We are pleased to share some of the highly cited papers from the Section “Bioinformatics and Data Analysis” published in Metabolites (ISSN: 2218-1989) in 2024 and 2025. In addition, some Special Issues related to this topic are currently open for submission.

The following is a list of notable articles and Special Issues:

1. “A Comprehensive LC–MS Metabolomics Assay for Quantitative Analysis of Serum and Plasma”
by Lun Zhang, Jiamin Zheng, Mathew Johnson, Rupasri Mandal, Meryl Cruz, Miriam Martínez-Huélamo, Cristina Andres-Lacueva and David S. Wishart
Metabolites 2024, 14(11), 622; https://doi.org/10.3390/metabo14110622
Available online: https://www.mdpi.com/2218-1989/14/11/622

2. “Explainable AI to Facilitate Understanding of Neural Network-Based Metabolite Profiling Using NMR Spectroscopy”
by Hayden Johnson and Aaryani Tipirneni-Sajja
Metabolites 2024, 14(6), 332; https://doi.org/10.3390/metabo14060332
Available online: https://www.mdpi.com/2218-1989/14/6/332

3. “Implementation of FAIR Practices in Computational Metabolomics Workflows—A Case Study”
by Mahnoor Zulfiqar, Michael R. Crusoe, Birgitta König-Ries, Christoph Steinbeck, Kristian Peters and Luiz Gadelha
Metabolites 2024, 14(2), 118; https://doi.org/10.3390/metabo14020118
Available online: https://www.mdpi.com/2218-1989/14/2/118

4. “Integrating TCGA and Single-Cell Sequencing Data for Hepatocellular Carcinoma: A Novel Glycosylation (GLY)/Tumor Microenvironment (TME) Classifier to Predict Prognosis and Immunotherapy Response”
by Yun Wu, Jiaru Chen, Riting Zhu, Guoliang Huang, Jincheng Zeng, Hongbing Yu, Zhiwei He and Cuifang Han
Metabolites 2024, 14(1), 51; https://doi.org/10.3390/metabo14010051
Available online: https://www.mdpi.com/2218-1989/14/1/51

5. “Temperature Dependence of Platelet Metabolism”
by Freyr Jóhannsson, James T. Yurkovich, Steinn Guðmundsson, Ólafur E. Sigurjónsson and Óttar Rolfsson
Metabolites 2024, 14(2), 91; https://doi.org/10.3390/metabo14020091
Available online: https://www.mdpi.com/2218-1989/14/2/91

6. “Analysis of In Vivo Plant Volatiles Using Active Sampling and TD-GC×GC-TOFMS”
by Sheri A. Schmidt, Ewenet Yemane Mesfin, Chaminda De Silva Weeraddana, A. Paulina de la Mata, Alejandro C. Costamagna and James J. Harynuk
Metabolites 2024, 14(11), 623; https://doi.org/10.3390/metabo14110623
Available online: https://www.mdpi.com/2218-1989/14/11/623

7. “Advanced Machine Learning for Comparative Synovial Fluid Analysis in Osteoarthritis and Rheumatoid Arthritis”
by Karolina Krystyna Kopeć, Gabrieleanselmo Uccheddu, Paweł Chodnicki, Antonio Noto, Cristina Piras, Martina Spada, Luigi Atzori and Vassilios Fanos
Metabolites 2025, 15(2), 112; https://doi.org/10.3390/metabo15020112  
Available online: https://www.mdpi.com/2218-1989/15/2/112

8. “A Comprehensive Comparison between Primary Liver Cancer and Liver Metastases through scRNA-Seq Data Analysis”
by Shuang Hao, Liqun Chen, Wenhui Du and Huiyan Sun
Metabolites 2024, 14(2), 90; https://doi.org/10.3390/metabo14020090
Available online: https://www.mdpi.com/2218-1989/14/2/90

9. “A Deep Mining Strategy for Peptide Rapid Identification in Lactobacillus reuteri Based on LC–MS/MS Integrated with FBMN and De Novo Sequencing”
by Yilang Zuo, Shilin Gong, Li Zhang, Jie Zhou, Jian-Lin Wu and Na Li
Metabolites 2024, 14(9), 467; https://doi.org/10.3390/metabo14090467
Available online: https://www.mdpi.com/2218-1989/14/9/467

10. “Intra-Individual Variations in How Insulin Sensitivity Responds to Long-Term Exercise: Predictions by Machine Learning Based on Large-Scale Serum Proteomics”
by Jonas Krag Viken, Thomas Olsen, Christian André Drevon, Marit Hjorth, Kåre Inge Birkeland, Frode Norheim and Sindre Lee-Ødegård
Metabolites 2024, 14(6), 335; https://doi.org/10.3390/metabo14060335
Available online: https://www.mdpi.com/2218-1989/14/6/335

Special Issues:

1. “Mechanism-Aware Machine Learning in Metabolomics and Clinical Translation: Signatures, Pathways, and Patient Impact”
Guest Editor: Dr. Vasuk Gautam
Submission deadline: 31 July 2026

2. “Machine Learning in Metabolomics: Unlocking the Future of Data Analysis”
Guest Editors: Dr. Boryana Petrova and Dr. Arzu Tugce Guler
Submission deadline: 31 May 2026

3. “Open-Source Software in Metabolomics, 2nd Edition”
Guest Editor: Prof. Dr. Seongho Kim
Submission deadline: 10 May 2026

If you are an active researcher in the field and are passionate about participating in cutting-edge research publications, please do not hesitate to contact the Metabolites Editorial Office (metabolites@mdpi.com).