Publications

Featured Publication:


"Unraveling the Pathogenesis of Crimean-Congo Hemorrhagic Fever: A Novel Approach via Non-Targeted Metabolomics by NMR Spectroscopy." (2023).

The application of metabolomics for studying modifications in host metabolism due to viral infections has proven to be a game-changing approach. Prior to our study, only one other ‘omics’ study has been carried out that investigates the interplay between the host and CCHFV and its subsequent pathogenesis. We employed NMR spectroscopy, given its advantages in terms of reproducibility, minimal sample preparation, and capability to analyze complex biofluids. Our methodology builds upon the proven success of metabolomics in the research of other viral hemorrhagic fevers such as Ebola, Marburg, and Dengue. Our research underlines the critical role of SAH, a metabolite involved in numerous biochemical reactions. We provide new insights into the metabolic alterations occurring in CCHF patients. These alterations not only shed light on the disease’s pathogenesis but also pave the way for potential biomarkers and therapeutic targets. Among all the metabolites detected, S-Adenosyl-L-homocysteine and Carnosine stood out as the most prevalent, warranting further exploration of their roles in CCHFV pathogenesis and their potential as therapeutic targets.

Dag, Cagdas, Oktay Göcenler, Kerem Kahraman, Derya Yapar, Yaren Kahraman, Cengizhan Büyükdag, Gülen Esken et al.

View 2006 - 2022 Publications 

538) FitzGerald, Garret. "Metabolomic Response to Non-Steroidal Anti-Inflammatory Drugs." (2024).

537) Abd Rahman, Mohamad Razlan, Zaiton Hassan, Mohd Sukri Hassan, Roshada Hashim, Ling Shing Wong, Maulidiani Maulidiani, Wai Yie Leong, Nur Ain Hannani Hamid, and Nur Maisarah Mohamad Sarbani. "1H NMR Milk Metabolomics Response from Goats Supplemented with Date (Phoenix Dactylifera L.) Pit Powder: Benefiting from Agricultural Waste Byproduct." Journal of Advanced Research in Applied Sciences and Engineering Technology (2024): 14-32.

536) Moots, Robert J., Farida Fortune, Richard Jackson, Tony Thornburn, Ann W. Morgan, Dan Carr, Philip Ian Murray, Graham Robert Wallace, and Deva Situnayake. "Infliximab versus alpha interferon in the treatment of Behçet's disease: the BIO BEHÇET'S RCT." Efficacy and Mechanism Evaluation 11, no. 17 (2024): 1-77.

535) Basile, Federico, Ana Cristina Abreu, Claudio Cannata, Rosario Paolo Mauro, María del Carmen Cerón-García, Cherubino Leonardi, and Ignacio Fernández. "Impact of Preharvest Silicon and Triacontanol Applications on Metabolite Accumulation and Storage Quality in Two Carrot Cultivars Differing for Root Colour." Available at SSRN 5048972.

534) Navarro Morillo, Ivan. "Effects of applying CSL to horticultural plants to improve their growth in different environmental conditions."

533) Huang, Xueying, Yu Wang, Feng Li, Hui Zhao, Liwang Zeng, Huiliang Li, Fenglin Gu et al. "Physiological activities, transcriptomes and metabolomes of Pyropia yezoensis conchocelis unveil the roles of pyPGK, pyBCKDHA, and pyDLD in response to freshwater soaking." International Journal of Biological Macromolecules (2024): 138193.

532) Montgomery, Keeton H., Aya Elhabashy, Maria Del Carmen Reynoso Rivas, Gurreet Brar, and V_V Krishnan. "NMR metabolomics as a complementary tool to brix-acid tests for navel orange quality control of long-term cold storage." Scientific Reports 14, no. 1 (2024): 1-10.

531) Kim, Hye-Jin, Dongheon Lee, Seungcheol Lee, Minwoo Choi, Soyoon Yun, Young Seung Lee, Dong Kyun Kim, Soo-Hyun Cho, and Cheorun Jo. " Chemometric Insights into the Flavor Development and Quality Changes in Jeju Crossbred Cattle Loin during Wet Aging." Food Science of Animal Resources (2024).

530) Ghosh, Soumita, Nick Lahens, Kayla Barekat, Soon-Yew Tang, Katherine N. Theken, Emanuela Ricciotti, Arjun Sengupta et al. "Metabolomic Response to Non-Steroidal Anti-Inflammatory Drugs." bioRxiv (2024): 2024-11.

529) Ngo, Trung Huy, Yoon‐Jin Lee, Hyukjae Choi, Kyung‐Sik Song, Kyu Joon Lee, and Joo‐Won Nam. "A Metabolomics Strategy Combining Countercurrent Separation and qNMR for the Comprehensive Chemical Evaluation of Polygoni Multiflori Radix Processing." Phytochemical Analysis (2024).

528) Nakorn, Sarun Na, Hasaya Dokduang, Nisana Namwat, Poramate Klanrit, Arporn Wangwiwatsin, Bundit Promraksa, Sirinya Sitthirak, Tinnapat Seaban, and Watcharin Loilome. "Antioxidant and longevity inducing properties of coconut water on human dermal fibroblasts." Heliyon (2024).

527) Chaudhari, Sachin R., Sachin P. Shinde, Suraj Payyadakkath, Anisha Biswas, Ganesh R. Hon, and Rajeshwar S. Matche. "Physiochemical Dynamics and Biochemical Transformations During Ripening of Indian Mangifera Indica L. Varieties: Insights from Multi-Parameter Analysis and Nmr Spectroscopy." Varieties: Insights from Multi-Parameter Analysis and Nmr Spectroscopy.

526) Granato, Alessandra, Simone Renwick, Christopher Yau, Tiffany Kong, Michelle C. Daigneault, Mikael Knip, Emma Allen-Vercoe, Jayne S. Danska, and DIABIMMUNE Study Group. "Analysis of early childhood intestinal microbial dynamics in a continuous-flow bioreactor." Microbiome 12 (2024): 255.

525) Shukla, Ananya, Khushbhu Meena, Ashish Gupta, and Rajat Sandhir. "1H NMR-Based Metabolomic Signatures in Rodent Models of Sporadic Alzheimer’s Disease and Metabolic Disorders." ACS Chemical Neuroscience (2024).

524) Utume, Laura, Jerome Nicolas Janssen, Peter Akomo, Daisy Shaw, William JS Edwards, Molly Muleya, Charoula Konstantia Nikolaou et al. "Toward holistic solutions to undernutrition: a comprehensive preclinical protocol for novel ready-to-use therapeutic foods testing." bioRxiv (2024): 2024-11.

523) Chistyakov, Dmitry V., Veronika V. Tiulina, Olga S. Gancharova, Viktoriia E. Baksheeva, Sergei V. Goriainov, Natalia G. Shebardina, Vasily A. Ivlev et al. "Targeting Oxidative Stress and Inflammation in the Eye: Insights from a New Model of Experimental Autoimmune Uveitis." International Journal of Molecular Sciences 25, no. 23 (2024): 12910.

522) Islam, Md Zohorul, Danica Jozipovic, Pablo Atienza Lopez, Lukasz Krych, Banny Silva Barbosa Correia, Hanne Christine Bertram, Axel Kornerup Hansen, and Camilla Hartmann Friis Hansen. "Wild-Mouse-Derived Gut Microbiome Transplantation in Laboratory Mice Partly Alleviates House-Dust-Mite-Induced Allergic Airway Inflammation." Microorganisms 12, no. 12 (2024): 2499.

521) Aluisio, Gaia Vertillo, Maria Lina Mezzatesta, Viviana Cafiso, Renata Scuderi, Stefania Stefani, and Maria Santagati. "Cell-free supernatant of Lactobacillus gasseri 1A-TV shows a promising activity to eradicate carbapenem-resistant Klebsiella pneumoniae colonization." Frontiers in Cellular and Infection Microbiology 14 (2024): 1471107.

520) Ferrier, Manon, Marin-Pierre Gémin, Magdalena Anna Malinowska, Cécile Abdallah, Florent Magot, Caroline Birer-Williams, Nathalie Giglioli-Guivarc’h, Christophe Hano, and Arnaud Lanoue. "Metabolomics applications in natural cosmetics: addressing the new challenges of bio-sourced ingredients." Phytochemistry Reviews (2024): 1-33.

519) Sorensen, Patrick, Ulas Karaoz, Harry R. Beller, Markus Bill, Nicholas J. Bouskill, Jillian F. Banfield, Rosalie K. Chu et al. "Coordinated organic and inorganic nitrogen transformations fuel soil microbial blooms and increase nitrogen retention during snowmelt." bioRxiv (2024): 2024-11.

518) de Oliveira, Paola Dias, Allana Cristina Faustino Martins, Roberto da Silva Gomes, Adilson Beatriz, Glaucia Braz Alcantara, and Ana Camila Micheletti. "Investigation of antibacterial mode of action of ω-aminoalkoxylxanthones by NMR-based metabolomics and molecular docking." Metabolomics 21, no. 1 (2025): 1-11.

517) Thibodeau, Alyssa. "The upcycling of liquid whey to produce a craft organic acid-based beverage with novel yeast and bacterial co-cultures." (2024).

516) Taheri, Salman, Jelmir Craveiro de Andrade, and Carlos Adam Conte-Junior. "Emerging perspectives on analytical techniques and machine learning for food metabolomics in the era of industry 4.0: a systematic review." Critical Reviews in Food Science and Nutrition (2024): 1-27.

515) Navarro Morillo, Ivan. "Effects of applying CSL to horticultural plants to improve their growth in different environmental conditions."

514) Zhao, Mingjian, Ruowen Li, Chengxu Miao, Paolo Miccoli, and Jinghui Lu. "Non-invasive diagnosis of papillary thyroid microcarcinoma using a novel metabolomics analysis of urine." Endocrine (2024): 1-12.

513) Kaihara, Julyane NS, Fabio Rogerio de Moraes, Priscila Rezeck Nunes, Marco G. Alves, Ricardo C. Cavalli, Ljubica Tasic, and Valeria Cristina Sandrim. "Plasma metabolic profile reveals signatures of maternal health during gestational hypertension and preeclampsia without and with severe features." PloS one 19, no. 11 (2024): e0314053.

512) Ugwuodo, Chika Jude, Fabrizio Colosimo, Jishnu Adhikari, Samuel O. Purvine, Elizabeth K. Eder, David W. Hoyt, Stephanie A. Wright, Mary S. Lipton, and Paula J. Mouser. "Aromatic amino acid metabolism and active transport regulation are implicated in microbial persistence in fractured shale reservoirs." ISME Communications (2024): ycae149.

511) Barekat, Kayla, Emanuela Ricciotti, Soumita Ghosh, Christin Herrmann, Karl Keat, Charles-Antoine Assenmacher, Ceylan Tanes et al. "Concomitant suppression of COX-1 and COX-2 is insufficient to induce enteropathy associated with chronic NSAID use." bioRxiv (2024): 2024-11.

510) Kumar, Umesh, Monika Sodhi, Dinesh Kumar, Prince Vivek, Saket K. Niranjan, Ranjit Singh Kataria, Sudarshan Kumar et al. "Characterizing metabolome signature of colostrum, transition and mature milk of indigenous cows (Bos indicus) adapted to high altitude environment of Leh-Ladakh." Food Chemistry 464 (2025): 141767.

509) Biswas, Anisha, Babasaheb Bhaskarrao Borse, and Sachin R. Chaudhari. "Quantitative NMR analysis of sugars in natural sweeteners: Profiling in honey, jaggery, date syrup, and coconut sugar." Food Research International (2024): 115358.

508) Hanyuda, Akiko, Yoshihiko Raita, Takahiro Ninomiya, Kazuki Hashimoto, Naoko Takada, Kota Sato, Jin Inoue et al. "Metabolomic Profiling of Open-Angle Glaucoma Etiologic Endotypes: Tohoku Multi-Omics Glaucoma Study." Investigative Ophthalmology & Visual Science 65, no. 13 (2024): 44-44.

507) Osthoff, Gernot, and Petronella Nieuwoudt. "Non-Targeted Metabolomics of White Rhinoceros Colostrum and Its Changes During Early Lactation by 1H Nuclear Magnetic Resonance Spectroscopy." Metabolites 14, no. 11 (2024): 637.

506) Sangermani, Matteo, Indri Desiati, Solveig M. Jørgensen, Jia V. Li, Trygve Andreassen, Tone F. Bathen, and Guro F. Giskeødegård. "Stability in fecal metabolites amid a diverse gut microbiome composition: a one-month longitudinal study of variability in healthy individuals." Gut Microbes 16, no. 1 (2024): 2427878.

505) Cerulli, Antonietta, Luciana Maria Polcaro, Milena Masullo, and Sonia Piacente. "Spinacia oleracea L. Baby Leaves as a Source of Bioactive Principles: The Chemical Profiling of Eco-Sustainable Extracts by Using LC-ESI/HRMS-and 1H NMR-Based Metabolomics." Foods 13, no. 22 (2024): 3699.

504) Polcaro, Luciana Maria, Antonietta Cerulli, Milena Masullo, and Sonia Piacente. "Metabolomics of Withania somnifera L. extracts by an integrated LC-MS and NMR approach and evaluation of their tyrosinase inhibitory activity." Journal of Pharmaceutical and Biomedical Analysis 253 (2025): 116520.

503) Giménez-Valero, Carlos, Alejandro Andy Maciá-Vázquez, Dámaris Núñez-Gómez, Juan José Martínez-Nicolás, Pilar Legua, and Pablo Melgarejo. "Metabolic Profile Evolution of Citrus sinensis ‘Navelina’Under Different Cultivation Techniques and Water-Saving Strategies." Horticulturae 10, no. 11 (2024): 1187.

502) Sievers, Michael, Jasmine A. Rasmussen, Benjamin Nielsen, Rune C. Steinfurth, Mogens R. Flindt, Steven D. Melvin, and Rod M. Connolly. "Restored seagrass rapidly provides high‐quality habitat for mobile animals." Restoration Ecology (2024): e14343.

501) Bhattacharyya, Dipanjan, Marcia A. LeVatte, Upasana Singh, Fleur Issac, Mahmoud Karim, Saira Ali, August Sieben, Suyenna Huang, and David S. Wishart. "A novel colorimetric assay for the detection of urinary N1, N12-diacetylspermine, a known biomarker for colorectal cancer." Analytical Biochemistry (2024): 115717.

500) McNeil, Jordyn. "Differential Metabolomic Response of the Red Eared Slider Turtle (Trachemys scripta) Ventricle and Brain to Prolonged Anoxia Exposure." Master's thesis, University of Alaska Anchorage, 2024.

499) de Sousa, Ashelley Kettyllem Alves, Keyla Silva Nobre Pires, Isadora Hart Cavalcante, Iasmin Cristina Lira Cavalcante, Julia Domingues Santos, Maiara Ingrid Cavalcante Queiroz, Ana Catarina Rezende Leite et al. "Polystyrene microplastics exposition on human placental explants induces time-dependent cytotoxicity, oxidative stress and metabolic alterations." Frontiers in Endocrinology 15 (2024): 1481014.

498) Botello-Marabotto, Marina, Emma Plana, M. Carmen Martínez-Bisbal, Pilar Medina, Andrea Bernardos, Ramón Martínez-Máñez, and Manuel Miralles. "Metabolomic study for the identification of symptomatic carotid plaque biomarkers." Talanta (2024): 127211.

497) Islam, Md Shiful. "Catechol-Escherichia coli UM146 interaction revealed through multi-omics." (2024).

496) Randall, David, Asil Alsam, Julius Kieswich, Susan Joseph, Joseph Aduse-Opoku, Jonathan Swann, Alan Boyde et al. "Oral dysbiosis initiates periodontal disease in experimental kidney disease." Nephrology Dialysis Transplantation (2024): gfae266.

495) Humphries, Josephine E., Steven D. Melvin, Chantal Lanctôt, Hamish McCallum, David Newell, and Laura F. Grogan. "Chytridiomycosis disrupts metabolic responses in amphibians at metamorphic climax." Microbes and Infection (2024): 105438.

494) SINGH, ANANYA. "METABOLOMICS IN BIOMEDICAL RESEARCH." Omics Applications and Avenues (2024): 190.

493) Ferreira, Osania Emerenciano, Halax Duart Martins Silva, Adriana Barboza Alves, Mariana Guerra de Aguilar, Lúcia Pinheiro Santos Pimenta, Gustavo Henrique Gravatim Costa, Mara Cristina Pessôa da Cruz, Augusto Cesar da Silva Bezerra, and Alan Rodrigues Teixeira Machado. "Biochar enhances soil interactions and the initial development of sugarcane." Scientific Reports 14, no. 1 (2024): 27610.

492) Wijaya, I. Dewa Made Rizky, Izwandy Idris, Wan Iryani Wan Ismail, Asnuzilawati Asari, Noor Aniza Harun, R. Rudiyanto, Kustiariyah Tarman, Faridah Abas, and M. Maulidiani. "Discrimination of Marine Polychaete Species of Different Harvest Times Using FTIR Metabolomics."

491) da Silva, Gustavo H. Rodrigues, Luís F. Mendes, Gabriela Geronimo, Ludmilla D. de Moura, Juliana S. Ruas, Roger F. Castilho, Helon G. Cordeiro, Carmen V. Ferreira, Eneida de Paula, and Iola F. Duarte. "Schwann Cells Exposed to Articaine Display Distinct Toxic Pathways Compared to Lidocaine." Chemico-Biological Interactions (2024): 111315.

490) Casarrubios, Laura, Mónica Cicuéndez, Alberto Polo-Montalvo, María José Feito, Álvaro Martínez-del-Pozo, Daniel Arcos, Iola F. Duarte, and María Teresa Portolés. "Metabolomic characterization of MC3T3-E1pre-osteoblast differentiation induced by ipriflavone-loaded mesoporous nanospheres." Biomaterials Advances 166 (2025): 214085.

489) Luo, Yunqing, Chengjun Zhao, and Fei Chen. "Multi-omics research: principles and challenges in integrated analysis." BioDesign Research.

488) Nolis, Pau. "NMR spectroscopy of small molecules in solution." (2024).

487) Mendes, Luiza Tomé, Marcos C. Gama-Almeida, Desirée Lopes Reis, Ana Carolina Pires E. Silva, Rômulo Leão Silva Neris, Rafael Mello Galliez, Terezinha Marta Pereira Pinto Castiñeiras et al. "Longitudinal 1H NMR-Based Metabolomics in Saliva Unveils Signatures of Transition from Acute to Post-Acute Phase of SARS-CoV-2 Infection." Viruses 16, no. 11 (2024): 1769.

486) Pasam, Tulasi, Hara Prasad Padhy, and Manoj P. Dandekar. "Lactobacillus Helveticus Improves Controlled Cortical Impact Injury-Generated Neurological Aberrations by Remodeling of Gut-Brain Axis Mediators." Neurochemical Research 50, no. 1 (2025): 3.

485) Surwaich, Arhana, Ali Maqbool, Sajid Ali Majeedaro, Agha Taymoor Ali, Bushra Arain, Khurram Anwar, Shaharyar Ahsan, and Maheen Ejaz. "Evaluating Preventive Health Strategies: Salivary Biomarkers as Non-Invasive Indicators of Caries Risk in School Children: Salivary Biomarkers for Caries Risk in Children." Pakistan Journal of Health Sciences (2024).

484) Kanagaraja, Abinaya, and Pachaiappan Raman. "Microbial Biotechniques Progressions: Fundamental of Analytic Techniques." In Industrial Microbiology and Biotechnology: A New Horizon of the Microbial World, pp. 183-245. Singapore: Springer Nature Singapore, 2024.

483) Chena, Hu, Patrick C. Blaufussa, Dong-Fang Denga, Fabio Casub, Emma K. Kracod, Brian Shepherdd, Wendy M. Sealeye, Aaron M. Watsonc, Matthew F. Digmanf, and Deborah A. Samacg. "Impacts of alfalfa nutrient concentrate on pellet physical attributes, growth performance, metabolism and nutritional quality of rainbow trout, Oncorhynchus mykiss 2."

482) Kumar, Umesh, Monika Sodhi, Dinesh Kumar, Prince Vivek, Saket K. Niranjan, Ranjit Singh Kataria, Sudarshan Kumar et al. "Characterizing metabolome signature of colostrum, transition and mature milk of indigenous cows (Bos indicus) adapted to high altitude environment of Leh-Ladakh." Food Chemistry (2024): 141767.

481) Chen, Guixia, Lifeng Chen, Huiya Wang, Jiyong Zhang, Xiaoling Sun, Xiaoxin Chen, Jianxia Fan, Zhiwei Jia, and Yinying Huang. "1H NMR-Based Metabolomic Profiling and Comparison of Human Milk Across Different Lactation Stages in Secretors and Non-Secretors: A Study of Chinese Lactating Women." The Journal of Nutrition (2024).

480) Kandasamy, Sujatha, Won-Seo Park, In-Seon Bae, Jayeon Yoo, Jeonghee Yun, Van-Ba Hoa, and Jun-Sang Ham. "HRMAS-NMR-Based Metabolomics Approach to Discover Key Differences in Cow and Goat Milk Yoghurt Metabolomes." Foods 13, no. 21 (2024): 3483.

479) Marokane-Radebe, Cynthia, Adekunle Raimi, Stephen Amoo, and Rasheed Adeleke. "Metabolomic profiling and 16 S rRNA metabarcoding of endophytes of two Aloe species revealed diverse metabolites." AMB Express 14, no. 1 (2024): 122.

478) Gowen, Niamh, Nan Gai, Seamus James A. O'Mahony, Jonathan O’Regan, and David Anthony Goulding. "Non-Protein Nitrogen in Dairy Ingredients: A Closer Look at its Contribution in Infant Nutritional Product Formulation." Jonathan and Goulding, David Anthony, Non-Protein Nitrogen in Dairy Ingredients: A Closer Look at its Contribution in Infant Nutritional Product Formulation.

477) Polcaro, Luciana Maria, Antonietta Cerulli, Milena Masullo, and Sonia Piacente. "Metabolomics of Withania somnifera L. extracts by an integrated LC-MS and NMR approach and evaluation of their tyrosinase inhibitory activity." Journal of Pharmaceutical and Biomedical Analysis (2024): 116520.

476) Hasan, Sk, Nafizul Alam, Gazi Abdullah Mashud, and Subodh Bhujel. "Neural Network for Enhancing Robot Assisted Rehabilitation: A Systematic Review." (2024).

475) D’Elia, Maria, Carmen Marino, Rita Celano, Enza Napolitano, Anna Maria D’Ursi, Mariateresa Russo, and Luca Rastrelli. "Impact of a Withania somnifera and Bacopa monnieri Formulation on SH-SY5Y Human Neuroblastoma Cells Metabolism Through NMR Metabolomic." (2024).

474) Laghi, Luca, Maria Àngels Ortiz, Giacomo Rossi, Eva Román, Carlo Mengucci, Elisabet Cantó, Lucia Biagini et al. "Biomarkers of Frailty in Patients with Advanced Chronic Liver Disease Undergoing a Multifactorial Intervention Consisting of Home Exercise, Branched-Chain Amino Acids, and Probiotics." Biomolecules 14, no. 11 (2024): 1410.

473) Katherinatama, Aldia, Yonathan Asikin, Kazuki Shimoda, Momoko Shimomura, Fumimasa Mitsube, Kensaku Takara, and Koji Wada. "Characterization of Free and Glycosidically Bound Volatile and Non-Volatile Components of Shiikuwasha (Citrus depressa Hayata) Fruit." Foods 13, no. 21 (2024): 3428.

472) Kumar, Sazal, Rafiquel Islam, Wayne O'Connor, Steve D. Melvin, Frederic DL Leusch, Allison Luengen, and Geoff R. MacFarlane. "A metabolomic analysis on the toxicological effects of the universal solvent, dimethyl sulfoxide." Comparative Biochemistry and Physiology Part C: Toxicology & Pharmacology (2024): 110073.

471) Dağ, Çağdaş, and Kerem Kahraman. "Exploring the Biochemical Landscape of Bacterial Medium with Pyruvate as the Exclusive Carbon Source for NMR Studies." bioRxiv (2024): 2024-10.

470) Yang, Zhibo, Chuan Song, Qiuyu Lan, Bin Hu, Zonghua Ao, Xiaole Jiang, Suyi Zhang et al. "High-Throughput Metabolomics Reveals Effect of Glutathione-Enriched Inactive Dry Yeast on Volatile and Non-Volatile Compounds of Kiwi Wine." Available at SSRN 4979109.

469) Wang, Gangqi, Bernard M. van den Berg, Sarantos Kostidis, Kelsey Pinkham, Marleen E. Jacobs, Arthur Liesz, Martin Giera, and Ton J. Rabelink. "Spatial quantitative metabolomics enables identification of remote and sustained ipsilateral cortical metabolic reprogramming after stroke." bioRxiv (2024): 2024-10.

468) Boisen, Gabriella, Susanne Brogårdh-Roth, Jessica Neilands, Alex Mira, Miguel Carda-Diéguez, and Julia R. Davies. "Oral biofilm composition and phenotype in caries-active and caries-free children." Frontiers in Oral Health 5 (2024): 1475361.

467) Msomi, Mhlonipheni, Garland More, Noluyolo Nogemane, and Gerhard Prinsloo. "1h-Nmr-Based Metabolomics and Antioxidant Enzymes of Maize (Zea Mays) in Response to Exogenously Applied Dicarboxylic Acids (Photon)." Available at SSRN 4891435.

466) McGivern, Bridget B., Jared B. Ellenbogen, David W. Hoyt, John A. Bouranis, Brooke P. Stemple, Rebecca A. Daly, Samantha H. Bosman et al. "Polyphenol rewiring of the microbiome reduces methane emissions." bioRxiv (2024): 2024-10.

465) Sink, Warren John, Russell Fling, Ali Yilmaz, Rance Nault, Delanie Goniwiecha, Jack Harkema, Stewart Graham, and Tim Zacharewski. "2, 3, 7, 8-Tetrachlorodibenzo-p-dioxin (TCDD) elicited dose-dependent shifts in the murine urinary metabolome associated with hepatic AHR-mediated differential gene expression." bioRxiv (2024): 2024-10.

464) Quifer-Rada, Paola, Laia Aguilar-Camprubí, Sara Samino, Nuria Amigó, Oria Soler, and Alba Padró-Arocas. "Metabolomics Approach to Identify Biomarkers of Acute and Subacute Mastitis in Milk Samples: A Pilot Case–Control Study." Metabolites 14, no. 10 (2024): 566.

463) Dias, Ana S., Catarina R. Almeida, Luisa Helguero, and Iola F. Duarte. "Antitumoral Activity and Metabolic Signatures of Dichloroacetate, 6-Aminonicotinamide and Etomoxir in Breast-Tumor-Educated Macrophages." Journal of Proteome Research (2024).

462) Lu, Jie, Jiawen Wang, Tuo Yao, Shengli Fu, Xiao Hu, and Lingtong Ye. "Metabolomic and enzymatic markers reveal critical air exposure threshold for Crassostrea hongkongensis quality." Food Research International (2024): 115309.

461) Young, Megan, Malene Aastrup, Nikayla Patel, Fenn Cullen, Esben SS Hansen, James E. Clark, Thomas R. Eykyn et al. "Altered systemic bioenergetic reserve in chronic kidney disease predisposes hearts to worse functional outcomes." bioRxiv (2024): 2024-10.

460) Brai, Annalaura, Cassia Neri, Franca Tarchi, Federica Poggialini, Chiara Vagaggini, Riccardo Frosinini, Sauro Simoni, Valeria Francardi, and Elena Dreassi. "Upcycling Milk Industry Byproducts into Tenebrio molitor Larvae: Investigation on Fat, Protein, and Sugar Composition." Foods 13, no. 21 (2024): 3450.

459) Martins, Cátia Falcão, Manolis Matzapetakis, David M. Ribeiro, Josipa Kuleš, Anita Horvatić, Nicholas Guillemin, Peter David Eckersall, João PB Freire, André M. Almeida, and José AM Prates. "Metabolomics and proteomics insights into hepatic responses of weaned piglets to dietary Spirulina inclusion and lysozyme supplementation." BMC Veterinary Research 20, no. 1 (2024): 505.

458) Casarrubios, Laura, Mónica Cicuéndez, Alberto Polo-Montalvo, María José Feito, Alvaro Martínez-del-Pozo, Daniel Arcos, Iola F. Duarte, and María Teresa Portolés. "Metabolomic characterization of MC3T3-E1pre-osteoblast differentiation induced by ipriflavone-loaded mesoporous nanospheres." Biomaterials Advances (2024): 214085.

457) Paglione, Marco, David CS Beddows, Anna Jones, Thomas Lachlan-Cope, Matteo Rinaldi, Stefano Decesari, Francesco Manarini et al. "Simultaneous organic aerosol source apportionment at two Antarctic sites reveals large-scale and eco-region specific components." Atmospheric Chemistry and Physics 24, no. 10 (2024): 6305-6322.

456) Li, Da-Wei, Rodrigo Cabrera Allpas, Munki Choo, Lei Bruschweiler-Li, Alexandar L. Hansen, and Rafael Brüschweiler. "COLMAR1d: A Web Server for Automated, Quantitative One-Dimensional Nuclear Magnetic Resonance-Based Metabolomics at Arbitrary Magnetic Fields." Analytical Chemistry (2024).

455) Singh, Rita, Sneh Bajpai, Amardeep Singh, Phulwanti Sharma, Yashwant Kumar, and Niraj Kumar. "Metabolomics of Chinese Hamster Ovary Cells." In Heterologous Protein Production in CHO Cells: Methods and Protocols, pp. 205-234. New York, NY: Springer US, 2024.

454) Qiu, Xu, and Xixiang Tang. "Metabolic adaptations of Shewanella eurypsychrophilus YLB-09 for survival in the high-pressure environment of the deep sea." Frontiers in Microbiology 15 (2024): 1467153.

453) Casarrubios Molina, Laura, Mónica Cicuéndez Maroto, Alberto Polo Montalvo, María José Feito Castellano, Álvaro Martínez Del Pozo, Daniel Arcos Navarrete, Iola F. Duarte, and María Teresa Portolés Pérez. "Metabolomic characterization of MC3T3-E1pre-osteoblast differentiation induced by ipriflavone-loaded mesoporous nanospheres." (2025).

452) de la Cabeza Fernández, María, Marta Sánchez, Laura Lozano-Chamizo, Ana Cristina Abreu, Ana Anguís-Morillas, Padreep K. Divakar, Marzia Marciello et al. "Electrospun nanofibers for localized drug release of a neuroprotective natural extract of USNEA ghattensis." European Journal of Pharmaceutics and Biopharmaceutics (2024): 114552.

451) Sahoo, Ashutosh, Deepanshu Verma, and Prajnadipta Panda. "A Gateway to Multi‐Omics‐Based Clinical Research." Applied Biotechnology and Bioinformatics: Agriculture, Pharmaceutical Research and Environment (2024): 235-256.

450) Hong, Natalie E., Alice Chaplin, Lin Di, Anastasia Ravodina, Graham H. Bevan, Huiyun Gao, Courteney Asase et al. "Nanoparticle-based itaconate treatment recapitulates low-cholesterol/low-fat diet-induced atherosclerotic plaque resolution." Cell Reports 43, no. 11 (2024).

449) Ruiz Coca, Mario, Cristian Perez-Fernandez, Ana Abreu, Ana Salmeron, Miguel Morales-Navas, Diego Ruiz-Sobremazas, Teresa Colomina, Ignacio Fernandez, and Fernando Sanchez-Santed. "Modulating Neurotoxic Effects of Prenatal Chlorpyrifos Exposure Through Probiotic and Vitamin D Gestational Supplementation: Unexpected Effects on Neurodevelopment and Sociability." bioRxiv (2024): 2024-11.

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447) Iovino, Margaud, Megan Colonval, Chloé Wilkin, Laurent L’homme, Cédric Lassence, Manon Campas, Olivier Peulen, Pascal de Tullio, Jacques Piette, and Sylvie Legrand-Poels. "Novel XBP1s-independent function of IRE1 RNase in HIF-1α-mediated glycolysis upregulation in human macrophages upon stimulation with LPS or saturated fatty acid." Frontiers in Immunology 14 (2023).

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440) Queiroz, Kamila A., Everton P. Vale, Manuel Martín-Pastor, Lílian GS Sólon, and Francisco FO Sousa. "Metabolomic Profile, Plasmatic Levels of Losartan and EXP3174, Blood Pressure Control in Hypertensive Patients and Their Correlation with COVID-19." Pharmaceuticals 16, no. 9 (2023): 1290.

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164) Luo, Donghui, Xuewu Zhang, and Xiaofei Xu. "1H NMR-based urinary metabolic analysis of high-dose cyclophosphamide-induced toxicity in mice." Analytical Biochemistry (2023): 115138.

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39) Cheon, Seongwon, Geonhee Kim, Jae-Han Bae, Dong Hyeon Lee, Hyunbin Seong, Hye Da Kim, Jung-Sook Han, Su-Youn Lim, and Nam Soo Han. "Comparative analysis of prebiotic effects of four oligosaccharides using in vitro gut model: digestibility, microbiome, and metabolome changes." FEMS Microbiology Ecology (2023).

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37) Martínez-Nicolás, Juan José, Francisca Hernández, Dámaris Núñez-Gómez, Francisco García-Sánchez, Rafael Martínez-Font, Pilar Legua, and Pablo Melgarejo. "Metabolomic Approach to Study the ‘Purple Queen’Pomegranate Cultivar Response to Alternative Culture Media and Phenological Stages." Foods 12, no. 2 (2023): 352.

36) Pinto, Bruna Cristina, Adriana Barboza Alves, Osania Emerenciano Ferreira, Gustavo Henrique Gravatim Costa, Magno André de Oliveira, Augusto Cesar da Silva Bezerra, and Alan Rodrigues Teixeira Machado. "Biochar influences the cane fields’ microbiota and the development of pre-sprouted sugarcane seedlings." Waste Disposal & Sustainable Energy (2023): 1-14.

35) Mráziková, Lucia, Silvie Hojná, Petra Vaculová, Štěpán Strnad, Vladimír Vrkoslav, Helena Pelantová, Marek Kuzma, Blanka Železná, Jaroslav Kuneš, and Lenka Maletínská. "Lipidized PrRP Analog Exhibits Strong Anti-Obesity and Antidiabetic Properties in Old WKY Rats with Obesity and Glucose Intolerance." Nutrients 15, no. 2 (2023): 280.

34) Miebach, Lea, Hager Mohamed, Kristian Wende, Vandana Miller, and Sander Bekeschus. "Pancreatic Cancer Cells Undergo Immunogenic Cell Death upon Exposure to Gas Plasma-Oxidized Ringers Lactate." Cancers 15, no. 1 (2023): 319.

33) Lai, Giacomo, Pierluigi Caboni, Cristina Piras, Massimo Pes, Maria Sitzia, Margherita Addis, Antonio Pirisi, and Paola Scano. "Development and Chemico-Physical Characterization of Ovine Milk-Based Ingredients for Infant Formulae." Applied Sciences 13, no. 1 (2023): 653.

32) Tiepo, Angelica N., Isabel D. Coutinho, Guilherme O. Machado, Halley C. Oliveira, José Antonio Pimenta, Liliane Marcia M. Henning, Luiz Alberto Colnago, and Renata Stolf-Moreira. "Phenolic Compounds from Leaves of Cariniana estrellensis (Raddi) Kuntze (Lecythidaceae): A Brazilian Atlantic Forest Tree." Journal of the Brazilian Chemical Society 34 (2023): 146-152.

31) Palomares, Cristofher Victor Vivas, Yan Borges Barreto, Natalia Marchesan Bexiga, Sergio Hiroshi Toma, Jonnatan Julival dos Santos, Koiti Araki, Adriano Mesquita Alencar, and Antonio Carlos Bloise. "Metabolic Profiling of Murine Macrophages Exposed to Silver Nanoparticles at Dose and Time Dependencies." Particle & Particle Systems Characterization: 2200191.

30) McCauley, Heather A., Anne Marie Riedman, Jacob R. Enriquez, Xinghao Zhang, Miki Watanabe-Chailland, J. Guillermo Sanchez, Daniel O. Kechele et al. "Enteroendocrine cells protect the stem cell niche by regulating crypt metabolism in response to nutrients." Cellular and Molecular Gastroenterology and Hepatology (2023).

29) Sun, Jialin, Sivan Osenberg, Austin Irwin, Li-Hua Ma, Nigel Lee, Yangfei Xiang, Feng Li et al. "Mutations in the transcriptional regulator MeCP2 severely impact key cellular and molecular signatures of human astrocytes during maturation." Cell Reports 42, no. 1 (2023): 111942.

28) Bouhajeb, Rim, Ana Cristina Abreu, Salima Selmi, Christoph Gerke, Ahlem Bellalah, Alexis Alvear-Jiménez, Laura Lozano Chamizo et al. "Implantable Electrospun Nanofibers with Wound-Healing Capabilities in the Reduction of Pressure Ulcers." ACS Applied Polymer Materials (2023).

27) Ganesan, Raja, Sang Jun Yoon, and Ki Tae Suk. "Microbiome and Metabolomics in Liver Cancer: Scientific Technology." International Journal of Molecular Sciences 24, no. 1 (2023): 537.

26) Zhang, Huan, Eric C. Johnson, Anne Carroll, Cecily Pryor, Kenneth Howe, Ryan Kramer, Naik Rajesh et al. "Profiling bourbons based on congener concentrations." Journal of Food Composition and Analysis 115 (2023): 105019.

25) Laketic, Katarina, Sophie Lalonde-Bester, Kim Smyth, Donna M. Slater, Suzanne C. Tough, Hiroaki Ishida, Hans J. Vogel, Gerald F. Giesbrecht, Chunlong Mu, and Jane Shearer. "Maternal Metabolites Indicative of Mental Health Status during Pregnancy." Metabolites 13, no. 1 (2023): 24.

24) Ruiz-Rico, María, Simone Renwick, Sarah J. Vancuren, Avery V. Robinson, Connor Gianetto-Hill, Emma Allen-Vercoe, and José M. Barat. "Impact of food preservatives based on immobilized phenolic compounds on an in vitro model of human gut microbiota." Food Chemistry 403 (2023): 134363.

23) Tripathi, Shweta, Manikyaprabhu Kairamkonda, Payal Gupta, and Krishna Mohan Poluri. "Dissecting the molecular mechanisms of producing biofuel and value-added products by cadmium tolerant microalgae as sustainable biorefinery approach." Chemical Engineering Journal 454 (2023): 140068.

22) Han, Dong Min, Ju Hye Baek, Byung Hee Chun, and Che Ok Jeon. "Fermentative features of Bacillus velezensis and Leuconostoc mesenteroides in doenjang-meju, a Korean traditional fermented soybean brick." Food Microbiology 110 (2023): 104186.

21) Baek, Ju Hye, Kyung Hyun Kim, Dong Min Han, Se Hee Lee, and Che Ok Jeon. "Effects of glutinous rice paste and fish sauce on kimchi fermentation." LWT 173 (2023): 114253.

20) Pereira, Tayla CS, Alzenir R. Souza, Paula B. Daltro, Maria GA Carosio, Antonio G. Ferreira, Regina V. Oliveira, Vitor Fortuna, and Paulo R. Ribeiro. "Blood plasma and bone marrow interstitial fluid metabolomics of sickle cell disease patients with osteonecrosis: An exploratory study to dissect biochemical alterations." Clinica Chimica Acta 539 (2023): 18-25.

19) Jiang, Lin, and Bo Wang. "Metabolomics study on southern hard clams (Mercenaria campechiensis) response to diclofenac exposure." Environmental Science: Advances (2023).

18) Bragulat, Ana P. Flores, Isabel Ortiz, Jaime Catalán, Jesus Dorado, Manuel Hidalgo, Luis Losinno, Marta Dordas-Perpinyà et al. "Time-lapse imaging and developmental competence of donkey eggs after ICSI: Effect of preovulatory follicular fluid during oocyte in vitro maturation." Theriogenology 195 (2023): 199-208.

17) Canella, Rita, Federica Brugnoli, Mariana Gallo, Jeffrey W. Keillor, Anna Terrazzan, Elena Ferrari, Silvia Grassilli et al. "A Multidisciplinary Approach Establishes a Link between Transglutaminase 2 and the Kv10. 1 Voltage-Dependent K+ Channel in Breast Cancer." Cancers 15, no. 1 (2023): 178.

16) Lee, Sheng-Han, Zhi-Yi Du, Wei-Chen Tseng, Wan-Yu Lin, Mei-Huei Chen, Ching-Chun Lin, Hao-Jan Liang et al. "Identification of serum metabolic signatures of environmental-leveled phthalate in the Taiwanese child population using NMR-based metabolomics." Environmental Pollution 316 (2023): 120454.

15) Yim, Dong-Gyun, Hyun Jun Kim, Sung-Su Kim, Hag Ju Lee, Jae-Kyung Kim, and Cheorun Jo. "Effects of different X-ray irradiation doses on quality traits and metabolites of marinated ground beef during storage." Radiation Physics and Chemistry 202 (2023): 110563.

14) Kunc, Martin, Pavel Dobeš, Rachel Ward, Saetbyeol Lee, Radim Čegan, Silvie Dostálková, Kateřina Holušová et al. "Omics-based analysis of honey bee (Apis mellifera) response to Varroa sp. parasitisation and associated factors reveals changes impairing winter bee generation." Insect Biochemistry and Molecular Biology 152 (2023): 103877.

13) Zakaria, Fauziahanim, Muhammad Tayyab Akhtar, Wan Ibrahim Wan Norhamidah, Abu Bakar Noraini, Azira Muhamad, Shamarina Shohaimi, Hafandi Ahmad, Intan Safinar Ismail, Nor Hadiani Ismail, and Khozirah Shaari. "Centella asiatica (L.) Urb. Extract ameliorates branched-chain amino acid (BCAA) metabolism in acute reserpine-induced stress zebrafish model via 1H Nuclear Magnetic Resonance (NMR)-based metabolomics approach." Comparative Biochemistry and Physiology Part C: Toxicology & Pharmacology 264 (2023): 109501.

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7) Verlander, Jill W., Hyun-Wook Lee, Susan M. Wall, Autumn N. Harris, and I. David Weiner. "The proximal tubule through an NBCe1-dependent mechanism regulates collecting duct phenotypic and remodeling responses to acidosis." American Journal of Physiology-Renal Physiology 324, no. 1 (2023): F12-F29.

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1) Huang, Feng, Tong Zhang, Bin Li, Shaosong Wang, Chang Xu, Caihua Huang, and Donghai Lin. "NMR-based metabolomic analysis for the effects of moxibustion on imiquimod-induced psoriatic mice." Journal of Ethnopharmacology 300 (2023): 115626.

Case Studies

The case studies below showcase various studies that were performed using Chenomx technology and services.

 

Analyzing the Metabolic Effects of Acetaminophen

 

Developing Biomarkers for Adverse Drug Responses

 

Pathways From Serological Metabolite Profiles

Acetaminophen is the most common identifiable cause of acute liver failure, and is an excellent model compound for studying liver toxicity. Acetaminophen toxicity has thus become a very active area of research. Identifying and quantifying metabolites associated with acetaminophen toxicity is an integral part of this research, and Chenomx is uniquely equipped to extract this information from biofluid samples.

Drug-induced liver injury is the leading reason that drug candidates fail. Identifying a suite of toxicity biomarkers for use in preclinical screening of drug candidates will allow drugs with harmful side effects to be identified earlier. Biomarkers that can be used to monitor or stage diseases will also offer insight into the net metabolic effect of a drug and can provide information for developing new drugs or adjusting treatment. Chenomx software offers powerful tools to aid in identifying these biomarkers.

Metabolomic data sets obtained using Chenomx NMR Suite often require additional analysis to place them in proper context. The GeneGo pathway analysis platform can help establish this context. In this note, we present an example analysis using serological metabolic profiles from Chenomx NMR Suite, known inflammatory markers from prior studies of the K/BxN mouse model and the GeneGo platform to generate a mechanistic hypothesis for the K/BxN mouse model.

Application Notes

Methods

Accurate CSI Quantification for Targeted Profiling

Accurately quantifying metabolites using targeted profiling in Chenomx NMR Suite requires using a chemical shape and shift indicator (CSI) of known concentration. As a result, the accuracy of the CSI concentration has a significant influence on quantification accuracy using this technique. Measuring ratios of the CSI peak area with that of a second, commercially available standard under optimal acquisition conditions offers a simple method of accurately measuring the concentration of the CSI.

 Optimizing Spectra for Metabolomics

Chenomx Processor allows you to work with NMR spectra from a variety of sources, helping you apply phasing and baseline correction through manual and semi-automated tools, and offering advanced lineshape correction through reference deconvolution. Processor also allows you to define chemical shape indicator (CSI) parameters and determine sample pH via indicator compounds. These are necessary prerequisites to analyzing your spectra with Chenomx Profiler.

Sample Types

Targeted Profiling of Common Metabolites in Saliva

Saliva is an excellent biofluid for analysis by targeted profiling. It is easily collected by individuals with minimal training, using noninvasive techniques. Targeted profiling of saliva samples can provide identification and quantification of many of the small molecule metabolites commonly found in saliva, and may allow the development of simple screening procedures for a variety of diseases. In this note we present a list of common metabolites found in human saliva, and techniques for targeted profiling of saliva spectra with Chenomx NMR Suite.

Metabolites in Blood Serum and Plasma

Blood serum and plasma are biofluids that are increasingly important in NMR-based metabolomics analysis. In this note we discuss several approaches to the analysis of serum using Chenomx NMR Suite, focusing on relaxation-edited NMR (CPMG) and physical separation of protein and metabolites using ultrafiltration. The CPMG method is simpler to apply, but the spectra are easier to analyze when protein is removed from a sample.

 

Targeted Profiling of Common Metabolites in Urine

Urine is a readily-collected, information-rich biofluid that can provide insight into the metabolic state of an organism. As a result, urine is often a focus in metabolomics investigations using NMR and MRI spectroscopy, in both diagnostic and monitoring applications. Targeted profiling is a powerful tool that can drive such studies, providing direct identification and quantification of a variety of metabolites. In this note we present a list of common metabolites found in many NMR spectra of human urine and several strategies for approaching targeted profiling of such spectra with Chenomx NMR Suite.

 

Identifying Metabolites in Biofluids

In this note we present a rapid, efficient method for identifying metabolites in biofluid NMR spectra using targeted profiling. Conventional techniques for identifying and quantifying metabolites in such spectra are labor-intensive and error-prone, as positions and linewidths of peaks can vary widely with changes in pH and other solution matrix effects. The length of time and level of operator skill needed to analyze large numbers of these complex spectra are significant barriers to the widespread application of NMR in metabolomics.

Statistical Analysis

Statistical Analysis of Targeted Profiling Data

Analysis of 1H NMR spectra in metabolomics studies often requires multivariate pattern recognition techniques to extract meaningful results. Targeted profiling offers the ability to analyze spectra based directly on the identity and quantities of individual compounds. Profiles created using targeted profiling in Chenomx NMR Suite can be used as input in statistical software packages such as Umetrics SIMCA-P. Performing PCA on Chenomx targeted profiles yields information-rich results that allow rapid biological interpretation, since group separation can be directly correlated to variations in specific metabolite concentrations.

Correcting Lineshapes in NMR Spectra

In this note we present a method for removing lineshape distortions from nuclear magnetic resonance (NMR) spectra prior to more detailed analysis. Reference deconvolution is a method of reconstructing an ideal spectrum by removing lineshape distortions caused by field inhomogeneity. Applying reference deconvolution has been found to improve the quality of fit of a spectrum using targeted profiling in Chenomx NMR Suite. However, successful application of reference deconvolution to a spectrum requires some preprocessing and the presence of an appropriate reference peak.

 

Statistical Analysis of Spectral Binning Data

Analysis of 1H NMR spectra in metabolomics studies often requires multivariate pattern recognition techniques to extract meaningful results. Spectral binning is an effective data reduction technique commonly used to prepare spectra for multivariate analysis. Spectral binning output from the Profiler module of Chenomx NMR Suite can readily be analyzed with multivariate analysis software packages like Umetrics SIMCA-P.