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

Evaluation of strategies for the assembly of diverse bacterial genomes using MinION long-read sequencing

(2019) Sarah Goldstein et al.   BMC GENOMICS

Bioinformatic Expansion and Discovery of Thiopeptide Antibiotics

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

Novel soil bacteria possess diverse genes for secondary metabolite biosynthesis

(2018) Alexander Crits-Christoph et al.   NATURE

A primer on deep learning in genomics

(2018) James Zou et al.   NATURE GENETICS

The antiSMASH database version 2: a comprehensive resource on secondary metabolite biosynthetic gene clusters

(2018) Kai Blin et al.   NUCLEIC ACIDS RESEARCH

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

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

RiPPMiner: a bioinformatics resource for deciphering chemical structures of RiPPs based on prediction of cleavage and cross-links

(2017) Priyesh Agrawal 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

Comparative analysis of chemical similarity methods for modular natural products with a hypothetical structure enumeration algorithm

(2017) Michael A. Skinnider et al.   Journal of Cheminformatics

Natural Products as Sources of New Drugs from 1981 to 2014

(2016) David J. Newman et al.   JOURNAL OF NATURAL PRODUCTS

Deep learning for computational biology

(2016) Christof Angermueller et al.   Molecular Systems Biology

New tools for reconstruction and heterologous expression of natural product biosynthetic gene clusters

(2016) Yunzi Luo et al.   NATURAL PRODUCT REPORTS

Polyketide and nonribosomal peptide retro-biosynthesis and global gene cluster matching

(2016) Chris A Dejong et al.   Nature Chemical Biology

Assembly and clustering of natural antibiotics guides target identification

(2016) Chad W Johnston et al.   Nature Chemical Biology

Dereplication of peptidic natural products through database search of mass spectra

(2016) Hosein Mohimani et al.   Nature Chemical Biology

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

Exploration of Nonribosomal Peptide Families with an Automated Informatic Search Algorithm

(2015) Lian Yang et al.   CHEMISTRY & BIOLOGY

Regulating malonyl-CoA metabolism via synthetic antisense RNAs for enhanced biosynthesis of natural products

(2015) Yaping Yang et al.   METABOLIC ENGINEERING

Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning

(2015) Babak Alipanahi et al.   NATURE BIOTECHNOLOGY

Computational approaches to natural product discovery

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

Genomes to natural products PRediction Informatics for Secondary Metabolomes (PRISM)

(2015) Michael A. Skinnider et al.   NUCLEIC ACIDS RESEARCH

An automated Genomes-to-Natural Products platform (GNP) for the discovery of modular natural products

(2015) Chad W. Johnston et al.   Nature Communications

Automated Genome Mining of Ribosomal Peptide Natural Products

(2014) Hosein Mohimani et al.   ACS Chemical Biology

Nucleophilic 1,4-Additions for Natural Product Discovery

(2014) Courtney L. Cox et al.   ACS Chemical Biology

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

(2014) Peter Cimermancic et al.   CELL

Automated Identification of Depsipeptide Natural Products by an Informatic Search Algorithm

(2014) Michael A. Skinnider et al.   CHEMBIOCHEM

NRPquest: Coupling Mass Spectrometry and Genome Mining for Nonribosomal Peptide Discovery

(2014) Hosein Mohimani et al.   JOURNAL OF NATURAL PRODUCTS

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

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

Heterologous Expression of the Thiopeptide Antibiotic GE2270 from Planobispora rosea ATCC 53733 in Streptomyces coelicolor Requires Deletion of Ribosomal Genes from the Expression Construct

(2014) Katrin Flinspach et al.   PLoS One

Structural investigation of ribosomally synthesized natural products by hypothetical structure enumeration and evaluation using tandem MS

(2014) Q. Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Pep2Path: Automated Mass Spectrometry-Guided Genome Mining of Peptidic Natural Products

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

Genome mining of the Streptomyces avermitilis genome and development of genome-minimized hosts for heterologous expression of biosynthetic gene clusters

(2013) Haruo Ikeda et al.   JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY

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

PKMiner: a database for exploring type II polyketide synthases

(2012) Jinki Kim et al.   BMC MICROBIOLOGY

Antibiotics: A New Hope

(2012) Gerard D. Wright   CHEMISTRY & BIOLOGY

Sequential deletion of all the polyketide synthase and nonribosomal peptide synthetase biosynthetic gene clusters and a 900-kb subtelomeric sequence of the linear chromosome of Streptomyces coelicolor

(2012) Min Zhou et al.   FEMS MICROBIOLOGY LETTERS

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

DoBISCUIT: a database of secondary metabolite biosynthetic gene clusters

(2012) Natsuko Ichikawa et al.   NUCLEIC ACIDS RESEARCH

ClusterMine360: a database of microbial PKS/NRPS biosynthesis

(2012) Kyle R. Conway et al.   NUCLEIC ACIDS RESEARCH

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

(2012) Nadine Ziemert et al.   PLoS One

Dereplicating nonribosomal peptides using an informatic search algorithm for natural products (iSNAP) discovery

(2012) A. Ibrahim et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

Genome-minimized Streptomyces host for the heterologous expression of secondary metabolism

(2010) M. Komatsu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Catalytic promiscuity in the biosynthesis of cyclic peptide secondary metabolites in planktonic marine cyanobacteria

(2010) B. Li et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Automated genome mining for natural products

(2009) Michael HT Li et al.   BMC BIOINFORMATICS

Drug Discovery and Natural Products: End of an Era or an Endless Frontier?

(2009) J. W.-H. Li et al.   SCIENCE