LargeMetabo: an out-of-the-box tool for processing and analyzing large-scale metabolomic data

Molecular Mechanism for the Allosteric Inhibition of the Human Serotonin Transporter by Antidepressant Escitalopram

(2022) Weiwei Xue et al.   ACS Chemical Neuroscience

POSREG: proteomic signature discovered by simultaneously optimizing its reproducibility and generalizability

(2022) Fengcheng Li et al.   BRIEFINGS IN BIOINFORMATICS

Comprehensive metabolomics expands precision medicine for triple-negative breast cancer

(2022) Yi Xiao et al.   CELL RESEARCH

Norm ISWSVR: A Data Integration and Normalization Approach for Large-Scale Metabolomics

(2022) Xian Ding et al.   ANALYTICAL CHEMISTRY

PFmulDL: a novel strategy enabling multi-class and multi-label protein function annotation by integrating diverse deep learning methods

(2022) Weiqi Xia et al.   COMPUTERS IN BIOLOGY AND MEDICINE

ConSIG: consistent discovery of molecular signature from OMIC data

(2022) Fengcheng Li et al.   BRIEFINGS IN BIOINFORMATICS

A novel multi-class classification model for schizophrenia, bipolar disorder and healthy controls using comprehensive transcriptomic data

(2022) Qingxia Yang et al.   COMPUTERS IN BIOLOGY AND MEDICINE

A Comparative Analysis of Biological Data Integration Systems Famous for Data Exploitation and Knowledge Discovery

(2021) Omer Irshad et al.   Current Bioinformatics

In Silico Analysis Revealed a Unique Binding but Ineffective Mode of Amantadine to Influenza Virus B M2 Channel

(2021) Yue Zhang et al.   Journal of Physical Chemistry Letters

The miRNA: a small but powerful RNA for COVID-19

(2021) Song Zhang et al.   BRIEFINGS IN BIOINFORMATICS

The maternal serum metabolome by multisegment injection-capillary electrophoresis-mass spectrometry: a high-throughput platform and standardized data workflow for large-scale epidemiological studies

(2021) Meera Shanmuganathan et al.   Nature Protocols

Advances of Mechanisms-Related Metabolomics in Parkinson’s Disease

(2021) Yanyan Zhang et al.   Frontiers in Neuroscience

Pharmacometabonomics: data processing and statistical analysis

(2021) Jianbo Fu et al.   BRIEFINGS IN BIOINFORMATICS

A metabolomics pipeline for the mechanistic interrogation of the gut microbiome

(2021) Shuo Han et al.   NATURE

MetaboAnalyst 5.0: narrowing the gap between raw spectra and functional insights

(2021) Zhiqiang Pang et al.   NUCLEIC ACIDS RESEARCH

A hierarchical approach to removal of unwanted variation for large-scale metabolomics data

(2021) Taiyun Kim et al.   Nature Communications

Dispersed foraging slime mould algorithm: Continuous and binary variants for global optimization and wrapper-based feature selection

(2021) Jiao Hu et al.   KNOWLEDGE-BASED SYSTEMS

Optimization of metabolomic data processing using NOREVA

(2021) Jianbo Fu et al.   Nature Protocols

VARIDT 2.0: structural variability of drug transporter

(2021) Tingting Fu et al.   NUCLEIC ACIDS RESEARCH

HMDB 5.0: the Human Metabolome Database for 2022

(2021) David S Wishart et al.   NUCLEIC ACIDS RESEARCH

Boosted binary Harris hawks optimizer and feature selection

(2020) Yanan Zhang et al.   ENGINEERING WITH COMPUTERS

NOREVA: enhanced normalization and evaluation of time-course and multi-class metabolomic data

(2020) Qingxia Yang et al.   NUCLEIC ACIDS RESEARCH

MetaFS: Performance assessment of biomarker discovery in metaproteomics

(2020) Jing Tang et al.   BRIEFINGS IN BIOINFORMATICS

In Silico Study of Membrane Lipid Composition Regulating Conformation and Hydration of Influenza Virus B M2 Channel

(2020) Yue Zhang et al.   Journal of Chemical Information and Modeling

A long non‐coding RNA signature for diagnostic prediction of sepsis upon ICU admission

(2020) Xueyan Liu et al.   Clinical and Translational Medicine

MRMkit: Automated Data Processing for Large-Scale Targeted Metabolomics Analysis

(2020) Guoshou Teo et al.   ANALYTICAL CHEMISTRY

Towards Augmented Kernel Extreme Learning Models for Bankruptcy Prediction: Algorithmic Behavior and Comprehensive Analysis

(2020) Yanan Zhang et al.   NEUROCOMPUTING

INTEDE: interactome of drug-metabolizing enzymes

(2020) Jiayi Yin et al.   NUCLEIC ACIDS RESEARCH

mrMLM v4.0: An R Platform for Multi-locus Genome-wide Association Studies

(2020) Ya-Wen Zhang et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

MMEASE: Online meta-analysis of metabolomic data by enhanced metabolite annotation, marker selection and enrichment analysis

(2020) Qingxia Yang et al.   Journal of Proteomics

Orthogonal learning covariance matrix for defects of grey wolf optimizer: Insights, balance, diversity, and feature selection

(2020) Jiao Hu et al.   KNOWLEDGE-BASED SYSTEMS

The Consortium of Metabolomics Studies (COMETS): Metabolomics in 47 Prospective Cohort Studies

(2019) Bing Yu et al.   AMERICAN JOURNAL OF EPIDEMIOLOGY

Convolutional neural network-based annotation of bacterial type IV secretion system effectors with enhanced accuracy and reduced false discovery

(2019) Jiajun Hong et al.   BRIEFINGS IN BIOINFORMATICS

A network-based algorithm for the identification of moonlighting noncoding RNAs and its application in sepsis

(2019) Xueyan Liu et al.   BRIEFINGS IN BIOINFORMATICS

Exploring the Binding Mechanism of Metabotropic Glutamate Receptor 5 Negative Allosteric Modulators in Clinical Trials by Molecular Dynamics Simulations

(2018) Tingting Fu et al.   ACS Chemical Neuroscience

Evaluation of batch effect elimination using quality control replicates in LC-MS metabolite profiling

(2018) Ángel Sánchez-Illana et al.   ANALYTICA CHIMICA ACTA

O-GlcNAcPRED-II: an integrated classification algorithm for identifying O-GlcNAcylation sites based on fuzzy undersampling and a K-means PCA oversampling technique

(2018) Cangzhi Jia et al.   BIOINFORMATICS

MetaboAnalystR: an R package for flexible and reproducible analysis of metabolomics data

(2018) Jasmine Chong et al.   BIOINFORMATICS

Developing a new intelligent system for the diagnosis of tuberculous pleural effusion

(2018) Chengye Li et al.   COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE

Clinical Success of Drug Targets Prospectively Predicted by In Silico Study

(2018) Feng Zhu et al.   TRENDS IN PHARMACOLOGICAL SCIENCES

Discovery of the Consistently Well-Performed Analysis Chain for SWATH-MS Based Pharmacoproteomic Quantification

(2018) Jianbo Fu et al.   Frontiers in Pharmacology

Using recursive feature elimination in random forest to account for correlated variables in high dimensional data

(2018) Burcu F. Darst et al.   BMC GENETICS

A joint analysis of metabolomic profiles associated with muscle mass and strength in Caucasian women

(2018) Qi Zhao et al.   Aging-US

Create, run, share, publish, and reference your LC–MS, FIA–MS, GC–MS, and NMR data analysis workflows with the Workflow4Metabolomics 3.0 Galaxy online infrastructure for metabolomics

(2017) Yann Guitton et al.   INTERNATIONAL JOURNAL OF BIOCHEMISTRY & CELL BIOLOGY

TCMID 2.0: a comprehensive resource for TCM

(2017) Lin Huang et al.   NUCLEIC ACIDS RESEARCH

NOREVA: normalization and evaluation of MS-based metabolomics data

(2017) Bo Li et al.   NUCLEIC ACIDS RESEARCH

DrugBank 5.0: a major update to the DrugBank database for 2018

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

Emerging applications of metabolomics in drug discovery and precision medicine

(2016) David S. Wishart   NATURE REVIEWS DRUG DISCOVERY

An efficient hybrid kernel extreme learning machine approach for early diagnosis of Parkinson׳s disease

(2016) Hui-Ling Chen et al.   NEUROCOMPUTING

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

MET-XAlign: A Metabolite Cross-Alignment Tool for LC/MS-Based Comparative Metabolomics

(2015) Wenchao Zhang et al.   ANALYTICAL CHEMISTRY

Structuring Microbial Metabolic Responses to Multiplexed Stimuli via Self-Organizing Metabolomics Maps

(2015) Cody R. Goodwin et al.   CHEMISTRY & BIOLOGY

An efficient machine learning approach for diagnosis of paraquat-poisoned patients

(2015) Lufeng Hu et al.   COMPUTERS IN BIOLOGY AND MEDICINE

Analysis of the Human Adult Urinary Metabolome Variations with Age, Body Mass Index, and Gender by Implementing a Comprehensive Workflow for Univariate and OPLS Statistical Analyses

(2015) Etienne A. Thévenot et al.   JOURNAL OF PROTEOME RESEARCH

Computational and statistical analysis of metabolomics data

(2015) Sheng Ren et al.   Metabolomics

ECMDB 2.0: A richer resource for understanding the biochemistry ofE. coli

(2015) Tanvir Sajed et al.   NUCLEIC ACIDS RESEARCH

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

Interactive XCMS Online: Simplifying Advanced Metabolomic Data Processing and Subsequent Statistical Analyses

(2014) Harsha Gowda et al.   ANALYTICAL CHEMISTRY

CFam: a chemical families database based on iterative selection of functional seeds and seed-directed compound clustering

(2014) Cheng Zhang et al.   NUCLEIC ACIDS RESEARCH

T3DB: the toxic exposome database

(2014) David Wishart et al.   NUCLEIC ACIDS RESEARCH

Detection of batch effects in liquid chromatography-mass spectrometry metabolomic data using guided principal component analysis

(2014) J. Kuligowski et al.   TALANTA

Utilization of metabolomics to identify serum biomarkers for hepatocellular carcinoma in patients with liver cirrhosis

(2012) Habtom W. Ressom et al.   ANALYTICA CHIMICA ACTA

XCMS Online: A Web-Based Platform to Process Untargeted Metabolomic Data

(2012) Ralf Tautenhahn et al.   ANALYTICAL CHEMISTRY

Normalizing and Integrating Metabolomics Data

(2012) Alysha M. De Livera et al.   ANALYTICAL CHEMISTRY

Batch effect removal methods for microarray gene expression data integration: a survey

(2012) C. Lazar et al.   BRIEFINGS IN BIOINFORMATICS

A support vector machine-recursive feature elimination feature selection method based on artificial contrast variables and mutual information

(2012) Xiaohui Lin et al.   JOURNAL OF CHROMATOGRAPHY B-ANALYTICAL TECHNOLOGIES IN THE BIOMEDICAL AND LIFE SCIENCES

A Critical Assessment of Feature Selection Methods for Biomarker Discovery in Clinical Proteomics

(2012) Christin Christin et al.   MOLECULAR & CELLULAR PROTEOMICS

Stability-based biomarker selection

(2011) Ron Wehrens et al.   ANALYTICA CHIMICA ACTA

Procedures for large-scale metabolic profiling of serum and plasma using gas chromatography and liquid chromatography coupled to mass spectrometry

(2011) Warwick B Dunn et al.   Nature Protocols

YMDB: the Yeast Metabolome Database

(2011) T. Jewison et al.   NUCLEIC ACIDS RESEARCH

metaP-Server: A Web-Based Metabolomics Data Analysis Tool

(2010) Gabi Kastenmüller et al.   JOURNAL OF BIOMEDICINE AND BIOTECHNOLOGY

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

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

Global metabolic profiling procedures for urine using UPLC–MS

(2010) Elizabeth J Want et al.   Nature Protocols

Metabolite identification via the Madison Metabolomics Consortium Database

(2008) Qiu Cui et al.   NATURE BIOTECHNOLOGY