Detecting and prioritizing biosynthetic gene clusters for bioactive compounds in bacteria and fungi

Panning for gold in mould: can we increase the odds for fungal genome mining?

(2018) Cameron L. M. Gilchrist et al.   ORGANIC & BIOMOLECULAR CHEMISTRY

HEx: A heterologous expression platform for the discovery of fungal natural products

(2018) Colin J. B. Harvey et al.   Science Advances

Resistance-gene-directed discovery of a natural-product herbicide with a new mode of action

(2018) Yan Yan et al.   NATURE

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

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

The Antibiotic Resistant Target Seeker (ARTS), an exploration engine for antibiotic cluster prioritization and novel drug target discovery

(2017) Mohammad Alanjary et al.   NUCLEIC ACIDS RESEARCH

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

Lateral Gene Transfer Dynamics in the Ancient Bacterial Genus Streptomyces

(2017) Bradon R. McDonald et al.   mBio

Resistance Gene-Guided Genome Mining: Serial Promoter Exchanges in Aspergillus nidulans Reveal the Biosynthetic Pathway for Fellutamide B, a Proteasome Inhibitor

(2016) Hsu-Hua Yeh 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

P450-Mediated Coupling of Indole Fragments To Forge Communesin and Unnatural Isomers

(2016) Hsiao-Ching Lin et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Genomic charting of ribosomally synthesized natural product chemical space facilitates targeted mining

(2016) Michael A. Skinnider et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Identification of Thiotetronic Acid Antibiotic Biosynthetic Pathways by Target-directed Genome Mining

(2015) Xiaoyu Tang et al.   ACS Chemical Biology

Azithromycin for the Prevention of COPD Exacerbations: The Good, Bad, and Ugly

(2015) Stephanie Parks Taylor et al.   AMERICAN JOURNAL OF MEDICINE

Elucidation of the Concise Biosynthetic Pathway of the Communesin Indole Alkaloids

(2015) Hsiao-Ching Lin et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Editorial: Yeast synthetic biology: new tools to unlock cellular function

(2015)   FEMS YEAST RESEARCH

Discovery of Unclustered Fungal Indole Diterpene Biosynthetic Pathways through Combinatorial Pathway Reassembly in Engineered Yeast

(2015) Man-Cheng Tang et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Efficient Biosynthesis of Fungal Polyketides Containing the Dioxabicyclo-octane Ring System

(2015) Xu-Ming Mao et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Computational approaches to natural product discovery

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

Translating biosynthetic gene clusters into fungal armor and weaponry

(2015) Nancy P Keller   Nature Chemical Biology

antiSMASH 3.0—a comprehensive resource for the genome mining of biosynthetic gene clusters

(2015) Tilmann Weber et al.   NUCLEIC ACIDS RESEARCH

Resistance is not futile: gliotoxin biosynthesis, functionality and utility

(2015) Stephen K. Dolan et al.   TRENDS IN MICROBIOLOGY

Complete genome sequence and comparative genomic analyses of the vancomycin-producing Amycolatopsis orientalis

(2014) Li Xu et al.   BMC GENOMICS

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

(2014) Peter Cimermancic et al.   CELL

Recent advances in natural product discovery

(2014) Yunzi Luo et al.   CURRENT OPINION IN BIOTECHNOLOGY

Generation of Complexity in Fungal Terpene Biosynthesis: Discovery of a Multifunctional Cytochrome P450 in the Fumagillin Pathway

(2014) Hsiao-Ching Lin et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Antibiotic resistance–mediated isolation of scaffold-specific natural product producers

(2014) Maulik N Thaker et al.   Nature Protocols

Identification and Characterization of a New Erythromycin Biosynthetic Gene Cluster in Actinopolyspora erythraea YIM90600, a Novel Erythronolide-Producing Halophilic Actinomycete Isolated from Salt Field

(2014) Dandan Chen et al.   PLoS One

The Fusarium graminearum Genome Reveals More Secondary Metabolite Gene Clusters and Hints of Horizontal Gene Transfer

(2014) Christian M. K. Sieber et al.   PLoS One

Diversity and evolution of secondary metabolism in the marine actinomycete genus Salinispora

(2014) N. Ziemert et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A comprehensive resource of genomic, epigenomic and transcriptomic sequencing data for the black truffle Tuber melanosporum

(2014) Pao-Yang Chen et al.   GigaScience

Multilocus Sequence Typing Reveals Evidence of Homologous Recombination Linked to Antibiotic Resistance in the Genus Salinispora

(2013) Kelle C. Freel et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Recent advances and new strategies in the NMR-based identification of natural products

(2013) Maria Halabalaki et al.   CURRENT OPINION IN BIOTECHNOLOGY

Prospects for new antibiotics: a molecule-centered perspective

(2013) Christopher T Walsh et al.   JOURNAL OF ANTIBIOTICS

The Fumagillin Biosynthetic Gene Cluster in Aspergillus fumigatus Encodes a Cryptic Terpene Cyclase Involved in the Formation of β-trans-Bergamotene

(2013) Hsiao-Ching Lin et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

antiSMASH 2.0—a versatile platform for genome mining of secondary metabolite producers

(2013) Kai Blin et al.   NUCLEIC ACIDS RESEARCH

BAGEL3: automated identification of genes encoding bacteriocins and (non-)bactericidal posttranslationally modified peptides

(2013) Auke J. van Heel et al.   NUCLEIC ACIDS RESEARCH

Genomic sequencing of uncultured microorganisms from single cells

(2012) Roger S. Lasken   NATURE REVIEWS MICROBIOLOGY

The Natural Product Domain Seeker NaPDoS: A Phylogeny Based Bioinformatic Tool to Classify Secondary Metabolite Gene Diversity

(2012) Nadine Ziemert et al.   PLoS One

Bacterial Self-Resistance to the Natural Proteasome Inhibitor Salinosporamide A

(2011) Andrew J. Kale et al.   ACS Chemical Biology

A new class of IMP dehydrogenase with a role in self-resistance of mycophenolic acid producing fungi

(2011) Bjarne G Hansen et al.   BMC MICROBIOLOGY

Phase 1 clinical trial of the novel proteasome inhibitor marizomib with the histone deacetylase inhibitor vorinostat in patients with melanoma, pancreatic and lung cancer based on in vitro assessments of the combination

(2011) Michael Millward et al.   INVESTIGATIONAL NEW DRUGS

antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences

(2011) Marnix H. Medema et al.   NUCLEIC ACIDS RESEARCH

Gene duplications in prokaryotes can be associated with environmental adaptation

(2010) Marit S Bratlie et al.   BMC GENOMICS

Deciphering chemotaxis pathways using cross species comparisons

(2010) Rebecca Hamer et al.   BMC Systems Biology

Horizontal Transfer of a Large and Highly Toxic Secondary Metabolic Gene Cluster between Fungi

(2010) Jason C. Slot et al.   CURRENT BIOLOGY

SMURF: Genomic mapping of fungal secondary metabolite clusters

(2010) Nora Khaldi et al.   FUNGAL GENETICS AND BIOLOGY

Avoidance of suicide in antibiotic-producing microbes

(2010) Eric Cundliffe et al.   JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY

Transannular Disulfide Formation in Gliotoxin Biosynthesis and Its Role in Self-Resistance of the Human PathogenAspergillus fumigatus

(2010) Daniel H. Scharf et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Natural Products Version 2.0: Connecting Genes to Molecules

(2010) Christopher T. Walsh et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Périgord black truffle genome uncovers evolutionary origins and mechanisms of symbiosis

(2010) Francis Martin et al.   NATURE

SBSPKS: structure based sequence analysis of polyketide synthases

(2010) Swadha Anand et al.   NUCLEIC ACIDS RESEARCH

BAGEL2: mining for bacteriocins in genomic data

(2010) Anne de Jong et al.   NUCLEIC ACIDS RESEARCH

Automated genome mining for natural products

(2009) Michael HT Li et al.   BMC BIOINFORMATICS

Coupling of the biosynthesis and export of the DNA gyrase inhibitor simocyclinone inStreptomyces antibioticus

(2009) Tung B. K. Le et al.   MOLECULAR MICROBIOLOGY

Ancient Horizontal Gene Transfer from Bacteria Enhances Biosynthetic Capabilities of Fungi

(2009) Imke Schmitt et al.   PLoS One

ClustScan : an integrated program package for the semi-automatic annotation of modular biosynthetic gene clusters and in silico prediction of novel chemical structures

(2008) Antonio Starcevic et al.   NUCLEIC ACIDS RESEARCH

Evidence for horizontal transfer of a secondary metabolite gene cluster between fungi

(2008) Nora Khaldi et al.   GENOME BIOLOGY