Product Diversity Revealed by Analysis of Lanthipeptide-Like Gene Clusters in Actinobacteria

(2015) Qi Zhang et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Chaxapeptin, a Lasso Peptide from Extremotolerant Streptomyces leeuwenhoekii Strain C58 from the Hyperarid Atacama Desert

(2015) Somayah S. Elsayed et al.   JOURNAL OF ORGANIC CHEMISTRY

Post-translational Introduction of d-Alanine into Ribosomally Synthesized Peptides by the Dehydroalanine Reductase NpnJ

(2015) Xiao Yang et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Taxonomy, Physiology, and Natural Products of Actinobacteria

(2015) Essaid Ait Barka et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Computational approaches to natural product discovery

(2015) Marnix H Medema et al.   Nature Chemical Biology

Discovery of microbial natural products by activation of silent biosynthetic gene clusters

(2015) Peter J. Rutledge et al.   NATURE REVIEWS MICROBIOLOGY

Insights into Secondary Metabolism from a Global Analysis of Prokaryotic Biosynthetic Gene Clusters

(2014) Peter Cimermancic et al.   CELL

A peptide ligase and the ribosome cooperate to synthesize the peptide pheganomycin

(2014) Motoyoshi Noike et al.   Nature Chemical Biology

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

The InterPro protein families database: the classification resource after 15 years

(2014) Alex Mitchell et al.   NUCLEIC ACIDS RESEARCH

Novel LanT Associated Lantibiotic Clusters Identified by Genome Database Mining

(2014) Mangal Singh et al.   PLoS One

A Systematic Computational Analysis of Biosynthetic Gene Cluster Evolution: Lessons for Engineering Biosynthesis

(2014) Marnix H. Medema et al.   PLoS Computational Biology

Bidirectional Best Hits Miss Many Orthologs in Duplication-Rich Clades such as Plants and Animals

(2013) Daniel A. Dalquen et al.   Genome Biology and Evolution

Drift time-specific collision energies enable deep-coverage data-independent acquisition proteomics

(2013) Ute Distler et al.   NATURE METHODS

Platforms for antibiotic discovery

(2013) Kim Lewis   NATURE REVIEWS DRUG DISCOVERY

A Tight Link between Orthologs and Bidirectional Best Hits in Bacterial and Archaeal Genomes

(2012) Yuri I. Wolf et al.   Genome Biology and Evolution

Erratum: Thoughts and facts about antibiotics: Where we are now and where we are heading

(2012) János Bérdy   JOURNAL OF ANTIBIOTICS

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

(2012) Paul G. Arnison et al.   NATURAL PRODUCT REPORTS

Structure and Biosynthesis of the Antibiotic Bottromycin D

(2012) Yanpeng Hou et al.   ORGANIC LETTERS

Metagenome Mining Reveals Polytheonamides as Posttranslationally Modified Ribosomal Peptides

(2012) M. F. Freeman et al.   SCIENCE

Posttranslational β-methylation and macrolactamidination in the biosynthesis of the bottromycin complex of ribosomal peptide antibiotics

(2012) Juan Pablo Gomez-Escribano et al.   Chemical Science

Identification and characterisation of the gene cluster for the anti-MRSA antibiotic bottromycin: expanding the biosynthetic diversity of ribosomal peptides

(2012) William J. K. Crone et al.   Chemical Science

Biosynthesis of Aminovinyl-Cysteine-Containing Peptides and Its Application in the Production of Potential Drug Candidates

(2011) Clarissa S. Sit et al.   ACCOUNTS OF CHEMICAL RESEARCH

The ATP-grasp enzymes

(2011) Maria V. Fawaz et al.   BIOORGANIC CHEMISTRY

Fix the antibiotics pipeline

(2011) Matthew A. Cooper et al.   NATURE

A mass spectrometry–guided genome mining approach for natural product peptidogenomics

(2011) Roland D Kersten et al.   Nature Chemical Biology

Exploiting the Natural Diversity of Microviridin Gene Clusters for Discovery of Novel Tricyclic Depsipeptides

(2010) N. Ziemert et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

MZmine 2: Modular framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile data

(2010) Tomáš Pluskal et al.   BMC BIOINFORMATICS

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Characterization of the ‘pristinamycin supercluster’ of Streptomyces pristinaespiralis

(2010) Yvonne Mast et al.   Microbial Biotechnology

Thiostrepton Biosynthesis: Prototype for a New Family of Bacteriocins

(2009) Wendy L. Kelly et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Synthesis of the Lantibiotic Lactocin S Using Peptide Cyclizations on Solid Phase

(2009) Avena C. Ross et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Discovery of proteinaceous N-modification in lysine biosynthesis of Thermus thermophilus

(2009) Akira Horie et al.   Nature Chemical Biology

Follow the leader: the use of leader peptides to guide natural product biosynthesis

(2009) Trent J Oman et al.   Nature Chemical Biology

Using Sequence Similarity Networks for Visualization of Relationships Across Diverse Protein Superfamilies

(2009) Holly J. Atkinson et al.   PLoS One

Functional expression of the Cre recombinase in actinomycetes

(2008) Marta Fedoryshyn et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY