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| | Issue Date | Title | Contributor(s) | Type | Cat. |
| 1 | 2024 | The Boosting | BECKER, Thijs; GEUBBELMANS, Melvin; ROUSSEAU, Axel-Jan; VALKENBORG, Dirk; BURZYKOWSKI, Tomasz | Journal Contribution | A2 |
| 2 | 2024 | Implementation of polygenic risk scores from sequencing data towards practice by utilizing large publicly available datasets | Rojo, Alejandro Correa; VALKENBORG, Dirk; Ertaylan, Gokhan | Journal Contribution | M |
| 3 | 2023 | Generalized linear models | BURZYKOWSKI, Tomasz; GEUBBELMANS, Melvin; ROUSSEAU, Axel-Jan; VALKENBORG, Dirk | Journal Contribution | A2 |
| 4 | 2023 | Validation of machine learning algorithms | BURZYKOWSKI, Tomasz; GEUBBELMANS, Melvin; ROUSSEAU, Axel-Jan; VALKENBORG, Dirk | Journal Contribution | A2 |
| 5 | 2023 | Introduction to machine learning | BURZYKOWSKI, Tomasz; ROUSSEAU, Axel-Jan; GEUBBELMANS, Melvin; VALKENBORG, Dirk | Journal Contribution | A2 |
| 6 | 2023 | Support vector machines | VALKENBORG, Dirk; ROUSSEAU, Axel-Jan; GEUBBELMANS, Melvin; BURZYKOWSKI, Tomasz | Journal Contribution | A2 |
| 7 | 2023 | Decision trees and random forests | BECKER, Thijs; ROUSSEAU, Axel-Jan; GEUBBELMANS, Melvin; BURZYKOWSKI, Tomasz; VALKENBORG, Dirk | Journal Contribution | A1 |
| 8 | 2023 | A compositional data model to predict the isotope distribution for average peptides using a compositional spline model | AGTEN, Annelies; VILENNE, Frédérique; PROSTKO, Piotr; VALKENBORG, Dirk | Journal Contribution | A1 |
| 9 | 2023 | High-dimensional data | GEUBBELMANS, Melvin; ROUSSEAU, Axel-Jan; VALKENBORG, Dirk; BURZYKOWSKI, Tomasz | Journal Contribution | A2 |
| 10 | 2023 | NMR-Metabolomics Reveals a Metabolic Shift after Surgical Resection of Non-Small Cell Lung Cancer | DERVEAUX, Elien; GEUBBELMANS, Melvin; Criel, Maarten; Demedts, Ingel; Himpe, Ulrike; Tournoy, Kurt; Vercauter, Piet; Johansson, Erik; VALKENBORG, Dirk; VANHOVE, Karolien; MESOTTEN, Liesbet; ADRIAENSENS, Peter; THOMEER, Michiel | Journal Contribution | A1 |
| 11 | 2023 | Supervised learning | VALKENBORG, Dirk; GEUBBELMANS, Melvin; ROUSSEAU, Axel-Jan; BURZYKOWSKI, Tomasz | Journal Contribution | A1 |
| 12 | 2023 | Unsupervised learning | VALKENBORG, Dirk; ROUSSEAU, Axel-Jan; GEUBBELMANS, Melvin; BURZYKOWSKI, Tomasz | Journal Contribution | A2 |
| 13 | 2023 | The isotope distribution: A rose with thorns | CLAESEN, Jurgen; Rockwood, Alan; Gorshkov, Mikhail; VALKENBORG, Dirk | Journal Contribution | A1 |
| 14 | 2023 | Machine learning approach for the prediction of the number of sulphur atoms in peptides using the theoretical aggregated isotope distribution | AGTEN, Annelies; CLAESEN, Jurgen; BURZYKOWSKI, Tomasz; VALKENBORG, Dirk | Journal Contribution | A1 |
| 15 | 2022 | Envemind: Accurate Monoisotopic Mass Determination Based On Isotopic Envelope | Radzinski, Piotr; VALKENBORG, Dirk; Startek, Michal Piotr; Gambin, Anna | Journal Contribution | A1 |
| 16 | 2022 | R Shiny App for the Automated Deconvolution of NMR Spectra to Quantify the Solid-State Forms of Pharmaceutical Mixtures | PROSTKO, Piotr; Pikkemaat, Jeroen; Selter, Philipp; Lukaschek, Michail; Wechselberger, Rainer; KHAMIAKOVA, Tatsiana; VALKENBORG, Dirk | Journal Contribution | A1 |
| 17 | 2022 | Four layer multi-omics reveals molecular responses to aneuploidy in Leishmania | Cuypers, Bart; Meysman, Pieter; Erb, Ionas; Bittremieux, Wout; VALKENBORG, Dirk; Baggerman, Geert; Mertens, Inge; Sundar, Shyam; Khanal, Basudha; Notredame, Cedric; Dujardin, Jean-Claude; Domagalska, Malgorzata A.; Laukens, Kris | Dataset | DS |
| 18 | 2022 | Four layer multi-omics reveals molecular responses to aneuploidy in Leishmania | Cuypers, Bart; Meysman, Pieter; Erb, Ionas; Bittremieux, Wout; VALKENBORG, Dirk; Baggerman, Geert; Mertens, Inge; Sundar, Shyam; Khanal, Basudha; Notredame, Cedric; Dujardin, Jean-Claude; Domagalska, Malgorzata A.; Laukens, Kris; Engwerda, Christian R. | Journal Contribution | A1 |
| 19 | 2022 | Evaluating Feature Attribution Methods in the Image Domain: Benchmark results and model parameters | Gevaert, Arne; ROUSSEAU, Axel-Jan; BECKER, Thijs; VALKENBORG, Dirk; De Bie, Tijl; Saeys, Yvan | Dataset | DS |
| 20 | 2022 | Evaluating Feature Attribution Methods in the Image Domain: High-Dimensional Datasets | Gevaert, Arne; ROUSSEAU, Axel-Jan; BECKER, Thijs; VALKENBORG, Dirk; De Bie, Tijl; Saeys, Yvan | Dataset | DS |
| 21 | 2022 | A prospective observational cohort study to identify inflammatory biomarkers for the diagnosis and prognosis of patients with sepsis | D'ONOFRIO, Valentino; HEYLEN, Dries; PUSPARUM, Murih; Grondman, Inge; VANWALLEGHEM, Johan; Meersman , Agnes; Cartuyvels, Reinoud; MESSIAEN, Peter; Joosten, Leo A. B.; Netea, Mihai G.; VALKENBORG, Dirk; Ertaylan, Gokhan; GYSSENS, Inge | Journal Contribution | A1 |
| 22 | 2021 | A Compositional Model to Predict the Aggregated Isotope Distribution for Average DNA and RNA Oligonucleotides | AGTEN, Annelies; PROSTKO, Piotr; GEUBBELMANS, Melvin; De Vijlder, Thomas; VALKENBORG, Dirk; Liu, Youzhong | Journal Contribution | A1 |
| 23 | 2021 | Masserstein: Linear regression of mass spectra by optimal transport | CIACH, Michal; Miasojedow, Blazej; Skoraczynski, Grzegorz; Majewski, Szymon; Startek, Michal; VALKENBORG, Dirk; Gambin, Anna | Journal Contribution | A1 |
| 24 | 2021 | Classification with a Deferral Option and Low-Trust Filtering for Automated Seizure Detection | BECKER, Thijs; Vandecasteele, Kaat; Chatzichristos, Christos; Van Paesschen, Wim; VALKENBORG, Dirk; Van Huffel, Sabine; De Vos, Maarten | Journal Contribution | A1 |
| 25 | 2021 | Post Training Uncertainty Calibration Of Deep Networks For Medical Image Segmentation | ROUSSEAU, Axel-Jan; BECKER, Thijs; Bertels, Jeroen; Blaschko, Matthew B.; VALKENBORG, Dirk | Proceedings Paper | C1 |
| 26 | 2021 | Constrained Standardization of Count Data from Massive Parallel Sequencing | VAN HOUTVEN, Joris; Cuypers , B; Meysman, P; HOOYBERGHS, Jef; Laukens, K; VALKENBORG, Dirk | Journal Contribution | A1 |
| 27 | 2021 | Towards Building a Quantitative Proteomics Toolbox in Precision Medicine: A Mini-Review | CORREA ROJO, Alejandro; HEYLEN, Dries; AERTS, Jan; THAS, Olivier; HOOYBERGHS, Jef; Ertaylan, Gokhan; VALKENBORG, Dirk | Journal Contribution | A1 |
| 28 | 2021 | CONSTANd: An Efficient Normalization Method for Relative Quantification in Small- and Large-Scale Omics Experiments in R BioConductor and Python | VAN HOUTVEN, Joris; HOOYBERGHS, Jef; Laukens, Kris; VALKENBORG, Dirk | Journal Contribution | A1 |
| 29 | 2021 | Constrained standardization of count data from massive parallel sequencing | VAN HOUTVEN, Joris; Cuypers, Bart; Meysman, Pieter; HOOYBERGHS, Jef; Laukens, Kris; VALKENBORG, Dirk | Preprint | O |
| 30 | 2021 | Analysis of Targeted Proteomics data across different datasets with reference characteristics | HEYLEN, Dries; PUSPARUM, Murih; D'ONOFRIO, Valentino; GYSSENS, Inge; VALKENBORG, Dirk; Ertaylan, Gökhan | Conference Material | C2 |
| 31 | 2021 | Predicting the number of sulfur atoms in peptides and small proteins based on the observed aggregated isotope distribution | CLAESEN, Jurgen; VALKENBORG, Dirk; BURZYKOWSKI, Tomasz | Journal Contribution | A1 |
| 32 | 2020 | IsoSpec2: Ultrafast Fine Structure Calculator | Lacki, Mateusz K.; VALKENBORG, Dirk; Startek, Michal P. | Journal Contribution | A1 |
| 33 | 2020 | MESSAR: Automated recommendation of metabolite substructures from tandem mass spectra | Liu, Youzhong; Mrzic, Aida; Meysman, Pieter; De Vijlder, Thomas; Romijn, Edwin P.; VALKENBORG, Dirk; Bittremieux, Wout; Laukens, Kris | Journal Contribution | A1 |
| 34 | 2020 | Urinary Protein Biomarker Panel for the Diagnosis of Antibody-Mediated Rejection in Kidney Transplant Recipients | Mertens, Inge; Willems, Hanny; Loon, Elisabet Van; Schildermans, Karin; Boonen, Kurt; Baggerman, Geert; VALKENBORG, Dirk; Gwinner, Wilfried; Anglicheau, Dany; Essig, Marie; Marquet, Pierre; Naesens, Maarten | Journal Contribution | A1 |
| 35 | 2020 | Visualizing the agreement of peptide assignments between different search engines | AGTEN, Annelies; VAN HOUTVEN, Joris; Askenazi, M; BURZYKOWSKI, Tomasz; Laukens, K; VALKENBORG, Dirk | Journal Contribution | A1 |
| 36 | 2020 | Deciphering the Morphology of Motor Evoked Potentials | YPERMAN, Jan; BECKER, Thijs; VALKENBORG, Dirk; HELLINGS, Niels; Cambron, M; Dive, D; Laureys, G.; POPESCU, Veronica; VAN WIJMEERSCH, Bart; PEETERS, Liesbet | Journal Contribution | A1 |
| 37 | 2020 | Machine learning analysis of motor evoked potential time series to predict disability progression in multiple sclerosis | YPERMAN, Jan; BECKER, Thijs; VALKENBORG, Dirk; POPESCU, Veronica; HELLINGS, Niels; VAN WIJMEERSCH, Bart; PEETERS, Liesbet | Journal Contribution | A1 |
| 38 | 2020 | PRiSM: A prototype for exhaustive, restriction-free database searching for mass spectrometry-based identification | VAN HOUTVEN, Joris; Boonen, Kurt; Geert Baggerman, |; Askenazi, Manor; Laukens, Kris; HOOYBERGHS, Jef; VALKENBORG, Dirk | Journal Contribution | A1 |
| 39 | 2020 | The (generalized) hydrogen rule for organic molecules | CLAESEN, Jurgen; VALKENBORG, Dirk; BURZYKOWSKI, Tomasz | Journal Contribution | A1 |
| 40 | 2020 | A “Refined Hydrogen Rule” and a “Refined Hydrogen and Halogen Rule” for Organic Molecules | CLAESEN, Jurgen; VALKENBORG, Dirk; BURZYKOWSKI, Tomasz | Journal Contribution | A1 |
| 41 | 2019 | The challenges of peptidomics in complementing proteomics in a clinical context | Maes, Evelyne; Oeyen, Eline; Boonen, Kurt; Schildermans, Karin; Mertens, Inge; Pauwels, Patrick; VALKENBORG, Dirk; Baggerman, Geert | Journal Contribution | A1 |
| 42 | 2019 | masstodon: A Tool for Assigning Peaks and Modeling Electron Transfer Reactions in Top-Down Mass Spectrometry | Lacki, Mateusz K.; Lermyte, Frederik; Miasojedow, Blazej; Startek, Michal P.; Sobott, Frank; VALKENBORG, Dirk; Gambin, Anna | Journal Contribution | A1 |
| 43 | 2019 | Beyond Genes: Re-Identifiability of Proteomic Data and Its Implications for Personalized Medicine | Boonen, Kurt; Hens, Kristien; Menschaert, Gerben; Baggerman, Geert; VALKENBORG, Dirk; Ertaylan, Gokhan | Journal Contribution | A1 |
| 44 | 2019 | Machine learning analysis of motor evoked potential time series to predict disability progression in multiple sclerosis | YPERMAN, Jan; BECKER, Thijs; VALKENBORG, Dirk; POPESCU, Veronica; HELLINGS, Niels; VAN WIJMEERSCH, Bart; PEETERS, Liesbet | Journal Contribution | M |
| 45 | 2019 | Deciphering morphology of Evoked Potentials | YPERMAN, Jan; BECKER, Thijs; VALKENBORG, Dirk; HELLINGS, Niels; Cambron, M.; Dive, D.; Laureys, G.; POPESCU, Veronica; VAN WIJMEERSCH, Bart; PEETERS, Liesbet | Journal Contribution | M |
| 46 | 2019 | QCQuan: a web tool for the automated assessment of protein expression and data quality of labeled mass spectrometry experiments. | VAN HOUTVEN, Joris; AGTEN, Annelies; Boonen, Kurt; Baggerman, Geert; HOOYBERGHS, Jef; Laukens, Kris; VALKENBORG, Dirk | Journal Contribution | A1 |
| 47 | 2019 | MIND: A Double-Linear Model To Accurately Determine Monoisotopic Precursor Mass in High-Resolution Top-Down Proteomics | Lermyte, Frederik; Dittwald, Piotr; CLAESEN, Jurgen; Baggerman, Geert; Sobott, Frank; O'Connor, Peter B.; Laukens, Kris; HOOYBERGHS, Jef; Gambin, Anna; VALKENBORG, Dirk | Journal Contribution | A1 |
| 48 | 2019 | De novo prediction of the elemental composition of peptides and proteins based on a single mass | CLAESEN, Jurgen; VALKENBORG, Dirk; BURZYKOWSKI, Tomasz | Journal Contribution | A1 |
| 49 | 2019 | Experimental design in quantitative proteomics | BURZYKOWSKI, Tomasz; CLAESEN, Jurgen; VALKENBORG, Dirk | Book Section | B2 |
| 50 | 2018 | Proceedings of the EuBIC developer's meeting 2018 | Willems, Sander; Bouyssie, David; Deforce, Dieter; Dorfer, Viktoria; Gorshkov, Vladimir; Kopczynski, Dominik; Laukens, Kris; Locard-Paulet, Marie; Schwammle, Veit; Uszkoreit, Julian; VALKENBORG, Dirk; Vaudel, Marc; Bittremieux, Wout | Journal Contribution | A1 |
| 51 | 2018 | A tutorial in small molecule identification via electrospray ionization-mass spectrometry: The practical art of structural elucidation | De Vijlder, Thomas; VALKENBORG, Dirk; Lemiere, Filip; Romijn, Edwin P.; Laukens, Kris; Cuyckens, Filip | Journal Contribution | A1 |
| 52 | 2018 | Radical solutions: Principles and application of electron-based dissociation in mass spectrometry-based analysis of protein structure | Lermyte, Frederik; VALKENBORG, Dirk; Loo, Joseph A.; Sobott, Frank | Journal Contribution | A1 |
| 53 | 2018 | Estimation of Rates of Reactions Triggered by Electron Transfer in Top-Down Mass Spectrometry | CIACH, Michal; Lacki, Mateusz Krzysztof; Miasojedow, Blazej; Lermyte, Frederik; VALKENBORG, Dirk; Sobott, Frank; Gambin, Anna | Journal Contribution | A1 |
| 54 | 2018 | Quantitative Peptidomics with Isotopic and Isobaric Tags | Boonen, Kurt; De Haes, Wouter; VAN HOUTVEN, Joris; VERDONCK, Rik; Baggerman, Geert; VALKENBORG, Dirk; Schoofs, Liliane | Book Section | B2 |
| 55 | 2017 | Messar: Automated Recommendation Of Metabolite Substructures From Tandem Mass Spectra | Mrzic, Aida; Meysman, Pieter; De Vijlder, Thomas; Romijn, Edwin P; VALKENBORG, Dirk; Bittremieux, Wout; Laukens, Kris | Dataset | DS |
| 56 | 2017 | A Biocompatible Synthetic Lung Fluid Based on Human Respiratory Tract Lining Fluid Composition | Kumar, Abhinav; Terakosolphan, Wachirun; Hassoun, Mireille; Vandera, Kalliopi-Kelli; Novicky, Astrid; Harvey, Richard; Royall, Paul G.; Bicer, Elif Melis; Eriksson, Jonny; Edwards, Katarina; VALKENBORG, Dirk; Nelissen, Inge; Hassall, Dave; Mudway, Ian S.; Forbes, Ben | Journal Contribution | A1 |
| 57 | 2017 | Estimation of Rates of Reactions Triggered by Electron Transfer in Top-Down Mass Spectrometry | Ciach, Michal Aleksander; Lacki, Mateusz Krzysztof; Miasojedow, Blazej; Lermyte, Frederik; VALKENBORG, Dirk; Sobott, Frank; Gambin, Anna | Proceedings Paper | C1 |
| 58 | 2017 | IsoSpec: Hyperfast Fine Structure Calculator | Lacki, Mateusz K.; Startek, Michal; VALKENBORG, Dirk; Gambin, Anna | Journal Contribution | A1 |
| 59 | 2017 | Conformational Space and Stability of ETD Charge Reduction Products of Ubiquitin | Lermyte, Frederik; Łącki, Mateusz Krzysztof; VALKENBORG, Dirk; Gambin, Anna; Sobott, Frank | Journal Contribution | A1 |
| 60 | 2017 | Computational quality control tools for mass spectrometry proteomics | Bittremieux, Wout; VALKENBORG, Dirk; Martens, Lennart; Laukens, Kris | Journal Contribution | A1 |
| 61 | 2017 | InSourcerer: a high-throughput method to search for unknown metabolite modifications by mass spectrometry | Mrzic, Aida; Lermyte, Frederik; Vu, Trung Nghia; VALKENBORG, Dirk; Laukens, Kris | Journal Contribution | A1 |
| 62 | 2017 | Thermodynamic framework to assess low abundance DNA mutation detection by hybridization | Willems, Hanny; Jacobs, An; Hadiwikarta, Wahyu Wijaya; Venken, Tom; VALKENBORG, Dirk; Van Roy, Nadine; Vandesompele, Jo; HOOYBERGHS, Jef | Journal Contribution | A1 |
| 63 | 2017 | The Analysis of Peptide-Centric Mass-Spectrometry Data Utilizing Information About the Expected Isotope Distribution | BURZYKOWSKI, Tomasz; CLAESEN, Jurgen; VALKENBORG, Dirk | Book Section | B2 |
| 64 | 2016 | Unsupervised Quality Assessment of Mass Spectrometry Proteomics Experiments by Multivariate Quality Control Metrics | Bittremieux, Wout; Meysman, Pieter; Martens, Lennart; VALKENBORG, Dirk; Laukens, Kris | Journal Contribution | A1 |
| 65 | 2016 | The use of elemental mass spectrometry in phosphoproteomic applications | Maes, Evelyne; Tirez, Kristof; Baggerman, Geert; VALKENBORG, Dirk; Schoofs, Liliane; Ruiz Encinar, Jorge; Mertens, Inge | Journal Contribution | A1 |
| 66 | 2016 | CONSTANd : a normalization method for isobaric labeled spectra by constrained optimization | Maes, Evelyne; Hadiwikarta, Wahyu Wijaya; Mertens, Inge; Baggerman, Geert; HOOYBERGHS, Jef; VALKENBORG, Dirk | Journal Contribution | A1 |
| 67 | 2016 | Designing biomedical proteomics experiments: state-of-the-art and future perspectives | Maes, Evelyne; Kelchtermans, Pieter; Bittremieux, Wout; De Grave, Kurt; Degroeve, Sven; HOOYBERGHS, Jef; Mertens, Inge; Baggerman, Geert; Ramon, Jan; Laukens, Kris; Martens, Lennart; VALKENBORG, Dirk | Journal Contribution | A1 |
| 68 | 2015 | Understanding reaction pathways in top-down ETD by dissecting isotope distributions: A mammoth task | Lermyte, Frederik; Lacki, Mateusz Krzysztof; VALKENBORG, Dirk; Baggerman, Geert; Gambin, Anna; Sobott, Frank | Journal Contribution | A1 |
| 69 | 2015 | A comparative study between spiral-filter press and belt press implemented in a cloudy apple juice production process | De Paepe, Domien; Coudijzer, Katleen; Noten, Bart; VALKENBORG, Dirk; Servaes, Kelly; De Loose, Marc; Diels, Ludo; Voorspoels, Stefan; Van Droogenbroeck, Bart | Journal Contribution | A1 |
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