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ORCIDJustin J. J. van der Hooft
2020 – today
- 2024
[j13]David Meijer, Marnix H. Medema, Justin J. J. van der Hooft
:
CineMol: a programmatically accessible direct-to-SVG 3D small molecule drawer. J. Cheminformatics 16(1): 58 (2024)- [j12]Niek F. de Jonge, Helge Hecht, Michael Strobel, Mingxun Wang, Justin J. J. van der Hooft, Florian Huber:
Reproducible MS/MS library cleaning pipeline in matchms. J. Cheminformatics 16(1): 88 (2024) - [c2]Francesco Russo, Filip Ottosson, Justin J. J. van der Hooft, Madeleine Ernst:
Deep Learning Models for LC-MS Untargeted Metabolomics Data Analysis. From Computational Logic to Computational Biology 2024: 128-144 - [c1]Roman Bushuiev, Anton Bushuiev, Niek F. de Jonge, Adamo Young, Fleming Kretschmer, Raman Samusevich, Janne Heirman, Fei Wang, Luke Zhang, Kai Dührkop, Marcus Ludwig, Nils A. Haupt, Apurva Kalia, Corinna Brungs, Robin Schmid, Russell Greiner, Bo Wang, David S. Wishart, Liping Liu, Juho Rousu, Wout Bittremieux, Hannes Rost, Tytus D. Mak, Soha Hassoun, Florian Huber, Justin J. J. van der Hooft, Michael A. Stravs, Sebastian Böcker, Josef Sivic, Tomás Pluskal:
MassSpecGym: A benchmark for the discovery and identification of molecules. NeurIPS 2024 - [i2]Roman Bushuiev, Anton Bushuiev, Niek F. de Jonge, Adamo Young, Fleming Kretschmer, Raman Samusevich, Janne Heirman, Fei Wang, Luke Zhang, Kai Dührkop, Marcus Ludwig, Nils A. Haupt, Apurva Kalia, Corinna Brungs, Robin Schmid, Russell Greiner, Bo Wang, David S. Wishart, Li-Ping Liu, Juho Rousu, Wout Bittremieux, Hannes Rost, Tytus D. Mak, Soha Hassoun, Florian Huber, Justin J. J. van der Hooft, Michael A. Stravs, Sebastian Böcker, Josef Sivic, Tomás Pluskal:
MassSpecGym: A benchmark for the discovery and identification of molecules. CoRR abs/2410.23326 (2024) - [i1]Timothy M. D. Ebbels, Soha Hassoun, Ewy A. Mathé, Justin J. J. van der Hooft, Haley Chatelaine:
Computational Metabolomics: Towards Molecules, Models, and their Meaning (Dagstuhl Seminar 24181). Dagstuhl Reports 14(4): 124-141 (2024) - 2023
- [j11]Barbara R. Terlouw, Kai Blin, Jorge C. Navarro-Muñoz, Nicole E. Avalon, Marc G. Chevrette, Susan Egbert, Sanghoon Lee, David Meijer, Michael J. Recchia, Zachary L. Reitz, Jeffrey A. van Santen, Nelly Sélem-Mojica, Thomas Tørring, Liana Zaroubi, Mohammad Alanjary, Gajender Aleti, César Aguilar, Suhad A. Al-Salihi, Hannah E. Augustijn, J. Abraham Avelar-Rivas, Luis A. Avitia-Domínguez, Francisco Barona-Gómez, Jordan Bernaldo-Agüero, Vincent A. Bielinski, Friederike Biermann, Thomas J. Booth, J. Carrion Bravo, Raquel Castelo-Branco, Fernanda O. Chagas, Pablo Cruz-Morales, Chao Du, Katherine R. Duncan, Athina Gavriilidou, Damien Gayrard, Karina Gutiérrez-García, Kristina Haslinger, Eric J. N. Helfrich, Justin J. J. van der Hooft, Afif P. Jati, Edward Kalkreuter, Nikolaos Kalyvas, Kyo Bin Kang, Satria A. Kautsar, Wonyong Kim, Aditya M. Kunjapur, Yong-Xin Li, Geng-Min Lin, Catarina Loureiro, Joris J. R. Louwen, Nico l L. Louwen, George Lund, Jonathan Parra, Benjamin Philmus, Bita Pourmohsenin, Lotte U. Pronk, Adriana Rego, Devasahayam Arokia Balaya Rex, Serina L. Robinson, L. Rodrigo Rosas-Becerra, Eve T. Roxborough, Michelle A. Schorn, Darren J. Scobie, Kumar Saurabh Singh, Nika Sokolova, Xiaoyu Tang, Daniel W. Udwary, Aruna Vigneshwari, Kristiina Vind, Sophie P. J. M. Vromans, Valentin Waschulin, Sam E. Williams, Jaclyn M. Winter, Thomas E. Witte, Huali Xie, Dong Yang, Jingwei Yu, Mitja Zdouc, Zheng Zhong, Jérôme Collemare, Roger G. Linington, Tilmann Weber, Marnix H. Medema:
MIBiG 3.0: a community-driven effort to annotate experimentally validated biosynthetic gene clusters. Nucleic Acids Res. 51(D1): 603-610 (2023) - [j10]Joris J. R. Louwen, Satria A. Kautsar, Sven van der Burg, Marnix H. Medema, Justin J. J. van der Hooft:
iPRESTO: Automated discovery of biosynthetic sub-clusters linked to specific natural product substructures. PLoS Comput. Biol. 19(2) (2023) - 2022
- [j9]Kevin Mildau, Justin J. J. van der Hooft, Mira Flasch, Benedikt Warth, Yasin El Abiead, Gunda Koellensperger, Jürgen Zanghellini, Christoph Bueschl:
Homologue series detection and management in LC-MS data with homologueDiscoverer. Bioinform. 38(22): 5139-5140 (2022) - 2021
- [j8]Fidele Ntie-Kang, Kiran K. Telukunta, Serge A. T. Fobofou, Victor Chukwudi Osamor, Samuel A. Egieyeh, Marilia Valli, Yannick Djoumbou Feunang, Maria Sorokina, Conrad Stork, Neann Mathai, Paul F. Zierep, Ana L. Chávez-Hernández, Miquel Duran-Frigola, Smith B. Babiaka, Romuald Tematio Fouedjou, Donatus B. Eni, Simeon Akame, Augustine B. Arreyetta-Bawak, Oyere T. Ebob, Jonathan A. Metuge, Boris D. Bekono, Mustafa A. Isa, Raphael Onuku, Daniel M. Shadrack, Thommas M. Musyoka, Vaishali M. Patil, Justin J. J. van der Hooft, Vanderlan da Silva Bolzani, José L. Medina-Franco, Johannes Kirchmair, Tilmann Weber, Özlem Tastan Bishop, Marnix H. Medema, Ludger A. Wessjohann, Jutta Ludwig-Müller:
Computational Applications in Secondary Metabolite Discovery (CAiSMD): an online workshop. J. Cheminformatics 13(1): 64 (2021) - [j7]Florian Huber, Sven van der Burg, Justin J. J. van der Hooft, Lars Ridder:
MS2DeepScore: a novel deep learning similarity measure to compare tandem mass spectra. J. Cheminformatics 13(1): 84 (2021) - [j6]Florian Huber, Lars Ridder, Stefan Verhoeven, Jurriaan H. Spaaks, Faruk Diblen, Simon Rogers, Justin J. J. van der Hooft:
Spec2Vec: Improved mass spectral similarity scoring through learning of structural relationships. PLoS Comput. Biol. 17(2) (2021) - [j5]Grímur Hjörleifsson Eldjárn, Andrew Ramsay, Justin J. J. van der Hooft, Katherine R. Duncan, Sylvia Soldatou, Juho Rousu, Rónán Daly, Joe Wandy, Simon Rogers:
Ranking microbial metabolomic and genomic links in the NPLinker framework using complementary scoring functions. PLoS Comput. Biol. 17(5) (2021) - 2020
- [j4]Florian Huber, Stefan Verhoeven, Christiaan Meijer, Hanno Spreeuw, Efraín Castilla, Cunliang Geng, Justin J. J. van der Hooft, Simon Rogers, Adam Belloum, Faruk Diblen, Jurriaan H. Spaaks:
matchms - processing and similarity evaluation of mass spectrometry data. J. Open Source Softw. 5(52): 2411 (2020) - [j3]Satria A. Kautsar, Kai Blin, Simon Shaw, Jorge C. Navarro-Muñoz, Barbara R. Terlouw, Justin J. J. van der Hooft, Jeffrey A. van Santen, Vittorio Tracanna, Hernando G. Suarez Duran, Victòria Pascal Andreu, Nelly Sélem-Mojica, Mohammad Alanjary, Serina L. Robinson, George Lund, Samuel C. Epstein, Ashley C. Sisto, Louise K. Charkoudian, Jérôme Collemare, Roger G. Linington, Tilmann Weber, Marnix H. Medema:
MIBiG 2.0: a repository for biosynthetic gene clusters of known function. Nucleic Acids Res. 48(Database-Issue): D454-D458 (2020)
2010 – 2019
- 2018
- [j2]Joe Wandy, Yunfeng Zhu, Justin J. J. van der Hooft, Rónán Daly, Michael P. Barrett, Simon Rogers:
Ms2lda.org: web-based topic modelling for substructure discovery in mass spectrometry. Bioinform. 34(2): 317-318 (2018) - [j1]Ricardo Roberto da Silva, Mingxun Wang, Louis-Félix Nothias, Justin J. J. van der Hooft, Andrés Mauricio Caraballo-Rodríguez, Evan Fox, Marcy J. Balunas, Jonathan L. Klassen, Norberto Peporine Lopes, Pieter C. Dorrestein:
Propagating annotations of molecular networks using in silico fragmentation. PLoS Comput. Biol. 14(4) (2018)
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