NPLinker
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Microbial natural products data mining by integrating genomics and metabolomics data
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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.
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What Paired omics data platform can do for you
- 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
Programming languages
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License
</>Source code
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Reference papers
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Book section
4- 1.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
- 2.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
- 3.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
- 4.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
Conference papers
2- 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
Journal articles
83- 1.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
- 2.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
- 3.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
- 4.Author(s): Martin BaunachPublished in Chem by Elsevier BV in 2024, page: 2948-295010.1016/j.chempr.2024.09.019
- 5.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
- 6.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
- 7.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 202410.1039/d4np00008k
- 8.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
- 9.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 202410.1016/j.chembiol.2024.07.011
- 10.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
- 11.Author(s): Yanan Bai, Junfang GuoPublished in Informatica by Slovenian Association Informatika in 202410.31449/inf.v48i9.4977
- 12.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
- 13.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 202410.1016/j.pbi.2024.102657
- 14.Author(s): Bablu Kumar, Erika Lorusso, Bruno Fosso, Graziano PesolePublished in Frontiers in Microbiology by Frontiers Media SA in 202410.3389/fmicb.2024.1343572
- 15.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
- 16.Author(s): Paolo Stincone, Amira Naimi, Anthony J. Saviola, Raphael Reher, Daniel PetrasPublished in PROTEOMICS by Wiley in 202310.1002/pmic.202200533
- 17.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
- 18.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
- 19.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
- 20.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
- 21.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
- 22.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
- 23.Author(s): Navid J. AyonPublished in Metabolites by MDPI AG in 2023, page: 62510.3390/metabo13050625
- 24.Author(s): Amelia PalermoPublished in Drug Discovery Today by Elsevier BV in 2023, page: 10346010.1016/j.drudis.2022.103460
- 25.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
- 26.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
- 27.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
- 28.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
- 29.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
- 30.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
- 31.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
- 32.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
- 33.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
- 34.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
- 35.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
- 36.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
- 37.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
- 38.Author(s): Junfang GuoPublished in Journal of Electrical and Computer Engineering by Hindawi Limited in 2023, page: 1-1110.1155/2023/9542465
- 39.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
- 40.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 in PNAS Nexus by Oxford University Press (OUP) in 202210.1093/pnasnexus/pgac257
- 41.Author(s): Kumar Saurabh Singh, Justin J. J. van der Hooft, Saskia C. M. van Wees, Marnix H. MedemaPublished in Natural Product Reports by Royal Society of Chemistry (RSC) in 2022, page: 1876-189610.1039/d2np00032f
- 42.Author(s): Juan Li, Aiping ChenPublished in International Journal of Computational Intelligence Systems by Springer Science and Business Media LLC in 202210.1007/s44196-022-00109-1
- 43.Author(s): Qihao Wu, Bailey A. Bell, Jia-Xuan Yan, Marc G. Chevrette, Nathan J. Brittin, Yanlong Zhu, Shaurya Chanana, Mitasree Maity, Doug R. Braun, Amelia M. Wheaton, Ilia A. Guzei, Ying Ge, Scott R. Rajski, Michael G. Thomas, Tim S. BugniPublished in Journal of the American Chemical Society by American Chemical Society (ACS) in 2022, page: 58-6910.1021/jacs.2c06410
- 44.Author(s): Cecilia Noecker, Alexander Eng, Efrat Muller, Elhanan BorensteinPublished in Bioinformatics by Oxford University Press (OUP) in 2022, page: 1615-162310.1093/bioinformatics/btac003
- 45.Author(s): Vida M. B. Leite, Leandro M. Garrido, Marcelo M. P. Tangerina, Leticia V. Costa-Lotufo, Marcelo J. P. Ferreira, Gabriel PadillaPublished in 3 Biotech by Springer Science and Business Media LLC in 202210.1007/s13205-022-03305-0
- 46.Author(s): Mary Ann Moran, Elizabeth B. Kujawinski, William F. Schroer, Shady A. Amin, Nicholas R. Bates, Erin M. Bertrand, Rogier Braakman, C. Titus Brown, Markus W. Covert, Scott C. Doney, Sonya T. Dyhrman, Arthur S. Edison, A. Murat Eren, Naomi M. Levine, Liang Li, Avena C. Ross, Mak A. Saito, Alyson E. Santoro, Daniel Segrè, Ashley Shade, Matthew B. Sullivan, Assaf VardiPublished in Nature Microbiology by Springer Science and Business Media LLC in 2022, page: 508-52310.1038/s41564-022-01090-3
- 47.Author(s): Sebastian Walesch, Joy Birkelbach, Gwenaëlle Jézéquel, F P Jake Haeckl, Julian D Hegemann, Thomas Hesterkamp, Anna K H Hirsch, Peter Hammann, Rolf MüllerPublished in EMBO reports by Springer Science and Business Media LLC in 202210.15252/embr.202256033
- 48.Author(s): Robert D. Hall, John C. D’Auria, Antonio C. Silva Ferreira, Yves Gibon, Dariusz Kruszka, Puneet Mishra, Rick van de ZeddePublished in Trends in Plant Science by Elsevier BV in 2022, page: 549-56310.1016/j.tplants.2022.02.001
- 49.Author(s): Sanghoon Lee, Jeffrey A. van Santen, Nima Farzaneh, Dennis Y. Liu, Cameron R. Pye, Tim U. H. Baumeister, Weng Ruh Wong, Roger G. LiningtonPublished in ACS Central Science by American Chemical Society (ACS) in 2022, page: 223-23410.1021/acscentsci.1c01108
- 50.Author(s): You-Shyang Chen, Chien-Ku Lin, Yu-Sheng Lin, Su-Fen Chen, Huei-Hua TsaoPublished in Sustainability by MDPI AG in 2022, page: 396410.3390/su14073964
Reports
1Thesis
4- 1.Author(s): Vincent NowakPublished by Victoria University of Wellington Library10.26686/wgtn.24187935
- 2.Author(s): Márcio Barczyszyn WeissPublished by Universidade de São Paulo. Agência de Bibliotecas e Coleções Digitais10.11606/d.9.2023.tde-08032024-115334
- 3.Author(s): Satria A. KautsarPublished by Wageningen University and Research10.18174/543999
- 4.Author(s): Sebastião Elias da SilveiraPublished by Universidade de São Paulo. Agência de Bibliotecas e Coleções Digitais10.11606/t.22.2023.tde-31082023-091131
Other
5- 1.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
- 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): 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
- 4.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
- 5.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
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