Research Explorer

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Researcher

Michiel Stock

Awards & Distinctions

70 Results

2024

Beyond correlations : a causal perspective on host-microbiome interactions

Steff TaelmanWim Van CriekingeMichiel StockLiesbeth Ceelen

DepoScope : accurate phage depolymerase annotation and domain delineation using large language models

Robby Concha-ElokoMichiel StockBernard De BaetsYves BriersRafael SanjuánPilar Domingo-CalapDimitri Boeckaerts

A1 Journal Article in PLOS COMPUTATIONAL BIOLOGY

Editorial : plant sensing and computing - PlantComp 2022

Michiel StockTom De SwaefFrancis wyffels

Editorial material

Engineering is evolution : a perspective on design processes to engineer biology

Simeon D. CastleMichiel StockThomas E. Gorochowski

A1 Journal Article in NATURE COMMUNICATIONS

Impedimetric biofilm characterization with microelectrode arrays using equivalent electrical circuit features and ensemble classifiers

Maxime Van HaeverbekeCharlotte CumsThijs VackierDries BraekenMichiel StockHans SteenackersBernard De Baets

A1 Journal Article in CHEMOMETRICS AND INTELLIGENT LABORATORY SYSTEMS

Machine-learning-based prediction of disability progression in multiple sclerosis : an observational, international, multi-center study

Edward De BrouwerThijs BeckerLorin Werthen-BrabantsPieter DewulfDimitrios IliadisCathérine DekeyserGuy LaureysBart Van WijmeerschVeronica PopescuTom Dhaene et al.

A2 Journal Article in PLOS DIGITAL HEALTH

Open-endedness in synthetic biology : a route to continual innovation for biological design

Michiel StockThomas E. Gorochowski

A1 Journal Article in SCIENCE ADVANCES

Plant science in the age of simulation intelligence

Michiel StockOlivier PietersTom De SwaefFrancis wyffels

A1 Journal Article in FRONTIERS IN PLANT SCIENCE

Prediction of Klebsiella phage-host specificity at the strain level

Dimitri BoeckaertsMichiel StockCelia Ferriol-GonzálezJesús Oteo-IglesiasRafael SanjuánPilar Domingo-CalapBernard De BaetsYves Briers

A1 Journal Article in NATURE COMMUNICATIONS

The role of Helicobacter suis, Fusobacterium gastrosuis, and the pars oesophageal microbiota in gastric ulceration in slaughter pigs receiving meal or pelleted feed

Emily TaillieuSteff TaelmanSofie De BruyckereEvy GoossensIlias ChantziarasChristophe Van SteenkistePeter YdeSteven HanssensDimitri De MeyerWim Van Criekinge et al.

A1 Journal Article in VETERINARY RESEARCH

2023

Advances in impedimetric modelling of electrochemical systems in engineering and the life sciences

Maxime Van HaeverbekeBernard De BaetsMichiel Stock

Biology-based machine learning to predict phage-host specificity for the clinical phage therapist

Dimitri BoeckaertsCélia PasAgnieszka ŁątkaMichiel StockCelia Ferriol-GonzálezRafael SanjuanPilar Domingo-CalapLars FieselerBernard De BaetsYves Briers

Evaluating the potential of Distribution of Relaxation Times analysis for plant agriculture

Maxime Van HaeverbekeBernard De BaetsMichiel Stock

A1 Journal Article in COMPUTERS AND ELECTRONICS IN AGRICULTURE

Exploiting data compositionality using tensor products and hyperdimensional computing

Pieter DewulfBernard De BaetsMichiel Stock

Plant impedance spectroscopy : a review of modeling approaches and applications

Maxime Van HaeverbekeBernard De BaetsMichiel Stock

A1 Journal Article in FRONTIERS IN PLANT SCIENCE

Predicting and understanding phage-host interactions with machine learning tools based on phage receptor-binding proteins

Dimitri BoeckaertsYves BriersBernard De BaetsMichiel Stock

2022

BioCCP.jl : collecting coupons in combinatorial biotechnology

Kirsten Van HuffelMichiel StockBernard De Baets

A1 Journal Article in BIOINFORMATICS

Covering the combinatorial design space of multiplex CRISPR/Cas experiments in plants

Kirsten Van HuffelMichiel StockTom RuttinkBernard De Baets

A1 Journal Article in FRONTIERS IN PLANT SCIENCE

Digital phagograms : predicting phage infectivity through a multilayer machine learning approach

Cédric LoodDimitri BoeckaertsMichiel StockBernard De BaetsRob LavigneVera van NoortYves Briers

A1 Journal Article in CURRENT OPINION IN VIROLOGY

Equivalent electrical circuits and their use across electrochemical impedance spectroscopy application domains

Maxime Van HaeverbekeMichiel StockBernard De Baets

A1 Journal Article in IEEE ACCESS

Identification of phage receptor-binding protein sequences with hidden Markov models and an extreme gradient boosting classifier

Dimitri BoeckaertsMichiel StockBernard De BaetsYves Briers

A1 Journal Article in VIRUSES-BASEL

Leveraging plant physiological dynamics using physical reservoir computing

Olivier PietersTom De SwaefMichiel StockFrancis wyffels

A1 Journal Article in SCIENTIFIC REPORTS

Machine learning techniques to characterize functional traits of plankton from image data

Eric C. OrensteinSakina‐Dorothée AyataFrédéric MapsÉrica C. BeckerFabio BenedettiTristan BiardThibault de Garidel‐ThoronJeffrey S. EllenFilippo FerrarioSarah L. C. Giering et al.

A1 Journal Article in LIMNOLOGY AND OCEANOGRAPHY

Machine learning to assist in large-scale, activity-based synthetic cannabinoid receptor agonist screening of serum samples

Liesl JanssensDimitri BoeckaertsSimon HudsonDaria MorozovaAnnelies CannaertDavid M. WoodCaitlin WolfeBernard De BaetsMichiel StockPaul, I Dargan et al.

A1 Journal Article in CLINICAL CHEMISTRY

Machine-learning-based prediction of disability progression in multiple sclerosis : an observational, international, multi-center study

Edward De BrouwerThijs BeckerLorin Werthen-BrabantsPieter DewulfDimitrios IliadisCathérine DekeyserGuy LaureysBart Van WijmeerschVeronica PopescuTom Dhaene et al.

On the pivotal role of water potential to model plant physiological processes

Tom De SwaefOlivier PietersSimon AppeltansIrene Borra-SerranoWillem CoudronValentin CouvreurSarah GarréPeter LootensBart NicolaïLeroi Pols et al.

A2 Journal Article in IN SILICO PLANTS

Optimising predictive models to prioritise viral discovery in zoonotic reservoirs

Daniel J BeckerGregory F AlberyAnna R SjodinTimothee PoisotLaura M BergnerBinqi ChenLily E CohenTad A DallasEvan A EskewAnna C Fagre et al.

A1 Journal Article in LANCET MICROBE

ProD : a tool for predictive design of tailored promoters in Escherichia coli

Friederike MeyJim ClauwaertMaarten Van BremptMichiel StockJo MaertensWillem WaegemanMarjan De Mey

Bookchapter in Prokaryotic gene regulation : methods and protocols

Rapid and high-throughput evaluation of diverse configura-tions of engineered lysins using the VersaTile technique

Lisa DuyvejonckHans GerstmansMichiel StockDennis GrimonRob LavigneYves Briers

Reservoir computing with plants

Olivier PietersFrancis wyffelsTom De SwaefMichiel Stock

Two novel approaches to identify phage receptor-binding protein sequences

Dimitri BoeckaertsMichiel StockBernard De BaetsYves Briers

2021

Cold-start problems in data-driven prediction of drug-drug interaction effects

Pieter DewulfMichiel StockBernard De Baets

A1 Journal Article in PHARMACEUTICALS

Crowdsourced mapping of unexplored target space of kinase inhibitors

Anna CichonskaBalaguru RavikumarRobert J. AllawayFangping WanSungjoon ParkOlexandr IsayevShuya LiMichael MasonAndrew LambZiaurrehman Tanoli et al.

A1 Journal Article in NATURE COMMUNICATIONS

Disentangling the information in species interaction networks

Michiel StockLaura HoebekeBernard De Baets

A1 Journal Article in ENTROPY

Optimal transportation theory for species interaction networks

Michiel StockTimothee PoisotBernard, de Baets

A1 Journal Article in ECOLOGY AND EVOLUTION

Otolith identification using a deep hierarchical classification model

Michiel StockBac Nguyen CongWouter CourtensHilbran VerstraeteEric StienenBernard De Baets

A1 Journal Article in COMPUTERS AND ELECTRONICS IN AGRICULTURE

Pairwise learning for predicting pollination interactions based on traits and phylogeny

Michiel StockNiels PiotSarah VanbesienJoris MeysGuy SmaggheBernard De Baets

A1 Journal Article in ECOLOGICAL MODELLING

PhaLP : a database for the study of phage lytic proteins and their evolution

Bjorn CrielSteff TaelmanWim Van CriekingeMichiel StockYves Briers

A1 Journal Article in VIRUSES-BASEL

Practical equivalent electrical circuit identification for electrochemical impedance spectroscopy analysis with gene expression programming

Maxime Van HaeverbekeMichiel StockBernard De Baets

A1 Journal Article in IEEE TRANSACTIONS ON INSTRUMENTATION AND MEASUREMENT

Predicting bacteriophage hosts based on sequences of annotated receptor-binding proteins

Dimitri BoeckaertsMichiel StockBjorn CrielHans GerstmansBernard De BaetsYves Briers

A1 Journal Article in SCIENTIFIC REPORTS

Rapid and high-throughput evaluation of diverse configurations of engineered lysins using the VersaTile technique

Lisa DuyvejonckHans GerstmansMichiel StockDennis GrimonRob LavigneYves Briers

A1 Journal Article in ANTIBIOTICS-BASEL

2020

A general-purpose toolbox for efficient Kronecker-based learning

Michiel StockTapio PahikkalaAntti AirolaBernard De Baets

Algebraic shortcuts for leave-one-out cross-validation in supervised network inference

Michiel StockTapio PahikkalaAntti AirolaWillem WaegemanBernard De Baets

A1 Journal Article in BRIEFINGS IN BIOINFORMATICS

Gloxinia—an open-source sensing platform to monitor the dynamic responses of plants

Olivier PietersTom De SwaefPeter LootensMichiel StockIsabel Roldán-RuizFrancis wyffels

A1 Journal Article in SENSORS

Information content in pollination network reveals missing interactions

Michiel StockNiels PiotSarah VanbesienBernard VaissièreClémentine Coiffait-GombaultGuy SmaggheBernard De Baets

A1 Journal Article in ECOLOGICAL MODELLING

Limitations of snapshot hyperspectral cameras to monitor plant response dynamics in stress-free conditions

Olivier PietersTom De SwaefPeter LootensMichiel StockIsabel Roldán-RuizFrancis wyffels

A1 Journal Article in COMPUTERS AND ELECTRONICS IN AGRICULTURE

Predicting pharmaceutical particle size distributions using kernel mean embedding

Daan Van HauwermeirenMichiel StockThomas De BeerIngmar Nopens

A1 Journal Article in PHARMACEUTICS

Predictive design of sigma factor-specific promoters

Maarten Van BremptJim ClauwaertFriederike MeyMichiel StockJo MaertensWillem WaegemanMarjan De Mey

A1 Journal Article in NATURE COMMUNICATIONS

2019

EcologicalNetworks.jl : analysing ecological networks of species interactions

Timothee PoisotZachary BelisleLaura HoebekeMichiel StockPiotr Szefer

A1 Journal Article in ECOGRAPHY

Guiding mineralization co-culture discovery using Bayesian optimization

Aisling DalyMichiel StockJan BaetensBernard De Baets

A1 Journal Article in ENVIRONMENTAL SCIENCE & TECHNOLOGY

Kernel mean embedding of distributions : a new data-driven model approach for modelling a continuous pharmaceutical twin-screw granulation process

Daan Van HauwermeirenMichiel StockThomas De BeerIngmar Nopens

X-ray microtomography and linear discriminant analysis enable detection of embolism-related acoustic emissions

Niels De BaerdemaekerMichiel StockJan Van den BulckeBernard De BaetsLuc Van HoorebekeKathy Steppe

A1 Journal Article in PLANT METHODS

2018

A comparative study of pairwise learning methods based on kernel ridge regression

Michiel StockTapio PahikkalaAntti AirolaBernard De BaetsWillem Waegeman

A1 Journal Article in NEURAL COMPUTATION

Liquid-to-solid ratio control as an advanced process control solution for continuous twin-screw wet granulation

Niels NicolaïFien De LeersnyderDana CopotMichiel StockClara-Mihaela IonescuKrist V GernaeyIngmar NopensThomas De Beer

A1 Journal Article in AICHE JOURNAL

2017

Exact and efficient algorithms for pairwise learning

Michiel StockBernard De BaetsWillem Waegeman

Linear filtering reveals false negatives in species interaction data

Michiel StockTimothée PoisotWillem WaegemanBernard De Baets

A1 Journal Article in SCIENTIFIC REPORTS

The use of shallow convolutional neural networks in predicting promotor strength in Eschericha coli

Jim ClauwaertMichiel StockMarjan De MeyWillem Waegeman

miSTAR : miRNA target prediction through modeling quantitative and qualitative miRNA binding site information in a stacked model structure

Gert Van PeerAyla De PaepeMichiel StockJasper AnckaertPieter-Jan VoldersJo VandesompeleBernard De BaetsWillem Waegeman

A1 Journal Article in NUCLEIC ACIDS RESEARCH

2016

Data-driven recipe completion using machine learning methods

Marlies De ClercqMichiel StockBernard De BaetsWillem Waegeman

A1 Journal Article in TRENDS IN FOOD SCIENCE & TECHNOLOGY

Exact and efficient top-K inference for multi-target prediction by querying separable linear relational models

Michiel StockKrzysztof DembczynskiBernard De BaetsWillem Waegeman

A1 Journal Article in DATA MINING AND KNOWLEDGE DISCOVERY

2015

A decoy-free approach to the identification of peptides

Giulia GonnelliMichiel StockJan VerwaerenDavy MaddeleinBernard De BaetsLennart MartensSven Degroeve

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

Recipe completion using machine learning techniques

Marlies De ClercqMichiel StockBernard De BaetsWillem Waegeman

2014

A community effort to assess and improve drug sensitivity prediction algorithms

James C CostelloLaura M HeiserElisabeth GeorgiiMehmet GönenMichael P MendenNicholas J WangMukesh BansalMuhammad Ammad-ud-dinPetteri HintsanenSuleiman A Khan et al.

A1 Journal Article in NATURE BIOTECHNOLOGY

A two-step learning approach for solving full and almost full cold start problems in dyadic prediction

Tapio PahikkalaMichiel StockAntti AirolaTero AittokallioBernard De BaetsWillem Waegeman

Identification of functionally related enzymes by learning-to-rank methods

Michiel StockThomas FoberEyke HüllermeierSerghei GlincaGerhard KlebeTapio PahikkalaAntti AirolaBernard De BaetsWillem Waegeman

A1 Journal Article in IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS

2013

Efficient regularized least-squares algorithms for conditional ranking on relational data

Tapio PahikkalaAntti AirolaMichiel StockBernard De BaetsWillem Waegeman

A1 Journal Article in MACHINE LEARNING

Exploration and prediction of interactions between methanotrophs and heterotrophs

Michiel StockSven HoefmanFrederiek-Maarten KerckhofNico BoonPaul De VosBernard De BaetsKim HeylenWillem Waegeman

A1 Journal Article in RESEARCH IN MICROBIOLOGY

2012

A kernel-based framework for learning graded relations from data

Willem WaegemanTapio PahikkalaAntti AirolaTapio SalakoskiMichiel StockBernard De Baets

A1 Journal Article in IEEE TRANSACTIONS ON FUZZY SYSTEMS

Conditional ranking algorithms for efﬁcient object retrieval and object querying on relational data

Willem WaegemanMichiel StockBernard De BaetsTapio PahikkalaAntti AirolaTapio Salakoski

Learning monadic and dyadic relations : three case studies in systems biology

Michiel StockTapio PahikkalaAntti AirolaTapio SalakoskiBernard De BaetsWillem Waegeman