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

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

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

(2014) Peter Cimermancic et al.   CELL

Analysis and Refactoring of the A-74528 Biosynthetic Pathway

(2013) Jay T. Fitzgerald et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Refactoring the Silent Spectinabilin Gene Cluster Using a Plug-and-Play Scaffold

(2013) Zengyi Shao et al.   ACS Synthetic Biology

Complete Genome Sequence of the Frog Pathogen Mycobacterium ulcerans Ecovar Liflandii

(2012) N. J. Tobias et al.   JOURNAL OF BACTERIOLOGY

Horizontal gene transfer and gene conversion drive evolution of modular polyketide synthases

(2012) Jurica Zucko et al.   JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY

Evolution of Secondary Metabolite Genes in Three Closely Related Marine Actinomycete Species

(2011) Kelle C. Freel et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Massive Genomic Decay in Serratia symbiotica, a Recently Evolved Symbiont of Aphids

(2011) Gaelen R. Burke et al.   Genome Biology and Evolution

MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods

(2011) K. Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

IMG: the integrated microbial genomes database and comparative analysis system

(2011) V. M. Markowitz et al.   NUCLEIC ACIDS RESEARCH

Open Babel: An open chemical toolbox

(2011) Noel M O'Boyle et al.   Journal of Cheminformatics

Cytoscape 2.8: new features for data integration and network visualization

(2010) M. E. Smoot et al.   BIOINFORMATICS

Biosynthesis of the Putative Siderophore Erythrochelin Requires Unprecedented Crosstalk between Separate Nonribosomal Peptide Gene Clusters

(2010) Orestis Lazos et al.   CHEMISTRY & BIOLOGY

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

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

Five hard truths for synthetic biology

(2010) Roberta Kwok   NATURE

Exploiting plug-and-play synthetic biology for drug discovery and production in microorganisms

(2010) Marnix H. Medema et al.   NATURE REVIEWS MICROBIOLOGY

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

Secondary metabolic gene clusters: evolutionary toolkits for chemical innovation

(2010) Anne Osbourn   TRENDS IN GENETICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Recurring cluster and operon assembly for Phenylacetate degradation genes

(2009) Fergal J Martin et al.   BMC EVOLUTIONARY BIOLOGY

Organisation of the Biosynthetic Gene Cluster and Tailoring Enzymes in the Biosynthesis of the Tetracyclic Quinone Glycoside Antibiotic Polyketomycin

(2009) Martina Daum  et al.   CHEMBIOCHEM

Evidence that a secondary metabolic biosynthetic gene cluster has grown by gene relocation during evolution of the filamentous fungusFusarium

(2009) Robert H. Proctor et al.   MOLECULAR MICROBIOLOGY

Genomic basis for natural product biosynthetic diversity in the actinomycetes

(2009) Markus Nett et al.   NATURAL PRODUCT REPORTS

Polyketide assembly lines of uncultivated sponge symbionts from structure-based gene targeting

(2009) Katja M Fisch et al.   Nature Chemical Biology

The Pfam protein families database

(2009) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Organization of the Biosynthetic Gene Cluster for the Polyketide Antitumor Macrolide, Pladienolide, inStreptomyces platensisMer-11107

(2008) Kazuhiro MACHIDA et al.   BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY

Optimizing Natural Products by Biosynthetic Engineering: Discovery of Nonquinone Hsp90 Inhibitors†

(2008) Ming-Qiang Zhang et al.   JOURNAL OF MEDICINAL CHEMISTRY

Exploiting the mosaic structure of trans-acyltransferase polyketide synthases for natural product discovery and pathway dissection

(2008) TuAnh Nguyen et al.   NATURE BIOTECHNOLOGY

PROMALS3D web server for accurate multiple protein sequence and structure alignments

(2008) J. Pei et al.   NUCLEIC ACIDS RESEARCH

A simple, fast, and accurate method of phylogenomic inference

(2008) Martin Wu et al.   GENOME BIOLOGY