Dereplication of microbial metabolites through database search of mass spectra

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

(2018) Alexey Gurevich et al.   Nature Microbiology

metaSPAdes: a new versatile metagenomic assembler

(2017) Sergey Nurk et al.   GENOME RESEARCH

Significance estimation for large scale metabolomics annotations by spectral matching

(2017) Kerstin Scheubert et al.   Nature Communications

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

(2017) Tal Luzzatto-Knaan et al.   eLife

Hydrogen Rearrangement Rules: Computational MS/MS Fragmentation and Structure Elucidation Using MS-FINDER Software

(2016) Hiroshi Tsugawa et al.   ANALYTICAL CHEMISTRY

Fast metabolite identification with Input Output Kernel Regression

(2016) Céline Brouard et al.   BIOINFORMATICS

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

Topic modeling for untargeted substructure exploration in metabolomics

(2016) Justin Johan Jozias van der Hooft et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

ClassyFire: automated chemical classification with a comprehensive, computable taxonomy

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

Spatial Molecular Architecture of the Microbial Community of a Peltigera Lichen

(2016) Neha Garg et al.   mSystems

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

The re-emergence of natural products for drug discovery in the genomics era

(2015) Alan L. Harvey et al.   NATURE REVIEWS DRUG DISCOVERY

Searching molecular structure databases with tandem mass spectra using CSI:FingerID

(2015) Kai Dührkop et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Using fragmentation trees and mass spectral trees for identifying unknown compounds in metabolomics

(2015) Arpana Vaniya et al.   TRAC-TRENDS IN ANALYTICAL CHEMISTRY

Competitive fragmentation modeling of ESI-MS/MS spectra for putative metabolite identification

(2014) Felicity Allen et al.   Metabolomics

MS/MS-based networking and peptidogenomics guided genome mining revealed the stenothricin gene cluster in Streptomyces roseosporus

(2013) Wei-Ting Liu et al.   JOURNAL OF ANTIBIOTICS

A New Approach to Evaluating Statistical Significance of Spectral Identifications

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

LipidBlast in silico tandem mass spectrometry database for lipid identification

(2013) Tobias Kind et al.   NATURE METHODS

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

Computational mass spectrometry for small molecules

(2013) Kerstin Scheubert et al.   Journal of Cheminformatics

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

Multiplex De Novo Sequencing of Peptide Antibiotics

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

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

A Single Streptomyces Symbiont Makes Multiple Antifungals to Support the Fungus Farming Ant Acromyrmex octospinosus

(2011) Ryan F. Seipke et al.   PLoS One

Sequencing cyclic peptides by multistage mass spectrometry

(2011) Hosein Mohimani et al.   PROTEOMICS

Metabolite identification and quantitation in LC-MS/MS-based metabolomics

(2011) Jun Feng Xiao et al.   TRAC-TRENDS IN ANALYTICAL CHEMISTRY

Computational mass spectrometry for metabolomics: Identification of metabolites and small molecules

(2010) Steffen Neumann et al.   ANALYTICAL AND BIOANALYTICAL CHEMISTRY

LC–high resolution MS in environmental analysis: from target screening to the identification of unknowns

(2010) Martin Krauss et al.   ANALYTICAL AND BIOANALYTICAL CHEMISTRY

Computing Fragmentation Trees from Tandem Mass Spectrometry Data

(2010) Florian Rasche et al.   ANALYTICAL CHEMISTRY

In silico fragmentation for computer assisted identification of metabolite mass spectra

(2010) Sebastian Wolf et al.   BMC BIOINFORMATICS

MassBank: a public repository for sharing mass spectral data for life sciences

(2010) Hisayuki Horai et al.   JOURNAL OF MASS SPECTROMETRY

Almiramides A−C: Discovery and Development of a New Class of Leishmaniasis Lead Compounds

(2010) Laura M. Sanchez et al.   JOURNAL OF MEDICINAL CHEMISTRY

Imaging mass spectrometry of intraspecies metabolic exchange revealed the cannibalistic factors of Bacillus subtilis

(2010) W.-T. Liu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Characterization of the ‘pristinamycin supercluster’ of Streptomyces pristinaespiralis

(2010) Yvonne Mast et al.   Microbial Biotechnology

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

(2009) J. W.-H. Li et al.   SCIENCE

Interferences and contaminants encountered in modern mass spectrometry

(2008) Bernd O. Keller et al.   ANALYTICA CHIMICA ACTA

Mass Spectral Metabonomics beyond Elemental Formula: Chemical Database Querying by Matching Experimental with Computational Fragmentation Spectra

(2008) Dennis W. Hill et al.   ANALYTICAL CHEMISTRY

Chemical substructures that enrich for biological activity

(2008) Justin Klekota et al.   BIOINFORMATICS

Clustering Millions of Tandem Mass Spectra

(2007) Ari M. Frank et al.   JOURNAL OF PROTEOME RESEARCH