Deep learning meets metabolomics: a methodological perspective

Metabolic alterations in immune cells associate with progression to type 1 diabetes

(2020) Partho Sen et al.   DIABETOLOGIA

Migrating from partial least squares discriminant analysis to artificial neural networks: a comparison of functionally equivalent visualisation and feature contribution tools using jupyter notebooks

(2020) Kevin M. Mendez et al.   Metabolomics

Software tools, databases and resources in metabolomics: updates from 2018 to 2019

(2020) Keiron O’Shea et al.   Metabolomics

Guiding the Refinement of Biochemical Knowledgebases with Ensembles of Metabolic Networks and Machine Learning

(2020) Gregory L. Medlock et al.   Cell Systems

Combining Machine Learning and Metabolomics to Identify Weight Gain Biomarkers

(2020) Flávia Luísa Dias-Audibert et al.   Frontiers in Bioengineering and Biotechnology

NormAE: Deep Adversarial Learning Model to Remove Batch Effects in Liquid Chromatography Mass Spectrometry-Based Metabolomics Data

(2020) Zhiwei Rong et al.   ANALYTICAL CHEMISTRY

An atlas of human metabolism

(2020) Jonathan L. Robinson et al.   Science Signaling

Rapid Prediction of Electron–Ionization Mass Spectrometry Using Neural Networks

(2019) Jennifer N. Wei et al.   ACS Central Science

Robust predictions of specialized metabolism genes through machine learning

(2019) Bethany M. Moore et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Primary fatty amides in plasma associated with brain amyloid burden, hippocampal volume, and memory in the European Medical Information Framework for Alzheimer's Disease biomarker discovery cohort

(2019) Min Kim et al.   Alzheimers & Dementia

Deep MS/MS-Aided Structural-Similarity Scoring for Unknown Metabolite Identification

(2019) Hongchao Ji et al.   ANALYTICAL CHEMISTRY

A White-Box Machine Learning Approach for Revealing Antibiotic Mechanisms of Action

(2019) Jason H. Yang et al.   CELL

Deep learning: new computational modelling techniques for genomics

(2019) Gökcen Eraslan et al.   NATURE REVIEWS GENETICS

Using deep learning to evaluate peaks in chromatographic data

(2019) Anne Bech Risum et al.   TALANTA

Metabolic reaction network-based recursive metabolite annotation for untargeted metabolomics

(2019) Xiaotao Shen et al.   Nature Communications

Machine and deep learning meet genome-scale metabolic modeling

(2019) Guido Zampieri et al.   PLoS Computational Biology

Human Systems Biology and Metabolic Modelling: A Review—From Disease Metabolism to Precision Medicine

(2019) Claudio Angione   Biomed Research International

Deep Neural Networks for Classification of LC-MS Spectral Peaks

(2019) Edward D. Kantz et al.   ANALYTICAL CHEMISTRY

Metabolomics meets machine learning: Longitudinal metabolite profiling in serum of normal versus overconditioned cows and pathway analysis

(2019) Morteza H. Ghaffari et al.   JOURNAL OF DAIRY SCIENCE

WiPP: Workflow for Improved Peak Picking for Gas Chromatography-Mass Spectrometry (GC-MS) Data

(2019) Borgsmüller et al.   Metabolites

Deep learning to generate in silico chemical property libraries and candidate molecules for small molecule identification in complex samples

(2019) Sean M. Colby et al.   ANALYTICAL CHEMISTRY

Peak alignment of gas chromatography–mass spectrometry data with deep learning

(2019) Mike Li et al.   JOURNAL OF CHROMATOGRAPHY A

The application of artificial neural networks in metabolomics: a historical perspective

(2019) Kevin M. Mendez et al.   Metabolomics

Toward Explainable Anticancer Compound Sensitivity Prediction via Multimodal Attention-Based Convolutional Encoders

(2019) Matteo Manica et al.   MOLECULAR PHARMACEUTICS

Urinary Metabolomic Markers of Protein Glycation, Oxidation, and Nitration in Early-Stage Decline in Metabolic, Vascular, and Renal Health

(2019) Jinit Masania et al.   Oxidative Medicine and Cellular Longevity

Deep Learning for the Precise Peak Detection in High-Resolution LC–MS Data

(2019) Arsenty D. Melnikov et al.   ANALYTICAL CHEMISTRY

A deep learning architecture for metabolic pathway prediction

(2019) Mayank Baranwal et al.   BIOINFORMATICS

Recent advances on constraint-based models by integrating machine learning

(2019) Pratip Rana et al.   CURRENT OPINION IN BIOTECHNOLOGY

Application of ensemble deep neural network to metabolomics studies

(2018) Taiga Asakura et al.   ANALYTICA CHIMICA ACTA

Application of a Deep Neural Network to Metabolomics Studies and Its Performance in Determining Important Variables

(2018) Yasuhiro Date et al.   ANALYTICAL CHEMISTRY

Guidelines and considerations for the use of system suitability and quality control samples in mass spectrometry assays applied in untargeted clinical metabolomic studies

(2018) David Broadhurst et al.   Metabolomics

Recon3D enables a three-dimensional view of gene variation in human metabolism

(2018) Elizabeth Brunk et al.   NATURE BIOTECHNOLOGY

Deep learning in biomedicine

(2018) Michael Wainberg et al.   NATURE BIOTECHNOLOGY

A primer on deep learning in genomics

(2018) James Zou et al.   NATURE GENETICS

Deep learning in imaging

(2018) Rita Strack   NATURE METHODS

Artificial Intelligence and amniotic fluid multiomics analysis: The prediction of perinatal outcome in asymptomatic short cervix

(2018) Ray O. Bahado-Singh et al.   ULTRASOUND IN OBSTETRICS & GYNECOLOGY

Machine learning applied to enzyme turnover numbers reveals protein structural correlates and improves metabolic models

(2018) David Heckmann et al.   Nature Communications

Metabolome-wide association studies for agronomic traits of rice

(2017) Julong Wei et al.   HEREDITY

Deep Learning Accurately Predicts Estrogen Receptor Status in Breast Cancer Metabolomics Data

(2017) Fadhl M. Alakwaa et al.   JOURNAL OF PROTEOME RESEARCH

HMDB 4.0: the human metabolome database for 2018

(2017) David S Wishart et al.   NUCLEIC ACIDS RESEARCH

Deep learning and 3D-DESI imaging reveal the hidden metabolic heterogeneity of cancer

(2017) Paolo Inglese et al.   Chemical Science

A Concise Review on Multi-Omics Data Integration for Terroir Analysis in Vitis vinifera

(2017) Pastor Jullian Fabres et al.   Frontiers in Plant Science

Selection of complementary foods based on optimal nutritional values

(2017) Partho Sen et al.   Scientific Reports

Artificial Neural Network for Probabilistic Feature Recognition in Liquid Chromatography Coupled to High-Resolution Mass Spectrometry

(2016) Michael Woldegebriel et al.   ANALYTICAL CHEMISTRY

Recon 2.2: from reconstruction to model of human metabolism

(2016) Neil Swainston et al.   Metabolomics

Deep learning for computational biology

(2016) Christof Angermueller et al.   Molecular Systems Biology

Human gut microbes impact host serum metabolome and insulin sensitivity

(2016) Helle Krogh Pedersen et al.   NATURE

Bioanalytical techniques in nontargeted clinical lipidomics

(2016) Tuulia Hyötyläinen et al.   Bioanalysis

Multi-omics integration accurately predicts cellular state in unexplored conditions for Escherichia coli

(2016) Minseung Kim et al.   Nature Communications

A tutorial review: Metabolomics and partial least squares-discriminant analysis – a marriage of convenience or a shotgun wedding

(2015) Piotr S. Gromski et al.   ANALYTICA CHIMICA ACTA

Optimizing the lipidomics workflow for clinical studies—practical considerations

(2015) Tuulia Hyötyläinen et al.   ANALYTICAL AND BIOANALYTICAL CHEMISTRY

Using Genome-scale Models to Predict Biological Capabilities

(2015) Edward J. O’Brien et al.   CELL

Deep learning

(2015) Yann LeCun et al.   NATURE

Predicting effects of noncoding variants with deep learning–based sequence model

(2015) Jian Zhou et al.   NATURE METHODS

MS-DIAL: data-independent MS/MS deconvolution for comprehensive metabolome analysis

(2015) Hiroshi Tsugawa et al.   NATURE METHODS

KEGG as a reference resource for gene and protein annotation

(2015) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

An integrated catalog of reference genes in the human gut microbiome

(2014) Junhua Li et al.   NATURE BIOTECHNOLOGY

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

(2014) Felicity Allen et al.   NUCLEIC ACIDS RESEARCH

Genome-scale metabolic modelling of hepatocytes reveals serine deficiency in patients with non-alcoholic fatty liver disease

(2014) Adil Mardinoglu et al.   Nature Communications

Simple topological properties predict functional misannotations in a metabolic network

(2013) Rodrigo Liberal et al.   BIOINFORMATICS

Supervised de novo reconstruction of metabolic pathways from metabolome-scale compound sets

(2013) M. Kotera et al.   BIOINFORMATICS

Integration of clinical data with a genome-scale metabolic model of the human adipocyte

(2013) A. Mardinoglu et al.   Molecular Systems Biology

A community-driven global reconstruction of human metabolism

(2013) Ines Thiele et al.   NATURE BIOTECHNOLOGY

Computational solutions for omics data

(2013) Bonnie Berger et al.   NATURE REVIEWS GENETICS

SMPDB 2.0: Big Improvements to the Small Molecule Pathway Database

(2013) Timothy Jewison et al.   NUCLEIC ACIDS RESEARCH

Predicting Network Activity from High Throughput Metabolomics

(2013) Shuzhao Li et al.   PLoS Computational Biology

Reconstruction of genome-scale metabolic models for 126 human tissues using mCADRE

(2012) Yuliang Wang et al.   BMC Systems Biology

Performance Evaluation of Algorithms for the Classification of Metabolic 1H NMR Fingerprints

(2012) Jochen Hochrein et al.   JOURNAL OF PROTEOME RESEARCH

Reconstruction of Genome-Scale Active Metabolic Networks for 69 Human Cell Types and 16 Cancer Types Using INIT

(2012) Rasmus Agren et al.   PLoS Computational Biology

The Human Serum Metabolome

(2011) Nikolaos Psychogios et al.   PLoS One

In silico fragmentation for computer assisted identification of metabolite mass spectra

(2010) Sebastian Wolf et al.   BMC BIOINFORMATICS

MZmine 2: Modular framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile data

(2010) Tomáš Pluskal et al.   BMC BIOINFORMATICS

A human gut microbial gene catalogue established by metagenomic sequencing

(2010) Junjie Qin et al.   NATURE

What is flux balance analysis?

(2010) Jeffrey D Orth et al.   NATURE BIOTECHNOLOGY

The challenges of integrating multi-omic data sets

(2010) Bernhard Palsson et al.   Nature Chemical Biology

Reactome: a database of reactions, pathways and biological processes

(2010) D. Croft et al.   NUCLEIC ACIDS RESEARCH

Dimensionality reduction for metabolome data using PCA, PLS, OPLS, and RFDA with differential penalties to latent variables

(2009) Hiroyuki Yamamoto et al.   CHEMOMETRICS AND INTELLIGENT LABORATORY SYSTEMS

Applications of genome-scale metabolic reconstructions

(2009) Matthew A Oberhardt et al.   Molecular Systems Biology

HMDB: a knowledgebase for the human metabolome

(2008) D. S. Wishart et al.   NUCLEIC ACIDS RESEARCH