A5015936316- Plant Molecular Biology Research
- Plant Reproductive Biology
- Protein Structure and Dynamics
- Genomics and Phylogenetic Studies
- Bioinformatics and Genomic Networks
- Photosynthetic Processes and Mechanisms
- Plant Gene Expression Analysis
- Plant biochemistry and biosynthesis
- Enzyme Structure and Function
- Genetic Mapping and Diversity in Plants and Animals
- Chromosomal and Genetic Variations
- RNA and protein synthesis mechanisms
- Microbial Metabolic Engineering and Bioproduction
- Microbial Natural Products and Biosynthesis
- Machine Learning in Bioinformatics
- Plant and animal studies
- Computational Drug Discovery Methods
- Plant Virus Research Studies
- Genetic and phenotypic traits in livestock
- Plant Parasitism and Resistance
- Plant nutrient uptake and metabolism
- Light effects on plants
- RNA Research and Splicing
- Plant Physiology and Cultivation Studies
- Biochemical and biochemical processes
Wageningen University & Research
2016-2025
University of Amsterdam
2024-2025
Research International (United States)
2010-2023
Plant (United States)
2012-2023
Graduate School Experimental Plant Sciences
2018-2020
Institute of Bioinformatics
2020
Centre for BioSystems Genomics
2009-2017
Centre for Medical Systems Biology
2012-2015
Bioscience (China)
2015
Max Planck Institute for Molecular Genetics
2013
Automated annotation of protein function is challenging. As the number sequenced genomes rapidly grows, overwhelming majority products can only be annotated computationally. If computational predictions are to relied upon, it crucial that accuracy these methods high. Here we report results from first large-scale community-based critical assessment (CAFA) experiment. Fifty-four representing state art for prediction were evaluated on a target set 866 proteins 11 organisms. Two findings stand...
Abstract Here we present version 2.0 of HADDOCK, which incorporates considerable improvements and new features. HADDOCK is now able to model not only protein–protein complexes but also other kinds biomolecular multi‐component ( N > 2) systems. In the absence any experimental and/or predicted information drive docking, offers two additional ab initio docking modes based on either random patch definition or center‐of‐mass restraints. The protocol has been considerably improved, supporting...
Abstract TEOSINTE BRANCHED1/CYCLOIDEA/PROLIFERATING CELL FACTOR1 (TCP) transcription factors control developmental processes in plants. The 24 TCP encoded the Arabidopsis (Arabidopsis thaliana) genome are divided into two classes, class I and II TCPs, which proposed to act antagonistically. We performed a detailed phenotypic analysis of tcp20 mutant, showing an increase leaf pavement cell sizes 10-d-old seedlings. Subsequently, glucocorticoid receptor induction assay was performed, aiming...
Plant MADS box proteins play important roles in a plethora of developmental processes. In order to regulate specific sets target genes, dimerize and are thought assemble into multimeric complexes. this study large-scale yeast three-hybrid screen is utilized provide insight the higher-order complex formation capacity Arabidopsis family. SEPALLATA3 (SEP3) has been shown mediate and, therefore, special attention paid factor study.In total, 106 complexes were identified; more than half these at...
Maize (Zea mays) is a major staple crop in Africa, where its yield and the livelihood of millions are compromised by parasitic witchweed Striga. Germination Striga induced strigolactones exuded from maize roots into rhizosphere. In germplasm collection, we identified two strigolactones, zealactol zealactonoic acid, which stimulate less germination than strigolactone, zealactone. We then showed that single cytochrome P450, ZmCYP706C37, catalyzes series oxidative steps maize-strigolactone...
Abstract The transition from vegetative to reproductive development is one of the most important phase changes in plant life cycle. This step controlled by various environmental signals that are integrated at molecular level so-called floral integrators. One such integrator Arabidopsis (Arabidopsis thaliana) MADS domain transcription factor SUPPRESSOR OF OVEREXPRESSION CONSTANS1 (SOC1). Despite extensive genetic studies, little known about transcriptional control SOC1, and we just starting...
Analyses of the functions TEOSINTE-LIKE1, CYCLOIDEA, and PROLIFERATING CELL FACTOR1 (TCP) transcription factors have been hampered by functional redundancy between its individual members. In general, putative functionally redundant genes are predicted based on sequence similarity confirmed genetic analysis. TCP family, however, identification is impeded relatively low overall similarity. a search for pairs that control Arabidopsis leaf development, this work performed an integrative...
Recent methodological developments in plant phenotyping, as well the growing importance of its applications science and breeding, are resulting a fast accumulation multidimensional data. There is great potential for expediting both discovery application if these data made publicly available analysis. However, collection storage phenotypic observations not yet sufficiently governed by standards that would ensure interoperability among providers precisely link specific phenotypes associated...
Summary N ootkatone is one of the major terpenes in heartwood ootka cypress C allitropsis nootkatensis . It an oxidized sesquiterpene, which has been postulated to be derived from valencene. Both valencene and nootkatone are used for flavouring citrus beverages considered among most valuable at commercial scale. Functional evaluation putative terpene synthase genes sourced by large‐scale EST sequencing wood revealed a gene ( n VS ) expression different tissues tree correlates well with...
Small Auxin-Upregulated RNA (SAUR) genes encode growth regulators that induce cell elongation. Arabidopsis contains more than 70 SAUR genes, of which the growth-promoting function has been unveiled in seedlings, while their role other tissues remained largely unknown. Here, we focus on regulatory regions to predict processes they play a role, and understand dynamics plant growth. In this study, characterized detail entire SAUR10-clade: SAUR8, SAUR9, SAUR10, SAUR12, SAUR16, SAUR50, SAUR51...
Abstract Motivation: Interfacial water, which plays an important role in mediating biomolecular interactions, has been neglected the modelling of complexes. Methods: We present a solvated docking approach that explicitly accounts for presence water protein–protein Our protocol is based on concept first encounter complex layer in-between molecules. It mimics pathway from this initial towards final assembly most waters have expelled interface. Docking performed biomolecules and are removed...
Abstract Protein–protein interactions play a key role in biological processes. Identifying the interacting residues is first step toward understanding these at structural level. In this study, interface prediction program WHISCY presented. It combines surface conservation and information to predict protein–protein interfaces. The accuracy of predictions more than three times higher random prediction. These have been combined with another program, ProMate [Neuvirth et al. J Mol Biol...
Inference of protein functions is one the most important aims modern biology. To fully exploit large volumes genomic data typically produced in modern-day experiments, automated computational methods for function prediction are urgently needed. Established use sequence or structure similarity to infer but those types do not suffice determine biological context which proteins act. Current high-throughput experiments produce amounts on interactions between proteins. Such can be used...
Strigolactones (SLs) are rhizosphere signalling molecules and phytohormones. The biosynthetic pathway of SLs in tomato has been partially elucidated, but the structural diversity predicts that additional steps required. Here, root RNA-seq data co-expression analysis were used for SL gene discovery. This strategy resulted a candidate list containing several cytochrome P450s. Heterologous expression Nicotiana benthamiana yeast showed one these, CYP712G1, can catalyse double oxidation...
Several genome-wide studies demonstrated that alternative splicing (AS) significantly increases the transcriptome complexity in plants. However, impact of AS on functional diversity proteins is difficult to assess using approaches. The availability detailed sequence annotations for specific genes and gene families allows a more assessment potential effect their function. One example plant MADS-domain transcription factor family, members which interact form protein complexes function...
Various environmental signals integrate into a network of floral regulatory genes leading to the final decision on when flower. Although wealth qualitative knowledge is available how flowering time regulate each other, only few studies incorporated this predictive models. Such models are invaluable as they enable investigate various types inputs combined give quantitative readout. To effect gene expression disturbances time, we developed dynamic model for regulation in Arabidopsis thaliana....
Floral induction in Tulipa gesneriana and Lilium longiflorum is triggered by contrasting temperature conditions, high low temperature, respectively. In Arabidopsis, the floral integrator FLOWERING LOCUS T (FT), a member of PEBP (phosphatidyl ethanolamine-binding protein) gene family, key player flowering time control. this study, one was identified characterized lily (LlFT) three genes were isolated from tulip (TgFT1, TgFT2 TgFT3). Overexpression these Arabidopsis thaliana resulted an early...