Wout Bittremieux

According to our database, Wout Bittremieux authored at least 19 papers between 2015 and 2025.

Collaborative distances:

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

2025

SpectriPy: Enhancing Cross-Language Mass Spectrometry Data Analysis with R and Python.

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

J. Open Source Softw., June, 2025

Foundation model for mass spectrometry proteomics.

Justin Sanders, Melih Yilmaz, Jacob H. Russell, Wout Bittremieux, William Fondrie, Nicholas M. Riley, Sewoong Oh, William Stafford Noble

CoRR, May, 2025

Strategic priorities for transformative progress in advancing biology with proteomics and artificial intelligence.

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

CoRR, February, 2025

2024

DRAM-Based Acceleration of Open Modification Search in Hyperdimensional Space.

Jaeyoung Kang, Weihong Xu, Wout Bittremieux, Niema Moshiri, Tajana Simunic Rosing

IEEE Trans. Comput. Aided Des. Integr. Circuits Syst., September, 2024

Reusability report: Annotating metabolite mass spectra with domain-inspired chemical formula transformers.

Janne Heirman, Wout Bittremieux

Nat. Mac. Intell., 2024

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".

Issar Arab, Kris Laukens, Wout Bittremieux

J. Chem. Inf. Model., 2024

Semisupervised Learning to Boost hERG, Nav1.5, and Cav1.2 Cardiac Ion Channel Toxicity Prediction by Mining a Large Unlabeled Small Molecule Data Set.

Issar Arab, Kris Laukens, Wout Bittremieux

J. Chem. Inf. Model., 2024

Benchmarking of Small Molecule Feature Representations for hERG, Nav1.5, and Cav1.2 Cardiotoxicity Prediction.

Issar Arab, Kristof Egghe, Kris Laukens, Ke Chen, Khaled H. Barakat, Wout Bittremieux

J. Chem. Inf. Model., 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 38: Annual Conference on Neural Information Processing Systems 2024, 2024

SpecHD: Hyperdimensional Computing Framework for FPGA-Based Mass Spectrometry Clustering.

Sumukh Pinge, Weihong Xu, Jaeyoung Kang, Tianqi Zhang, Niema Moshiri, Wout Bittremieux, Tajana Rosing

Proceedings of the Design, Automation & Test in Europe Conference & Exhibition, 2024

RapidOMS: FPGA-based Open Modification Spectral Library Searching with HD Computing.

Sumukh Pinge, Weihong Xu, Wout Bittremieux, Niema Moshiri, Sang-Woo Jun, Tajana Rosing

Proceedings of the IEEE Biomedical Circuits and Systems Conference, 2024

2023

The pitfalls of negative data bias for the T-cell epitope specificity challenge.

Ceder Dens, Kris Laukens, Wout Bittremieux, Pieter Meysman

Nat. Mac. Intell., October, 2023

2022

De novo mass spectrometry peptide sequencing with a transformer model.

Melih Yilmaz, William Fondrie, Wout Bittremieux, Sewoong Oh, William S. Noble

Proceedings of the International Conference on Machine Learning, 2022

Massively Parallel Open Modification Spectral Library Searching with Hyperdimensional Computing.

Jaeyoung Kang, Weihong Xu, Wout Bittremieux, Tajana Rosing

Proceedings of the International Conference on Parallel Architectures and Compilation Techniques, 2022

2021

Current challenges for unseen-epitope TCR interaction prediction and a new perspective derived from image classification.

Pieter Moris, Joey De Pauw, Anna Postovskaya, Sofie Gielis, Nicolas De Neuter, Wout Bittremieux, Benson Ogunjimi, Kris Laukens, Pieter Meysman

Briefings Bioinform., 2021

2019

Mining the Enriched Subgraphs for Specific Vertices in a Biological Graph.

Pieter Meysman, Yvan Saeys, Ehsan Sabaghian, Wout Bittremieux, Yves Van de Peer, Bart Goethals, Kris Laukens

IEEE ACM Trans. Comput. Biol. Bioinform., 2019

2018

Grasping frequent subgraph mining for bioinformatics applications.

Aida Mrzic, Pieter Meysman, Wout Bittremieux, Pieter Moris, Boris Cule, Bart Goethals, Kris Laukens

BioData Min., 2018

2017

Computational solutions for quality control of mass spectrometry-based proteomics

Wout Bittremieux

PhD thesis, 2017

2015

A primer to frequent itemset mining for bioinformatics.

Stefan Naulaerts, Pieter Meysman, Wout Bittremieux, Trung-Nghia Vu, Wim Vanden Berghe, Bart Goethals, Kris Laukens

Briefings Bioinform., 2015