Computational approaches to natural product discovery

MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

(2015) Dinghua Li et al.   BIOINFORMATICS

Computational approaches to natural product discovery

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

IMG-ABC: A Knowledge Base To Fuel Discovery of Biosynthetic Gene Clusters and Novel Secondary Metabolites

(2015) Michalis Hadjithomas et al.   mBio

Automated Genome Mining of Ribosomal Peptide Natural Products

(2014) Hosein Mohimani et al.   ACS Chemical Biology

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

(2014) Peter Cimermancic et al.   CELL

eSNaPD: A Versatile, Web-Based Bioinformatics Platform for Surveying and Mining Natural Product Biosynthetic Diversity from Metagenomes

(2014) Boojala Vijay B. Reddy et al.   CHEMISTRY & BIOLOGY

Metagenomic small molecule discovery methods

(2014) Zachary Charlop-Powers et al.   CURRENT OPINION IN MICROBIOLOGY

Motif-Independent Prediction of a Secondary Metabolism Gene Cluster Using Comparative Genomics: Application to Sequenced Genomes of Aspergillus and Ten Other Filamentous Fungal Species

(2014) Itaru Takeda et al.   DNA RESEARCH

In silico tools for the analysis of antibiotic biosynthetic pathways

(2014) Tilmann Weber   INTERNATIONAL JOURNAL OF MEDICAL MICROBIOLOGY

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

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

Secondary metabolomics: the impact of mass spectrometry-based approaches on the discovery and characterization of microbial natural products

(2014) Daniel Krug et al.   NATURAL PRODUCT REPORTS

Mass spectrometry of natural products: current, emerging and future technologies

(2014) Amina Bouslimani et al.   NATURAL PRODUCT REPORTS

An environmental bacterial taxon with a large and distinct metabolic repertoire

(2014) Micheal C. Wilson et al.   NATURE

Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes

(2014) H Bjørn Nielsen et al.   NATURE BIOTECHNOLOGY

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

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

Improved Lanthipeptide Detection and Prediction for antiSMASH

(2014) Kai Blin et al.   PLoS One

Tackling soil diversity with the assembly of large, complex metagenomes

(2014) Adina Chuang Howe et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

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

Metagenomic Approaches for Exploiting Uncultivated Bacteria as a Resource for Novel Biosynthetic Enzymology

(2013) Micheal C. Wilson et al.   CHEMISTRY & BIOLOGY

“Function-First” Lead Discovery: Mode of Action Profiling of Natural Product Libraries Using Image-Based Screening

(2013) Christopher J. Schulze et al.   CHEMISTRY & BIOLOGY

Design-based re-engineering of biosynthetic gene clusters: plug-and-play in practice

(2013) Hans-Jörg Frasch et al.   CURRENT OPINION IN BIOTECHNOLOGY

The phenomenon of microbial uncultivability

(2013) SS Epstein   CURRENT OPINION IN MICROBIOLOGY

Bioinformatics tools for genome mining of polyketide and non-ribosomal peptides

(2013) Christopher N. Boddy   JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY

Databases of the thiotemplate modular systems (CSDB) and their in silico recombinants (r-CSDB)

(2013) Janko Diminic et al.   JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY

Predicting substrate specificity of adenylation domains of nonribosomal peptide synthetases and other protein properties by latent semantic indexing

(2013) Damir Baranašić et al.   JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY

Detecting Sequence Homology at the Gene Cluster Level with MultiGeneBlast

(2013) Marnix H. Medema et al.   MOLECULAR BIOLOGY AND EVOLUTION

Insights into the phylogeny and coding potential of microbial dark matter

(2013) Christian Rinke et al.   NATURE

Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes

(2013) Mads Albertsen et al.   NATURE BIOTECHNOLOGY

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

(2013) Kai Blin et al.   NUCLEIC ACIDS RESEARCH

The ChEMBL bioactivity database: an update

(2013) A. Patrícia Bento 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

KNApSAcK Metabolite Activity Database for Retrieving the Relationships Between Metabolites and Biological Activities

(2013) Y. Nakamura et al.   PLANT AND CELL PHYSIOLOGY

Classification of the Adenylation and Acyl-Transferase Activity of NRPS and PKS Systems Using Ensembles of Substrate Specific Hidden Markov Models

(2013) Barzan I. Khayatt et al.   PLoS One

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

Metagenomic natural product discovery in lichen provides evidence for a family of biosynthetic pathways in diverse symbioses

(2013) A. Kampa et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Glycogenomics as a mass spectrometry-guided genome-mining method for microbial glycosylated molecules

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

Mapping gene clusters within arrayed metagenomic libraries to expand the structural diversity of biomedically relevant natural products

(2013) J. G. Owen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Using Functional Signature Ontology (FUSION) to Identify Mechanisms of Action for Natural Products

(2013) M. B. Potts et al.   Science Signaling

Gene fragmentation in bacterial draft genomes: extent, consequences and mitigation

(2012) Jonathan L Klassen et al.   BMC GENOMICS

The spectral networks paradigm in high throughput mass spectrometry

(2012) Adrian Guthals et al.   Molecular BioSystems

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

Genomic sequencing of uncultured microorganisms from single cells

(2012) Roger S. Lasken   NATURE REVIEWS MICROBIOLOGY

StreptomeDB: a resource for natural compounds isolated from Streptomyces species

(2012) X. Lucas et al.   NUCLEIC ACIDS RESEARCH

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 ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013

(2012) Janna Hastings 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

Genome streamlining and chemical defense in a coral reef symbiosis

(2012) J. C. Kwan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ray Meta: scalable de novo metagenome assembly and profiling

(2012) Sébastien Boisvert et al.   GENOME BIOLOGY

NRPSsp: non-ribosomal peptide synthase substrate predictor

(2011) Carlos Prieto et al.   BIOINFORMATICS

Bacterial symbionts and natural products

(2011) Jason M. Crawford et al.   CHEMICAL COMMUNICATIONS

Cycloquest: Identification of Cyclopeptides via Database Search of Their Mass Spectra against Genome Databases

(2011) Hosein Mohimani et al.   JOURNAL OF PROTEOME RESEARCH

Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications

(2011) Pelin Yilmaz et al.   NATURE BIOTECHNOLOGY

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

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

NRPSpredictor2—a web server for predicting NRPS adenylation domain specificity

(2011) Marc Röttig et al.   NUCLEIC ACIDS RESEARCH

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

The Pfam protein families database

(2011) M. Punta et al.   NUCLEIC ACIDS RESEARCH

Chemical Analyses of Wasp-Associated Streptomyces Bacteria Reveal a Prolific Potential for Natural Products Discovery

(2011) Michael Poulsen et al.   PLoS One

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

SMURF: Genomic mapping of fungal secondary metabolite clusters

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

ChemSpider: An Online Chemical Information Resource

(2010) Harry E. Pence et al.   JOURNAL OF CHEMICAL EDUCATION

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

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

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

MapsiDB: an integrated web database for type I polyketide synthases

(2009) Hongseok Tae et al.   BIOPROCESS AND BIOSYSTEMS ENGINEERING

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

Entomopathogenic bacteria as a source of secondary metabolites

(2009) Helge B Bode   CURRENT OPINION IN CHEMICAL BIOLOGY

CLUSEAN: A computer-based framework for the automated analysis of bacterial secondary metabolite biosynthetic gene clusters

(2009) T. Weber et al.   JOURNAL OF BIOTECHNOLOGY

A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea

(2009) Dongying Wu et al.   NATURE

PubChem: a public information system for analyzing bioactivities of small molecules

(2009) Y. Wang et al.   NUCLEIC ACIDS RESEARCH

Antibiotics for Emerging Pathogens

(2009) M. A. Fischbach et al.   SCIENCE

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