Justin J. J. van der Hooft

According to our database, Justin J. J. van der Hooft authored at least 23 papers between 2018 and 2026.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

2026

NPLinker 2: a modular and customizable framework for paired omics analyses.

Cunliang Geng, Giulia Crocioni, Helge Hecht, Arjan Draisma, Annette Lien, Laura Rosina Torres Ortega, Dora Ferreira, Pablo Lopez-Tarifa, Katherine R. Duncan, Marnix H. Medema, Justin J. J. van der Hooft

J. Open Source Softw., May, 2026

2025

Translating community-wide spectral library into actionable chemical knowledge: a proof of concept with monoterpene indole alkaloids.

Sarah Szwarc, Adriano Rutz, Kyungha Lee, Yassine Mejri, Olivier Bonnet, Hazrina Hazni, Adrien Jagora, Rany B. Mbeng Obame, Jin Kyoung Noh, Elvis Otogo N'Nang, Stephenie C. Alaribe, Khalijah Awang, Guillaume Bernadat, Young Hae Choi, Vincent Courdavault, Michel Frederich, Thomas Gaslonde, Florian Huber, Toh-Seok Kam, Yun Yee Low, Erwan Poupon, Justin J. J. van der Hooft, Kyo Bin Kang, Pierre Le Pogam, Mehdi A. Beniddir

J. Cheminformatics, December, 2025

Chemical characteristics vectors map the chemical space of natural biomes from untargeted mass spectrometry data.

Pilleriin Peets, Aristeidis Litos, Kai Dührkop, Daniel R. Garza, Justin J. J. van der Hooft, Sebastian Böcker, Bas E. Dutilh

J. Cheminformatics, December, 2025

Biosynfoni: a biosynthesis-informed and interpretable lightweight molecular fingerprint.

Lucina-May Nollen, David Meijer, Maria Sorokina, Justin J. J. van der Hooft

J. Cheminformatics, December, 2025

To Bin or not to Bin: Alternative Representations of Mass Spectra.

Niek F. de Jonge, Justin J. J. van der Hooft, Daniel Probst

CoRR, February, 2025

Strategies for community-sourced biocuration in bioinformatics: a case study on MIBiG 4.0.

Kai Blin, Catarina Loureiro, Nico l L. Louwen, Jorge C. Navarro-Muñoz, Hans Gerstmans, Serina L. Robinson, Adriano Rutz, Zachary L. Reitz, Drew T. Doering, Justin J. J. van der Hooft, Tilmann Weber, Marnix H. Medema, Mitja Zdouc

Briefings Bioinform., 2025

2024

CineMol: a programmatically accessible direct-to-SVG 3D small molecule drawer.

David Meijer, Marnix H. Medema, Justin J. J. van der Hooft

J. Cheminformatics, December, 2024

Reproducible MS/MS library cleaning pipeline in matchms.

Niek F. de Jonge, Helge Hecht, Michael Strobel, Mingxun Wang, Justin J. J. van der Hooft, Florian Huber

J. Cheminformatics, December, 2024

Computational Metabolomics: Towards Molecules, Models, and their Meaning (Dagstuhl Seminar 24181).

Timothy M. D. Ebbels, Soha Hassoun, Ewy A. Mathé, Justin J. J. van der Hooft, Haley Chatelaine

Dagstuhl Reports, 2024

Combined LC-MS/MS feature grouping, statistical prioritization, and interactive networking in msFeaST.

Kevin Mildau, Christoph Bueschl, Jürgen Zanghellini, Justin J. J. van der Hooft

Bioinform., 2024

MassSpecGym: A benchmark for the discovery and identification of molecules.

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

Proceedings of the Advances in Neural Information Processing Systems 37: Annual Conference on Neural Information Processing Systems 2024, 2024

Deep Learning Models for LC-MS Untargeted Metabolomics Data Analysis.

Francesco Russo, Filip Ottosson, Justin J. J. van der Hooft, Madeleine Ernst

Proceedings of the From Computational Logic to Computational Biology, 2024

2023

iPRESTO: Automated discovery of biosynthetic sub-clusters linked to specific natural product substructures.

Joris J. R. Louwen, Satria A. Kautsar, Sven van der Burg, Marnix H. Medema, Justin J. J. van der Hooft

PLoS Comput. Biol., February, 2023

MIBiG 3.0: a community-driven effort to annotate experimentally validated biosynthetic gene clusters.

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

Nucleic Acids Res., January, 2023

2022

Homologue series detection and management in LC-MS data with <i>homologueDiscoverer</i>.

Kevin Mildau, Justin J. J. van der Hooft, Mira Flasch, Benedikt Warth, Yasin El Abiead, Gunda Koellensperger, Jürgen Zanghellini, Christoph Bueschl

Bioinform., November, 2022

2021

Spec2Vec: Improved mass spectral similarity scoring through learning of structural relationships.

Florian Huber, Lars Ridder, Stefan Verhoeven, Jurriaan H. Spaaks, Faruk Diblen, Simon Rogers, Justin J. J. van der Hooft

PLoS Comput. Biol., 2021

Ranking microbial metabolomic and genomic links in the NPLinker framework using complementary scoring functions.

Grímur Hjörleifsson Eldjárn, Andrew Ramsay, Justin J. J. van der Hooft, Katherine R. Duncan, Sylvia Soldatou, Juho Rousu, Rónán Daly, Joe Wandy, Simon Rogers

PLoS Comput. Biol., 2021

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

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

J. Cheminformatics, 2021

MS2DeepScore: a novel deep learning similarity measure to compare tandem mass spectra.

Florian Huber, Sven van der Burg, Justin J. J. van der Hooft, Lars Ridder

J. Cheminformatics, 2021

2020

MIBiG 2.0: a repository for biosynthetic gene clusters of known function.

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

Nucleic Acids Res., 2020

matchms - processing and similarity evaluation of mass spectrometry data.

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

J. Open Source Softw., 2020

2018

Propagating annotations of molecular networks using in silico fragmentation.

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

PLoS Comput. Biol., 2018

Ms2lda.org: web-based topic modelling for substructure discovery in mass spectrometry.

Joe Wandy, Yunfeng Zhu, Justin J. J. van der Hooft, Rónán Daly, Michael P. Barrett, Simon Rogers

Bioinform., 2018