Wout Bittremieux

ORCID

Publication Activity (10 Years)

Years Active: 2017-2024
Publications (10 Years): 63

Top Venues

Journal of proteome research

Nature communications

Journal of the American Society for Mass Spectrometry

Nature biotechnology

University of California San Diego

University of Antwerp (PHD)

This page only lists publications with an associated author ORCID identifier.

Affiliation History

University of California San Diego Jul 01 2019

United States

Postdoctoral fellow :: Skaggs School of Pharmacy & Pharmaceutical Sciences

University of Antwerp Mar 01 2017

Belgium

Postdoctoral researcher :: Department of Mathematics and Computer Science

University of Washington Sep 18 2017 - Jun 30 2019

United States

Postdoctoral fellow :: Department of Genome Sciences

Stellenbosch University Sep 12 2016 - Dec 04 2016

South Africa

Visiting researcher :: Division of Molecular Biology and Human Genetics

Education History

University of Antwerp Mar 01 2013 - Feb 28 2017

Belgium

PHD :: Department of Mathematics and Computer Science

Hasselt University Sep 01 2010 - Jun 30 2012

Belgium

MSC

Hasselt University Sep 01 2007 - Jun 30 2010

Belgium

BSC

Publications

Melih Yilmaz, William E Fondrie, Wout Bittremieux, Carlo F Melendez, Rowan Nelson, Varun Ananth, Sewoong Oh, William Stafford Noble
Sequence-to-sequence translation from mass spectra to peptides with a transformer model. Nature communications 15 (1) (2024)
Margaret R Martin, Wout Bittremieux, Soha Hassoun
Molecular structure discovery for untargeted metabolomics using biotransformation rules and global molecular networking. bioRxiv : the preprint server for biology (2024)
Chris Bielow, Nils Hoffmann, David Jimenez-Morales, Tim Van Den Bossche, Juan Antonio Vizcaino, David L Tabb, Wout Bittremieux, Mathias Walzer
Communicating Mass Spectrometry Quality Information in mzQC with Python, R, and Java. Journal of the American Society for Mass Spectrometry 35 (8) (2024)
Wout Bittremieux
From data to discovery: The essential role of computational tools in proteomics. Proteomics 24 (8) (2024)
Carlo Melendez, Justin Sanders, Melih Yilmaz, Wout Bittremieux, William E Fondrie, Sewoong Oh, William Stafford Noble
Accounting for Digestion Enzyme Bias in Casanovo. Journal of proteome research (2024)
Charlotte Adams, Wassim Gabriel, Kris Laukens, Mario Picciani, Mathias Wilhelm, Wout Bittremieux, Kurt Boonen
Fragment ion intensity prediction improves the identification rate of non-tryptic peptides in timsTOF. Nature communications 15 (1) (2024)
Wout Bittremieux
From data to discovery: The essential role of computational tools in proteomics. Proteomics 24 (8) (2024)
Ceder Dens, Charlotte Adams, Kris Laukens, Wout Bittremieux
Machine Learning Strategies to Tackle Data Challenges in Mass Spectrometry-Based Proteomics. Journal of the American Society for Mass Spectrometry (2024)
Chris Bielow, Nils Hoffmann, David Jimenez-Morales, Tim Van Den Bossche, Juan Antonio Vizcaino, David L Tabb, Wout Bittremieux, Mathias Walzer
Communicating Mass Spectrometry Quality Information in mzQC with Python, R, and Java. Journal of the American Society for Mass Spectrometry (2024)
Charlotte Adams, Wassim Gabriel, Kris Laukens, Mario Picciani, Mathias Wilhelm, Wout Bittremieux, Kurt Boonen
Fragment ion intensity prediction improves the identification rate of non-tryptic peptides in timsTOF. Nature communications 15 (1) (2024)
Melih Yilmaz, William E Fondrie, Wout Bittremieux, Carlo F Melendez, Rowan Nelson, Varun Ananth, Sewoong Oh, William Stafford Noble
Sequence-to-sequence translation from mass spectra to peptides with a transformer model. Nature communications 15 (1) (2024)
Issar Arab, Kris Laukens, Wout Bittremieux
Semisupervised Learning to Boost hERG, Nav1.5, and Cav1.2 Cardiac Ion Channel Toxicity Prediction by Mining a Large Unlabeled Small Molecule Data Set. Journal of chemical information and modeling 64 (16) (2024)
Melih Yilmaz, William E Fondrie, Wout Bittremieux, Carlo F Melendez, Rowan Nelson, Varun Ananth, Sewoong Oh, William Stafford Noble
Sequence-to-sequence translation from mass spectra to peptides with a transformer model. Nature communications 15 (1) (2024)
Issar Arab, Kris Laukens, Wout Bittremieux
Semisupervised Learning to Boost hERG, Nav1.5, and Cav1.2 Cardiac Ion Channel Toxicity Prediction by Mining a Large Unlabeled Small Molecule Data Set. Journal of chemical information and modeling (2024)
Chris Bielow, Nils Hoffmann, David Jimenez-Morales, Tim Van Den Bossche, Juan Antonio Vizcaino, David L Tabb, Wout Bittremieux, Mathias Walzer
Communicating Mass Spectrometry Quality Information in mzQC with Python, R, and Java. Journal of the American Society for Mass Spectrometry 35 (8) (2024)
Chris Bielow, Nils Hoffmann, David Jimenez-Morales, Tim Van Den Bossche, Juan Antonio Vizcaino, David L Tabb, Wout Bittremieux, Mathias Walzer
Communicating Mass Spectrometry Quality Information in mzQC with Python, R, and Java. Journal of the American Society for Mass Spectrometry 35 (8) (2024)
Eric W Deutsch, Juan Antonio Vizcaino, Andrew R Jones, Pierre-Alain Binz, Henry H N Lam, Joshua Klein, Wout Bittremieux, Yasset Perez Riverol, David L Tabb, Mathias Walzer, Sylvie Ricard-Blum, Henning Hermjakob, Steffen Neumann, Tytus D Mak, Shin-Ichiro Kawano, Luis Mendoza, Tim Van Den Bossche, Ralf Gabriels, Nuno Bandeira, Jeremy J Carver, Benjamin S Pullman, Zhi Sun, Nils Hoffmann, Jim Shofstahl, Yunping Zhu, Luana Licata, Federica Quaglia, Silvio C E Tosatto, Sandra E Orchard
Proteomics Standards Initiative at Twenty Years: Current Activities and Future Work. Journal of proteome research 22 (2) (2023)
Eric W Deutsch, Juan Antonio Vizcaino, Andrew R Jones, Pierre-Alain Binz, Henry H N Lam, Joshua Klein, Wout Bittremieux, Yasset Perez Riverol, David L Tabb, Mathias Walzer, Sylvie Ricard-Blum, Henning Hermjakob, Steffen Neumann, Tytus D Mak, Shin-Ichiro Kawano, Luis Mendoza, Tim Van Den Bossche, Ralf Gabriels, Nuno Bandeira, Jeremy J Carver, Benjamin S Pullman, Zhi Sun, Nils Hoffmann, Jim Shofstahl, Yunping Zhu, Luana Licata, Federica Quaglia, Silvio C E Tosatto, Sandra E Orchard
Proteomics Standards Initiative at Twenty Years: Current Activities and Future Work. Journal of proteome research (2023)
Weihong Xu, Jaeyoung Kang, Wout Bittremieux, Niema Moshiri, Tajana Rosing
HyperSpec: Ultrafast Mass Spectra Clustering in Hyperdimensional Space. Journal of proteome research (2023)
Wout Bittremieux, Lev I Levitsky, Matteo Pilz, Timo Sachsenberg, Florian Huber, Mingxun Wang, Pieter C Dorrestein
Unified and Standardized Mass Spectrometry Data Processing in Python Using spectrum_utils. Journal of proteome research 22 (2) (2023)
Julia M Gauglitz, Kiana A West, Wout Bittremieux, Candace L Williams, Kelly C Weldon, Morgan Panitchpakdi, Francesca Di Ottavio, Christine M Aceves, Elizabeth Brown, Nicole C Sikora, Alan K Jarmusch, Cameron Martino, Anupriya Tripathi, Michael J Meehan, Kathleen Dorrestein, Justin P Shaffer, Roxana Coras, Fernando Vargas, Lindsay DeRight Goldasich, Tara Schwartz, MacKenzie Bryant, Gregory Humphrey, Abigail J Johnson, Katharina Spengler, Pedro Belda Ferre, Edgar Diaz, Daniel McDonald, Qiyun Zhu, Emmanuel O Elijah, Mingxun Wang, Clarisse Marotz, Kate E Sprecher, Daniela Vargas-Robles, Dana Withrow, Gail Ackermann, Lourdes Herrera, Barry J Bradford, Lucas Maciel Mauriz Marques, Juliano Geraldo Amaral, Rodrigo Moreira da Silva, Flavio Protasio Veras, Thiago Mattar Cunha, Rene Donizeti Ribeiro Oliveira, Paulo Louzada-Junior, Robert H Mills, Paulina K Piotrowski, Stephanie L Servetas, Sandra M Da Silva, Christina M Jones, Nancy J Lin, Katrice A Lippa, Scott A Jackson, Rima Kaddurah Daouk, Douglas Galasko, Parambir S Dulai, Tatyana I Kalashnikova, Curt Wittenberg, Robert Terkeltaub, Megan M Doty, Jae H Kim, David J Gonzalez, Julia Beauchamp-Walters, Kenneth P Wright, Maria Gloria Dominguez Bello, Mark Manary, Michelli F Oliveira, Brigid S Boland, Norberto Peporine Lopes, Monica Guma, Austin D Swafford, Rachel J Dutton, Rob Knight, Pieter C Dorrestein
Author Correction: Enhancing untargeted metabolomics using metadata-based source annotation. Nature biotechnology (2023)
Charlotte Adams, Kris Laukens, Wout Bittremieux, Kurt Boonen
Machine learning-based peptide-spectrum match rescoring opens up the immunopeptidome. Proteomics (2023)
Eric W Deutsch, Juan Antonio Vizcaino, Andrew R Jones, Pierre-Alain Binz, Henry H N Lam, Joshua Klein, Wout Bittremieux, Yasset Perez Riverol, David L Tabb, Mathias Walzer, Sylvie Ricard-Blum, Henning Hermjakob, Steffen Neumann, Tytus D Mak, Shin-Ichiro Kawano, Luis Mendoza, Tim Van Den Bossche, Ralf Gabriels, Nuno Bandeira, Jeremy J Carver, Benjamin S Pullman, Zhi Sun, Nils Hoffmann, Jim Shofstahl, Yunping Zhu, Luana Licata, Federica Quaglia, Silvio C E Tosatto, Sandra E Orchard
Proteomics Standards Initiative at Twenty Years: Current Activities and Future Work. Journal of proteome research 22 (2) (2023)
Wout Bittremieux, Nicole E Avalon, Sydney P Thomas, Sarvar A Kakhkhorov, Alexander A Aksenov, Paulo Wender Portal Gomes, Christine M Aceves, Andrés Mauricio Caraballo-Rodríguez, Julia M Gauglitz, William H Gerwick, Tao Huan, Alan K Jarmusch, Rima F Kaddurah-Daouk, Kyo-Bin Kang, Hyun Woo Kim, Todor Kondić, Helena M Russo, Michael J Meehan, Alexey V Melnik, Louis-Felix Nothias, Claire O'Donovan, Morgan Panitchpakdi, Daniel Petras, Robin Schmid, Emma L Schymanski, Justin Johan Jozias van der Hooft, Kelly C Weldon, Heejung Yang, Shipei Xing, Jasmine Zemlin, Mingxun Wang, Pieter C Dorrestein
Open access repository-scale propagated nearest neighbor suspect spectral library for untargeted metabolomics. Nature communications 14 (1) (2023)
Eric W Deutsch, Juan Antonio Vizcaino, Andrew R Jones, Pierre-Alain Binz, Henry H N Lam, Joshua Klein, Wout Bittremieux, Yasset Perez Riverol, David L Tabb, Mathias Walzer, Sylvie Ricard-Blum, Henning Hermjakob, Steffen Neumann, Tytus D Mak, Shin-Ichiro Kawano, Luis Mendoza, Tim Van Den Bossche, Ralf Gabriels, Nuno Bandeira, Jeremy J Carver, Benjamin S Pullman, Zhi Sun, Nils Hoffmann, Jim Shofstahl, Yunping Zhu, Luana Licata, Federica Quaglia, Silvio C E Tosatto, Sandra E Orchard
Proteomics Standards Initiative at Twenty Years: Current Activities and Future Work. Journal of proteome research (2023)
Eric W Deutsch, Juan Antonio Vizcaino, Andrew R Jones, Pierre-Alain Binz, Henry H N Lam, Joshua Klein, Wout Bittremieux, Yasset Perez Riverol, David L Tabb, Mathias Walzer, Sylvie Ricard-Blum, Henning Hermjakob, Steffen Neumann, Tytus D Mak, Shin-Ichiro Kawano, Luis Mendoza, Tim Van Den Bossche, Ralf Gabriels, Nuno Bandeira, Jeremy J Carver, Benjamin S Pullman, Zhi Sun, Nils Hoffmann, Jim Shofstahl, Yunping Zhu, Luana Licata, Federica Quaglia, Silvio C E Tosatto, Sandra E Orchard
Proteomics Standards Initiative at Twenty Years: Current Activities and Future Work. Journal of proteome research 22 (2) (2023)
Wout Bittremieux, Lev I Levitsky, Matteo Pilz, Timo Sachsenberg, Florian Huber, Mingxun Wang, Pieter C Dorrestein
Unified and Standardized Mass Spectrometry Data Processing in Python Using spectrum_utils. Journal of proteome research 22 (2) (2023)
Wout Bittremieux, Nicole E Avalon, Sydney P Thomas, Sarvar A Kakhkhorov, Alexander A Aksenov, Paulo Wender Portal Gomes, Christine M Aceves, Andrés Mauricio Caraballo-Rodríguez, Julia M Gauglitz, William H Gerwick, Tao Huan, Alan K Jarmusch, Rima F Kaddurah-Daouk, Kyo-Bin Kang, Hyun Woo Kim, Todor Kondić, Helena M Russo, Michael J Meehan, Alexey V Melnik, Louis-Felix Nothias, Claire O'Donovan, Morgan Panitchpakdi, Daniel Petras, Robin Schmid, Emma L Schymanski, Justin Johan Jozias van der Hooft, Kelly C Weldon, Heejung Yang, Shipei Xing, Jasmine Zemlin, Mingxun Wang, Pieter C Dorrestein
Open access repository-scale propagated nearest neighbor suspect spectral library for untargeted metabolomics. Nature communications 14 (1) (2023)
Wout Bittremieux, Nicole E Avalon, Sydney P Thomas, Sarvar A Kakhkhorov, Alexander A Aksenov, Paulo Wender Portal Gomes, Christine M Aceves, Andrés Mauricio Caraballo-Rodríguez, Julia M Gauglitz, William H Gerwick, Tao Huan, Alan K Jarmusch, Rima F Kaddurah-Daouk, Kyo-Bin Kang, Hyun Woo Kim, Todor Kondić, Helena M Russo, Michael J Meehan, Alexey V Melnik, Louis-Felix Nothias, Claire O'Donovan, Morgan Panitchpakdi, Daniel Petras, Robin Schmid, Emma L Schymanski, Justin Johan Jozias van der Hooft, Kelly C Weldon, Heejung Yang, Shipei Xing, Jasmine Zemlin, Mingxun Wang, Pieter C Dorrestein
Open access repository-scale propagated nearest neighbor suspect spectral library for untargeted metabolomics. Nature communications 14 (1) (2023)
Eric W Deutsch, Juan Antonio Vizcaino, Andrew R Jones, Pierre-Alain Binz, Henry H N Lam, Joshua Klein, Wout Bittremieux, Yasset Perez Riverol, David L Tabb, Mathias Walzer, Sylvie Ricard-Blum, Henning Hermjakob, Steffen Neumann, Tytus D Mak, Shin-Ichiro Kawano, Luis Mendoza, Tim Van Den Bossche, Ralf Gabriels, Nuno Bandeira, Jeremy J Carver, Benjamin S Pullman, Zhi Sun, Nils Hoffmann, Jim Shofstahl, Yunping Zhu, Luana Licata, Federica Quaglia, Silvio C E Tosatto, Sandra E Orchard
Proteomics Standards Initiative at Twenty Years: Current Activities and Future Work. Journal of proteome research 22 (2) (2023)
Wout Bittremieux, Lev I Levitsky, Matteo Pilz, Timo Sachsenberg, Florian Huber, Mingxun Wang, Pieter C Dorrestein
Unified and Standardized Mass Spectrometry Data Processing in Python Using spectrum_utils. Journal of proteome research (2023)
Wout Bittremieux, Nicole E Avalon, Sydney P Thomas, Sarvar A Kakhkhorov, Alexander A Aksenov, Paulo Wender Portal Gomes, Christine M Aceves, Andrés Mauricio Caraballo-Rodríguez, Julia M Gauglitz, William H Gerwick, Tao Huan, Alan K Jarmusch, Rima F Kaddurah-Daouk, Kyo-Bin Kang, Hyun Woo Kim, Todor Kondić, Helena M Russo, Michael J Meehan, Alexey V Melnik, Louis-Felix Nothias, Claire O'Donovan, Morgan Panitchpakdi, Daniel Petras, Robin Schmid, Emma L Schymanski, Justin Johan Jozias van der Hooft, Kelly C Weldon, Heejung Yang, Shipei Xing, Jasmine Zemlin, Mingxun Wang, Pieter C Dorrestein
Open access repository-scale propagated nearest neighbor suspect spectral library for untargeted metabolomics. Nature communications 14 (1) (2023)
Wout Bittremieux, Lev I Levitsky, Matteo Pilz, Timo Sachsenberg, Florian Huber, Mingxun Wang, Pieter C Dorrestein
Unified and Standardized Mass Spectrometry Data Processing in Python Using spectrum_utils. Journal of proteome research 22 (2) (2023)
Issar Arab, William E Fondrie, Kris Laukens, Wout Bittremieux
Semisupervised Machine Learning for Sensitive Open Modification Spectral Library Searching. Journal of proteome research 22 (2) (2023)
Issar Arab, William E Fondrie, Kris Laukens, Wout Bittremieux
Semisupervised Machine Learning for Sensitive Open Modification Spectral Library Searching. Journal of proteome research 22 (2) (2023)
Wout Bittremieux, Nicole E Avalon, Sydney P Thomas, Sarvar A Kakhkhorov, Alexander A Aksenov, Paulo Wender Portal Gomes, Christine M Aceves, Andrés Mauricio Caraballo-Rodríguez, Julia M Gauglitz, William H Gerwick, Tao Huan, Alan K Jarmusch, Rima F Kaddurah-Daouk, Kyo-Bin Kang, Hyun Woo Kim, Todor Kondić, Helena M Russo, Michael J Meehan, Alexey V Melnik, Louis-Felix Nothias, Claire O'Donovan, Morgan Panitchpakdi, Daniel Petras, Robin Schmid, Emma L Schymanski, Justin Johan Jozias van der Hooft, Kelly C Weldon, Heejung Yang, Shipei Xing, Jasmine Zemlin, Mingxun Wang, Pieter C Dorrestein
Open access repository-scale propagated nearest neighbor suspect spectral library for untargeted metabolomics. Nature communications 14 (1) (2023)
Issar Arab, William E Fondrie, Kris Laukens, Wout Bittremieux
Semisupervised Machine Learning for Sensitive Open Modification Spectral Library Searching. Journal of proteome research (2023)
Eric W Deutsch, Juan Antonio Vizcaino, Andrew R Jones, Pierre-Alain Binz, Henry H N Lam, Joshua Klein, Wout Bittremieux, Yasset Perez Riverol, David L Tabb, Mathias Walzer, Sylvie Ricard-Blum, Henning Hermjakob, Steffen Neumann, Tytus D Mak, Shin-Ichiro Kawano, Luis Mendoza, Tim Van Den Bossche, Ralf Gabriels, Nuno Bandeira, Jeremy J Carver, Benjamin S Pullman, Zhi Sun, Nils Hoffmann, Jim Shofstahl, Yunping Zhu, Luana Licata, Federica Quaglia, Silvio C E Tosatto, Sandra E Orchard
Proteomics Standards Initiative at Twenty Years: Current Activities and Future Work. Journal of proteome research 22 (2) (2023)
Issar Arab, Kristof Egghe, Kris Laukens, Ke Chen, Khaled H Barakat, Wout Bittremieux
Benchmarking of Small Molecule Feature Representations for hERG, Nav1.5, and Cav1.2 Cardiotoxicity Prediction. Journal of chemical information and modeling (2023)
Issar Arab, William E Fondrie, Kris Laukens, Wout Bittremieux
Semisupervised Machine Learning for Sensitive Open Modification Spectral Library Searching. Journal of proteome research 22 (2) (2023)
Julia M Gauglitz, Kiana A West, Wout Bittremieux, Candace L Williams, Kelly C Weldon, Morgan Panitchpakdi, Francesca Di Ottavio, Christine M Aceves, Elizabeth Brown, Nicole C Sikora, Alan K Jarmusch, Cameron Martino, Anupriya Tripathi, Michael J Meehan, Kathleen Dorrestein, Justin P Shaffer, Roxana Coras, Fernando Vargas, Lindsay DeRight Goldasich, Tara Schwartz, MacKenzie Bryant, Gregory Humphrey, Abigail J Johnson, Katharina Spengler, Pedro Belda Ferre, Edgar Diaz, Daniel McDonald, Qiyun Zhu, Emmanuel O Elijah, Mingxun Wang, Clarisse Marotz, Kate E Sprecher, Daniela Vargas-Robles, Dana Withrow, Gail Ackermann, Lourdes Herrera, Barry J Bradford, Lucas Maciel Mauriz Marques, Juliano Geraldo Amaral, Rodrigo Moreira da Silva, Flavio Protasio Veras, Thiago Mattar Cunha, Rene Donizeti Ribeiro Oliveira, Paulo Louzada-Junior, Robert H Mills, Paulina K Piotrowski, Stephanie L Servetas, Sandra M Da Silva, Christina M Jones, Nancy J Lin, Katrice A Lippa, Scott A Jackson, Rima Kaddurah Daouk, Douglas Galasko, Parambir S Dulai, Tatyana I Kalashnikova, Curt Wittenberg, Robert Terkeltaub, Megan M Doty, Jae H Kim, David J Gonzalez, Julia Beauchamp-Walters, Kenneth P Wright, Maria Gloria Dominguez Bello, Mark Manary, Michelli F Oliveira, Brigid S Boland, Norberto Peporine Lopes, Monica Guma, Austin D Swafford, Rachel J Dutton, Rob Knight, Pieter C Dorrestein
Enhancing untargeted metabolomics using metadata-based source annotation. Nature biotechnology (2022)
Raphael Reher, Allegra T Aron, Pavla Fajtová, Paolo Stincone, Berenike Wagner, Alicia I Pérez-Lorente, Chenxi Liu, Ido Y Ben Shalom, Wout Bittremieux, Mingxun Wang, Kyowon Jeong, Marie L Matos-Hernández, Kelsey L Alexander, Eduardo J E Caro-Diaz, C Benjamin Naman, J H William Scanlan, Phil M M Hochban, Wibke E Diederich, Carlos Molina-Santiago, Diego Romero, Khaled A Selim, Peter Sass, Heike Brötz-Oesterhelt, Chambers C Hughes, Pieter C Dorrestein, Anthony J O'Donoghue, William H Gerwick, Daniel Petras
Native metabolomics identifies the rivulariapeptolide family of protease inhibitors. Nature communications 13 (1) (2022)
Xiyang Luo, Wout Bittremieux, Johannes Griss, Eric W Deutsch, Timo Sachsenberg, Lev I Levitsky, Mikhail V Gorshkov, Julia A Bubis, Ralf Gabriels, Henry Webel, Aniel Sanchez, Mingze Bai, Lukas Käll, Yasset Perez Riverol
A Comprehensive Evaluation of Consensus Spectrum Generation Methods in Proteomics. Journal of proteome research 21 (6) (2022)
Wout Bittremieux, Damon H May, Jeffrey Bilmes, William Stafford Noble
A learned embedding for efficient joint analysis of millions of mass spectra. Nature methods 19 (6) (2022)
Justin P Shaffer, Louis-Felix Nothias, Luke R Thompson, Jon G Sanders, Rodolfo A Salido, Sneha P Couvillion, Asker D Brejnrod, Franck Lejzerowicz, Niina Haiminen, Shi Huang, Holly L Lutz, Qiyun Zhu, Cameron Martino, James T Morton, Smruthi Karthikeyan, Mélissa Nothias-Esposito, Kai Dührkop, Sebastian Böcker, Hyun Woo Kim, Alexander A Aksenov, Wout Bittremieux, Jeremiah J Minich, Clarisse Marotz, MacKenzie M Bryant, Karenina Sanders, Tara Schwartz, Greg Humphrey, Yoshiki Vásquez-Baeza, Anupriya Tripathi, Laxmi Parida, Anna Paola Carrieri, Kristen L Beck, Promi Das, Antonio González, Daniel McDonald, Joshua Ladau, Søren M Karst, Mads Albertsen, Gail Ackermann, Jeff DeReus, Torsten Thomas, Daniel Petras, Ashley Shade, James Stegen, Se Jin Song, Thomas O Metz, Austin D Swafford, Pieter C Dorrestein, Janet K Jansson, Jack A Gilbert, Rob Knight, null null
Standardized multi-omics of Earth's microbiomes reveals microbial and metabolite diversity. Nature microbiology 7 (12) (2022)
Richard D LeDuc, Eric W Deutsch, Pierre-Alain Binz, Ryan T Fellers, Anthony J Cesnik, Joshua A Klein, Tim Van Den Bossche, Ralf Gabriels, Arshika Yalavarthi, Yasset Perez Riverol, Jeremy Carver, Wout Bittremieux, Shin Kawano, Benjamin Pullman, Nuno Bandeira, Michael P Snyder, Paul M Thomas, Juan Antonio Vizcaino
Proteomics Standards Initiative's ProForma 2.0: Unifying the Encoding of Proteoforms and Peptidoforms. Journal of proteome research 21 (4) (2022)
Wout Bittremieux, Robin Schmid, Florian Huber, Justin Johan Jozias van der Hooft, Mingxun Wang, Pieter C Dorrestein
Comparison of Cosine, Modified Cosine, and Neutral Loss Based Spectrum Alignment For Discovery of Structurally Related Molecules. Journal of the American Society for Mass Spectrometry 33 (9) (2022)
Wout Bittremieux, Rohit S Advani, Alan K Jarmusch, Shaden Aguirre, Aileen Lu, Pieter C Dorrestein, Shirley M Tsunoda
Physicochemical properties determining drug detection in skin. Clinical and translational science (2021)
Wout Bittremieux, Charlotte Adams, Kris Laukens, Pieter C Dorrestein, Nuno Bandeira
Open Science Resources for the Mass Spectrometry-Based Analysis of SARS-CoV-2. Journal of proteome research 20 (3) (2021)
Eric W Deutsch, Yasset Perez Riverol, Jeremy Carver, Shin-Ichiro Kawano, Luis Mendoza, Tim Van Den Bossche, Ralf Gabriels, Pierre-Alain Binz, Benjamin Pullman, Zhi Sun, Jim Shofstahl, Wout Bittremieux, Tytus D Mak, Joshua Klein, Yunping Zhu, Henry H N Lam, Juan Antonio Vizcaino, Nuno Bandeira
Universal Spectrum Identifier for mass spectra. Nature methods 18 (7) (2021)
Wout Bittremieux, Kris Laukens, William Stafford Noble, Pieter C Dorrestein
Large-scale tandem mass spectrum clustering using fast nearest neighbor searching. Rapid communications in mass spectrometry : RCM (2021)
Samantha L Wilson, Gregory P Way, Wout Bittremieux, Jean Paul Armache, Melissa A Haendel, Michael M Hoffman
Sharing biological data: why, when, and how. FEBS letters 595 (7) (2021)
William E Fondrie, Wout Bittremieux, William Stafford Noble
ppx: Programmatic Access to Proteomics Data Repositories. Journal of proteome research 20 (9) (2021)
Wout Bittremieux, David Bouyssié, Viktoria Dorfer, Marie Locard-Paulet, Yasset Perez Riverol, Veit Schwämmle, Julian Uszkoreit, Tim Van Den Bossche
The European Bioinformatics Community for Mass Spectrometry (EuBIC-MS): an open community for bioinformatics training and research. Rapid communications in mass spectrometry : RCM (2021)
Alexander A Aksenov, Ivan Laponogov, Zheng Zhang, Sophie L F Doran, Ilaria Belluomo, Dennis Veselkov, Wout Bittremieux, Louis-Felix Nothias, Mélissa Nothias-Esposito, Katherine N Maloney, Biswapriya B Misra, Alexey V Melnik, Aleksandr Smirnov, Xiuxia Du, Kenneth L Jones, Kathleen Dorrestein, Morgan Panitchpakdi, Madeleine Ernst, Justin Johan Jozias van der Hooft, Mabel Gonzalez, Chiara Carazzone, Adolfo Amézquita, Chris Callewaert, James T Morton, Robert A Quinn, Amina Bouslimani, Andrea Albarracín Orio, Daniel Petras, Andrea M Smania, Sneha P Couvillion, Meagan C Burnet, Carrie D Nicora, Erika M Zink, Thomas O Metz, Viatcheslav Artaev, Elizabeth Humston-Fulmer, Rachel Gregor, Michael M Meijler, Itzhak Mizrahi, Stav Eyal, Brooke Anderson, Rachel Dutton, Raphaël Lugan, Pauline Le Boulch, Yann Guitton, Stephanie Prevost, Audrey Poirier, Gaud Dervilly, Abdoulaye Zié Koné, Aaron Fait, Noga Sikron Persi, Chao Song, Kelem Gashu, Roxana Coras, Monica Guma, Julia Manasson, Jose U Scher, Dinesh Kumar Barupal, Saleh Alseekh, Alisdair Robert Fernie, Reza Mirnezami, Vasilis Vasiliou, Robin Schmid, Roman S Borisov, Larisa N Kulikova, Rob Knight, Mingxun Wang, George B Hanna, Pieter C Dorrestein, Kirill Veselkov
Auto-deconvolution and molecular networking of gas chromatography-mass spectrometry data. Nature biotechnology 39 (2) (2020)
Youzhong Liu, Aida Mrzic, Pieter Meysman, Thomas De Vijlder, Edwin P Romijn, Dirk Valkenborg, Wout Bittremieux, Kris Laukens
MESSAR: Automated recommendation of metabolite substructures from tandem mass spectra. PloS one 15 (1) (2020)
Charlie Beirnaert, Laura Peeters, Pieter Meysman, Wout Bittremieux, Kenn Foubert, Deborah Custers, Anastasia Van der Auwera, Matthias Cuykx, Luc Pieters, Adrian Covaci, Kris Laukens
Using Expert Driven Machine Learning to Enhance Dynamic Metabolomics Data Analysis. Metabolites 9 (3) (2019)
Wout Bittremieux
spectrum_utils: A Python Package for Mass Spectrometry Data Processing and Visualization. Analytical chemistry 92 (1) (2019)
Wout Bittremieux, Kris Laukens, William Stafford Noble
Extremely Fast and Accurate Open Modification Spectral Library Searching of High-Resolution Mass Spectra Using Feature Hashing and Graphics Processing Units. Journal of proteome research 18 (10) (2019)
Lindsay K Pino, Andy Lin, Wout Bittremieux
2018 YPIC Challenge: A Case Study in Characterizing an Unknown Protein Sample. Journal of proteome research 18 (11) (2019)
Wout Bittremieux, Pieter Meysman, William Stafford Noble, Kris Laukens
Fast Open Modification Spectral Library Searching through Approximate Nearest Neighbor Indexing. Journal of proteome research 17 (10) (2018)
Wout Bittremieux, Mathias Walzer, Stefan Tenzer, Weimin Zhu, Reza M Salek, Martin Eisenacher, David L Tabb
The Human Proteome Organization-Proteomics Standards Initiative Quality Control Working Group: Making Quality Control More Accessible for Biological Mass Spectrometry. Analytical chemistry 89 (8) (2017)
Eric W Deutsch, Sandra Orchard, Pierre-Alain Binz, Wout Bittremieux, Martin Eisenacher, Henning Hermjakob, Shin Kawano, Henry Lam, Gerhard Mayer, Gerben Menschaert, Yasset Perez-Riverol, Reza M Salek, David L Tabb, Stefan Tenzer, Juan Antonio Vizcaíno, Mathias Walzer, Andrew R Jones
Proteomics Standards Initiative: Fifteen Years of Progress and Future Work. Journal of proteome research 16 (12) (2017)

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Publication Activity (10 Years)

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Wout Bittremieux