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Author Details

Aalt D J van Dijk
Wageningen University and Research
2001
96
32
PMIDPaper TitleJournal TitlePublished Year
38009929A gene regulatory network critical for axillary bud dormancy directly controlled by Arabidopsis BRANCHED1.New Phytol2024
37965720Protein interaction mapping reveals widespread targeting of development-related host transcription factors by phytoplasma effectors.Plant J2024
36255594Individual lipid transfer proteins from Tanacetum parthenium show different specificity for extracellular accumulation of sesquiterpenes.Plant Mol Biol2023
37707440Interploidy Introgression Shaped Adaptation during the Origin and Domestication History of Brassica napus.Mol Biol Evol2023
36603079Maize resistance to witchweed through changes in strigolactone biosynthesis.Science2023
34597400Domestication Shapes Recombination Patterns in Tomato.Mol Biol Evol2022
35612785The tomato cytochrome P450 CYP712G1 catalyses the double oxidation of orobanchol en route to the rhizosphere signalling strigolactone, solanacol.New Phytol2022
36659927Beyond sequence: Structure-based machine learning.Comput Struct Biotechnol J2022
36037906Detoxification of monoterpenes by a family of plant glycosyltransferases.Phytochemistry2022
33552126Prior Biological Knowledge Improves Genomic Prediction of Growth-Related Traits in <i>Arabidopsis thaliana</i>.Front Genet2021
33561242Chasing breeding footprints through structural variations in Cucumis melo and wild relatives.G3 (Bethesda)2021
33750949Integrating structure-based machine learning and co-evolution to investigate specificity in plant sesquiterpene synthases.PLoS Comput Biol2021
31431299Designing Eukaryotic Gene Expression Regulation Using Machine Learning.Trends Biotechnol2020
32090266Novel routes towards bioplastics from plants: elucidation of the methylperillate biosynthesis pathway from Salvia dorisiana trichomes.J Exp Bot2020
31820490Meiotic recombination profiling of interspecific hybrid F1 tomato pollen by linked read sequencing.Plant J2020
33364579Machine learning in plant science and plant breeding.iScience2020
33121934The santalene synthase from Cinnamomum camphora: Reconstruction of a sesquiterpene synthase from a monoterpene synthase.Arch Biochem Biophys2020
33381814Geometricus represents protein structures as shape-mers derived from moment invariants.Bioinformatics2020
32831124CAPICE: a computational method for Consequence-Agnostic Pathogenicity Interpretation of Clinical Exome variations.Genome Med2020
32592463Coevolution-based prediction of protein-protein interactions in polyketide biosynthetic assembly lines.Bioinformatics2020
32368333Caretta - A multiple protein structure alignment and feature extraction suite.Comput Struct Biotechnol J2020
30446165An analysis of characterized plant sesquiterpene synthases.Phytochemistry2019
30903633Comprehensive phenotyping reveals interactions and functions of Arabidopsis thaliana TCP genes in yield determination.Plant J2019
30398547Improved inference of intermolecular contacts through protein-protein interaction prediction using coevolutionary analysis.Bioinformatics2019
29088399Tulipa gesneriana and Lilium longiflorum PEBP Genes and Their Putative Roles in Flowering Time Control.Plant Cell Physiol2018
29808512DNA sequence and shape are predictive for meiotic crossovers throughout the plant kingdom.Plant J2018
29940855Comparative analysis of binding patterns of MADS-domain proteins in Arabidopsis thaliana.BMC Plant Biol2018
29471492Corrigendum: Towards recommendations for metadata and data handling in plant phenotyping.J Exp Bot2018
29192027Transcription Factor-Mediated Control of Anthocyanin Biosynthesis in Vegetative Tissues.Plant Physiol2018
27814969Cross-Family Transcription Factor Interactions: An Additional Layer of Gene Regulation.Trends Plant Sci2017
28439467Floral pathway integrator gene expression mediates gradual transmission of environmental and endogenous cues to flowering time.PeerJ2017
28149201An interactomics overview of the human and bovine milk proteome over lactation.Proteome Sci2017
29258424Divergent regulation of Arabidopsis SAUR genes: a focus on the SAUR10-clade.BMC Plant Biol2017
28797052Similarities between plant traits based on their connection to underlying gene functions.PLoS One2017
28547871Sequence-based analysis of protein degradation rates.Proteins2017
27797425Distribution, position and genomic characteristics of crossovers in tomato recombinant inbred lines derived from an interspecific cross between Solanum lycopersicum and Solanum pimpinellifolium.Plant J2017
27987170Species-Specific Genome Sequence Databases: A Practical Review.Methods Mol Biol2017
27604469An expanded evaluation of protein function prediction methods shows an improvement in accuracy.Genome Biol2016
28105910Selected proceedings of Machine Learning in Systems Biology: MLSB 2016.BMC Bioinformatics2016
25719734A quantitative and dynamic model of the Arabidopsis flowering time gene regulatory network.PLoS One2015
26044092Towards recommendations for metadata and data handling in plant phenotyping.J Exp Bot2015
24112147Valencene synthase from the heartwood of Nootka cypress (Callitropsis nootkatensis) for biotechnological production of valencene.Plant Biotechnol J2014
25492368Prioritization of candidate genes in QTL regions based on associations between traits and biological processes.BMC Plant Biol2014
25344813Rice cytochrome P450 MAX1 homologs catalyze distinct steps in strigolactone biosynthesis.Nat Chem Biol2014
24913630The (r)evolution of gene regulatory networks controlling Arabidopsis plant reproduction: a two-decade history.J Exp Bot2014
24699171Inferring the gene network underlying the branching of tomato inflorescence.PLoS One2014
24275492Structural determinants of DNA recognition by plant MADS-domain transcription factors.Nucleic Acids Res2014
23353650A large-scale evaluation of computational protein function prediction.Nat Methods2013
24129704Analysis of functional redundancies within the Arabidopsis TCP transcription factor family.J Exp Bot2013
23994444N-glycan occupancy of Arabidopsis N-glycoproteins.J Proteomics2013
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Collaborators

Alexandre M J J Bonvin
Bijvoet Center for Biomolecular Research, Utrecht University
Co-authored papers 13
Miguel Correa Marrero
Wageningen University and Research
Co-authored papers 4
Rolf Boelens
Utrecht University
Co-authored papers 4
Christopher Funk
University of Colorado School of Medicine
Co-authored papers 2
Sean D Mooney
University of Washington
Co-authored papers 2
Patricia C Babbitt
University of California san francisco
Co-authored papers 2
Hai Fang
University of Bristol
Co-authored papers 2
Stefano Toppo
University of Padova
Co-authored papers 2
Tobias Hamp
Inc. San Diego
Co-authored papers 2
Cyril Pommier
Universite Paris-Saclay
Co-authored papers 2
Asa Ben-Hur
Colorado State University
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Michal Linial
Institute of Life Sciences, The Hebrew University of Jerusalem
Co-authored papers 2
Karin Verspoor
National Centre for Infections in Cancer, 5Peter MacCallum Cancer Centre
Co-authored papers 2
Daisuke Kihara
Purdue University
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Iddo Friedberg
Iowa State University
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David T Jones
University College London
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Nives ??kunca
ETH Zurich, Universitatstrasse 19
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Wyatt T Clark
BioMarin Pharmaceutical Inc.
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Joachim W Bargsten
Wageningen University and Research Centre
Co-authored papers 2
Steven E Brenner
University of California berkeley
Co-authored papers 2
Weidong Tian
Institute of Biostatistics, Fudan University
Co-authored papers 2
Rita Casadio
Department of Pharmacy and Biotechnology, University of Bologna
Co-authored papers 2
Yuanpeng Zhou
Fudan University
Co-authored papers 2
Burkhard Rost
Technical University of Munich (TUM)
Co-authored papers 2
Victor L Hsu
Co-authored papers 2
Domenico Cozzetto
Imperial College London
Co-authored papers 2
Prajwal Bhat
Royal Holloway University of London
Co-authored papers 2
Panagiotis L Kastritis
Interdisciplinary Research Center HALOmem, Martin Luther University Halle-Wittenberg
Co-authored papers 2
Kevin Bryson
University of Glasgow
Co-authored papers 2
Pekka Koskinen
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