Increased diversity of peptidic natural products revealed by modification-tolerant database search of mass spectra

MSFragger: ultrafast and comprehensive peptide identification in mass spectrometry–based proteomics

(2017) Andy T Kong et al.   NATURE METHODS

Digitizing mass spectrometry data to explore the chemical diversity and distribution of marine cyanobacteria and algae

(2017) Tal Luzzatto-Knaan et al.   eLife

Dereplication, sequencing and identification of peptidic natural products: from genome mining to peptidogenomics to spectral networks

(2016) Hosein Mohimani et al.   NATURAL PRODUCT REPORTS

Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking

(2016) Mingxun Wang et al.   NATURE BIOTECHNOLOGY

Dereplication of peptidic natural products through database search of mass spectra

(2016) Hosein Mohimani et al.   Nature Chemical Biology

IMG-ABC: new features for bacterial secondary metabolism analysis and targeted biosynthetic gene cluster discovery in thousands of microbial genomes

(2016) Michalis Hadjithomas et al.   NUCLEIC ACIDS RESEARCH

ClassyFire: automated chemical classification with a comprehensive, computable taxonomy

(2016) Yannick Djoumbou Feunang et al.   Journal of Cheminformatics

Indexing the Pseudomonas specialized metabolome enabled the discovery of poaeamide B and the bananamides

(2016) Don D. Nguyen et al.   Nature Microbiology

Molecular Networking and Pattern-Based Genome Mining Improves Discovery of Biosynthetic Gene Clusters and their Products from Salinispora Species

(2015) Katherine R. Duncan et al.   CHEMISTRY & BIOLOGY

A new antibiotic kills pathogens without detectable resistance

(2015) Losee L. Ling et al.   NATURE

Minimum Information about a Biosynthetic Gene cluster

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

Illuminating the dark matter in metabolomics: Fig. 1.

(2015) Ricardo R. da Silva et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Automated Genome Mining of Ribosomal Peptide Natural Products

(2014) Hosein Mohimani et al.   ACS Chemical Biology

Isolation and structural determination of a new hydrophobic peptide venepeptide from Streptomyces venezuelae

(2014) Shinya Kodani et al.   JOURNAL OF ANTIBIOTICS

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

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

Image-Based 384-Well High-Throughput Screening Method for the Discovery of Skyllamycins A to C as Biofilm Inhibitors and Inducers of Biofilm Detachment in Pseudomonas aeruginosa

(2013) Gabriel Navarro et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Surugamides A–E, Cyclic Octapeptides with Four d-Amino Acid Residues, from a Marine Streptomyces sp.: LC–MS-Aided Inspection of Partial Hydrolysates for the Distinction of d- and l-Amino Acid Residues in the Sequence

(2013) Kentaro Takada et al.   JOURNAL OF ORGANIC CHEMISTRY

A New Approach to Evaluating Statistical Significance of Spectral Identifications

(2013) Hosein Mohimani et al.   JOURNAL OF PROTEOME RESEARCH

Discovery and development of first in class antifungal caspofungin (CANCIDAS®)—A case study

(2013) James M. Balkovec et al.   NATURAL PRODUCT REPORTS

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

StreptomeDB: a resource for natural compounds isolated from Streptomyces species

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

Mass spectral molecular networking of living microbial colonies

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

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

Small Molecule Databases and Chemical Descriptors Useful in Chemoinformatics: An Overview

(2011) Rafael Gozalbes et al.   COMBINATORIAL CHEMISTRY & HIGH THROUGHPUT SCREENING

Multiplex De Novo Sequencing of Peptide Antibiotics

(2011) Hosein Mohimani et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

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

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

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 hidden diversity of ribosomal peptide natural products

(2010) Eric W Schmidt   BMC BIOLOGY

Dereplication and de novo sequencing of nonribosomal peptides

(2009) Julio Ng et al.   NATURE METHODS