Publications by authors named "Aalt D J van Dijk"

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BADDADAN: Mechanistic modelling of time-series gene module expression.
Ben Noordijk, Marcel Reinders, Aalt D J van Dijk, Dick de Ridder

Quant Plant Biol· September 2025

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Root microbiota regulates tiller number in rice.
Jingying Zhang, Bing Wang, Haoran Xu, Weidong Liu, Jingwei Yu, Aalt Dirk Jan van Dijk

Cell· June 2025

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Chinese chestnut did not induce negative plant soil feedback during centuries of growth.
Xu Cheng, Zhichun Yan, Qian Li, Lucas Schmitz, Jundi Yan, Aalt D J van Dijk

Sci Total Environ· March 2025

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Penalized factorial regression as a flexible and computationally attractive reaction norm model for prediction in the presence of GxE.
Vahe Avagyan, Martin P Boer, Junita Solin, Aalt D J van Dijk, Daniela Bustos-Korts

Theor Appl Genet· March 2025

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Comparative Assessment of Protein Large Language Models for Enzyme Commission Number Prediction.
João Capela, Maria Zimmermann-Kogadeeva, Aalt D J van Dijk, Dick de Ridder, Oscar Dias

BMC Bioinformatics· February 2025

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Enzyme structure correlates with variant effect predictability.
Floris van der Flier, Dave Estell, Sina Pricelius, Lydia Dankmeyer, Sander van Stigt Thans, Aalt D J van Dijk

Comput Struct Biotechnol J· December 2024

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Evolutionary origin and functional investigation of the widely conserved plant PEBP gene STEPMOTHER OF FT AND TFL1 (SMFT).
Francesca Bellinazzo, Judit Nadal Bigas, Rensco A H Hogers, Jan Kodde, Froukje van der Wal, Aalt D J van Dijk

Plant J· November 2024

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Uncoupling FRUITFULL's functions through modification of a protein motif identified by co-ortholog analysis.
Kai Thoris, Miguel Correa Marrero, Martijn Fiers, Xuelei Lai, Iris E Zahn, Aalt D J van Dijk

Nucleic Acids Res· November 2024

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Contribution of homoeologous exchange to domestication of polyploid Brassica.
Tianpeng Wang, Aalt D J van Dijk, Ranze Zhao, Guusje Bonnema, Xiaowu Wang

Genome Biol· August 2024

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The rise of scientific machine learning: a perspective on combining mechanistic modelling with machine learning for systems biology.
Ben Noordijk, Monica L Garcia Gomez, Kirsten H W J Ten Tusscher, Dick de Ridder, Aalt D J van Dijk

Front Syst Biol· August 2024

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A catalogue of recombination coldspots in interspecific tomato hybrids.
Roven Rommel Fuentes, Ronald Nieuwenhuis, Jihed Chouaref, Thamara Hesselink, Willem van Dooijeweert, Aalt D J van Dijk

PLoS Genet· July 2024

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Root branching under high salinity requires auxin-independent modulation of LATERAL ORGAN BOUNDARY DOMAIN 16 function.
Yanxia Zhang, Yiyun Li, Thijs de Zeeuw, Kilian Duijts, Dorota Kawa, Aalt D J van Dijk

Plant Cell· March 2024

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Protein interaction mapping reveals widespread targeting of development-related host transcription factors by phytoplasma effectors.
Miguel Correa Marrero, Sylvain Capdevielle, Weijie Huang, Ali M Al-Subhi, Marco Busscher, Aalt D J van Dijk

Plant J· February 2024

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A gene regulatory network critical for axillary bud dormancy directly controlled by Arabidopsis BRANCHED1.
Sam W van Es, Aitor Muñoz-Gasca, Francisco J Romero-Campero, Eduardo González-Grandío, Pedro de Los Reyes, Aalt D J van Dijk

New Phytol· February 2024

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Interploidy Introgression Shaped Adaptation during the Origin and Domestication History of Brassica napus.
Tianpeng Wang, Aalt D J van Dijk, Johan Bucher, Jianli Liang, Jian Wu

Mol Biol Evol· September 2023

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Genomic prediction in plants: opportunities for ensemble machine learning based approaches.
Muhammad Farooq, Aalt D J van Dijk, Harm Nijveen, Shahid Mansoor, Dick de Ridder

F1000Res· April 2023

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Individual lipid transfer proteins from Tanacetum parthenium show different specificity for extracellular accumulation of sesquiterpenes.
Arman Beyraghdar Kashkooli, Aalt D J van Dijk, Harro Bouwmeester, Alexander van der Krol

Plant Mol Biol· January 2023

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Beyond sequence: Structure-based machine learning.
Janani Durairaj, Dick de Ridder, Aalt D J van Dijk

Comput Struct Biotechnol J· December 2022

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Detoxification of monoterpenes by a family of plant glycosyltransferases.
Rumyana Karlova, Jeroen Busscher, Florence M Schempp, Markus Buchhaupt, Aalt D J van Dijk

Phytochemistry· November 2022

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The tomato cytochrome P450 CYP712G1 catalyses the double oxidation of orobanchol en route to the rhizosphere signalling strigolactone, solanacol.
Yanting Wang, Janani Durairaj, Hernando G Suárez Duran, Robin van Velzen, Kristyna Flokova, Aalt D J van Dijk

New Phytol· September 2022

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Editorial: Artificial Intelligence and Machine Learning Applications in Plant Genomics and Genetics.
Aalt D J van Dijk, Shin-Han Shiu, Dick de Ridder

Front Artif Intell· June 2022

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Domestication Shapes Recombination Patterns in Tomato.
Roven Rommel Fuentes, Dick de Ridder, Aalt D J van Dijk, Sander A Peters

Mol Biol Evol· January 2022

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Integrating structure-based machine learning and co-evolution to investigate specificity in plant sesquiterpene synthases.
Janani Durairaj, Elena Melillo, Harro J Bouwmeester, Jules Beekwilder, Dick de Ridder, Aalt D J van Dijk

PLoS Comput Biol· March 2021

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Prior Biological Knowledge Improves Genomic Prediction of Growth-Related Traits in .
Muhammad Farooq, Aalt D J van Dijk, Harm Nijveen, Mark G M Aarts, Willem Kruijer

Front Genet· January 2021

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Chasing breeding footprints through structural variations in Cucumis melo and wild relatives.
Sevgin Demirci, Roven Rommel Fuentes, Willem van Dooijeweert, Saulo Aflitos, Elio Schijlen, Aalt D J van Dijk

G3 (Bethesda)· January 2021

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