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23 results on '"Djoumbou Feunang, Yannick"'

1. Perspective: Dietary Biomarkers of Intake and Exposure—Exploration with Omics Approaches

Author

Maruvada, Padma, Lampe, Johanna W, Wishart, David S, Barupal, Dinesh, Chester, Deirdra N, Dodd, Dylan, Djoumbou-Feunang, Yannick, Dorrestein, Pieter C, Dragsted, Lars O, Draper, John, Duffy, Linda C, Dwyer, Johanna T, Emenaker, Nancy J, Fiehn, Oliver, Gerszten, Robert E, B Hu, Frank, Karp, Robert W, Klurfeld, David M, Laughlin, Maren R, Little, A Roger, Lynch, Christopher J, Moore, Steven C, Nicastro, Holly L, O'Brien, Diane M, Ordovás, José M, Osganian, Stavroula K, Playdon, Mary, Prentice, Ross, Raftery, Daniel, Reisdorph, Nichole, Roche, Helen M, Ross, Sharon A, Sang, Shengmin, Scalbert, Augustin, Srinivas, Pothur R, and Zeisel, Steven H

Subjects
Prevention, Nutrition, Metabolic and endocrine, Oral and gastrointestinal, Cancer, Biomarkers, Diet, Food, Genomics, Humans, Metabolomics, Metagenomics, Nutritional Physiological Phenomena, Nutritional Sciences, Nutritional Status, Reproducibility of Results, dietary biomarkers, dietary intervention studies, diet, nutrition, metabolomics, Nutrition and Dietetics
Abstract

While conventional nutrition research has yielded biomarkers such as doubly labeled water for energy metabolism and 24-h urinary nitrogen for protein intake, a critical need exists for additional, equally robust biomarkers that allow for objective assessment of specific food intake and dietary exposure. Recent advances in high-throughput MS combined with improved metabolomics techniques and bioinformatic tools provide new opportunities for dietary biomarker development. In September 2018, the NIH organized a 2-d workshop to engage nutrition and omics researchers and explore the potential of multiomics approaches in nutritional biomarker research. The current Perspective summarizes key gaps and challenges identified, as well as the recommendations from the workshop that could serve as a guide for scientists interested in dietary biomarkers research. Topics addressed included study designs for biomarker development, analytical and bioinformatic considerations, and integration of dietary biomarkers with other omics techniques. Several clear needs were identified, including larger controlled feeding studies, testing a variety of foods and dietary patterns across diverse populations, improved reporting standards to support study replication, more chemical standards covering a broader range of food constituents and human metabolites, standardized approaches for biomarker validation, comprehensive and accessible food composition databases, a common ontology for dietary biomarker literature, and methodologic work on statistical procedures for intake biomarker discovery. Multidisciplinary research teams with appropriate expertise are critical to moving forward the field of dietary biomarkers and producing robust, reproducible biomarkers that can be used in public health and clinical research.

Published
2020

2. The NORMAN Suspect List Exchange (NORMAN-SLE): facilitating European and worldwide collaboration on suspect screening in high resolution mass spectrometry

Author

Mohammed Taha, Hiba, Aalizadeh, Reza, Alygizakis, Nikiforos, Antignac, Jean-Philippe, Arp, Hans Peter H., Bade, Richard, Baker, Nancy, Belova, Lidia, Bijlsma, Lubertus, Bolton, Evan E., Brack, Werner, Celma, Alberto, Chen, Wen-Ling, Cheng, Tiejun, Chirsir, Parviel, Čirka, Ľuboš, D’Agostino, Lisa A., Djoumbou Feunang, Yannick, Dulio, Valeria, Fischer, Stellan, Gago-Ferrero, Pablo, Galani, Aikaterini, Geueke, Birgit, Głowacka, Natalia, Glüge, Juliane, Groh, Ksenia, Grosse, Sylvia, Haglund, Peter, Hakkinen, Pertti J., Hale, Sarah E., Hernandez, Felix, Janssen, Elisabeth M.-L., Jonkers, Tim, Kiefer, Karin, Kirchner, Michal, Koschorreck, Jan, Krauss, Martin, Krier, Jessy, Lamoree, Marja H., Letzel, Marion, Letzel, Thomas, Li, Qingliang, Little, James, Liu, Yanna, Lunderberg, David M., Martin, Jonathan W., McEachran, Andrew D., McLean, John A., Meier, Christiane, Meijer, Jeroen, Menger, Frank, Merino, Carla, Muncke, Jane, Muschket, Matthias, Neumann, Michael, Neveu, Vanessa, Ng, Kelsey, Oberacher, Herbert, O’Brien, Jake, Oswald, Peter, Oswaldova, Martina, Picache, Jaqueline A., Postigo, Cristina, Ramirez, Noelia, Reemtsma, Thorsten, Renaud, Justin, Rostkowski, Pawel, Rüdel, Heinz, Salek, Reza M., Samanipour, Saer, Scheringer, Martin, Schliebner, Ivo, Schulz, Wolfgang, Schulze, Tobias, Sengl, Manfred, Shoemaker, Benjamin A., Sims, Kerry, Singer, Heinz, Singh, Randolph R., Sumarah, Mark, Thiessen, Paul A., Thomas, Kevin V., Torres, Sonia, Trier, Xenia, van Wezel, Annemarie P., Vermeulen, Roel C. H., Vlaanderen, Jelle J., von der Ohe, Peter C., Wang, Zhanyun, Williams, Antony J., Willighagen, Egon L., Wishart, David S., Zhang, Jian, Thomaidis, Nikolaos S., Hollender, Juliane, Slobodnik, Jaroslav, and Schymanski, Emma L.

Published
2022
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3. Computational Applications in Secondary Metabolite Discovery (CAiSMD): an online workshop

Author

Ntie-Kang, Fidele, Telukunta, Kiran K., Fobofou, Serge A. T., Chukwudi Osamor, Victor, Egieyeh, Samuel A., Valli, Marilia, Djoumbou-Feunang, Yannick, Sorokina, Maria, Stork, Conrad, Mathai, Neann, Zierep, Paul, Chávez-Hernández, Ana L., Duran-Frigola, Miquel, Babiaka, Smith B., Tematio Fouedjou, Romuald, Eni, Donatus B., Akame, Simeon, Arreyetta-Bawak, Augustine B., Ebob, Oyere T., Metuge, Jonathan A., Bekono, Boris D., Isa, Mustafa A., Onuku, Raphael, Shadrack, Daniel M., Musyoka, Thommas M., Patil, Vaishali M., van der Hooft, Justin J. J., da Silva Bolzani, Vanderlan, Medina-Franco, José L., Kirchmair, Johannes, Weber, Tilmann, Tastan Bishop, Özlem, Medema, Marnix H., Wessjohann, Ludger A., and Ludwig-Müller, Jutta

Published
2021
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6. ChemFOnt: the chemical functional ontology resource

Author

Wishart, David S, primary, Girod, Sagan, additional, Peters, Harrison, additional, Oler, Eponine, additional, Jovel, Juan, additional, Budinski, Zachary, additional, Milford, Ralph, additional, Lui, Vicki W, additional, Sayeeda, Zinat, additional, Mah, Robert, additional, Wei, William, additional, Badran, Hasan, additional, Lo, Elvis, additional, Yamamoto, Mai, additional, Djoumbou-Feunang, Yannick, additional, Karu, Naama, additional, and Gautam, Vasuk, additional

Published
2022
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7. The NORMAN Suspect List Exchange (NORMAN-SLE): Facilitating European and worldwide collaboration on suspect screening in high resolution mass spectrometry

Author

IRAS OH Epidemiology Chemical Agents, Mohammed Taha, Hiba, Aalizadeh, Reza, Alygizakis, Nikiforos, Antignac, Jean-Philippe, Arp, Hans Peter H, Bade, Richard, Baker, Nancy, Belova, Lidia, Bijlsma, Lubertus, Bolton, Evan E, Brack, Werner, Celma, Alberto, Chen, Wen-Ling, Cheng, Tiejun, Chirsir, Parviel, Čirka, Ľuboš, D'Agostino, Lisa A, Djoumbou Feunang, Yannick, Dulio, Valeria, Fischer, Stellan, Gago-Ferrero, Pablo, Galani, Aikaterini, Geueke, Birgit, Głowacka, Natalia, Glüge, Juliane, Groh, Ksenia, Grosse, Sylvia, Haglund, Peter, Hakkinen, Pertti J, Hale, Sarah E, Hernandez, Felix, Janssen, Elisabeth M-L, Jonkers, Tim, Kiefer, Karin, Kirchner, Michal, Koschorreck, Jan, Krauss, Martin, Krier, Jessy, Lamoree, Marja H, Letzel, Marion, Letzel, Thomas, Li, Qingliang, Little, James, Liu, Yanna, Lunderberg, David M, Martin, Jonathan W, McEachran, Andrew D, McLean, John A, Meier, Christiane, Meijer, Jeroen, Menger, Frank, Merino, Carla, Muncke, Jane, Muschket, Matthias, Neumann, Michael, Neveu, Vanessa, Ng, Kelsey, Oberacher, Herbert, O'Brien, Jake, Oswald, Peter, Oswaldova, Martina, Picache, Jaqueline A, Postigo, Cristina, Ramirez, Noelia, Reemtsma, Thorsten, Renaud, Justin, Rostkowski, Pawel, Rüdel, Heinz, Salek, Reza M, Samanipour, Saer, Scheringer, Martin, Schliebner, Ivo, Schulz, Wolfgang, Schulze, Tobias, Sengl, Manfred, Shoemaker, Benjamin A, Sims, Kerry, Singer, Heinz, Singh, Randolph R, Sumarah, Mark, Thiessen, Paul A, Thomas, Kevin V, Torres, Sonia, Trier, Xenia, van Wezel, Annemarie P, Vermeulen, Roel C H, Vlaanderen, Jelle J, von der Ohe, Peter C, Wang, Zhanyun, Williams, Antony J, Willighagen, Egon L, Wishart, David S, Zhang, Jian, Thomaidis, Nikolaos S, Hollender, Juliane, Slobodnik, Jaroslav, Schymanski, Emma L, IRAS OH Epidemiology Chemical Agents, Mohammed Taha, Hiba, Aalizadeh, Reza, Alygizakis, Nikiforos, Antignac, Jean-Philippe, Arp, Hans Peter H, Bade, Richard, Baker, Nancy, Belova, Lidia, Bijlsma, Lubertus, Bolton, Evan E, Brack, Werner, Celma, Alberto, Chen, Wen-Ling, Cheng, Tiejun, Chirsir, Parviel, Čirka, Ľuboš, D'Agostino, Lisa A, Djoumbou Feunang, Yannick, Dulio, Valeria, Fischer, Stellan, Gago-Ferrero, Pablo, Galani, Aikaterini, Geueke, Birgit, Głowacka, Natalia, Glüge, Juliane, Groh, Ksenia, Grosse, Sylvia, Haglund, Peter, Hakkinen, Pertti J, Hale, Sarah E, Hernandez, Felix, Janssen, Elisabeth M-L, Jonkers, Tim, Kiefer, Karin, Kirchner, Michal, Koschorreck, Jan, Krauss, Martin, Krier, Jessy, Lamoree, Marja H, Letzel, Marion, Letzel, Thomas, Li, Qingliang, Little, James, Liu, Yanna, Lunderberg, David M, Martin, Jonathan W, McEachran, Andrew D, McLean, John A, Meier, Christiane, Meijer, Jeroen, Menger, Frank, Merino, Carla, Muncke, Jane, Muschket, Matthias, Neumann, Michael, Neveu, Vanessa, Ng, Kelsey, Oberacher, Herbert, O'Brien, Jake, Oswald, Peter, Oswaldova, Martina, Picache, Jaqueline A, Postigo, Cristina, Ramirez, Noelia, Reemtsma, Thorsten, Renaud, Justin, Rostkowski, Pawel, Rüdel, Heinz, Salek, Reza M, Samanipour, Saer, Scheringer, Martin, Schliebner, Ivo, Schulz, Wolfgang, Schulze, Tobias, Sengl, Manfred, Shoemaker, Benjamin A, Sims, Kerry, Singer, Heinz, Singh, Randolph R, Sumarah, Mark, Thiessen, Paul A, Thomas, Kevin V, Torres, Sonia, Trier, Xenia, van Wezel, Annemarie P, Vermeulen, Roel C H, Vlaanderen, Jelle J, von der Ohe, Peter C, Wang, Zhanyun, Williams, Antony J, Willighagen, Egon L, Wishart, David S, Zhang, Jian, Thomaidis, Nikolaos S, Hollender, Juliane, Slobodnik, Jaroslav, and Schymanski, Emma L

Published
2022

8. The NORMAN Suspect List Exchange (NORMAN-SLE):facilitating European and worldwide collaboration on suspect screening in high resolution mass spectrometry

Author

Mohammed Taha, Hiba, Aalizadeh, Reza, Alygizakis, Nikiforos, Antignac, Jean Philippe, Arp, Hans Peter H., Bade, Richard, Baker, Nancy, Belova, Lidia, Bijlsma, Lubertus, Bolton, Evan E., Brack, Werner, Celma, Alberto, Chen, Wen Ling, Cheng, Tiejun, Chirsir, Parviel, Čirka, Ľuboš, D’Agostino, Lisa A., Djoumbou Feunang, Yannick, Dulio, Valeria, Fischer, Stellan, Gago-Ferrero, Pablo, Galani, Aikaterini, Geueke, Birgit, Głowacka, Natalia, Glüge, Juliane, Groh, Ksenia, Grosse, Sylvia, Haglund, Peter, Hakkinen, Pertti J., Hale, Sarah E., Hernandez, Felix, Janssen, Elisabeth M.L., Jonkers, Tim, Kiefer, Karin, Kirchner, Michal, Koschorreck, Jan, Krauss, Martin, Krier, Jessy, Lamoree, Marja H., Letzel, Marion, Letzel, Thomas, Li, Qingliang, Little, James, Liu, Yanna, Lunderberg, David M., Martin, Jonathan W., McEachran, Andrew D., McLean, John A., Meier, Christiane, Meijer, Jeroen, Menger, Frank, Merino, Carla, Muncke, Jane, Muschket, Matthias, Neumann, Michael, Neveu, Vanessa, Ng, Kelsey, Oberacher, Herbert, O’Brien, Jake, Oswald, Peter, Oswaldova, Martina, Picache, Jaqueline A., Postigo, Cristina, Ramirez, Noelia, Reemtsma, Thorsten, Renaud, Justin, Rostkowski, Pawel, Rüdel, Heinz, Salek, Reza M., Samanipour, Saer, Scheringer, Martin, Schliebner, Ivo, Schulz, Wolfgang, Schulze, Tobias, Sengl, Manfred, Shoemaker, Benjamin A., Sims, Kerry, Singer, Heinz, Singh, Randolph R., Sumarah, Mark, Thiessen, Paul A., Thomas, Kevin V., Torres, Sonia, Trier, Xenia, van Wezel, Annemarie P., Vermeulen, Roel C.H., Vlaanderen, Jelle J., von der Ohe, Peter C., Wang, Zhanyun, Williams, Antony J., Willighagen, Egon L., Wishart, David S., Zhang, Jian, Thomaidis, Nikolaos S., Hollender, Juliane, Slobodnik, Jaroslav, Schymanski, Emma L., Mohammed Taha, Hiba, Aalizadeh, Reza, Alygizakis, Nikiforos, Antignac, Jean Philippe, Arp, Hans Peter H., Bade, Richard, Baker, Nancy, Belova, Lidia, Bijlsma, Lubertus, Bolton, Evan E., Brack, Werner, Celma, Alberto, Chen, Wen Ling, Cheng, Tiejun, Chirsir, Parviel, Čirka, Ľuboš, D’Agostino, Lisa A., Djoumbou Feunang, Yannick, Dulio, Valeria, Fischer, Stellan, Gago-Ferrero, Pablo, Galani, Aikaterini, Geueke, Birgit, Głowacka, Natalia, Glüge, Juliane, Groh, Ksenia, Grosse, Sylvia, Haglund, Peter, Hakkinen, Pertti J., Hale, Sarah E., Hernandez, Felix, Janssen, Elisabeth M.L., Jonkers, Tim, Kiefer, Karin, Kirchner, Michal, Koschorreck, Jan, Krauss, Martin, Krier, Jessy, Lamoree, Marja H., Letzel, Marion, Letzel, Thomas, Li, Qingliang, Little, James, Liu, Yanna, Lunderberg, David M., Martin, Jonathan W., McEachran, Andrew D., McLean, John A., Meier, Christiane, Meijer, Jeroen, Menger, Frank, Merino, Carla, Muncke, Jane, Muschket, Matthias, Neumann, Michael, Neveu, Vanessa, Ng, Kelsey, Oberacher, Herbert, O’Brien, Jake, Oswald, Peter, Oswaldova, Martina, Picache, Jaqueline A., Postigo, Cristina, Ramirez, Noelia, Reemtsma, Thorsten, Renaud, Justin, Rostkowski, Pawel, Rüdel, Heinz, Salek, Reza M., Samanipour, Saer, Scheringer, Martin, Schliebner, Ivo, Schulz, Wolfgang, Schulze, Tobias, Sengl, Manfred, Shoemaker, Benjamin A., Sims, Kerry, Singer, Heinz, Singh, Randolph R., Sumarah, Mark, Thiessen, Paul A., Thomas, Kevin V., Torres, Sonia, Trier, Xenia, van Wezel, Annemarie P., Vermeulen, Roel C.H., Vlaanderen, Jelle J., von der Ohe, Peter C., Wang, Zhanyun, Williams, Antony J., Willighagen, Egon L., Wishart, David S., Zhang, Jian, Thomaidis, Nikolaos S., Hollender, Juliane, Slobodnik, Jaroslav, and Schymanski, Emma L.

Abstract

Background: The NORMAN Association (https://www.norman-network.com/) initiated the NORMAN Suspect List Exchange (NORMAN-SLE; https://www.norman-network.com/nds/SLE/) in 2015, following the NORMAN collaborative trial on non-target screening of environmental water samples by mass spectrometry. Since then, this exchange of information on chemicals that are expected to occur in the environment, along with the accompanying expert knowledge and references, has become a valuable knowledge base for “suspect screening” lists. The NORMAN-SLE now serves as a FAIR (Findable, Accessible, Interoperable, Reusable) chemical information resource worldwide. Results: The NORMAN-SLE contains 99 separate suspect list collections (as of May 2022) from over 70 contributors around the world, totalling over 100,000 unique substances. The substance classes include per- and polyfluoroalkyl substances (PFAS), pharmaceuticals, pesticides, natural toxins, high production volume substances covered under the European REACH regulation (EC: 1272/2008), priority contaminants of emerging concern (CECs) and regulatory lists from NORMAN partners. Several lists focus on transformation products (TPs) and complex features detected in the environment with various levels of provenance and structural information. Each list is available for separate download. The merged, curated collection is also available as the NORMAN Substance Database (NORMAN SusDat). Both the NORMAN-SLE and NORMAN SusDat are integrated within the NORMAN Database System (NDS). The individual NORMAN-SLE lists receive digital object identifiers (DOIs) and traceable versioning via a Zenodo community (https://zenodo.org/communities/norman-sle), with a total of > 40,000 unique views, > 50,000 unique downloads and 40 citations (May 2022). NORMAN-SLE content is progressively integrated into large open chemical databases such as PubChem (https://pubchem.ncbi.nlm.nih.gov/) and the US EPA’s CompTox Chemicals Dashboard (https://comptox.epa.

Published
2022

9. The NORMAN Suspect List Exchange (NORMAN-SLE): facilitating European and worldwide collaboration on suspect screening in high resolution mass spectrometry

Author

Ministerio de Ciencia e Innovación (España), European Commission, 0000-0001-7820-4335, 0000-0001-9167-9060, 0000-0002-5727-4999, 0000-0001-9512-9314, 0000-0002-0747-8838, 0000-0003-2724-9183, 0000-0002-8351-9435, 0000-0001-7147-384X, 0000-0001-7005-8775, 0000-0002-5959-6190, 0000-0001-9269-6524, 0000-0001-9763-8737, 0000-0001-5143-0543, 0000-0002-4486-3356, 0000-0002-9932-8609, 0000-0001-9351-6855, 0000-0002-9734-324X, 0000-0001-7850-184X, 0000-0002-9436-9954, 0000-0002-5987-0399, 0000-0003-1112-6867, 0000-0002-0749-3982, 0000-0002-1740-9422, 0000-0003-1997-2750, 0000-0002-3778-4721, 0000-0003-2293-7913, 0000-0002-8295-9738, 0000-0002-7743-9199, 0000-0003-1268-3083, 0000-0002-5475-6730, 0000-0002-6415-6173, 0000-0002-6917-3431, 0000-0002-1043-3278, 0000-0002-0362-4244, 0000-0001-6986-5545, 0000-0002-7373-7738, 0000-0003-1008-8790, 0000-0002-6453-236X, 0000-0001-7893-9876, 0000-0002-4439-9194, 0000-0001-6265-4294, 0000-0003-1423-330X, 0000-0001-8918-6419, 0000-0003-3126-5186, 0000-0002-4551-6823, 0000-0002-1808-8835, 0000-0002-8793-5516, 0000-0002-6942-0594, 0000-0001-6672-8414, 0000-0002-2558-4431, 0000-0002-8501-7789, 0000-0003-2396-2993, 0000-0002-0963-8268, 0000-0001-9336-9656, 0000-0003-3088-9771, 0000-0002-1948-9243, 0000-0002-7344-7044, 0000-0002-9251-0790, 0000-0003-1606-0764, 0000-0001-6974-0224, 0000-0001-9778-4283, 0000-0002-4175-4787, 0000-0001-8604-1732, 0000-0001-8270-6979, 0000-0002-0809-7826, 0000-0002-1553-3868, 0000-0002-9744-8914, 0000-0002-1356-285X, 0000-0001-6273-4083, 0000-0002-8542-3699, 0000-0003-4500-3400, 0000-0003-0977-1656, 0000-0002-1992-2086, 0000-0002-2155-100X, 0000-0001-8881-0793, 0000-0001-6067-8321, 0000-0002-6875-957X, 0000-0003-4082-8163, 0000-0001-7350-8962, 0000-0001-9914-7659, 0000-0002-2668-4821, 0000-0001-7542-0286, 0000-0002-3207-2434, 0000-0002-6192-4632, 0000-0002-4624-4735, 0000-0002-4660-274X, 0000-0003-2622-6318, 0000-0001-6868-8145, Mohammed Taha, Hiba, Aalizadeh, Reza, Alygizakis, Nikiforos, Antignac, Jean-Philippe, Arp, Hans Peter H., Bade, Richard, Baker, Nancy, Belova, Lidia, Bijlsma, Lubertus, Bolton, Evan E., Brack, Werner, Celma, Alberto, Chen, Wen-Ling, Cheng, Tiejun, Chirsir, Parviel, Čirka, Ľuboš, D'Agostino, Lisa A., Djoumbou Feunang, Yannick, Dulio, Valeria, Fischer, Stellan, Gago-Ferrero, Pablo, Galani, Aikaterini, Geueke, Birgit, Głowacka, Natalia, Glüge, Juliane, Groh, Ksenia, Grosse, Sylvia, Haglund, Peter, Hakkinen, Pertti J., Hale, Sarah E., Hernandez, Felix, Janssen, Elisabeth M-L., Jonkers, Tim, Kiefer, Karin, Kirchner, Michal, Koschorreck, Jan, Krauss, Martin, Krier, Jessy, Lamoree, Marja H., Letzel, Marion, Letzel, Thomas, Li, Qingliang, Little, James, Liu, Yanna, Lunderberg, David M., Martin, Jonathan W., McEachran, Andrew D., McLean, John A., Meier, Christiane, Meijer, Jeroen, Menger, Frank, Merino, Carla, Muncke, Jane, Muschket, Matthias, Neumann, Michael, Neveu, Vanessa, Ng, Kelsey, Oberacher, Herbert, O'Brien, Jake, Oswald, Peter, Oswaldova, Martina, Picache, Jaqueline A., Postigo, Cristina, Ramírez, Noelia, Reemtsma, Thorsten, Renaud, Justin, Rostkowski, Pawel, Rüdel, Heinz, Salek, Reza M., Samanipour, Saer, Scheringer, Martin, Schliebner, Ivo, Schulz, Wolfgang, Schulze, Tobias, Sengl, Manfred, Shoemaker, Benjamin A., Sims, Kerry, Singer, Heinz, Singh, Randolph R., Sumarah, Mark, Thiessen, Paul A., Thomas, Kevin V., Torres, Sonia, Trier, Xenia, van Wezel, Annemarie P., Vermeulen, Roel C. H., Vlaanderen, Jelle J., von der Ohe, Peter C., Wang, Zhanyun, Williams, Antony J., Willighagen, Egon L., Wishart, David S., Zhang, Jian, Thomaidis, Nikolaos S., Hollender, Juliane, Slobodnik, Jaroslav, Schymanski, Emma L., Ministerio de Ciencia e Innovación (España), European Commission, 0000-0001-7820-4335, 0000-0001-9167-9060, 0000-0002-5727-4999, 0000-0001-9512-9314, 0000-0002-0747-8838, 0000-0003-2724-9183, 0000-0002-8351-9435, 0000-0001-7147-384X, 0000-0001-7005-8775, 0000-0002-5959-6190, 0000-0001-9269-6524, 0000-0001-9763-8737, 0000-0001-5143-0543, 0000-0002-4486-3356, 0000-0002-9932-8609, 0000-0001-9351-6855, 0000-0002-9734-324X, 0000-0001-7850-184X, 0000-0002-9436-9954, 0000-0002-5987-0399, 0000-0003-1112-6867, 0000-0002-0749-3982, 0000-0002-1740-9422, 0000-0003-1997-2750, 0000-0002-3778-4721, 0000-0003-2293-7913, 0000-0002-8295-9738, 0000-0002-7743-9199, 0000-0003-1268-3083, 0000-0002-5475-6730, 0000-0002-6415-6173, 0000-0002-6917-3431, 0000-0002-1043-3278, 0000-0002-0362-4244, 0000-0001-6986-5545, 0000-0002-7373-7738, 0000-0003-1008-8790, 0000-0002-6453-236X, 0000-0001-7893-9876, 0000-0002-4439-9194, 0000-0001-6265-4294, 0000-0003-1423-330X, 0000-0001-8918-6419, 0000-0003-3126-5186, 0000-0002-4551-6823, 0000-0002-1808-8835, 0000-0002-8793-5516, 0000-0002-6942-0594, 0000-0001-6672-8414, 0000-0002-2558-4431, 0000-0002-8501-7789, 0000-0003-2396-2993, 0000-0002-0963-8268, 0000-0001-9336-9656, 0000-0003-3088-9771, 0000-0002-1948-9243, 0000-0002-7344-7044, 0000-0002-9251-0790, 0000-0003-1606-0764, 0000-0001-6974-0224, 0000-0001-9778-4283, 0000-0002-4175-4787, 0000-0001-8604-1732, 0000-0001-8270-6979, 0000-0002-0809-7826, 0000-0002-1553-3868, 0000-0002-9744-8914, 0000-0002-1356-285X, 0000-0001-6273-4083, 0000-0002-8542-3699, 0000-0003-4500-3400, 0000-0003-0977-1656, 0000-0002-1992-2086, 0000-0002-2155-100X, 0000-0001-8881-0793, 0000-0001-6067-8321, 0000-0002-6875-957X, 0000-0003-4082-8163, 0000-0001-7350-8962, 0000-0001-9914-7659, 0000-0002-2668-4821, 0000-0001-7542-0286, 0000-0002-3207-2434, 0000-0002-6192-4632, 0000-0002-4624-4735, 0000-0002-4660-274X, 0000-0003-2622-6318, 0000-0001-6868-8145, Mohammed Taha, Hiba, Aalizadeh, Reza, Alygizakis, Nikiforos, Antignac, Jean-Philippe, Arp, Hans Peter H., Bade, Richard, Baker, Nancy, Belova, Lidia, Bijlsma, Lubertus, Bolton, Evan E., Brack, Werner, Celma, Alberto, Chen, Wen-Ling, Cheng, Tiejun, Chirsir, Parviel, Čirka, Ľuboš, D'Agostino, Lisa A., Djoumbou Feunang, Yannick, Dulio, Valeria, Fischer, Stellan, Gago-Ferrero, Pablo, Galani, Aikaterini, Geueke, Birgit, Głowacka, Natalia, Glüge, Juliane, Groh, Ksenia, Grosse, Sylvia, Haglund, Peter, Hakkinen, Pertti J., Hale, Sarah E., Hernandez, Felix, Janssen, Elisabeth M-L., Jonkers, Tim, Kiefer, Karin, Kirchner, Michal, Koschorreck, Jan, Krauss, Martin, Krier, Jessy, Lamoree, Marja H., Letzel, Marion, Letzel, Thomas, Li, Qingliang, Little, James, Liu, Yanna, Lunderberg, David M., Martin, Jonathan W., McEachran, Andrew D., McLean, John A., Meier, Christiane, Meijer, Jeroen, Menger, Frank, Merino, Carla, Muncke, Jane, Muschket, Matthias, Neumann, Michael, Neveu, Vanessa, Ng, Kelsey, Oberacher, Herbert, O'Brien, Jake, Oswald, Peter, Oswaldova, Martina, Picache, Jaqueline A., Postigo, Cristina, Ramírez, Noelia, Reemtsma, Thorsten, Renaud, Justin, Rostkowski, Pawel, Rüdel, Heinz, Salek, Reza M., Samanipour, Saer, Scheringer, Martin, Schliebner, Ivo, Schulz, Wolfgang, Schulze, Tobias, Sengl, Manfred, Shoemaker, Benjamin A., Sims, Kerry, Singer, Heinz, Singh, Randolph R., Sumarah, Mark, Thiessen, Paul A., Thomas, Kevin V., Torres, Sonia, Trier, Xenia, van Wezel, Annemarie P., Vermeulen, Roel C. H., Vlaanderen, Jelle J., von der Ohe, Peter C., Wang, Zhanyun, Williams, Antony J., Willighagen, Egon L., Wishart, David S., Zhang, Jian, Thomaidis, Nikolaos S., Hollender, Juliane, Slobodnik, Jaroslav, and Schymanski, Emma L.

Abstract

The NORMAN Association (https://www.norman-network.com/) initiated the NORMAN Suspect List Exchange (NORMAN-SLE; https://www.norman-network.com/nds/SLE/) in 2015, following the NORMAN collaborative trial on non-target screening of environmental water samples by mass spectrometry. Since then, this exchange of information on chemicals that are expected to occur in the environment, along with the accompanying expert knowledge and references, has become a valuable knowledge base for "suspect screening" lists. The NORMAN-SLE now serves as a FAIR (Findable, Accessible, Interoperable, Reusable) chemical information resource worldwide.

Published
2022

11. Additional file 2 of The NORMAN Suspect List Exchange (NORMAN-SLE): facilitating European and worldwide collaboration on suspect screening in high resolution mass spectrometry

Author

Mohammed Taha, Hiba, Aalizadeh, Reza, Alygizakis, Nikiforos, Antignac, Jean-Philippe, Arp, Hans Peter H., Bade, Richard, Baker, Nancy, Belova, Lidia, Bijlsma, Lubertus, Bolton, Evan E., Brack, Werner, Celma, Alberto, Chen, Wen-Ling, Cheng, Tiejun, Chirsir, Parviel, Čirka, Ľuboš, D’Agostino, Lisa A., Djoumbou Feunang, Yannick, Dulio, Valeria, Fischer, Stellan, Gago-Ferrero, Pablo, Galani, Aikaterini, Geueke, Birgit, Głowacka, Natalia, Glüge, Juliane, Groh, Ksenia, Grosse, Sylvia, Haglund, Peter, Hakkinen, Pertti J., Hale, Sarah E., Hernandez, Felix, Janssen, Elisabeth M.-L., Jonkers, Tim, Kiefer, Karin, Kirchner, Michal, Koschorreck, Jan, Krauss, Martin, Krier, Jessy, Lamoree, Marja H., Letzel, Marion, Letzel, Thomas, Li, Qingliang, Little, James, Liu, Yanna, Lunderberg, David M., Martin, Jonathan W., McEachran, Andrew D., McLean, John A., Meier, Christiane, Meijer, Jeroen, Menger, Frank, Merino, Carla, Muncke, Jane, Muschket, Matthias, Neumann, Michael, Neveu, Vanessa, Ng, Kelsey, Oberacher, Herbert, O’Brien, Jake, Oswald, Peter, Oswaldova, Martina, Picache, Jaqueline A., Postigo, Cristina, Ramirez, Noelia, Reemtsma, Thorsten, Renaud, Justin, Rostkowski, Pawel, Rüdel, Heinz, Salek, Reza M., Samanipour, Saer, Scheringer, Martin, Schliebner, Ivo, Schulz, Wolfgang, Schulze, Tobias, Sengl, Manfred, Shoemaker, Benjamin A., Sims, Kerry, Singer, Heinz, Singh, Randolph R., Sumarah, Mark, Thiessen, Paul A., Thomas, Kevin V., Torres, Sonia, Trier, Xenia, van Wezel, Annemarie P., Vermeulen, Roel C. H., Vlaanderen, Jelle J., von der Ohe, Peter C., Wang, Zhanyun, Williams, Antony J., Willighagen, Egon L., Wishart, David S., Zhang, Jian, Thomaidis, Nikolaos S., Hollender, Juliane, Slobodnik, Jaroslav, and Schymanski, Emma L.

Subjects
Pharmacology, Ecology, 39999 Chemical Sciences not elsewhere classified, FOS: Chemical sciences, FOS: Biological sciences, Computational Biology, Marine Biology, Biochemistry, Molecular Biology, Biotechnology, Cancer
Abstract

Additional file 2: Overview of the NORMAN-SLE website (DOCX format) as of 30 May 2022 [82].

Published
2022
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12. ChemFOnt: the chemical functional ontology resource.

Author

Wishart, David S, Girod, Sagan, Peters, Harrison, Oler, Eponine, Jovel, Juan, Budinski, Zachary, Milford, Ralph, Lui, Vicki W, Sayeeda, Zinat, Mah, Robert, Wei, William, Badran, Hasan, Lo, Elvis, Yamamoto, Mai, Djoumbou-Feunang, Yannick, Karu, Naama, and Gautam, Vasuk

Published
2023
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13. Additional file 2 of Computational Applications in Secondary Metabolite Discovery (CAiSMD): an online workshop

Author

Ntie-Kang, Fidele, Telukunta, Kiran K., Fobofou, Serge A. T., Chukwudi Osamor, Victor, Egieyeh, Samuel A., Valli, Marilia, Djoumbou-Feunang, Yannick, Sorokina, Maria, Stork, Conrad, Mathai, Neann, Zierep, Paul, Chávez-Hernández, Ana L., Duran-Frigola, Miquel, Babiaka, Smith B., Tematio Fouedjou, Romuald, Eni, Donatus B., Akame, Simeon, Arreyetta-Bawak, Augustine B., Ebob, Oyere T., Metuge, Jonathan A., Bekono, Boris D., Isa, Mustafa A., Onuku, Raphael, Shadrack, Daniel M., Musyoka, Thommas M., Patil, Vaishali M., van der Hooft, Justin J. J., da Silva Bolzani, Vanderlan, Medina-Franco, José L., Kirchmair, Johannes, Weber, Tilmann, Tastan Bishop, Özlem, Medema, Marnix H., Wessjohann, Ludger A., and Ludwig-Müller, Jutta

Abstract

Additional file 2. CAiSMD Feedback form.

Published
2021
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14. Additional file 1 of Computational Applications in Secondary Metabolite Discovery (CAiSMD): an online workshop

Author

Ntie-Kang, Fidele, Telukunta, Kiran K., Fobofou, Serge A. T., Chukwudi Osamor, Victor, Egieyeh, Samuel A., Valli, Marilia, Djoumbou-Feunang, Yannick, Sorokina, Maria, Stork, Conrad, Mathai, Neann, Zierep, Paul, Chávez-Hernández, Ana L., Duran-Frigola, Miquel, Babiaka, Smith B., Tematio Fouedjou, Romuald, Eni, Donatus B., Akame, Simeon, Arreyetta-Bawak, Augustine B., Ebob, Oyere T., Metuge, Jonathan A., Bekono, Boris D., Isa, Mustafa A., Onuku, Raphael, Shadrack, Daniel M., Musyoka, Thommas M., Patil, Vaishali M., van der Hooft, Justin J. J., da Silva Bolzani, Vanderlan, Medina-Franco, José L., Kirchmair, Johannes, Weber, Tilmann, Tastan Bishop, Özlem, Medema, Marnix H., Wessjohann, Ludger A., and Ludwig-Müller, Jutta

Subjects
Data_FILES
Abstract

Additional file 1. Workshop statistics.

Published
2021
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15. Computational Applications in Secondary Metabolite Discovery (CAiSMD):an online workshop

Author

Ntie-Kang, Fidele, Telukunta, Kiran K., Fobofou, Serge A.T., Chukwudi Osamor, Victor, Egieyeh, Samuel A., Valli, Marilia, Djoumbou-Feunang, Yannick, Sorokina, Maria, Stork, Conrad, Mathai, Neann, Zierep, Paul, Chávez-Hernández, Ana L., Duran-Frigola, Miquel, Babiaka, Smith B., Tematio Fouedjou, Romuald, Eni, Donatus B., Akame, Simeon, Arreyetta-Bawak, Augustine B., Ebob, Oyere T., Metuge, Jonathan A., Bekono, Boris D., Isa, Mustafa A., Onuku, Raphael, Shadrack, Daniel M., Musyoka, Thommas M., Patil, Vaishali M., van der Hooft, Justin J.J., da Silva Bolzani, Vanderlan, Medina-Franco, José L., Kirchmair, Johannes, Weber, Tilmann, Tastan Bishop, Özlem, Medema, Marnix H., Wessjohann, Ludger A., Ludwig-Müller, Jutta, Ntie-Kang, Fidele, Telukunta, Kiran K., Fobofou, Serge A.T., Chukwudi Osamor, Victor, Egieyeh, Samuel A., Valli, Marilia, Djoumbou-Feunang, Yannick, Sorokina, Maria, Stork, Conrad, Mathai, Neann, Zierep, Paul, Chávez-Hernández, Ana L., Duran-Frigola, Miquel, Babiaka, Smith B., Tematio Fouedjou, Romuald, Eni, Donatus B., Akame, Simeon, Arreyetta-Bawak, Augustine B., Ebob, Oyere T., Metuge, Jonathan A., Bekono, Boris D., Isa, Mustafa A., Onuku, Raphael, Shadrack, Daniel M., Musyoka, Thommas M., Patil, Vaishali M., van der Hooft, Justin J.J., da Silva Bolzani, Vanderlan, Medina-Franco, José L., Kirchmair, Johannes, Weber, Tilmann, Tastan Bishop, Özlem, Medema, Marnix H., Wessjohann, Ludger A., and Ludwig-Müller, Jutta

Abstract

We report the major conclusions of the online open-access workshop “Computational Applications in Secondary Metabolite Discovery (CAiSMD)” that took place from 08 to 10 March 2021. Invited speakers from academia and industry and about 200 registered participants from five continents (Africa, Asia, Europe, South America, and North America) took part in the workshop. The workshop highlighted the potential applications of computational methodologies in the search for secondary metabolites (SMs) or natural products (NPs) as potential drugs and drug leads. During 3 days, the participants of this online workshop received an overview of modern computer-based approaches for exploring NP discovery in the “omics” age. The invited experts gave keynote lectures, trained participants in hands-on sessions, and held round table discussions. This was followed by oral presentations with much interaction between the speakers and the audience. Selected applicants (early-career scientists) were offered the opportunity to give oral presentations (15 min) and present posters in the form of flash presentations (5 min) upon submission of an abstract. The final program available on the workshop website (https://caismd.indiayouth.info/) comprised of 4 keynote lectures (KLs), 12 oral presentations (OPs), 2 round table discussions (RTDs), and 5 hands-on sessions (HSs). This meeting report also references internet resources for computational biology in the area of secondary metabolites that are of use outside of the workshop areas and will constitute a long-term valuable source for the community. The workshop concluded with an online survey form to be completed by speakers and participants for the goal of improving any subsequent editions.

Published
2021

18. Recent advances in computational metabolite structure predictions and altered metabolic pathways assessment to inform drug development processes.

Author

Schleiff, Mary Alexandra, Dhaware, Deepika, Sodhi, Jasleen K., de Bruyn Kops, Christina, Stork, Conrad, Šícho, Martin, Kochev, Nikolay, Svozil, Daniel, Jeliazkova, Nina, Kirchmair, Johannes, Djoumbou-Feunang, Yannick, Fiamoncini, Jarlei, Gil-de-la-Fuente, Alberto, Greiner, Russell, Manach, Claudine, Wishart, David S., Hughes, Tyler B., Le Dang, Na, Kumar, Ayush, and Flynn, Noah R.

Subjects
DRUG development, DRUG side effects, DRUG interactions, DRUG metabolism, DRUG efficacy, GENETIC polymorphisms
Abstract

Many drug candidates fail during preclinical and clinical trials due to variable or unexpected metabolism which may lead to variability in drug efficacy or adverse drug reactions. The drug metabolism field aims to address this important issue from many angles which range from the study of drug–drug interactions, pharmacogenomics, computational metabolic modeling, and others. This manuscript aims to provide brief but comprehensive manuscript summaries highlighting the conclusions and scientific importance of seven exceptional manuscripts published in recent years within the field of drug metabolism. Two main topics within the field are reviewed: novel computational metabolic modeling approaches which provide complex outputs beyond site of metabolism predictions, and experimental approaches designed to discern the impacts of interindividual variability and species differences on drug metabolism. The computational approaches discussed provide novel outputs in metabolite structure and formation likelihood and/or extend beyond the saturated field of drug phase I metabolism, while the experimental metabolic pathways assessments aim to highlight the impacts of genetic polymorphisms and clinical animal model metabolic differences on human metabolism and subsequent health outcomes. [ABSTRACT FROM AUTHOR]

Published
2021
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23. YMDB 2.0: a significantly expanded version of the yeast metabolome database.

Author

Ramirez-Gaona M, Marcu A, Pon A, Guo AC, Sajed T, Wishart NA, Karu N, Djoumbou Feunang Y, Arndt D, and Wishart DS

Subjects
Metabolic Networks and Pathways, Web Browser, Computational Biology methods, Databases, Factual, Metabolome, Metabolomics methods, Software, Yeasts metabolism
Abstract

YMDB or the Yeast Metabolome Database (http://www.ymdb.ca/) is a comprehensive database containing extensive information on the genome and metabolome of Saccharomyces cerevisiae Initially released in 2012, the YMDB has gone through a significant expansion and a number of improvements over the past 4 years. This manuscript describes the most recent version of YMDB (YMDB 2.0). More specifically, it provides an updated description of the database that was previously described in the 2012 NAR Database Issue and it details many of the additions and improvements made to the YMDB over that time. Some of the most important changes include a 7-fold increase in the number of compounds in the database (from 2007 to 16 042), a 430-fold increase in the number of metabolic and signaling pathway diagrams (from 66 to 28 734), a 16-fold increase in the number of compounds linked to pathways (from 742 to 12 733), a 17-fold increase in the numbers of compounds with nuclear magnetic resonance or MS spectra (from 783 to 13 173) and an increase in both the number of data fields and the number of links to external databases. In addition to these database expansions, a number of improvements to YMDB's web interface and its data visualization tools have been made. These additions and improvements should greatly improve the ease, the speed and the quantity of data that can be extracted, searched or viewed within YMDB. Overall, we believe these improvements should not only improve the understanding of the metabolism of S. cerevisiae, but also allow more in-depth exploration of its extensive metabolic networks, signaling pathways and biochemistry., (© The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.)

Published
2017
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