Wout Bittremieux

25 papers A* 2A 1B 1Journal 19Unranked 1

Year	Rank	Type	Title / Venue / Authors
2025	J	`jnl`	Foundation model for mass spectrometry proteomics. CoRR Justin Sanders, Melih Yilmaz, Jacob H. Russell, Wout Bittremieux, William Fondrie, Nicholas M. Riley, Sewoong Oh, William Stafford Noble
2025	J	`jnl`	MetaboT: AI-based agent for natural language-based interaction with metabolomics knowledge graphs. CoRR Madina Bekbergenova, Lucas Pradi, Benjamin Navet, Emma Tysinger, Franck Michel, Matthieu Feraud, Yousouf Taghzouti, Yan Zhou Chen, Olivier Kirchhoffer, Florence Mehl, Martin Legrand, Tao Jiang, Marco Pagni, Soha Hassoun, Jean-Luc Wolfender, Wout Bittremieux, Fabien Gandon, Louis-Félix Nothias
2025	J	`jnl`	SpectriPy: Enhancing Cross-Language Mass Spectrometry Data Analysis with R and Python. J. Open Source Softw. Marilyn De Graeve, Wout Bittremieux, Thomas Naake, Carolin Huber, Matthias Anagho-Mattanovich, Nils Hoffmann, Pierre Marchal, Victor Chrone, Philippine Louail, Helge Hecht, Michael Witting, Johannes Rainer
2025	J	`jnl`	Strategic priorities for transformative progress in advancing biology with proteomics and artificial intelligence. CoRR Yingying Sun, Jun A, Zhiwei Liu, Rui Sun, Liujia Qian, Samuel H. Payne, Wout Bittremieux, Markus Ralser, Chen Li, Yi Chen, Zhen Dong, Yasset Pérez-Riverol, Asif Khan, Chris Sander, Ruedi Aebersold, Juan Antonio Vizcaíno, Jonathan R. Krieger, Jianhua Yao, Han Wen, Linfeng Zhang, Yunping Zhu, Yue Xuan, Benjamin Boyang Sun, Liang Qiao, Henning Hermjakob, Haixu Tang, Huanhuan Gao, Yamin Deng, Qing Zhong, Cheng Chang, Nuno Bandeira, Ming Li, Weinan E, Siqi Sun, Yuedong Yang, Gilbert S. Omenn, Yue Zhang, Ping Xu, Yan Fu, Xiaowen Liu, Christopher M. Overall, Yu Wang, Eric W. Deutsch, Luonan Chen, Jürgen Cox, Vadim Demichev, Fuchu He, Jiaxing Huang, Huilin Jin, Chao Liu, Nan Li, Zhongzhi Luan, Jiangning Song, Kaicheng Yu, Wanggen Wan, Tai Wang, Kang Zhang, Le Zhang, Peter A. Bell, Matthias Mann, Bing Zhang, Tiannan Guo
2024	J	`jnl`	Benchmarking of Small Molecule Feature Representations for hERG, Nav1.5, and Cav1.2 Cardiotoxicity Prediction. J. Chem. Inf. Model. Issar Arab, Kristof Egghe, Kris Laukens, Ke Chen, Khaled H. Barakat, Wout Bittremieux
2024	J	`jnl`	Correction to "Semisupervised Learning to Boost hERG, Nav1.5, and Cav1.2 Cardiac Ion Channel Toxicity Prediction by Mining a Large Unlabeled Small Molecule Data Set". J. Chem. Inf. Model. Issar Arab, Kris Laukens, Wout Bittremieux
2024	J	`jnl`	DRAM-Based Acceleration of Open Modification Search in Hyperdimensional Space. IEEE Trans. Comput. Aided Des. Integr. Circuits Syst. Jaeyoung Kang, Weihong Xu, Wout Bittremieux, Niema Moshiri, Tajana Simunic Rosing
2024	A*	`conf`	MassSpecGym: A benchmark for the discovery and identification of molecules. NeurIPS 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
2024	J	`jnl`	MassSpecGym: A benchmark for the discovery and identification of molecules. CoRR 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
2024	—	`conf`	RapidOMS: FPGA-based Open Modification Spectral Library Searching with HD Computing. BioCAS Sumukh Pinge, Weihong Xu, Wout Bittremieux, Niema Moshiri, Sang-Woo Jun, Tajana Rosing
2024	J	`jnl`	RapidOMS: FPGA-based Open Modification Spectral Library Searching with HD Computing. CoRR Sumukh Pinge, Weihong Xu, Wout Bittremieux, Niema Moshiri, Sang-Woo Jun, Tajana Rosing
2024	J	`jnl`	Reusability report: Annotating metabolite mass spectra with domain-inspired chemical formula transformers. Nat. Mac. Intell. Janne Heirman, Wout Bittremieux
2024	J	`jnl`	Semisupervised Learning to Boost hERG, Nav1.5, and Cav1.2 Cardiac Ion Channel Toxicity Prediction by Mining a Large Unlabeled Small Molecule Data Set. J. Chem. Inf. Model. Issar Arab, Kris Laukens, Wout Bittremieux
2024	A	`conf`	SpecHD: Hyperdimensional Computing Framework for FPGA-Based Mass Spectrometry Clustering. DATE Sumukh Pinge, Weihong Xu, Jaeyoung Kang, Tianqi Zhang, Niema Moshiri, Wout Bittremieux, Tajana Rosing
2023	J	`jnl`	Accelerating open modification spectral library searching on tensor core in high-dimensional space. Bioinform. Jaeyoung Kang, Weihong Xu, Wout Bittremieux, Niema Moshiri, Tajana Rosing
2023	J	`jnl`	SpecHD: Hyperdimensional Computing Framework for FPGA-based Mass Spectrometry Clustering. CoRR Sumukh Pinge, Weihong Xu, Jaeyoung Kang, Tianqi Zhang, Niema Moshiri, Wout Bittremieux, Tajana Rosing
2023	J	`jnl`	The pitfalls of negative data bias for the T-cell epitope specificity challenge. Nat. Mac. Intell. Ceder Dens, Kris Laukens, Wout Bittremieux, Pieter Meysman
2022	A*	`conf`	De novo mass spectrometry peptide sequencing with a transformer model. ICML Melih Yilmaz, William Fondrie, Wout Bittremieux, Sewoong Oh, William S. Noble
2022	B	`conf`	Massively Parallel Open Modification Spectral Library Searching with Hyperdimensional Computing. PACT Jaeyoung Kang, Weihong Xu, Wout Bittremieux, Tajana Rosing
2022	J	`jnl`	Massively Parallel Open Modification Spectral Library Searching with Hyperdimensional Computing. CoRR Jaeyoung Kang, Weihong Xu, Wout Bittremieux, Tajana Rosing
2021	J	`jnl`	Current challenges for unseen-epitope TCR interaction prediction and a new perspective derived from image classification. Briefings Bioinform. Pieter Moris, Joey De Pauw, Anna Postovskaya, Sofie Gielis, Nicolas De Neuter, Wout Bittremieux, Benson Ogunjimi, Kris Laukens, Pieter Meysman
2019	J	`jnl`	Mining the Enriched Subgraphs for Specific Vertices in a Biological Graph. IEEE ACM Trans. Comput. Biol. Bioinform. Pieter Meysman, Yvan Saeys, Ehsan Sabaghian, Wout Bittremieux, Yves Van de Peer, Bart Goethals, Kris Laukens
2018	J	`jnl`	Grasping frequent subgraph mining for bioinformatics applications. BioData Min. Aida Mrzic, Pieter Meysman, Wout Bittremieux, Pieter Moris, Boris Cule, Bart Goethals, Kris Laukens
2017	—	`—`	Computational solutions for quality control of mass spectrometry-based proteomics Wout Bittremieux
2015	J	`jnl`	A primer to frequent itemset mining for bioinformatics. Briefings Bioinform. Stefan Naulaerts, Pieter Meysman, Wout Bittremieux, Trung-Nghia Vu, Wim Vanden Berghe, Bart Goethals, Kris Laukens