Vladimir Mironov

Norwegian University of Science and Technology | NTNU

The BioGateway App is a plugin for the Cytoscape network editor, allowing users to interactively build biological networks by querying the Biogateway Resource Description Framework (RDF) triple store. BioGateway contains information from several curated resources including UniProtKB, IntAct, Gene Ontology Annotations, various datasets containing tr...

The BioGateway App is a Cytoscape (version 3) plugin designed to provide easy query access to the BioGateway RDF triple store, which contains functional and interaction information for proteins from several curated resources. For explorative network building, we have added a comprehensive dataset with regulatory relationships of mammalian DNA bindi...

Network-based approaches for the analysis of large-scale genomics data have become well established. Biological networks provide a knowledge scaffold against which the patterns and dynamics of ‘omics’ data can be interpreted. The background information required for the construction of such networks is often dispersed across a multitude of knowledge...

The present invention relates generally to the field of molecular biology and concerns a method for improving plant growth characteristics relative to corresponding wild type plants. More specifically, the present invention concerns a method for improving plant growth characteristics comprising modulating expression in a plant of a nucleic acid enc...

The Semantic Web standards OWL and RDF are often used to represent biomedical information as Linked Data, however, the OWL/RDF syntax, which combines both, was never optimised for querying. By combining two formal paradigms for modelling Linked Data, namely multi-digraphs and Description Logic, many precise terms for relations have emerged that are...

The comparison of genes and gene products across species depends on high quality tools to determine the relationships between gene or protein sequences from various species. Although some excellent applications are available and widely used, their performance leaves room for improvement. We developed orthAgogue: a multithreaded C++ application for...

The present invention concerns a method for improving growth characteristics of plants by increasing expression and/or activity in a plant of an LRR receptor kinase or a homologue thereof. One such method comprises introducing into a plant an RLK827 nucleic acid molecule or functional variant thereof. The invention also relates to transgenic plants...

Over the last decade the biological sciences have been widely embracing Systems Biology and its various data integration approaches to discover new knowledge. Molecular Systems Biology aims to develop hypotheses based on integrated, or modelled data. These hypotheses can be subsequently used to design new experiments for testing, leading to an impr...

The last decade has seen the emergence of Systems Biology: an integrative approach to understand how biological systems are built and operate. In parallel, the Semantic Web has started to offer new technologies that make data on the web comprehensible for computers. The merger of the two, in Semantic Systems Biology, offers new opportunities for da...

Transcriptional regulation of gene expression is an important mechanism in many biological processes. Aberrations in this mechanism have been implicated in cancer and other diseases. Effective investigation of gene expression mechanisms requires a system-wide integration and assessment of all available knowledge of the underlying molecular networks...

Background Semantic Web technologies have been developed to overcome the limitations of the current Web and conventional data integration solutions. The Semantic Web is expected to link all the data present on the Internet instead of linking just documents. One of the foundations of the Semantic Web technologies is the knowledge representation lang...

This file contains all the additional results referred to in the description of the use cases I and II. Subsection I: Use case I - Lists the ancestor terms for CCO:F0000391. Subsection II: Use case I - Lists the ancestor terms for CCO:F0000759. Subsection III: Use case I - Lists the overlapping terms generates as part of step 2. Subsection IV: Use...

SPARQL queries. This file contains the SPARQL code of the 24 queries used for testing the stores.

We have exploited semantic annotations of biological entities to develop a novel approach to infer new knowledge. We demonstrate this in four use cases based on the Gene Expression Ontology, an applied ontology that we developed to serve the needs of researchers involved in the analysis of genes and proteins implicated in transcriptional control of...

Ontologies have become indispensable in the Life Sciences for managing large amounts of knowledge. The use of logics in ontologies ranges from sound modelling to practical querying of that knowledge, thus adding a considerable value. We conceive reasoning on bio-ontologies as a semi-automated process in three steps: (i) defining a logic-based repre...

The Cell Cycle Ontology (CCO) has the aim to provide a ‘one stop shop’ for scientists interested in the biology of the cell cycle that would like to ask questions from a molecular and/or systems perspective: what are the genes, proteins, and so on involved in the regulation of cell division? How do they interact to produce the effects observed in t...

The vast amounts of knowledge in the biomedical domain have paved the way for a new paradigm in biological research called Systems Biology, essentially an approach that relies on the integration of all available knowledge of a biological system in a single model. This approach promotes a comprehensive understanding of biological systems, driven by...

Currently, the OBO Foundry plays an important role by setting guidelines to formalise the concepts within the biomedical domain. The ontologies within the OBO Foundry are usually represented in the OBO ontology language. While being human-readable, this language lacks the computational rigour required for the Semantic Web (SW). Consequently, the RD...

The biosciences increasingly face the challenge of integrating a wide variety of available data, information and knowledge in order to gain an understanding of biological systems. Data integration is supported by a diverse series of tools, but the lack of a consistent terminology to label these data still presents significant hurdles. As a conseque...

We have compared the performance of five non-commercial triple stores, Virtuoso-open source, Jena SDB, Jena TDB, SWIFT-OWLIM and 4Store. We examined three performance aspects: the query execution time, scalability and run-to-run reproducibility. The queries we chose addressed different ontological or biological topics, and we obtained evidence that...

We have compared the performance of five non-commercial triple stores, Virtuoso-open source, Jena SDB, Jena TDB, SWIFT-OWLIM and 4Store. We examined three performance aspects: the query execution time, scalability and run-to-run reproducibility. The queries we chose addressed different ontological or biological topics, and we obtained evidence that...

IntroductionKnowledge representation languages and tools for building bio-ontologiesBest practices for building bio-ontologiesConclusion AcknowledgementsReferences

Life scientists need help in coping with the plethora of fast growing and scattered knowledge resources. Ideally, this knowledge should be integrated in a form that allows them to pose complex questions that address the properties of biological systems, independently from the origin of the knowledge. Semantic Web technologies prove to be well suite...

The Cell Cycle Ontology (CCO) is an application ontology that automatically captures and integrates detailed knowledge on the cell cycle process by combining, interlinking and enriching knowledge from various sources. CCO uses Semantic Web technologies, and it is accessible via the web for browsing, visualising, advanced querying, and computational...

While OWL, the Web Ontology Language, is often regarded as the preferred language for Knowledge Representation in the world of the Semantic Web, the potential of direct representation in RDF, the Resource Description Framework, is underestimated. Here we show how ontologies adequately represented in RDF could be semantically enriched with SPARUL. T...

New knowledge is produced at a continuously increasing speed, and the list of papers, databases and other knowledge sources that a researcher in the life sciences needs to cope with is actually turning into a problem rather than an asset. The adequate management of knowledge is therefore becoming fundamentally important for life scientists, especia...

The Cell Cycle Ontology (http://www.CellCycleOntology.org) is an application ontology that automatically captures and integrates detailed knowledge on the cell cycle process. Cell Cycle Ontology is enabled by semantic web technologies, and is accessible via the web for browsing, visualizing, advanced querying, and computational reasoning. Cell Cycl...

The application of Semantic Web technologies in the life sciences for data integration is still nascent. We have recently built Bio-Gateway, an RDF store that integrates all the candidate OBO Foundry ontologies with other resources such as SWISS-PROT. In the course of developing BioGateway, we faced challenges that are common to other projects that...

Many biomedical ontologies use OBO or OWL as knowledge representation language. The rapid increase of such ontologies calls for adequate tools to facilitate their use. In particular, there is a pressing need to programmatically deal with such ontologies in many applications, including data integration, text mining, as well as semantic applications...

Kip-related proteins (KRPs) play a major role in the regulation of the plant cell cycle. We report the identification of five putative rice (Oryza sativa) proteins that share characteristic motifs with previously described plant KRPs. To investigate the function of KRPs in rice development, we generated transgenic plants overexpressing the Orysa;KR...

The goal of the EU FP6 project DIAMONDS is to build a computational platform for studying the cell-cycle regulation process in several different (model) organisms (S. cerevisiae, S. pombe, A. thaliana and human). This platform will enable wet-lab biologists to use a systems biology approach encompassing data integration, modeling and simulation, th...

Cell-cycle regulation plays a crucial role in organogenesis, morphogenesis, growth and differentiation and conceptually offers a means to design a next generation of crop plants that outperform traditionally bred ones. However, cell-cycle regulation involves a large, highly redundant, set of genes, which complicates unravelling of function in the c...

Although the majority of cyclin-dependent kinases (CDKs) play a key role in cell cycle progression, recent evidence has shown that CDKs are also implicated in transcription regulation. Here, we describe two Arabidopsis CDKs designated Arath;CDKC;1 and Arath; CDKC;2. These CDKs share a PITAIRE signature in the cyclin-binding domain and the structura...

Progression through the cell cycle is driven by cyclin-dependent kinases (CDKs) whose activity is controlled by regulatory subunits called cyclins. The expression of cyclins is subject to numerous controls at multiple levels, not least at the level of transcription. As a first step to unravel the mechanisms that regulate expression of B-cyclins in...

Progression through the cell cycle is driven by cyclin-dependent kinases (CDKs) whose activity is controlled by regulatory subunits called cyclins. The expression of cyclins is subject to numerous controls at multiple levels, not least at the level of transcription. As a first step to unravel the mechanisms that regulate expression of B-cyclins in...

Tools for mutagenesis and expression analyses are needed to study the role of bacterial genes. Here, we report the construction of pMH11, a small, mobilizable plasmid that replicates in Escherichia coli, but not in Azorhizobium caulinodans, a nodulating microsymbiont of Sesbania rostrata, and that contains a unique BamHI restriction site upstream o...

Cyclin-dependent kinases (CDKs) control the key transitions in the eukaryotic cell cycle. All the CDKs known to control G(2)/M progression in yeast and animals are distinguished by the characteristic PSTAIRE motif in their cyclin-binding domain and are closely related. Higher plants contain in addition a number of more divergent non-PSTAIRE CDKs wi...

The effect of Rhodococcus fascians, the causal agent of leafy gall disease, on the mitotic behavior of synchronized tobacco Bright Yellow-2 (BY-2) cells was investigated. Incubation of aphidicolin-synchronized BY-2 cells with R. fascians cells specifically resulted in a broader mitotic index peak, an effect that was linked to an intact and expresse...

We have analyzed five mutant alleles of two cyclin-dependent kinases from Arabidopsis thaliana , CDC2aAt and CDC2bAt , in Schizosaccharomyces pombe . Two of the five mutant alleles produced similar phenotypes for both cyclin-dependent kinases. The other three mutants caused phenotypes dependent on the particular cyclin-dependent kinase. Of all the...

β-Glucuronidase (gus) is widely used as a reporter gene to study transcriptional regulation in transgenic plants, based on the assumption that the level of GUS activity is indicative of the rate of gus transcription driven by the promoter investigated. Here we examined tobacco BY-2 cultures transformed with Arabidopsis cyclin promoters fused to gus...

Considerable progress has been achieved in the identification and molecular characterisation of genes and/or cDNAs coding for cyclin-dependent kinases (CDK) as well as cyclins in diverse plant species including Arabidopsis thaliana. Their transcriptional control during the cell cycle progression and the response to developmental cues and environmen...

In the past 7-8 years considerable effort has been expended to produce transgenic plants that resist virus infection, insects, herbicides and disease development. The crop improvement and the desired phenotype is conferred by transformation, usually with a single foreign gene. Selection of transformants demands the use of selectable markers, which...

Cyclins are cell cycle regulators whose proteins oscillate dramatically during the cell cycle. Cyclin steady-state mRNA levels also fluctuate, and there are indications that both their rate of transcription and mRNA stability are under cell cycle control. Here, we demonstrate the transcriptional regulation of higher eukaryote cyclins throughout the...

We have sequenced 6006 bp DNA of a region from the Bacillus subtilis SHgw chromosome known to contain riboflavin biosynthesis genes (rib gene cluster, 210 degrees on the B. subtilis genetic map). Five of the seven open reading frames found within the sequence are shown to represent the genes ribG, ribB, ribA, ribH and ribTD. The calculated molecula...

Seventeen cis-dominant mutations leading to riboflavin overproduction in Bacillus subtilis were localized to the region between nucleotides +37 and +159 relative to the transcription initiation site of the riboflavin operon. This region displays an unusual structure for regulatory sequences. The main part of it represents clusters of A/T and G/C-ri...

We describe several improvements of chain-termination DNA sequencing procedure of Sanger et al. For template preparation we use 0.3 ml cultures of M13 clones, grown in standard 1,5 ml polypropylene tubes. The sequencing experiment differs from the previously described by the use of deoxyNTP, labelled with phosphorus-33 (a low energy isotope with a...

Double stranded multimers and (C2A6C2)n,(C2A6G2)n, and (C2A6G2)n, were prepared from chemically synthesized oligonucleotldes to study the influence of sequences flanking the An tract on the curvature of DNA. All these duplexes, including polypurine . polypyrimidine one, exhibit strong retardation in polyacrylamide gel which is indicative of pronoun...

In vitro mutagenesis with methylhydroxylamine and nitrosomethylurea was used to obtain a number of Bacillus subtilis mutants impaired in flavin-dependent response. Mutants displayed varying degree of flavin-dependent repression of riboflavin synthase and of 6,7-dimethyl-8-ribityl-lumasine accumulation. Single nucleotide substitutions were detected...

Genes controlling sporulation of Bacillus subtilis SHgW are localized in the region of 210 degrees of Bac. subtilis chromosome between lys genes and the rib operon. The method of constructing deletions of definite size was used in the deletion mapping.

All the structural genes of riboflavin biosynthesis are shown to be located on the 2.8 MD DNA fragment, using the collection of plasmids, carrying the Bacillus subtilis riboflavin operon fragments and Bacillus subtilis strains, containing various deletions of rib-operon for analysis. The proximal Bgl II site is shown to be located between promoter...

http://www.psb.ugent.be/cbd/ Abstract. The goal of the EU FP6 project DIAMONDS 1 is to build a computational platform for studying the cell-cycle regulation process in several different (model) organisms (S. cerevisiae, S. pombe, A. thaliana and human). This platform will enable wet-lab biologists to use a systems biology approach encompassing data...