Announcements

1. “Approaches to Integrating Metabolomics and Multi-Omics Data: A Primer”
   by Takoua Jendoubi
   Metabolites 2021, 11(3), 184; https://doi.org/10.3390/metabo11030184
   Available online: https://www.mdpi.com/2218-1989/11/3/184
   

2. “Next-Generation Genome-Scale Metabolic Modeling through Integration of Regulatory Mechanisms”
   *Feature Paper
   by Carolina H. Chung, Da-Wei Lin, Alec Eames and Sriram Chandrasekaran
   Metabolites 2021, 11(9), 606; https://doi.org/10.3390/metabo11090606
   Available online: https://www.mdpi.com/2218-1989/11/9/606
   

3. “Amino Acid Metabolism in Apicomplexan Parasites”
   by Aarti Krishnan and Dominique Soldati-Favre
   Metabolites 2021, 11(2), 61; https://doi.org/10.3390/metabo11020061
   Available online: https://www.mdpi.com/2218-1989/11/2/61
   

4. “Reconstruction of a Genome-Scale Metabolic Model of Streptomyces albus J1074: Improved Engineering Strategies in Natural Product Synthesis”
   *Feature Paper
   by Cheewin Kittikunapong, Suhui Ye, Patricia Magadán-Corpas, Álvaro Pérez-Valero, Claudio J. Villar, Felipe Lombó and Eduard J. Kerkhoven
   Metabolites 2021, 11(5), 304; https://doi.org/10.3390/metabo11050304
   Available online: https://www.mdpi.com/2218-1989/11/5/304
   

5. “Investigating Global Lipidome Alterations with the Lipid Network Explorer”
   by Nikolai Köhler, Tim Daniel Rose, Lisa Falk and Josch Konstantin Pauling
   Metabolites 2021, 11(8), 488; https://doi.org/10.3390/metabo11080488
   Available online: https://www.mdpi.com/2218-1989/11/8/488
   

6. “MSCAT: A Machine Learning Assisted Catalog of Metabolomics Software Tools”
   by Jonathan Dekermanjian, Wladimir Labeikovsky, Debashis Ghosh and Katerina Kechris
   Metabolites 2021, 11(10), 678; https://doi.org/10.3390/metabo11100678
   Available online: https://www.mdpi.com/2218-1989/11/10/678
   

7. “Diverse Taxonomies for Diverse Chemistries: Enhanced Representation of Natural Product Metabolism in UniProtKB”
   by Marc Feuermann, Emmanuel Boutet, Anne Morgat, Kristian B. Axelsen, Parit Bansal, Jerven Bolleman, Edouard de Castro, Elisabeth Coudert, Elisabeth Gasteiger, Sébastien Géhant et al.
   Metabolites 2021, 11(1), 48; https://doi.org/10.3390/metabo11010048
   Available online: https://www.mdpi.com/2218-1989/11/1/48
   

8. “Pathway Tools Visualization of Organism-Scale Metabolic Networks”
   by Suzanne Paley, Richard Billington, James Herson, Markus Krummenacker and Peter D. Karp
   Metabolites 2021, 11(2), 64; https://doi.org/10.3390/metabo11020064
   Available online: https://www.mdpi.com/2218-1989/11/2/64
   

1. “Uncoupling Thermotolerance and Growth Performance in Chinook Salmon: Blood Biochemistry and Immune Capacity”
   by Ronald Lulijwa, Tim Young, Jane E. Symonds, Seumas P. Walker, Natalí J. Delorme and Andrea C. Alfaro
   Metabolites 2021, 11(8), 547; https://doi.org/10.3390/metabo11080547
   Available online: https://www.mdpi.com/2218-1989/11/8/547
   

2. “Oral Supplementation of an Alkylglycerol Mix Comprising Different Alkyl Chains Effectively Modulates Multiple Endogenous Plasmalogen Species in Mice”
   by Sudip Paul, Aliki A. Rasmiena, Kevin Huynh, Adam Alexander T. Smith, Natalie A. Mellett, Karin Jandeleit-Dahm, Graeme I. Lancaster and Peter J. Meikle
   Metabolites 2021, 11(5), 299; https://doi.org/10.3390/metabo11050299
   Available online: https://www.mdpi.com/2218-1989/11/5/299
   

3. “Simultaneous Measurement of Amino Acid Enantiomers in Aged Mouse Brain Samples by LC/MS/MS Combined with Derivatization Using N^α-(5-Fluoro-2,4-dinitrophenyl)-l-leucinamide (l-FDLA)”
   by Taiji Yamamoto, Keisuke Yaku and Takashi Nakagawa
   Metabolites 2021, 11(1), 57; https://doi.org/10.3390/metabo11010057
   Available online: https://www.mdpi.com/2218-1989/11/1/57
   

4. “Correlation between Pre-Ovulatory Follicle Diameter and Follicular Fluid Metabolome Profiles in Lactating Beef Cows”
   by Casey C. Read, Lannett Edwards, Neal Schrick, Justin D. Rhinehart, Rebecca R. Payton, Shawn R. Campagna, Hector F. Castro, Jessica L. Klabnik, Emma J. Horn and Sarah E. Moorey
   Metabolites 2021, 11(9), 623; https://doi.org/10.3390/metabo11090623
   Available online: https://www.mdpi.com/2218-1989/11/9/623
   

5. “Exploring the Lipids Involved in the Formation of Characteristic Lactones in Japanese Black Cattle”
   by Shuji Ueda, Ryo Sasaki, Rio Nakabayashi, Minoru Yamanoue, Yasuhito Sirai and Eiji Iwamoto
   Metabolites 2021, 11(4), 203; https://doi.org/10.3390/metabo11040203
   Available online: https://www.mdpi.com/2218-1989/11/4/203
   

6. “Metabolites Secreted by Bovine Embryos In Vitro Predict Pregnancies That the Recipient Plasma Metabolome Cannot, and Vice Versa”
   *Editor’s Choice Paper
   by Enrique Gomez, Nuria Canela, Pol Herrero, Adrià Cereto, Isabel Gimeno, Susana Carrocera, David Martin-Gonzalez, Antonio Murillo and Marta Muñoz
   Metabolites 2021, 11(3), 162; https://doi.org/10.3390/metabo11030162
   Available online: https://www.mdpi.com/2218-1989/11/3/162
   

7. “The Effects of Live Transport on Metabolism and Stress Responses of Abalone (Haliotis iris)”
   by Andrea C. Alfaro, Thao V. Nguyen, Leonie Venter, Jessica A. Ericson, Shaneel Sharma, Norman L. C. Ragg and Craig Mundy
   Metabolites 2021, 11(11), 748; https://doi.org/10.3390/metabo11110748
   Available online: https://www.mdpi.com/2218-1989/11/11/748
   

8. “High Throughput Procedure for Comparative Analysis of In Vivo Cardiac Glucose or Amino Acids Use in Cardiovascular Pathologies and Pharmacological Treatments”
   *Editor’s Choice Paper
   by Marta Tomczyk, Mariola Olkowicz, Ewa M. Slominska and Ryszard T. Smolenski
   Metabolites 2021, 11(8), 497; https://doi.org/10.3390/metabo11080497
   Available online: https://www.mdpi.com/2218-1989/11/8/497
   

As a leading open access publisher, MDPI provides scholars with a high-quality and rich academic exchange platform by continuously expanding into new and exciting research areas.

In December 2022, MDPI launched five new journals, covering multiple subjects such as life sciences, biology, medicine and pharmacology, social sciences and humanities. These new journals are being edited by established scholars across the world.

If you are interested in creating more open access journals with us to publish cutting-edge research, please send your journal proposal application to newjournal-committee@mdpi.com.

MDPI is pleased to announce that we now display the co-authors’ email addresses in addition to the corresponding author’s email address on the webpage of published papers, protected by Captcha. For more information about this change, please visit the journal’s instructions for authors page. 

We believe this change will facilitate academic discussions and advance our cause of open science and research. The corresponding authors are responsible for communicating with their co-authors and indicating in our system (https://susy.mdpi.com/) if co-authors would prefer for their email addresses not to be displayed.

On 9 February 2023, Clarivate, a global leader in providing trusted insights and analytics, added the Preprint Citation Index to the Web of Science platform, streamlining the research process by allowing researchers to locate and link to preprints alongside other trusted content in the database.

The Preprint Citation Index will act as a bridge to connect cutting-edge preprints with peer-reviewed journal articles published within the Web of Science Core Collection. Alerts can be easily set to monitor new research across several repositories and authors will also be able to include preprints on their Web of Science Research Profile to more accurately display their various research outputs.

As of its launch, the Preprint Citation Index will provide nearly two million preprints from various repositories, including MDPI’s own Preprints.org.

MDPI's Preprints Platform – Preprints.org

To advance Open Science and the fast dissemination of research, MDPI offers researchers a free multidisciplinary preprint platform. Preprints.org accepts submissions from all research areas and offers authors high visibility, permanent archiving, article-level Metrics and immediately citable content by assigning a Digital Object Identifier (DOI) to all preprints.

During submission to any MDPI journal, authors have the option to share their research as a preprint. After an initial screening, the manuscript is available online in 48 hours or less. Once online, preprints can be downloaded, shared, commented on, and cited, providing authors maximum visibility.

We invite you to join the ranks of the over 100k researchers using Preprints.org and share your research.

For more information, please visit Preprints.org.

Conference: 11th National Conference on Bioinformatics and Systems Biology
Date: 25–27 February 2023
Place: Guangzhou, China

MDPI will be attending the 11th National Conference on Bioinformatics and Systems Biology (CCBSB2023) as the exhibitor. The National Academic Conference on Bioinformatics and Systems Biology has been successfully held for ten sessions since its first session in 1998. It is a national event with the highest academic level and the greatest influence in the field of bioinformatics research in China. The theme of the conference is "The Latest Frontier Research of Bioinformatics and Systems Biology and Their Applications", and the topics cover translational informatics and data sharing security, biomedical data mining and computing, genome informatics, artificial intelligence and life sciences, group bioinformatics and integrated biology, non-coding RNA and RNA informatics, network biology, major disease omics informatics, biological macromolecular structure prediction and simulation, bioinformatics algorithm research, biological data resources, bioinformatics and drugs discovery, computational synthetic biology, agricultural and forestry informatics and other bioinformatics, and other frontier directions.

The following MDPI journals will be represented:

• Genes;
• JPM;
• Cardiogenetics;
• Bioengineering;
• Biomolecules;
• Metabolites;
• Cells;
• Symmetry;
• Biomedicines;
• Computers;
• COVID;
• Epigenomes.

If you are attending this conference, please feel free to start a conversation with us. Our delegates look forward to meeting you in person and answering any questions that you may have. For more information about the conference, please visit https://ccbsb2022.casconf.cn/.

We are pleased to highlight several papers published in Metabolites (ISSN: 2218-1989) from the last three years. We invite you to read the selection of published papers listed below.

1. “Discovery and Validation of Potential Serum Biomarkers with Pro-Inflammatory and DNA Damage Activities in Ulcerative Colitis: A Comprehensive Untargeted Metabolomic Study”
by Boli Zhang (张伯礼)
Available online: https://www.mdpi.com/2218-1989/12/10/997

2. “Apple Polyphenol Extract Suppresses Clostridioides difficile Infection in a Mouse Model”
by Lanjuan Li (李兰娟)
Available online: https://www.mdpi.com/2218-1989/12/11/1042

3. “Targeted Metabolomics Analysis of Bile Acids in Patients with Idiosyncratic Drug-Induced Liver Injury”
by Lanjuan Li (李兰娟)
Available online: https://www.mdpi.com/2218-1989/11/12/852

4. “Comparison of the Three Most Commonly Used Metabolic Syndrome Definitions in the Chinese Population: A Prospective Study”
by Runlin Gao (高润霖)
Available online: https://www.mdpi.com/2218-1989/13/1/12

5. “Identification of Biomarkers for Methamphetamine Exposure Time Prediction in Mice Using Metabolomics and Machine Learning Approaches”
by Guangji Wang (王广基)
Available online: https://www.mdpi.com/2218-1989/12/12/1250

6. “Identification of Morphine and Heroin-Treatment in Mice Using Metabonomics”
by Guangji Wang (王广基)
Available online: https://www.mdpi.com/2218-1989/11/9/607

7. “Metabolites Associated with the Main Nutrients in Two Varieties of Purple Rice Processed to Polished Rice”
by Hongcheng Zhang (张洪程)
Available online: https://www.mdpi.com/2218-1989/13/1/7

8. “Untargeted Metabolomics Reveals the Function of GPRC6A in Amino Acid and Lipid Metabolism in Mice”
by Yulong Yin (印遇龙)
Available online: https://www.mdpi.com/2218-1989/12/9/776

9. “GPRC6A Mediates Glucose and Amino Acid Homeostasis in Mice”
by Yulong Yin (印遇龙)
Available online: https://www.mdpi.com/2218-1989/12/8/740

10. “Quantitative Profiling of Bile Acids in Feces of Humans and Rodents by Ultra-High-Performance Liquid Chromatography–Quadrupole Time-of-Flight Mass Spectrometry”
by Fazheng Ren (任发政)
Available online: https://www.mdpi.com/2218-1989/12/7/633

11. “Muscle Nutritive Metabolism Changes after Dietary Fishmeal Replaced by Cottonseed Meal in Golden Pompano (Trachinotus ovatus)”
by Kangsen Mai (麦康森)
Available online: https://www.mdpi.com/2218-1989/12/7/576

12. “Simultaneous Quantification of Trace and Micro Phenolic Compounds by Liquid Chromatography Tandem-Mass Spectrometry”
by Peiwu Li (李培武)
Available online: https://www.mdpi.com/2218-1989/11/9/589

13. “Identification and Validation of Metabolic Markers for Adulteration Detection of Edible Oils Using Metabolic Networks”
by Peiwu Li (李培武)
Available online: https://www.mdpi.com/2218-1989/10/3/85

It is our great honor to congratulate the publications that have been distinguished as highly cited papers by Clarivate^TM from 2020 to 2022, according to the Web of Science data. As of December 2022, these highly cited papers received enough citations to place them in the top 1% of the academic field of the “Biochemistry and Molecular Biology” category, based on a high citation threshold for the field and the publication year analyzed in the “Essential Science Indicators”, distinguishing them as hugely influential within their research areas.

1. “Major Nutritional Metabolic Alterations Influencing the Reproductive System of Postpartum Dairy Cows”
by Abdul Sammad, Muhammad Zahoor Khan, Zaheer Abbas, Lirong Hu, Qudrat Ullah, Yajing Wang, Huabin Zhu and Yachun Wang
Metabolites 2022, 12(1), 60; https://doi.org/10.3390/metabo12010060
Full text available online: https://www.mdpi.com/2218-1989/12/1/60

2. “Glucagon-Like Peptide-1 Receptor Agonists for Treatment of Nonalcoholic Fatty Liver Disease and Nonalcoholic Steatohepatitis: An Updated Meta-Analysis of Randomized Controlled Trials”
by Alessandro Mantovani, Graziana Petracca, Giorgia Beatrice, Alessandro Csermely, Amedeo Lonardo and Giovanni Targher
Metabolites 2021, 11(2), 73; https://doi.org/10.3390/metabo11020073
Full text available online: https://www.mdpi.com/2218-1989/11/2/73

3. “Comprehensive Meta-Analysis of COVID-19 Global Metabolomics Datasets”
by Zhiqiang Pang, Guangyan Zhou, Jasmine Chong and Jianguo Xia
Metabolites 2021, 11(1), 44; https://doi.org/10.3390/metabo11010044
Full text available online: https://www.mdpi.com/2218-1989/11/1/44

4. “The Potential of Metabolomics in Biomedical Applications”
by Vanessa Gonzalez-Covarrubias, Eduardo Martínez-Martínez and Laura del Bosque-Plata
Metabolites 2022, 12(2), 194; https://doi.org/10.3390/metabo12020194
Full text available online: https://www.mdpi.com/2218-1989/12/2/194

5. “Gut Microbiota Dysbiosis Is Associated with Elevated Bile Acids in Parkinson's Disease”
by Peipei Li, Bryan A. Killinger, Elizabeth Ensink, Ian Beddows, Ali Yilmaz, Noah Lubben, Jared Lamp, Meghan Schilthuis, Irving E. Vega and Randy Woltjer et al.
Metabolites 2021, 11(1), 29; https://doi.org/10.3390/metabo11010029
Full text available online: https://www.mdpi.com/2218-1989/11/1/29

6. “L-Carnitine and Acylcarnitines: Mitochondrial Biomarkers for Precision Medicine”
by Marc R. McCann, Mery Vet George De la Rosa, Gus R. Rosania and Kathleen A. Stringer
Metabolites 2021, 11(1), 51; https://doi.org/10.3390/metabo11010051
Full text available online: https://www.mdpi.com/2218-1989/11/1/51

7. “MetaboAnalystR 3.0: Toward an Optimized Workflow for Global Metabolomics”
by Zhiqiang Pang, Jasmine Chong, Shuzhao Li and Jianguo Xia
Metabolites 2020, 10(5), 186; https://doi.org/10.3390/metabo10050186
Full text available online: https://www.mdpi.com/2218-1989/10/5/186

8. “Gut Microbiota Metabolites in Major Depressive Disorder-Deep Insights into Their Pathophysiological Role and Potential Translational Applications”
by Miguel A. Ortega, Miguel Angel Alvarez-Mon, Cielo García-Montero, Oscar Fraile-Martinez, Luis G. Guijarro, Guillermo Lahera, Jorge Monserrat, Paula Valls, Fernando Mora and Roberto Rodríguez-Jiménez et al.
Metabolites 2022, 12(1), 50; https://doi.org/10.3390/metabo12010050
Full text available online: https://www.mdpi.com/2218-1989/12/1/50

9. “The Role of Fructose as a Cardiovascular Risk Factor: An Update”
by Stefan-Sebastian Busnatu, Teodor Salmen, Maria-Alexandra Pana, Manfredi Rizzo, Tiziana Stallone, Nikolaos Papanas, Djordje Popovic, Denisa Tanasescu, Dragos Serban and Anca Pantea Stoian
Metabolites 2022, 12(1), 67; https://doi.org/10.3390/metabo12010067
Full text available online: https://www.mdpi.com/2218-1989/12/1/67

We are pleased to announce the launch of a new initiative—the MDPI Special Issue Mentor Program.

This program will enable early career researchers (who must hold a Ph.D. in a related field) to experience editing a Special Issue in MDPI journals, under the mentorship of our experienced Editorial Board Members or other experienced scientists. The mentor program will provide an excellent opportunity for early career scientists to gain editorial experience, and to cultivate their ability to edit scientific research.

The mentee’s responsibilities include:

• Proposing a Special Issue title and assisting the mentor in preparing a summary (around 200–400 words) and 3–10 keywords describing the background, importance, and goal of the Issue;
• Writing a brief promotion plan for the Special Issue;
• Preparing a list of scholars who may be interested in the Issue and personally e-mailing invitations on behalf of Guest Editors;
• Writing an editorial for the online Special Issue together with the mentor.

The mentor’s responsibilities include:

• Conducting a final check before the Special Issue is published online;
• Performing editorial control of the Special Issue and quality control of the publications, both of which must be carried out in a timely manner;
• Providing suggestions to younger scholars if they have any doubts or concerns regarding submissions;
• Organizing video calls with young scholars and the Editorial Office regularly to discuss problems and improvement suggestions for the Special Issue;
• Making and submitting decisions regarding submissions with the assistance of mentees.

Certificates and awards:
After the Special Issue closes, the Editorial Office will provide official certificates for all the mentors and early career researchers.

If you are interested in this opportunity, please send your Special Issue proposal to the Editorial Office of a journal you choose, and we will discuss the process (i.e., mentor collaboration, Special Issue topic feasibility analysis, etc.) in further detail. The full list of MDPI journals is as follows: https://www.mdpi.com/about/journals.

In addition to the new Special Issue Mentor Program, we will continue to welcome all Special Issue proposals focusing on hot research topics.

MDPI has just become the first open access (OA) publisher to reach the milestone of one million articles published. That is one million articles freely available to all, to circulate and build upon! We are proud to share this special moment with the global scientific community.

This landmark has been reached thanks to the immeasurable support of more than 600,000 expert reviewers, 66,000 editorial board members and 6700 hard-working colleagues across MDPI’s global offices.

Within more than 25 years of publishing, our journals received 2.1 million manuscripts and generated 4.6 million peer review reports to get to one million papers published.

Reaching the milestone of one million articles published reinforces our mission to remove any existing barriers and to make scientific research accessible to all. Since its inception, MDPI’s goal has been to create reliable processes to make science open. This is a path towards facilitating the dissemination of novel insights in scientific communities.

Regular feedback from authors and reviewers shows that our service is greatly appreciated and needed. At the same time, the feedback helps us identify areas for further improvement.

As it stands, a significant share of published research findings remain closed access. More than half of the content published with the most well-known legacy publishers stays behind a paywall, and that is not including articles published in hybrid OA journals, or made available months or years after publication.

A new policy announced by the US administration in August 2022 requires that, as of January 2026, all US federally funded research be made freely and immediately available after publication. While the new policy does not mandate articles be published under an open access license, it is aligned with the open access movement in removing all barriers to research. Similarly, some of the most advanced research institutions in the world intend to have all funded research articles published in open access by 2025.

MDPI is proud to be the leading agent of the transition to open access.

"Thanks a Million" to all the contributors!