Improved Small Molecule Identification through Learning Combinations of Kernel Regression Models

SIRIUS 4: a rapid tool for turning tandem mass spectra into metabolite structure information

(2019) Kai Dührkop et al.   NATURE METHODS

ADAPTIVE: leArning DAta-dePendenT, concIse molecular VEctors for fast, accurate metabolite identification from tandem mass spectra

(2019) Dai Hai Nguyen et al.   BIOINFORMATICS

CFM-ID 3.0: Significantly Improved ESI-MS/MS Prediction and Compound Identification

(2019) Yannick Djoumbou-Feunang et al.   Metabolites

ChemDistiller: an engine for metabolite annotation in mass spectrometry

(2018) Ivan Laponogov et al.   BIOINFORMATICS

SIMPLE: Sparse Interaction Model over Peaks of moLEcules for fast, interpretable metabolite identification from tandem mass spectra

(2018) Dai Hai Nguyen et al.   BIOINFORMATICS

OUP accepted manuscript

(2018)   BRIEFINGS IN BIOINFORMATICS

Multimodal Machine Learning: A Survey and Taxonomy

(2018) Tadas Baltrusaitis et al.   IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE

Critical Assessment of Small Molecule Identification 2016: automated methods

(2017) Emma L. Schymanski et al.   Journal of Cheminformatics

The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching

(2017) Egon L. Willighagen et al.   Journal of Cheminformatics

Fast metabolite identification with Input Output Kernel Regression

(2016) Céline Brouard et al.   BIOINFORMATICS

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

(2016) Mingxun Wang et al.   NATURE BIOTECHNOLOGY

MetFrag relaunched: incorporating strategies beyond in silico fragmentation

(2016) Christoph Ruttkies et al.   Journal of Cheminformatics

Fragmentation trees reloaded

(2016) Sebastian Böcker et al.   Journal of Cheminformatics

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

Metabolite identification through multiple kernel learning on fragmentation trees

(2014) Huibin Shen et al.   BIOINFORMATICS

CFM-ID: a web server for annotation, spectrum prediction and metabolite identification from tandem mass spectra

(2014) Felicity Allen et al.   NUCLEIC ACIDS RESEARCH

Metabolite identification and molecular fingerprint prediction through machine learning

(2012) M. Heinonen et al.   BIOINFORMATICS

In silico fragmentation for computer assisted identification of metabolite mass spectra

(2010) Sebastian Wolf et al.   BMC BIOINFORMATICS

Extended-Connectivity Fingerprints

(2010) David Rogers et al.   Journal of Chemical Information and Modeling

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

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

Towards de novo identification of metabolites by analyzing tandem mass spectra

(2008) S. Bocker et al.   BIOINFORMATICS

Chemical substructures that enrich for biological activity

(2008) Justin Klekota et al.   BIOINFORMATICS