Journal Papers (ISI)

Biblio logo(48) Engineering is evolution : a perspective on design processes to engineer biology
S. D. Castle, M. Stock and T. E. Gorochowski
Biblio logo(47) Plant science in the age of simulation intelligence
M. Stock, O. Pieters, T. De Swaef and F. wyffels
(2024) FRONTIERS IN PLANT SCIENCE. 14, 1299208.
Biblio logo(46) The role of Helicobacter suis, Fusobacterium gastrosuis, and the pars oesophageal microbiota in gastric ulceration in slaughter pigs receiving meal or pelleted feed
E. 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
Biblio logo(45) Open-endedness in synthetic biology: A route to continual innovation for biological design
M. Stock and T. E. Gorochowski
(2024) SCIENCE ADVANCES. 10, eadi3621.
Biblio logo(44) Impedimetric biofilm characterisation with microelectrode arrays using equivalent electrical circuit features and ensemble classifiers
M. Van Haeverbeke, C. Cums, T. Vackier, D. Braeken, M. Stock, H. Steenackers and B. De Baets
Biblio logo(43) Evaluating the potential of Distribution of Relaxation Times analysis for plant agriculture
M. Van Haeverbeke, B. De Baets and M. Stock
Biblio logo(42) Plant impedance spectroscopy: a review of modeling approaches and applications
M. Van Haeverbeke, B. De Baets and M. Stock
(2023) FRONTIERS IN PLANT SCIENCE. 14, 1187573.
Biblio logo(41) Optimising predictive models to prioritise viral discovery in zoonotic reservoirs
D.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.
Biblio logo(40) Leveraging plant physiological dynamics using physical reservoir computing
O. Pieters, T. De Swaef, M. Stock and F. wyffels
(2022) SCIENTIFIC REPORTS. 12, 12594.
Biblio logo(39) Machine learning techniques to characterize functional traits of plankton from image data
E. 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.
Biblio logo(38) Machine learning to assist in large-scale, activity-based synthetic cannabinoid receptor agonist screening of serum samples
L. 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.
Biblio logo(37) Covering the combinatorial design space of multiplex CRISPR/Cas experiments in plants
K. Van Huffel, M. Stock, T. Ruttink and B. De Baets
(2022) FRONTIERS IN PLANT SCIENCE. 13, 907095.
Biblio logo(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.
Biblio logo(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.
Biblio logo(34) Hydraulics and beyond: a review on water potential as pivotal driver of physiological processes in plant models
T. 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.
Biblio logo(33) BioCCP.jl: Collecting Coupons in combinatorial biotechnology
K. Van Huffel, M. Stock and B. De Baets
(2022) BIOINFORMATICS. 38, 1144-1145.
Biblio logo(32) Digital phagograms: predicting phage infectivity through a multi-layer machine learning approach
C. Lood, D. Boeckaerts, M. Stock, B. De Baets, R. Lavigne, V. Van Noort and Y. Briers
(2022) CURRENT OPINION IN VIROLOGY. 52, 174-181.
Biblio logo(31) Practical equivalent electrical circuit identification for electrochemical impedance spectroscopy analysis with gene expression programming
M. Van Haeverbeke, M. Stock and B. De Baets
Biblio logo(30) Crowdsourced mapping of unexplored target space of kinase inhibitors
A. 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
Biblio logo(29) PhaLP: A database for the study of phage lytic proteins and their evolution
B. Criel, S. Taelman, W. Van Criekinge, M. Stock and Y. Briers
(2021) VIRUSES. 13, 1240.
Biblio logo(28) Disentangling the information in species interaction networks
M. Stock, L. Hoebeke and B. De Baets
(2021) ENTROPY. 23, 703.
Biblio logo(27) Optimal transportation theory for species interaction networks
M. Stock, T. Poisot and B. De Baets
(2021) ECOLOGY AND EVOLUTION. 11, 3841-3855.
Biblio logo(26) Cold-start problems in data-driven prediction of drug-drug interaction effects
P. Dewulf, M. Stock and B. De Baets
(2021) PHARMACEUTICALS. 14, 429.
Biblio logo(25) Pairwise learning for predicting pollination interactions based on traits and phylogeny
M. Stock, N. Piot, S. Vanbesien, J. Meys, G. Smagghe and B. De Baets
(2021) ECOLOGICAL MODELLING. 451, 109508.
Biblio logo(24) Rapid and high-throughput evaluation of diverse configurations of engineered lysins using the VersaTile technique
L. Duyvejonck, H. Gerstmans, M. Stock, D. Grimon, R. Lavigne and Y. Briers
(2021) ANTIBIOTICS. 10, 293.
Biblio logo(23) Predicting bacteriophage hosts based on sequences of annotated receptor-binding proteins
D. Boeckaerts, M. Stock, B. Criel, H. Gerstmans, B. De Baets and Y. Briers
(2021) SCIENTIFIC REPORTS. 11, 1467.
Biblio logo(22) Otolith identification using a deep hierarchical classification model
M. Stock, B. Nguyen, W. Courtens, H. Verstraete, E. Stienen and B. De Baets
Biblio logo(21) Predictive design of sigma factor-specific promoters
M. Van Brempt, J. Clauwaert, F. Mey, M. Stock, J. Maertens, W. Waegeman and M. De Mey
Biblio logo(20) Limitations of snapshot hyperspectral cameras to monitor plant response dynamics in stress-free conditions
O. Pieters, T. De Swaef, P. Lootens, M. Stock, I. Roldán-Ruiz and F. wyffels
Biblio logo(19) Information content in pollination network reveals missing interactions
M. Stock, N. Piot, S. Vanbesien, B. Vaissière, C. Coiffait-Gombault, G. Smagghe and B. De Baets
(2020) ECOLOGICAL MODELLING. 431, 109161.
Biblio logo(18) Gloxinia - An open-source sensing platform to monitor the dynamic responses of plants
O. Pieters, T. De Swaef, P. Lootens, M. Stock, I. Roldán-Ruiz and F. wyffels
(2020) SENSORS. 20, 3055.
Biblio logo(17) Predicting pharmaceutical particle size distributions using kernel mean embedding
D. Van Hauwermeiren, M. Stock, T. De Beer and I. Nopens
(2020) PHARMACEUTICS. 12, 271.
Biblio logo(16) Algebraic shortcuts for leave-one-out cross-validation in supervised network inference
M. Stock, T. Pahikkala, A. Airola, W. Waegeman and B. De Baets
Biblio logo(15) X-ray microtomography and linear discriminant analysis enable extraction of embolism-related acoustic emissions
N.J.F. De Baerdemaker, M. Stock, J. Van Den Bulcke, B. De Baets, L. Van Hoorebeke and K. Steppe
(2019) PLANT METHODS. 15, 153.
Biblio logo(14) Guiding mineralization co-culture discovery using Bayesian optimization
A.J. Daly, M. Stock, J.M. Baetens and B. De Baets
Biblio logo(13) EcologicalNetworks.jl: analysing ecological networks of species interactions
T. Poisot, Z. Bélisle, L. Hoebeke, M. Stock and P. Szefer
(2019) ECOGRAPHY. 42, 1850-1861.
Biblio logo(12) Liquid-to-solid ratio control as an advanced process control solution for continuous twin-screw wet granulation
N. 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.
Biblio logo(11) A comparative study of pairwise learning methods based on Kernel Ridge Regression
M. Stock, T. Pahikkala, A. Airola, B. De Baets and W. Waegeman
(2018) NEURAL COMPUTATION. 30, 2245-2283.
Biblio logo(10) miSTAR: miRNA target prediction through modeling quantitative and qualitative miRNA binding site information in a stacked model structure
G. Van Peer, A. De Paepe, M. Stock, J. Anckaert, P-J. Volders, J. Vandesompele, B. De Baets and W. Waegeman
Biblio logo(9) Linear filtering reveals false negatives in species interaction data
M. Stock, T. Poisot, W. Waegeman and B. De Baets
(2017) SCIENTIFIC REPORTS. 7, 45908.
Biblio logo(8) Exact and efficient top-K inference for multi-target prediction by querying separable linear relational models
M. Stock, K. Dembczyński, B. De Baets and W. Waegeman
Biblio logo(7) Data-driven recipe completion using machine learning methods
M. De Clercq, M. Stock, B. De Baets and W. Waegeman
Biblio logo(6) A decoy-free approach to the identification of peptides
G. Gonnelli, M. Stock, J. Verwaeren, D. Maddelein, B. De Baets, L. Martens and S. Degroeve
(2015) JOURNAL OF PROTEOME RESEARCH. 14, 1792-1798.
Biblio logo(5) A community effort to assess and improve drug sensitivity prediction algorithms
J.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.
Biblio logo(4) Identification of functionally-related enzymes by learning-to-rank methods and cavity-based similarity measures
M. Stock, T. Fober, E. Hüllermeier, S. Glinca, G. Klebe, T. Pahikkala, A. Airola, B. De Baets and W. Waegeman
Biblio logo(3) Exploration and prediction of interactions between methanotrophs and heterotrophs
M. 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.
Biblio logo(2) Efficient regularized least-squares algorithms for conditional ranking on relational data
T. Pahikkala, A. Airola, M. Stock, B. De Baets and W. Waegeman
(2013) MACHINE LEARNING. 93, 321-356.
Biblio logo(1) A kernel-based framework for learning graded relations from data
W. Waegeman, T. Pahikkala, A. Airola, T. Salakoski, M. Stock and B. De Baets