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Wout Bittremieux · SciRah

Researcher profile · Semantic Scholar

Wout Bittremieux

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Wout Bittremieux — researcher profile on SciRah

h-index: 35
Works: 154
Citations: 3,826

Most-cited papers

The underappreciated diversity of bile acid modifications
Ipsita Mohanty, H. Mannochio-Russo, Joshua V. Schweer, Yasin El Abiead +24 more
2024Cell195 citations Open access
Semantic Scholar
Standardized multi-omics of Earth’s microbiomes reveals microbial and metabolite diversity
J. Shaffer, L. Nothias, L. Thompson, Jon G. Sanders +47 more
2022Nature Microbiology172 citations Open access
Semantic Scholar
The critical role that spectral libraries play in capturing the metabolomics community knowledge
Wout Bittremieux, Mingxun Wang, P. Dorrestein
2022Metabolomics137 citations Open access
Semantic Scholar
Sequence-to-sequence translation from mass spectra to peptides with a transformer model
Melih Yilmaz, William E. Fondrie, Wout Bittremieux, Carlo Melendez +4 more
2024bioRxiv123 citations Open access
Semantic Scholar
De novo mass spectrometry peptide sequencing with a transformer model
Melih Yilmaz, William E. Fondrie, Wout Bittremieux, Sewoong Oh +1 more
2022bioRxiv93 citations Open access
Semantic Scholar
Open access repository-scale propagated nearest neighbor suspect spectral library for untargeted metabolomics
Wout Bittremieux, Nicole E. Avalon, Sydney P. Thomas, Sarvar A. Kakhkhorov +28 more
2023bioRxiv83 citations Open access
Semantic Scholar
MassSpecGym: A benchmark for the discovery and identification of molecules
Roman Bushuiev, Anton Bushuiev, Niek F. de Jonge, A. Young +26 more
2024Neural Information Processing Systems80 citations
Semantic Scholar
Comparison of Cosine, Modified Cosine, and Neutral Loss Based Spectrum Alignment For Discovery of Structurally Related Molecules
Wout Bittremieux, Robin Schmid, Florian Huber, J. J. J. van der Hooft +2 more
2022bioRxiv77 citations Open access
Semantic Scholar
Enhancing untargeted metabolomics using metadata-based source annotation
J. Gauglitz, Kiana A. West, Wout Bittremieux, C. Williams +69 more
2022Nature Biotechnology73 citations Open access
Semantic Scholar
Sharing biological data: why, when, and how
S. Wilson, G. Way, Wout Bittremieux, J. Armache +2 more
2021FEBS Letters56 citations Open access
Semantic Scholar
The pitfalls of negative data bias for the T-cell epitope specificity challenge
Ceder Dens, K. Laukens, Wout Bittremieux, P. Meysman
2023bioRxiv51 citations Open access
Semantic Scholar
Proteomics Standards Initiative at Twenty Years: Current Activities and Future Work
E. Deutsch, J. Vizcaíno, Andrew R. Jones, P. Binz +25 more
2023Journal of Proteome Research50 citations Open access
Semantic Scholar
Native metabolomics identifies the rivulariapeptolide family of protease inhibitors
R. Reher, Allegra T. Aron, Pavla Fajtová, P. Stincone +24 more
2021Nature Communications50 citations Open access
Semantic Scholar
A Universal Language for Finding Mass Spectrometry Data Patterns
Alan K. Jarmusch, Allegra T. Aron, D. Petráš, Vanessa V. Phelan +65 more
2022bioRxiv44 citations Open access
Semantic Scholar
Proteomics Standards Initiative’s ProForma 2.0: Unifying the Encoding of Proteoforms and Peptidoforms
Richard D. LeDuc, E. Deutsch, P. Binz, Ryan T. Fellers +14 more
2021Journal of Proteome Research41 citations Open access
Semantic Scholar
Large-scale tandem mass spectrum clustering using fast nearest neighbor searching
Wout Bittremieux, K. Laukens, William Stafford Noble, P. Dorrestein
2021bioRxiv36 citations Open access
Semantic Scholar
Discovery of metabolites prevails amid in-source fragmentation
Yasin El Abiead, Adriano Rutz, Simone Zuffa, Bashar Amer +22 more
2025Nature Metabolism35 citations Open access
Semantic Scholar
A Universal Language for Finding Mass Spectrometry Data Patterns
T. Damiani, A. Jarmusch, Allegra T. Aron, D. Petráš +70 more
2025Nature Methods35 citations Open access
Semantic Scholar
Deep Learning Methods for De Novo Peptide Sequencing
Wout Bittremieux, V. Ananth, William E. Fondrie, Carlo Melendez +5 more
2024Mass spectrometry reviews (Print)35 citations Open access
Semantic Scholar
Benchmarking of Small Molecule Feature Representations for hERG, Nav1.5, and Cav1.2 Cardiotoxicity Prediction
Issar Arab, Kristof Egghe, K. Laukens, Ke Chen +2 more
2023bioRxiv34 citations Open access
Semantic Scholar
Fragment ion intensity prediction improves the identification rate of non-tryptic peptides in timsTOF
Charlotte Adams, Wassim Gabriel, K. Laukens, Mario Picciani +3 more
2024bioRxiv28 citations Open access
Semantic Scholar
Current and future deep learning algorithms for MS/MS-based small molecule structure elucidation.
Youzhong Liu, Thomas de Vijlder, Wout Bittremieux, K. Laukens +1 more
2021Rapid Communications in Mass Spectrometry21 citations Open access
Semantic Scholar
HyperSpec: Ultrafast Mass Spectra Clustering in Hyperdimensional Space
Weihong Xu, Jaeyoung Kang, Wout Bittremieux, Niema Moshiri +1 more
2023Journal of Proteome Research20 citations Open access
Semantic Scholar
Four layer multi-omics reveals molecular responses to aneuploidy in Leishmania
B. Cuypers, P. Meysman, Ionas Erb, Wout Bittremieux +9 more
2021bioRxiv19 citations Open access
Semantic Scholar
Machine learning strategies to tackle data challenges in mass spectrometry-based proteomics
Ceder Dens, Charlotte Adams, Kris Laukens, Wout Bittremieux
2024bioRxiv18 citations Open access
Semantic Scholar
Interpretable deep learning to uncover the molecular binding patterns determining TCR–epitope interaction predictions
Ceder Dens, Wout Bittremieux, F. Affaticati, K. Laukens +1 more
2023ImmunoInformatics18 citations Open access
Semantic Scholar
Unified and standardized mass spectrometry data processing in Python using spectrum_utils
Wout Bittremieux, L. Levitsky, Matteo Pilz, T. Sachsenberg +3 more
2022bioRxiv18 citations Open access
Semantic Scholar
Open-Source and FAIR Research Software for Proteomics
Yasset Pérez-Riverol, Wout Bittremieux, W. Noble, L. Martens +16 more
2025Journal of Proteome Research15 citations Open access
Semantic Scholar
Machine learning‐based peptide‐spectrum match rescoring opens up the immunopeptidome
Charlotte Adams, Kris Laukens, Wout Bittremieux, K. Boonen
2023Proteomics14 citations Open access
Semantic Scholar
Massively Parallel Open Modification Spectral Library Searching with Hyperdimensional Computing
Jaeyoung Kang, Weihong Xu, Wout Bittremieux, Tajana S. Rosing
2022International Conference on Parallel Architectures and Compilation Techniques14 citations Open access
Semantic Scholar
Accelerating open modification spectral library searching on tensor core in high-dimensional space
Jaeyoung Kang, Weihong Xu, Wout Bittremieux, Niema Moshiri +1 more
2023Bioinform.13 citations Open access
Semantic Scholar
Accounting for digestion enzyme bias in Casanovo
Carlo Melendez, Justin A. Sanders, Melih Yilmaz, Wout Bittremieux +3 more
2024bioRxiv12 citations Open access
Semantic Scholar
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
2024Journal of Chemical Information and Modeling12 citations
Semantic Scholar
Semi-supervised machine learning for sensitive open modification spectral library searching
Issar Arab, William E. Fondrie, K. Laukens, Wout Bittremieux
2022bioRxiv12 citations Open access
Semantic Scholar
Open Modification Searching of SARS-CoV-2–Human Protein Interaction Data Reveals Novel Viral Modification Sites
Charlotte Adams, K. Boonen, K. Laukens, Wout Bittremieux
2022bioRxiv11 citations Open access
Semantic Scholar
Communicating Mass Spectrometry Quality Information in mzQC with Python, R, and Java
Chris Bielow, Nils Hoffmann, David Jimenez-Morales, T. Van Den Bossche +4 more
2024bioRxiv10 citations Open access
Semantic Scholar
DRAM-Based Acceleration of Open Modification Search in Hyperdimensional Space
Jaeyoung Kang, Weihong Xu, Wout Bittremieux, Niema Moshiri +1 more
2024IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems10 citations
Semantic Scholar
Improvements to Casanovo, a deep learning de novo peptide sequencer
Gwenneth Straub, V. Ananth, William E. Fondrie, Chris Hsu +11 more
2025bioRxiv9 citations Open access
Semantic Scholar
The Proteomics Standards Initiative Standardized Formats for Spectral Libraries and Fragment Ion Peak Annotations: mzSpecLib and mzPAF
J. Klein, Henry Lam, Tytus D. Mak, Wout Bittremieux +22 more
2024Analytical Chemistry9 citations Open access
Semantic Scholar
SpecHD: Hyperdimensional Computing Framework for FPGA-Based Mass Spectrometry Clustering
Sumukh Pinge, Weihong Xu, Jaeyoung Kang, Tian-Qi Zhang +3 more
2023Design, Automation and Test in Europe9 citations
Semantic Scholar
A Comprehensive Evaluation of Consensus Spectrum Generation Methods in Proteomics
Xiyang Luo, Wout Bittremieux, J. Griss, E. Deutsch +10 more
2022bioRxiv9 citations Open access
Semantic Scholar
Comparing the applicability of de facto population markers for spatiotemporal trend analysis in wastewater-based epidemiology.
Maarten Quireyns, Tim Boogaerts, Juan S. Giraldo, Natan Van Wichelen +10 more
2025Journal of Hazardous Materials8 citations
Semantic Scholar
A resource to empirically establish drug exposure records directly from untargeted metabolomics data
H. Zhao, K. Kvitne, Corinna Brungs, Siddharth Mohan +55 more
2025Nature Communications8 citations Open access
Semantic Scholar
Open Science Resources for the Mass Spectrometry-Based Analysis of SARS-CoV-2.
Wout Bittremieux, Charlotte Adams, K. Laukens, P. Dorrestein +1 more
2021Journal of Proteome Research8 citations Open access
Semantic Scholar
ppx: Programmatic access to proteomics data repositories
William E. Fondrie, Wout Bittremieux, William Stafford Noble
2021bioRxiv8 citations Open access
Semantic Scholar
Bridging complexity and accessibility in metabolomics with MetaboApps
Helena Mannochio-Russo, W. D. Gonçalves Nunes, H. Zhao, K. Kvitne +18 more
2026Nature Methods7 citations Open access
Semantic Scholar
A 2025 perspective on the role of machine learning for biomarker discovery in clinical proteomics
Charlotte Adams, Wout Bittremieux
2025Espert Review of Proteomics7 citations
Semantic Scholar
Scalability of mass spectrometry-based metabolomics for natural extracts libraries exploration: current status, challenges, and opportunities.
Adriano Rutz, Wout Bittremieux, Robin Schmid, Olivier Cailloux +2 more
2025Natural product reports (Print)7 citations Open access
Semantic Scholar
Strategic priorities for transformative progress in advancing biology with proteomics and artificial intelligence
Yingying Sun, A. Jun, Zhiwei Liu, Rui Sun +58 more
2025arXiv.org7 citations
Semantic Scholar
RapidOMS: FPGA-based Open Modification Spectral Library Searching with HD Computing
Sumukh Pinge, Wei-Hong Xu, Wout Bittremieux, Niema Moshiri +2 more
2024Biomedical Circuits and Systems Conference7 citations Open access
Semantic Scholar

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