NPLinker
NP
Microbial natural products data mining by integrating genomics and metabolomics data
Updated 10 months ago
1 5
Get started
766 commitsLast commit ≈ 39 months ago6 stars4 forks
Ctrl K
Paired omics data platform
If you do metabolomics experiments with mass spectra and have sequenced the genomes of the samples, then the platform can help you link them.
112
mentions
2
contributors
Cite this software
Description
- Provides web form to describe a metabolomics project
- Is the document repository to store links between gene clusters and mass spectra
- Is source for training datasets for software trying to find links between gene cluster and mass spectra
- Uses JSON schema to validate projects
- Constructed together the metabolomics/genomics community
Keywords
License
Participating organisations
Reference papers
Mentions
- 1.Author(s): Derrick A. Ousley, Xiaofeng Wang, Lisa S. Mydy, Roland D. KerstenPublished in Methods in Enzymology by Elsevier in 202510.1016/bs.mie.2025.04.007
- 2.Author(s): Millena C. Barros Santos, Cathleen Mirande-Ney, Thomas Dussarrat, Guillaume Marti, Alain Bouchereau, Younès Dellero, Sylvain Prigent, Pierre PétriacqPublished in CABI Biotechnology Series, High-Throughput Plant Metabolomics by CABI in 2025, page: 38-6610.1079/9781800626911.0003
- 3.Author(s): Pieter M. M. van der Velden, Robert S. JansenPublished in Metabolomics by Springer International Publishing in 2023, page: 165-20810.1007/978-3-031-39094-4_6
- 4.Author(s): Paulo Wender P. Gomes, Talita Carla de Tralia Medeiros, Naydja Moralles Maimone, Tiago F. Leão, Luiz Alberto Beraldo de Moraes, Anelize BauermeisterPublished in Advances in Experimental Medicine and Biology, Microbial Natural Products Chemistry by Springer International Publishing in 2023, page: 225-24810.1007/978-3-031-41741-2_9
- 5.Author(s): Jonna Teikari, Martin Baunach, Elke DittmannPublished in Methods in Molecular Biology, Engineering Natural Product Biosynthesis by Springer US in 2022, page: 269-28710.1007/978-1-0716-2273-5_14
- 6.Author(s): Joseph Bamidele Awotunde, Rasheed Gbenga Jimoh, Roseline Oluwaseun Ogundokun, Sanjay Misra, Oluwakemi Christiana AbikoyePublished in Internet of Things, Artificial Intelligence for Cloud and Edge Computing by Springer International Publishing in 2022, page: 181-20810.1007/978-3-030-80821-1_9
- 1.Author(s): Xiaojun TangPublished in 2023 International Conference on Applied Physics and Computing (ICAPC) by IEEE in 2023, page: 525-53010.1109/icapc61546.2023.00103
- 2.Author(s): Zhang Yanxia, Shi Jie, Yu Linlin, Zhuo ZhaoPublished in 2023 IEEE 3rd International Conference on Data Science and Computer Application (ICDSCA) by IEEE in 2023, page: 1447-145110.1109/icdsca59871.2023.10392334
- 1.Author(s): Somayah J. Jarallah, Fahad A. Almughem, Nada K. Alhumaid, Nojoud AL Fayez, Ibrahim Alradwan, Khulud A. Alsulami, Essam A. Tawfik, Abdullah A. AlshehriPublished in International Journal of Pharmaceutics by Elsevier BV in 2025, page: 12578910.1016/j.ijpharm.2025.125789
- 2.Author(s): Mohammed Salim Dason, Davide Corà, Angela RePublished in mSystems by American Society for Microbiology in 202510.1128/msystems.00333-25
- 3.Author(s): Faezeh Ebrahimi, Hadi Maleki, Mansour Ebrahimi, Amir Hossein BeikiPublished in Endocrinología, Diabetes y Nutrición (English ed.) by Elsevier BV in 2025, page: 50156110.1016/j.endien.2025.501561
- 4.Author(s): David Meijer, Mehdi A. Beniddir, Connor W. Coley, Yassine M. Mejri, Meltem Öztürk, Justin J. J. van der Hooft, Marnix H. Medema, Adam SkiredjPublished in Natural Product Reports by Royal Society of Chemistry (RSC) in 2025, page: 654-66210.1039/d4np00008k
- 5.Author(s): Jakob K. Reinhardt, David Craft, Jing-Ke WengPublished in Trends in Biochemical Sciences by Elsevier BV in 2025, page: 311-32110.1016/j.tibs.2025.01.010
- 6.Author(s): Jaime Lorenzo N. Dinglasan, Hiroshi Otani, Drew T. Doering, Daniel Udwary, Nigel J. MounceyPublished in Nature Reviews Microbiology by Springer Science and Business Media LLC in 2025, page: 338-35410.1038/s41579-024-01141-y
- 7.Author(s): Lucas Farndale, Robert Insall, Ke YuanPublished in Medical Image Analysis by Elsevier BV in 2025, page: 10347910.1016/j.media.2025.103479
- 8.Author(s): Natavan Dudkina, Hyun Bong Park, Deguang Song, Abhishek Jain, Sajid A. Khan, Richard A. Flavell, Caroline H. Johnson, Noah W. Palm, Jason M. CrawfordPublished in Cell Chemical Biology by Elsevier BV in 2025, page: 126-144.e1810.1016/j.chembiol.2024.07.011
- 9.Author(s): Faezeh Ebrahimi, Hadi Maleki, Mansour Ebrahimi, Amir Hossein BeikiPublished in Endocrinología, Diabetes y Nutrición by Elsevier BV in 2025, page: 50156110.1016/j.endinu.2025.501561
- 10.Author(s): De-Gao Wang, Jia-Qi Hu, Chao-Yi Wang, Teng Liu, Yue-Zhong Li, Changsheng WuPublished in Natural Product Reports by Royal Society of Chemistry (RSC) in 202510.1039/d4np00065j
- 11.Author(s): Sophie Jin, Fabrizio AlbertiPublished in Natural Product Reports by Royal Society of Chemistry (RSC) in 2025, page: 1367-138610.1039/d5np00017c
- 12.Author(s): Kekeletso H. Chele, Lizelle A. Piater, Justin J. J. van der Hooft, Fidele TugizimanaPublished in Metabolites by MDPI AG in 2025, page: 36210.3390/metabo15060362
- 13.Author(s): César Aguilar, Amir Alwali, Madeline Mair, Lorena Rodriguez-Orduña, Haydeé Contreras-Peruyero, Ramya Modi, Carson Roberts, Nelly Sélem-Mojica, Cuauhtemoc Licona-Cassani, Elizabeth Ivy ParkinsonPublished in Microbial Genomics by Microbiology Society in 202410.1099/mgen.0.001253
- 14.Author(s): Carolina Cano-Prieto, Agustina Undabarrena, Ana Calheiros de Carvalho, Jay D. Keasling, Pablo Cruz-MoralesPublished in Annual Review of Biochemistry by Annual Reviews in 2024, page: 411-44510.1146/annurev-biochem-032620-104731
- 15.Author(s): Cecilia Noecker, Peter J. TurnbaughPublished in Nature Metabolism by Springer Science and Business Media LLC in 2024, page: 1225-123610.1038/s42255-024-01074-z
- 16.Author(s): Martin BaunachPublished in Chem by Elsevier BV in 2024, page: 2948-295010.1016/j.chempr.2024.09.019
- 17.Author(s): Mahnoor Zulfiqar, Vinay Singh, Christoph Steinbeck, Maria SorokinaPublished in Critical Reviews in Microbiology by Informa UK Limited in 2024, page: 1053-109210.1080/1040841x.2024.2306465
- 18.Author(s): Moustafa M. Zohair, Wang Dongmei, Kuniyoshi ShimizuPublished in Metabolomics by Springer Science and Business Media LLC in 202410.1007/s11306-024-02138-7
- 19.Author(s): Hao Li, Yuling Chen, Bingqing Tang, Zhengjie Liu, Bo Peng, Jiajun Li, Han Gao, Sibao Wang, Zhiyong LiPublished in Journal of Natural Products by American Chemical Society (ACS) in 2024, page: 2695-270810.1021/acs.jnatprod.4c00740
- 20.Author(s): Scarlet Ferrinho, Helen Connaris, Nigel J. Mouncey, Rebecca J.M. GossPublished in Water Research by Elsevier BV in 2024, page: 12149210.1016/j.watres.2024.121492
- 21.Author(s): Martin Baunach, Arthur Guljamow, María Miguel-Gordo, Elke DittmannPublished in Natural Product Reports by Royal Society of Chemistry (RSC) in 2024, page: 347-36910.1039/d3np00045a
- 22.Author(s): Jonathan R. Chekan, Lisa S. Mydy, Michael A. Pasquale, Roland D. KerstenPublished in Natural Product Reports by Royal Society of Chemistry (RSC) in 2024, page: 1020-105910.1039/d3np00042g
- 23.Author(s): Yanan Bai, Junfang GuoPublished in Informatica by Slovenian Association Informatika in 202410.31449/inf.v48i9.4977
- 24.Author(s): Felicia C. Wolters, Elena Del Pup, Kumar Saurabh Singh, Klaas Bouwmeester, M. Eric Schranz, Justin J.J. van der Hooft, Marnix H. MedemaPublished in Current Opinion in Plant Biology by Elsevier BV in 2024, page: 10265710.1016/j.pbi.2024.102657
- 25.Author(s): Bablu Kumar, Erika Lorusso, Bruno Fosso, Graziano PesolePublished in Frontiers in Microbiology by Frontiers Media SA in 202410.3389/fmicb.2024.1343572
- 26.Author(s): Joris J. R. Louwen, Marnix H. Medema, Justin J. J. van der HooftPublished in Microbiome by Springer Science and Business Media LLC in 202310.1186/s40168-022-01444-3
- 27.Author(s): Paolo Stincone, Amira Naimi, Anthony J. Saviola, Raphael Reher, Daniel PetrasPublished in PROTEOMICS by Wiley in 202310.1002/pmic.202200533
- 28.Author(s): Shi Qiu, Ying Cai, Hong Yao, Chunsheng Lin, Yiqiang Xie, Songqi Tang, Aihua ZhangPublished in Signal Transduction and Targeted Therapy by Springer Science and Business Media LLC in 202310.1038/s41392-023-01399-3
- 29.Author(s): Francesc Puig-Castellví, Romina Pacheco-Tapia, Maxime Deslande, Manyi Jia, Petros Andrikopoulos, Kanta Chechi, Amélie Bonnefond, Philippe Froguel, Marc-Emmanuel DumasPublished in TrAC Trends in Analytical Chemistry by Elsevier BV in 2023, page: 11724810.1016/j.trac.2023.117248
- 30.Author(s): Michael W. Mullowney, Katherine R. Duncan, Somayah S. Elsayed, Neha Garg, Justin J. J. van der Hooft, Nathaniel I. Martin, David Meijer, Barbara R. Terlouw, Friederike Biermann, Kai Blin, Janani Durairaj, Marina Gorostiola González, Eric J. N. Helfrich, Florian Huber, Stefan Leopold-Messer, Kohulan Rajan, Tristan de Rond, Jeffrey A. van Santen, Maria Sorokina, Marcy J. Balunas, Mehdi A. Beniddir, Doris A. van Bergeijk, Laura M. Carroll, Chase M. Clark, Djork-Arné Clevert, Chris A. Dejong, Chao Du, Scarlet Ferrinho, Francesca Grisoni, Albert Hofstetter, Willem Jespers, Olga V. Kalinina, Satria A. Kautsar, Hyunwoo Kim, Tiago F. Leao, Joleen Masschelein, Evan R. Rees, Raphael Reher, Daniel Reker, Philippe Schwaller, Marwin Segler, Michael A. Skinnider, Allison S. Walker, Egon L. Willighagen, Barbara Zdrazil, Nadine Ziemert, Rebecca J. M. Goss, Pierre Guyomard, Andrea Volkamer, William H. Gerwick, Hyun Uk Kim, Rolf Müller, Gilles P. van Wezel, Gerard J. P. van Westen, Anna K. H. Hirsch, Roger G. Linington, Serina L. Robinson, Marnix H. MedemaPublished in Nature Reviews Drug Discovery by Springer Science and Business Media LLC in 2023, page: 895-91610.1038/s41573-023-00774-7
- 31.Author(s): Bin Yu, Yan Hu, Yun Kang, Mingjie CaiPublished in International Journal of Approximate Reasoning by Elsevier BV in 2023, page: 88-10410.1016/j.ijar.2023.03.002
- 32.Author(s): Monica Thukral, Andrew E Allen, Daniel PetrasPublished in The ISME Journal by Oxford University Press (OUP) in 2023, page: 2147-215910.1038/s41396-023-01532-8
- 33.Author(s): Alexander B Chase, Alexander Bogdanov, Alyssa M Demko, Paul R JensenPublished in The ISME Journal by Oxford University Press (OUP) in 2023, page: 976-98310.1038/s41396-023-01410-3
- 34.Author(s): Navid J. AyonPublished in Metabolites by MDPI AG in 2023, page: 62510.3390/metabo13050625
- 35.Author(s): Amelia PalermoPublished in Drug Discovery Today by Elsevier BV in 2023, page: 10346010.1016/j.drudis.2022.103460
- 36.Author(s): Lindsay K. Caesar, Fatma A. Butun, Matthew T. Robey, Navid J. Ayon, Raveena Gupta, David Dainko, Jin Woo Bok, Grant Nickles, Robert J. Stankey, Don Johnson, David Mead, Kristof B. Cank, Cody E. Earp, Huzefa A. Raja, Nicholas H. Oberlies, Nancy P. Keller, Neil L. KelleherPublished in Nature Chemical Biology by Springer Science and Business Media LLC in 2023, page: 846-85410.1038/s41589-023-01276-8
- 37.Author(s): Mitja M. Zdouc, Justin J.J. van der Hooft, Marnix H. MedemaPublished in Trends in Pharmacological Sciences by Elsevier BV in 2023, page: 532-54110.1016/j.tips.2023.06.004
- 38.Author(s): César R. Balcázar-Zumaeta, Efraín M. Castro-Alayo, Ilse S. Cayo-Colca, Guillermo Idrogo-Vásquez, Lucas D. Muñoz-AsteckerPublished in Food Research International by Elsevier BV in 2023, page: 11219010.1016/j.foodres.2022.112190
- 39.Author(s): Allyson McAtamney, Casey Heaney, Itzel Lizama-Chamu, Laura M SanchezPublished in Analytical Chemistry by American Chemical Society (ACS) in 2023, page: 16775-1678510.1021/acs.analchem.3c02408
- 40.Author(s): Henning Otto Brinkhaus, Kohulan Rajan, Jonas Schaub, Achim Zielesny, Christoph SteinbeckPublished in Current Opinion in Structural Biology by Elsevier BV in 2023, page: 10254210.1016/j.sbi.2023.102542
- 41.Author(s): Bartosz Jan Bartmanski, Miguel Rocha, Maria Zimmermann-KogadeevaPublished in Current Opinion in Chemical Biology by Elsevier BV in 2023, page: 10232410.1016/j.cbpa.2023.102324
- 42.Author(s): Lexiang Zhang, Rokshana Parvin, Mingshuo Chen, Dingmeng Hu, Qihui Fan, Fangfu YePublished in Biosensors and Bioelectronics by Elsevier BV in 2023, page: 11521310.1016/j.bios.2023.115213
- 43.Author(s): Yi-Yuan Lee, Mustafa Guler, Desnor N. Chigumba, Shen Wang, Neel Mittal, Cameron Miller, Benjamin Krummenacher, Haodong Liu, Liu Cao, Aditya Kannan, Keshav Narayan, Samuel T. Slocum, Bryan L. Roth, Alexey Gurevich, Bahar Behsaz, Roland D. Kersten, Hosein MohimaniPublished in Nature Communications by Springer Science and Business Media LLC in 202310.1038/s41467-023-39905-4
- 44.Author(s): Anna A. Baranova, Vera A. Alferova, Vladimir A. Korshun, Anton P. TyurinPublished in Life by MDPI AG in 2023, page: 107310.3390/life13051073
- 45.Author(s): Susana P. Gaudêncio, Engin Bayram, Lada Lukić Bilela, Mercedes Cueto, Ana R. Díaz-Marrero, Berat Z. Haznedaroglu, Carlos Jimenez, Manolis Mandalakis, Florbela Pereira, Fernando Reyes, Deniz TasdemirPublished in Marine Drugs by MDPI AG in 2023, page: 30810.3390/md21050308
- 46.Author(s): Cecilia H Deng, Sushma Naithani, Sunita Kumari, Irene Cobo-Simón, Elsa H Quezada-Rodríguez, Maria Skrabisova, Nick Gladman, Melanie J Correll, Akeem Babatunde Sikiru, Olusola O Afuwape, Annarita Marrano, Ines Rebollo, Wentao Zhang, Sook JungPublished in Database by Oxford University Press (OUP) in 202310.1093/database/baad088
- 47.Author(s): Cantin Baron, Sarah Cherkaoui, Sandra Therrien-Laperriere, Yann Ilboudo, Raphaël Poujol, Pamela Mehanna, Melanie E. Garrett, Marilyn J. Telen, Allison E. Ashley-Koch, Pablo Bartolucci, John D. Rioux, Guillaume Lettre, Christine Des Rosiers, Matthieu Ruiz, Julie G. HussinPublished in iScience by Elsevier BV in 2023, page: 10847310.1016/j.isci.2023.108473
- 48.Author(s): Kayla Wilson, Tristan de Rond, Immo Burkhardt, Taylor S. Steele, Rebecca J. B. Schäfer, Sheila Podell, Eric E. Allen, Bradley S. MoorePublished in Proceedings of the National Academy of Sciences by Proceedings of the National Academy of Sciences in 202310.1073/pnas.2220934120
- 49.Author(s): Junfang GuoPublished in Journal of Electrical and Computer Engineering by Wiley in 2023, page: 1-1110.1155/2023/9542465
- 50.Author(s): Timothy M.D. Ebbels, Justin J.J. van der Hooft, Haley Chatelaine, Corey Broeckling, Nicola Zamboni, Soha Hassoun, Ewy A. MathéPublished in Current Opinion in Chemical Biology by Elsevier BV in 2023, page: 10228810.1016/j.cbpa.2023.102288
- 1.Author(s): Márcio Barczyszyn WeissPublished by Universidade de São Paulo. Agência de Bibliotecas e Coleções Digitais10.11606/d.9.2023.tde-08032024-115334
- 2.Author(s): Satria A. KautsarPublished by Wageningen University and Research10.18174/543999
- 3.Author(s): Sebastião Elias da SilveiraPublished by Universidade de São Paulo. Agência de Bibliotecas e Coleções Digitais10.11606/t.22.2023.tde-31082023-091131
- 4.Author(s): Vincent NowakPublished by Victoria University of Wellington Library10.26686/wgtn.24187935
- 1.Author(s): Pablo Cruz-Morales, Ana Calheiros de Carvalho, Naiara Hurtado-Lopez, Carolina Cano-Prieto, Miriam von Bargen, Luis Damas-Ramos, Agustina Undabarrena, Daniela Rago, Ling Chen, Adrian Gadar-Lopez, Sidharth Jayachandran, Luisa Trejo-Alarcon, Xiaowei Li, Dushica Arsovska, Linda Ahonen, Vijayalakshmi Kandasamy, Line Sondt-Marcussenv, Mariana Arango-Saavedra, Iason Karyofyllis, Kealan Exley, Charissa de Bekker, Jay KeaslingPublished by Springer Science and Business Media LLC in 202510.21203/rs.3.rs-6105887/v1
- 2.Author(s): Cecilia H. Deng, Sushma Naithani, Sunita Kumari, Irene Cobo-Simon, Elsa H. Quezada-Rodriguez, Maria Skrabisova, Nick Gladman, Melanie J. Correll, Akeem Babatunde Sikiru, Olusola O. Afuwape, Annarita Marrano, Ines Rebollo, Wentao Zhang, Sook JungPublished by MDPI AG in 202310.20944/preprints202306.1013.v1
- 3.Author(s): Henning Otto Brinkhaus, Kohulan Rajan, Jonas Schaub, Achim Zielesny, Christoph SteinbeckPublished by American Chemical Society (ACS) in 202310.26434/chemrxiv-2022-dgcm6-v2
- 4.Author(s): Tiago F. Leão, Mingxun Wang, Ricardo da Silva, Alexey Gurevich, Anelize Bauermeister, Paulo Wender P. Gomes, Asker Brejnrod, Evgenia Glukhov, Allegra T. Aron, Joris J. R. Louwen, Hyun Woo Kim, Raphael Reher, Marli F. Fiore, Justin J.J. van der Hooft, Lena Gerwick, William H. Gerwick, Nuno Bandeira, Pieter C. DorresteinPublished by Cold Spring Harbor Laboratory in 202110.1101/2021.10.05.463235
- 5.Author(s): Alexander B. Chase, Douglas Sweeney, Mitchell N. Muskat, Dulce Guillén-Matus, Paul R. JensenPublished by Cold Spring Harbor Laboratory in 202010.1101/2020.12.19.423547
- 6.Author(s): Alexander B. Chase, Douglas Sweeney, Mitchell N. Muskat, Dulce Guillén-Matus, Paul R. JensenPublished in 2020
Contributors
Contact person
MS
Michelle Schorn
Wageningen University & Research
Netherlands eScience Center
Related projects
Integrated omics analysis for small molecule-mediated host-microbiome interactions
Advancing our understanding of molecular mechanisms of health and disease
Updated 34 months ago
Finished