 (52) Hyperdimensional computing: a fast, robust and interpretable paradigm for biological dataM. Stock, D. Boeckaerts, P. Dewulf, S. Taelman, M. Van Haeverbeke, W. Van Criekinge and B. De Baets(2024) PLOS COMPUTATIONAL BIOLOGY. 20, e1012426 . |
| (51) DepoScope: accurate phage depolymerase annotation
and domain delineation using large language modelsR. Concha-Eloko, M. Stock, B. De Baets, Y. Briers, R. Sanjuan,
P. Domingo-Calap and D. Boeckaerts(2024) PLOS COMPUTATIONAL BIOLOGY. 20, e1011831. |
| (50) Link prediction in stagewise graphsP. Dewulf, M. Stock and B. De Baets(2024) IEEE TRANSACTIONS ON DATA AND KNOWLEDGE ENGINEERING. 36, 3252-3264. |
| (49) Prediction of Klebsiella phage-host specificity at the strain levelD. Boeckaerts, M. Stock, C. Ferriol-González, J. Oteo-Iglesias, R. Sanjuán, P. Domingo-Calap, B. De Baets and Y. Briers(2024) NATURE COMMUNICATIONS. 15, 4355. |
| (48) Engineering is evolution : a perspective on design processes to engineer biologyS. D. Castle, M. Stock and T. E. Gorochowski(2024) NATURE COMMUNICATIONS. 15, 3640. |
| (47) Plant science in the age of simulation intelligenceM. Stock, O. Pieters, T. De Swaef and F. wyffels(2024) FRONTIERS IN PLANT SCIENCE. 14, 1299208. |
| (46) The role of Helicobacter suis, Fusobacterium gastrosuis, and the pars oesophageal microbiota in gastric ulceration in slaughter pigs receiving meal or pelleted feedE. Taillieu, S. Taelman, S. De Bruyckere, E. Goossens, I. Chantziaras, C. Van Steenkiste, P. Yde, S. Hanssens, D. De Meyer, W. Van Criekinge, M. Stock, D. Maes, K. Chiers and F. Haesebrouck (2024) VETERINARY RESEARCH. 55, 15. |
| (45) Open-endedness in synthetic biology: A route to continual innovation for biological designM. Stock and T. E. Gorochowski(2024) SCIENCE ADVANCES. 10, eadi3621. |
| (44) Impedimetric biofilm characterisation with microelectrode arrays using equivalent electrical circuit features and ensemble classifiersM. Van Haeverbeke, C. Cums, T. Vackier, D. Braeken, M. Stock, H. Steenackers and B. De Baets(2024) CHEMOMETRICS AND INTELLIGENT LABORATORY SYSTEMS. 244, 105048. |
| (43) Evaluating the potential of Distribution of Relaxation Times analysis for plant agricultureM. Van Haeverbeke, B. De Baets and M. Stock(2023) COMPUTERS AND ELECTRONICS IN AGRICULTURE. 213, 108249. |
| (42) Plant impedance spectroscopy: a review of modeling approaches and applicationsM. Van Haeverbeke, B. De Baets and M. Stock(2023) FRONTIERS IN PLANT SCIENCE. 14, 1187573. |
| (41) Optimising predictive models to prioritise viral discovery in zoonotic reservoirsD.J. Becker, G.F. Albery, A.R. Sjodin, T. Poisot, L.M. Bergner, B. Chen, L.E. Cohen, T.A. Dallas, E.A. Eskew, A.C. Fagre, M.J. Farrell, S. Guth, B.A. Han, N.B. Simmons, M. Stock, E.C. Teeling and C.J. Carlson(2022) THE LANCET MICROBE. 3, e625-e637. |
| (40) Leveraging plant physiological dynamics using physical reservoir computingO. Pieters, T. De Swaef, M. Stock and F. wyffels(2022) SCIENTIFIC REPORTS. 12, 12594. |
| (39) Machine learning techniques to characterize functional traits of plankton from image dataE. Orenstein, S.-D. Ayata, F. Maps, T. Biard, E. Becker, F. Benedetti, T. de Garidel-Thoron, J.S. Ellen, F. Ferrario, S.L.C. Giering, T. Guy-Haim, L. Hoebeke, M. Iversen, T. Kiørboe, J.-F. Lalonde, A. Lana, M. Laviale, F. Lombard, T. Lorimer, S. Martini, A. Meyer, K.O. Möller, B. Niehoff, M. Ohman, C. Pradalier, J.-B. Romagnan, S.-M. Schröder, V. Sonnet, H.M. Sosik, L. Stemmann, M. Stock, T. Terbiyik-Kurt, N. Valcàrcel-Pérez, L. Vilgrain, G. Wacquet, A. Waite and J.-O. Irisson(2022) LIMNOLOGY AND OCEANOGRAPHY. 67, 1647-1669. |
| (38) Machine learning to assist in large-scale, activity-based synthetic cannabinoid receptor agonist screening of serum samplesL. Janssens, D. Boeckaerts, S. Hudson, D. Morozova, A. Cannaert, D.M. Wood, C. Wolfe, B. De Baets, M. Stock, P.I. Dargan and C.P. Stove(2022) CLINICAL CHEMISTRY. 68, 906-916. |
| (37) Covering the combinatorial design space of multiplex CRISPR/Cas experiments in plantsK. Van Huffel, M. Stock, T. Ruttink and B. De Baets(2022) FRONTIERS IN PLANT SCIENCE. 13, 907095. |
| (36) Identification of phage receptor-binding protein sequences with hidden Markov models
and an extreme gradient boosting classifier
D. Boeckaerts, M. Stock, B. De Baets and Y. Briers(2022) VIRUSES. 14, 1329. |
| (35) Equivalent electrical circuits and their use across electrochemical impedance spectroscopy application domains
M. Van Haeverbeke, M. Stock and B. De Baets(2022) IEEE ACCESS. 10, 51363-51379. |
| (34) Hydraulics and beyond: a review on water potential as pivotal driver of physiological processes in plant modelsT. De Swaef, O. Pieters, S. Appeltans, I. Borra-Serrano, W. Coudron, V. Couvreur, S. Garré, P. Lootens, B. Nicolaï, L. Pols, C. Saint Cast, J. Šalagovič, M. Van Haeverbeke, M. Stock and F. wyffels(2022) IN SILICO PLANTS. 4, 1-28. |
| (33) BioCCP.jl: Collecting Coupons in combinatorial biotechnologyK. Van Huffel, M. Stock and B. De Baets(2022) BIOINFORMATICS. 38, 1144-1145. |
| (32) Digital phagograms: predicting phage infectivity through a multi-layer machine learning approachC. Lood, D. Boeckaerts, M. Stock, B. De Baets, R. Lavigne, V. Van Noort and Y. Briers(2022) CURRENT OPINION IN VIROLOGY. 52, 174-181. |
| (31) Practical equivalent electrical circuit identification for electrochemical impedance spectroscopy analysis with gene expression programmingM. Van Haeverbeke, M. Stock and B. De Baets(2021) IEEE TRANSACTIONS ON INSTRUMENTATION AND MEASUREMENT. 70, 2514612. |
| (30) Crowdsourced mapping of unexplored target space of kinase inhibitorsA. Cichonska, B. Ravikumar, R. J. Allaway, F. Wan, S. Park, O. Isayev, S. Li, M. Mason, A. Lamb, Z. Tanoli, M. Jeon, S. Kim, M. Popova, S. Capuzzi, J. Zeng, K. Dang, G. Koytiger, J. Kang, C. I. Wells, T. M. Willson, M. Tan, C.-H. Huang, E. S. C. Shih, T.-M. Chen, C.-H. Wu, W.-Q. Fang, J.-Y. Chen, M.-J. Hwang, X. Wang, M. B. Guebila, B. Shamsaei, S. Singh, T. Nguyen, M. Karimi, D. Wu, Z. Wang, Y. Shen, H. Öztürk, E. Ozkirimli, A. Özgür, H. Lim, L. Xie, G. K. Kanev, A. J. Kooistra, B. A. Westerman, P. Terzopoulos, K. Ntagiantas, C. Fotis, L. Alexopoulos, D. Boeckaerts, M. Stock, B. De Baets, Y. Briers, F. Wan, S. Li, Y. Luo, H. Hu, J. Peng, J. Zeng, T. Dogan, A. S. Rifaioglu, H. Atas, R. C. Atalay, V. Atalay, M. J. Martin, S. Park, M. Jeon, S. Kim, J. Lee, S. Yun, B. Kim, B. Chang, J. Kang, M. Popova, S. Capuzzi, O. Isayev, G. Turu, Á. Misák, B. Szalai, L. Hunyady, M. Lienhard, P. Prasse, I. Bachmann, J. Ganzlin, G. Barel, R. Herwig, D. Oršolić, B. Lučić, V. Stepanić, T. Šmuc, T. I. Oprea, A. Schlessinger, D. H. Drewry, G. Stolovitzky, K. Wennerberg, J. Guinney, T. Aittokallio(2021) NATURE COMMUNICATIONS. 12, 3307. |
| (29) PhaLP: A database for the study of phage lytic proteins and their evolutionB. Criel, S. Taelman, W. Van Criekinge, M. Stock and Y. Briers(2021) VIRUSES. 13, 1240. |
| (28) Disentangling the information in species interaction networksM. Stock, L. Hoebeke and B. De Baets(2021) ENTROPY. 23, 703. |
| (27) Optimal transportation theory for species interaction networksM. Stock, T. Poisot and B. De Baets(2021) ECOLOGY AND EVOLUTION. 11, 3841-3855. |
| (26) Cold-start problems in data-driven prediction of drug-drug interaction effectsP. Dewulf, M. Stock and B. De Baets(2021) PHARMACEUTICALS. 14, 429. |
| (25) Pairwise learning for predicting pollination interactions based on traits and phylogenyM. Stock, N. Piot, S. Vanbesien, J. Meys, G. Smagghe and B. De Baets(2021) ECOLOGICAL MODELLING. 451, 109508. |
| (24) Rapid and high-throughput evaluation of diverse configurations of engineered lysins using the VersaTile techniqueL. Duyvejonck, H. Gerstmans, M. Stock, D. Grimon, R. Lavigne and Y. Briers(2021) ANTIBIOTICS. 10, 293. |
| (23) Predicting bacteriophage hosts based on sequences of annotated receptor-binding proteinsD. Boeckaerts, M. Stock, B. Criel, H. Gerstmans, B. De Baets and Y. Briers(2021) SCIENTIFIC REPORTS. 11, 1467. |
| (22) Otolith identification using a deep hierarchical classification modelM. Stock, B. Nguyen, W. Courtens, H. Verstraete, E. Stienen and B. De Baets(2021) COMPUTERS AND ELECTRONICS IN AGRICULTURE. 180, 105883. |
| (21) Predictive design of sigma factor-specific promotersM. Van Brempt, J. Clauwaert, F. Mey, M. Stock, J. Maertens, W. Waegeman and M. De Mey(2020) NATURE COMMUNICATIONS. 11, 5822. |
| (20) Limitations of snapshot hyperspectral cameras to monitor plant response dynamics in stress-free conditionsO. Pieters, T. De Swaef, P. Lootens, M. Stock, I. Roldán-Ruiz and F. wyffels(2020) COMPUTERS AND ELECTRONICS IN AGRICULTURE. 179, 105825. |
| (19) Information content in pollination network reveals missing interactionsM. Stock, N. Piot, S. Vanbesien, B. Vaissière, C. Coiffait-Gombault, G. Smagghe and B. De Baets(2020) ECOLOGICAL MODELLING. 431, 109161. |
| (18) Gloxinia - An open-source sensing platform to monitor the dynamic responses of plantsO. Pieters, T. De Swaef, P. Lootens, M. Stock, I. Roldán-Ruiz and F. wyffels(2020) SENSORS. 20, 3055. |
| (17) Predicting pharmaceutical particle size distributions using kernel mean embeddingD. Van Hauwermeiren, M. Stock, T. De Beer and I. Nopens(2020) PHARMACEUTICS. 12, 271. |
| (16) Algebraic shortcuts for leave-one-out cross-validation in supervised network inferenceM. Stock, T. Pahikkala, A. Airola, W. Waegeman and B. De Baets(2020) BRIEFINGS IN BIOINFORMATICS. 21, 262-271. |
| (15) X-ray microtomography and linear discriminant analysis enable extraction of embolism-related acoustic emissionsN.J.F. De Baerdemaker, M. Stock, J. Van Den Bulcke, B. De Baets, L. Van Hoorebeke and K. Steppe(2019) PLANT METHODS. 15, 153. |
| (14) Guiding mineralization co-culture discovery using Bayesian optimizationA.J. Daly, M. Stock, J.M. Baetens and B. De Baets(2019) ENVIRONMENTAL SCIENCE AND TECHNOLOGY. 53, 14459-14469. |
| (13) EcologicalNetworks.jl: analysing ecological networks of species interactionsT. Poisot, Z. Bélisle, L. Hoebeke, M. Stock and P. Szefer(2019) ECOGRAPHY. 42, 1850-1861. |
| (12) Liquid-to-solid ratio control as an advanced process control solution for continuous twin-screw wet granulationN. Nicolaï, F. De Leersnyder, D. Copot, M. Stock, C.-M. Ionescu, K.V. Gernaey, I. Nopens and T. De Beer(2018) AICHE JOURNAL. 64, 2500-2514. |
| (11) A comparative study of pairwise learning methods based on Kernel Ridge RegressionM. Stock, T. Pahikkala, A. Airola, B. De Baets and W. Waegeman(2018) NEURAL COMPUTATION. 30, 2245-2283. |
| (10) miSTAR: miRNA target prediction through modeling quantitative and qualitative miRNA binding site information in a stacked model structureG. Van Peer, A. De Paepe, M. Stock, J. Anckaert, P-J. Volders, J. Vandesompele, B. De Baets and W. Waegeman(2017) NUCLEIC ACIDS RESEARCH. 45, e51. |
| (9) Linear filtering reveals false negatives in species interaction dataM. Stock, T. Poisot, W. Waegeman and B. De Baets(2017) SCIENTIFIC REPORTS. 7, 45908. |
| (8) Exact and efficient top-K inference for multi-target prediction by querying separable linear relational modelsM. Stock, K. Dembczyński, B. De Baets and W. Waegeman(2016) DATA MINING AND KNOWLEDGE DISCOVERY. 30, 1370-1394. |
| (7) Data-driven recipe completion using machine learning methodsM. De Clercq, M. Stock, B. De Baets and W. Waegeman(2016) TRENDS IN FOOD SCIENCE & TECHNOLOGY. 49, 1-13. |
| (6) A decoy-free approach to the identification of peptidesG. Gonnelli, M. Stock, J. Verwaeren, D. Maddelein, B. De Baets, L. Martens and S. Degroeve(2015) JOURNAL OF PROTEOME RESEARCH. 14, 1792-1798. |
| (5) A community effort to assess and improve drug sensitivity prediction algorithmsJ.C. Costello, L.M. Heiser, E. Georgii, M. Gönen, M.P. Menden, N.J. Wang, M. Bansal, M. Ammad-ud-din, P. Hintsanen, S.A. Khan, J.-P. Mpindi, O. Kallioniemi, A. Honkela, T. Aittokallio, K. Wennerberg, J.-P. Abbuehl, J. Allen, R.B. Altman, S. Balcome, A. Battle, A. Bender, B. Berger, J. Bernard, M. Bhattacharjee, K. Bhuvaneshwar, A.A. Bieberich, F. Boehm, A. Califano, C. Chan, B. Chen, T.-H. Chen, J. Choi, L.P. Coelho, T. Cokelaer, C.J. Creighton, J. Cui, W. Dampier, V.J. Davisson, B. De Baets, R. Deshpande, B. DiCamillo, M. Dundar, Z. Duren, A. Ertel, H. Fan, H. Fang, R. Gauba, A. Gottlieb, M. Grau, Y. Gusev, M.J. Ha, L. Han, M. Harris, N. Henderson, H.A. Hejase, K. Homicsko, J.P. Hou, W. Hwang, A.P. Ijzerman, B. Karacali, S. Keles, C. Kendziorski, J. Kim, M. Kim, Y. Kim, D.A. Knowles, D. Koller, J. Lee, J.K. Lee, E.B. Lenselink, B. Li, B. Li, J. Li, H. Liang, J. Ma, S. Madhavan, S. Mooney, C.L. Myers, M.A Newton, J.P. Overington, R. Pal, J. Peng, R. Pestell, R.J. Prill, P. Qiu, B. Rajwa, A. Sadanandam, F. Sambo, H. Shin, J. Song, L. Song, A. Sridhar, M. Stock, W. Sun, T. Ta, M. Tadesse, M. Tan, H. Tang, D. Theodorescu, G.M. Toffolo, A. Tozeren, W. Trepicchio, N. Varoquaux, J.-P. Vert, W. Waegeman, T. Walter, Q. Wan, D. Wang, W. Wang, Y. Wang, Z. Wang, J.K. Wegner, T. Wu, T. Xia, G. Xiao, Y. Xie, Y. Xu, J. Yang, Y. Yuan, S. Zhang, X.-S. Zhang, J. Zhao, C. Zuo, H.W.T. van Vlijmen, G.J.P. van Westen, J.J. Collins, D. Gallahan, D. Singer, J. Saez-Rodriguez, S. Kaski, J.W. Gray and G. Stolovitzky(2014) NATURE BIOTECHNOLOGY. 32, 1202-1212. |
| (4) Identification of functionally-related enzymes by learning-to-rank methods and cavity-based similarity measuresM. Stock, T. Fober, E. Hüllermeier, S. Glinca, G. Klebe, T. Pahikkala, A. Airola, B. De Baets and W. Waegeman(2014) IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS. 11, 1157-1169. |
| (3) Exploration and prediction of interactions between methanotrophs and heterotrophsM. Stock, S. Hoefman, F.-M. Kerckhof, N. Boon, P. De Vos, B. De Baets, K. Heylen and W. Waegeman(2013) RESEARCH IN MICROBIOLOGY. 10, 1045-1054. |
| (2) Efficient regularized least-squares algorithms for conditional ranking on relational dataT. Pahikkala, A. Airola, M. Stock, B. De Baets and W. Waegeman(2013) MACHINE LEARNING. 93, 321-356. |
| (1) A kernel-based framework for learning graded relations from dataW. Waegeman, T. Pahikkala, A. Airola, T. Salakoski, M. Stock and B. De Baets(2012) IEEE TRANSACTIONS ON FUZZY SYSTEMS. 20, 1090-1101. |