A5038211775- Bioinformatics and Genomic Networks
- Genomics and Phylogenetic Studies
- Insect symbiosis and bacterial influences
- Machine Learning in Bioinformatics
- Plant Pathogens and Resistance
- Insect-Plant Interactions and Control
- RNA and protein synthesis mechanisms
- Plant Disease Resistance and Genetics
- Chromosomal and Genetic Variations
- Plant Pathogens and Fungal Diseases
- Plant-Microbe Interactions and Immunity
- Plant Molecular Biology Research
- Plant Virus Research Studies
- Protein Structure and Dynamics
- Gene expression and cancer classification
- Metabolomics and Mass Spectrometry Studies
- Plant Reproductive Biology
- RNA Research and Splicing
- Phytochemistry and Biological Activities
- Ethnobotanical and Medicinal Plants Studies
- Fungal Biology and Applications
- Photosynthetic Processes and Mechanisms
- Insect behavior and control techniques
- Machine Learning and Algorithms
- Evolution and Genetic Dynamics
Wageningen University & Research
2003-2023
KeyGene (Netherlands)
2012-2023
Delft University of Technology
2018-2020
Agro Business Park
2019
Centre for BioSystems Genomics
2007-2015
Utrecht University
1992-2013
Research International (United States)
2003-2011
Centro de Astrobiología
2000-2004
Universitat de València
1998-2003
Astrobiology Center
2003
The plant-pathogenic fungus Mycosphaerella graminicola (asexual stage: Septoria tritici) causes septoria tritici blotch, a disease that greatly reduces the yield and quality of wheat. This is economically important in most wheat-growing areas worldwide threatens global food production. Control has been hampered by limited understanding genetic biochemical bases pathogenicity, including mechanisms infection resistance host. Unlike other plant pathogens, M. long latent period during which it...
We have sequenced the genome of intracellular symbiont Buchnera aphidicola from aphid Baizongia pistacea . This strain diverged 80–150 million years ago common ancestor two previously strains. Here, a field-collected, nonclonal sample insects was used as source material for laboratory procedures. As consequence, assembly unveiled intrapopulational variation, consisting ≈1,200 polymorphic sites. Comparison 618-kb (kbp) with other genomes revealed nearly perfect gene-order conservation,...
Solanum pennellii is a wild tomato species endemic to Andean regions in South America, where it has evolved thrive arid habitats. Because of its extreme stress tolerance and unusual morphology, an important donor germplasm for the cultivated lycopersicum. Introgression lines (ILs) which large genomic S. lycopersicum are replaced with corresponding segments from can show remarkably superior agronomic performance. Here we describe high-quality genome assembly parents IL population. By...
Genetic variation in the tomato clade was explored by sequencing a selection of 84 accessions and related wild species representative for Lycopersicon, Arcanum, Eriopersicon, Neolycopersicon groups. We present reconstruction three new reference genomes support our comparative genome analyses. Sequence diversity commercial breeding lines appears extremely low, indicating dramatic genetic erosion crop tomatoes. This is reflected SNP count which can exceed 10 million i.e. 20 fold higher than...
We sequenced and compared the genomes of Dothideomycete fungal plant pathogens Cladosporium fulvum (Cfu) (syn. Passalora fulva) Dothistroma septosporum (Dse) that are closely related phylogenetically, but have different lifestyles hosts. Although both fungi grow extracellularly in close contact with host mesophyll cells, Cfu is a biotroph infecting tomato, while Dse hemibiotroph pine. The these similar set genes (70% gene content homologs), differ significantly size (Cfu >61.1-Mb; 31.2-Mb),...
Bacterial symbioses are widespread among insects, probably being one of the key factors their evolutionary success. We present complete genome sequence Blochmannia floridanus , primary endosymbiont carpenter ants. Although these ants feed on a complex diet, this symbiosis very likely has nutritional basis: is able to supply nitrogen and sulfur compounds host while it takes advantage metabolic machinery. Remarkably, bacteria lack all known genes involved in replication initiation ( dna A, pri...
Protein function prediction is a difficult bioinformatics problem. Many recent methods use deep neural networks to learn complex sequence representations and predict from these. Deep supervised models require lot of labeled training data which are not available for this task. However, very large amount protein sequences without functional labels available.We applied an existing model that had been pretrained in unsupervised setting on the task molecular prediction. We found feature...
Potato is a member of the Solanaceae, plant family that includes several other economically important species, such as tomato, eggplant, petunia, tobacco and pepper. The Genome Sequencing Consortium (PGSC) aims to elucidate complete genome sequence potato, third most food crop in world. PGSC collaboration between 13 research groups from China, India, Poland, Russia, Netherlands, Ireland, Argentina, Brazil, Chile, Peru, USA, New Zealand UK. potato consists 12 chromosomes has (haploid) length...
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...
The genome of tomato ( Solanum lycopersicum L.) is being sequenced by an international consortium 10 countries (Korea, China, the United Kingdom, India, Netherlands, France, Japan, Spain, Italy, and States) as part larger “International Solanaceae Genome Project (SOL): Systems Approach to Diversity Adaptation” initiative. sequencing project uses ordered bacterial artificial chromosome (BAC) approach generate a high‐quality euchromatic sequence for use reference euasterids. Sequence deposited...
Explainable Artificial Intelligence (XAI) is an increasingly important field of research required to bring AI the next level in real-world applications. Global sensitivity analysis methods play role XAI, as they can provide understanding which (groups of) parameters have high influence predictions machine learning models and output simulators processes. In this paper, we conduct a survey into global XAI context present both qualitative quantitative these under different conditions. addition...
A restriction‐site analysis of chloroplast DNA from 44 species, representing 19 genera and all six subfamilies the Crassulaceae was conducted using 12 restriction endonucleases. total 969 variable sites detected, 608 which were phylogenetically informative used in parsimony analysis. Estimated values nucleotide sequence divergence to construct a distance tree by neighbor‐joining method. Maximum family ~7%. Different inference methods yielded only moderately different topologies. The amount...
Within the framework of International Solanaceae Genome Project, genome tomato (Solanum lycopersicum) is currently being sequenced. We follow a 'BAC-by-BAC' approach that aims to deliver high-quality sequences euchromatin part genome. BACs are selected from various libraries on basis markers F2.2000 linkage map. Prior sequencing, we validated precise physical location chromosomes by five-colour high-resolution fluorescent in situ hybridization (FISH) mapping. This paper describes strategies...
Like all plants, potato has evolved a surveillance system consisting of large array genes encoding for immune receptors that confer resistance to pathogens and pests. The majority these so-called or R proteins belong the super-family harbour nucleotide binding leucine-rich-repeat domain (NB-LRR). Here, sequence information conserved NB was used investigate genome-wide genetic distribution NB-LRR gene loci in potato. We analysed sequences 288 unique BAC clones selected using filter...
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....
We have explored compositional variation at synonymous (codon usage) and nonsynonymous (amino acid positions in three complete genomes of Buchnera , endosymbiotic bacteria aphids, also their orthologs Escherichia coli a close free-living relative. sought to discriminate genes variable expression levels order weigh the relative contributions mutational bias selection genomic changes following symbiosis. identified clear strand asymmetries, distribution biases (putative high-expression were...
Protein sequences encompass tertiary structures and contain information about specific molecular interactions, which in turn determine biological functions of proteins. Knowledge how protein define interaction specificity is largely missing, particular for paralogous families with high sequence similarity, such as the plant MADS domain transcription factor family. In comparison to situation mammalian species, this important family regulators has expanded enormously species contains over 100...
Abstract Motivation: Matching both the retention index (RI) and mass spectrum of an unknown compound against a spectral reference library provides strong evidence for correct identification that compound. Data on indices are, however, available only small fraction compounds in such libraries. We propose quantitative structure-RI model enables ranking filtering putative identifications which predicted RI falls outside predefined window. Results: constructed multiple linear regression support...
Although Arabidopsis (Arabidopsis thaliana) is the best studied plant species, biological role of one-third its proteins still unknown. We developed a probabilistic protein function prediction method that integrates information from sequences, protein-protein interactions, and gene expression. The was applied to Arabidopsis. Evaluation performance showed our has improved compared with single source-based approaches two existing integration approaches. An innovative feature it enables...
Abstract Motivation Most automatic functional annotation methods assign Gene Ontology (GO) terms to proteins based on annotations of highly similar proteins. We advocate that are less still informative. Also, despite their simplicity and structure, GO seem be hard for computers learn, in particular the Biological Process ontology, which has most (>29 000). propose use Label-Space Dimensionality Reduction (LSDR) techniques exploit redundancy transform them into a more compact latent...