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

Metabolic engineering of antibiotic factories: new tools for antibiotic production in actinomycetes

(2015) Tilmann Weber et al.   TRENDS IN BIOTECHNOLOGY

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

(2014) Peter Cimermancic et al.   CELL

In silico tools for the analysis of antibiotic biosynthetic pathways

(2014) Tilmann Weber   INTERNATIONAL JOURNAL OF MEDICAL MICROBIOLOGY

A roadmap for natural product discovery based on large-scale genomics and metabolomics

(2014) James R Doroghazi et al.   Nature Chemical Biology

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Formation of 1,3-Cyclohexanediones and Resorcinols Catalyzed by a Widely Occuring Ketosynthase

(2013) Sebastian W. Fuchs et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

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

(2013) Kai Blin et al.   NUCLEIC ACIDS RESEARCH

Pfam: the protein families database

(2013) Robert D. Finn 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

MS/MS networking guided analysis of molecule and gene cluster families

(2013) D. D. Nguyen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The RAVEN Toolbox and Its Use for Generating a Genome-scale Metabolic Model for Penicillium chrysogenum

(2013) Rasmus Agren et al.   PLoS Computational Biology

EFICAz2.5: application of a high-precision enzyme function predictor to 396 proteomes

(2012) Narendra Kumar et al.   BIOINFORMATICS

Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data

(2012) M. Kearse et al.   BIOINFORMATICS

Natural Products As Sources of New Drugs over the 30 Years from 1981 to 2010

(2012) David J. Newman et al.   JOURNAL OF NATURAL PRODUCTS

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

Constraining the metabolic genotype–phenotype relationship using a phylogeny of in silico methods

(2012) Nathan E. Lewis et al.   NATURE REVIEWS MICROBIOLOGY

MultiMetEval: Comparative and Multi-Objective Analysis of Genome-Scale Metabolic Models

(2012) Piotr Zakrzewski et al.   PLoS One

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

SMURF: Genomic mapping of fungal secondary metabolite clusters

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

SBSPKS: structure based sequence analysis of polyketide synthases

(2010) Swadha Anand et al.   NUCLEIC ACIDS RESEARCH

Biopython: freely available Python tools for computational molecular biology and bioinformatics

(2009) P. J. A. Cock et al.   BIOINFORMATICS

A comparative genomics study of genetic products potentially encoding ladderane lipid biosynthesis

(2009) Jayne E Rattray et al.   Biology Direct

Automated genome mining for natural products

(2009) Michael HT Li et al.   BMC BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

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