A5058635802- Microbial Metabolic Engineering and Bioproduction
- Gene Regulatory Network Analysis
- Bioinformatics and Genomic Networks
- Metabolomics and Mass Spectrometry Studies
- Protein Structure and Dynamics
- Scientific Computing and Data Management
- Gene expression and cancer classification
- Iron Metabolism and Disorders
- Fungal and yeast genetics research
- Trace Elements in Health
- Genetics, Bioinformatics, and Biomedical Research
- Biofuel production and bioconversion
- Hemoglobinopathies and Related Disorders
- Biomedical Text Mining and Ontologies
- RNA Research and Splicing
- Enzyme Catalysis and Immobilization
- Fermentation and Sensory Analysis
- Mitochondrial Function and Pathology
- Computational Drug Discovery Methods
- Oral microbiology and periodontitis research
- Advanced Proteomics Techniques and Applications
- Evolution and Genetic Dynamics
- Advanced Control Systems Optimization
- Bacterial Genetics and Biotechnology
- RNA and protein synthesis mechanisms
University of Connecticut
2016-2025
UConn Health
2013-2021
Rede de Química e Tecnologia
2020
Quantitative BioSciences
2017
University of Manchester
2007-2016
Czech Academy of Sciences, Institute of Biotechnology
2016
Virginia Tech
2004-2013
Cancer Research UK Manchester Institute
2012
Wake Forest University
2009-2011
Uninova
2008
Abstract Motivation: Molecular biotechnology now makes it possible to build elaborate systems models, but the biology community needs information standards if models are be shared, evaluated and developed cooperatively. Results: We summarize Systems Biology Markup Language (SBML) Level 1, a free, open, XML-based format for representing biochemical reaction networks. SBML is software-independent language describing common research in many areas of computational biology, including cell...
Abstract Motivation: Simulation and modeling is becoming a standard approach to understand complex biochemical processes. Therefore, there big need for software tools that allow access diverse simulation methods as well support the usage of these methods. Results: Here, we present COPASI, platform-independent user-friendly simulator offers several unique features. We discuss numerical issues with features; in particular, criteria switch between stochastic deterministic methods, hybrid...
ChEBI is a database and ontology containing information about chemical entities of biological interest. It currently includes over 46 000 entries, each which classified within the assigned multiple annotations including (where relevant) structure, cross-references, synonyms literature citations. All content freely available can be accessed online at http://www.ebi.ac.uk/chebi. In this update paper, we describe recent improvements additions to offering. We have substantially extended our...
Carmen G. Moles1, Pedro Mendes2, and Julio R. Banga1,3 Process Engineering Group, Instituto de Investigaciones Marinas (CSIC), 36208 Vigo, Spain Virginia Bioinformatics Institute, Polytechnic Institute State University, Blacksburg, 24061, USA
Abstract MOTIVATION: The simulation of biochemical kinetic systems is a powerful approach that can be used for: (i) checking the consistency postulated model with set experimental measurements, (ii) answering 'what if?' questions and (iii) exploring possible behaviours model. Here we describe generic to combine numerical optimization methods simulations, which suitable for use in rational design improved metabolic pathways industrial significance (metabolic engineering) solving inverse...
Most of the published quantitative models in biology are lost for community because they either not made available or insufficiently characterized to allow them be reused. The lack a standard description format, stringent reviewing and authors' carelessness main causes incomplete model descriptions. With today's increased interest detailed biochemical models, it is necessary define minimum quality encoding those models. We propose set rules curating biological systems. These procedures...
Abstract Motivation: A major challenge of systems biology is to infer biochemical interactions from large-scale observations, such as transcriptomics, proteomics and metabolomics. We propose use a partial correlation analysis construct approximate Undirected Dependency Graphs data. This approach enables distinction between direct indirect compounds, thereby inferring the underlying network topology. Results: The method first thoroughly evaluated with large set simulated Results indicate that...
GEPASI is a software system for modelling chemical and biochemical reaction networks on computers running Microsoft Windows. For any of up to 45 metabolites reactions, each with user-defined or one 35 predefined rate equations, can produce trajectories the metabolite concentrations obtain steady state (if it does exist). When steady-state solutions are produced, elasticity control coefficients, as defined in metabolic analysis, calculated. also allows automatic generation sequence...
Abstract Two biosynthetic pathways for ascorbate (l-ascorbic acid [AsA]; vitamin C) in plants are presently known, the mannose/l-galactose pathway and an l-GalUA pathway. Here, we present molecular biochemical evidence a possible route using myo-inositol (MI) as initial substrate. A MI oxygenase (MIOX) gene was identified chromosome 4 (miox4) of Arabidopsis ecotype Columbia, its enzymatic activity confirmed bacterially expressed recombinant protein. Miox4 primarily flowers leaves wild-type...
GC-MS-based metabolite profiling was used to analyse the response of Medicago truncatula cell cultures elicitation with methyl jasmonate (MeJa), yeast elicitor (YE), or ultraviolet light (UV). Marked changes in levels primary metabolites, including several amino acids, organic and carbohydrates, were observed following MeJa. A similar, but attenuated YE elicitation, whereas little UV elicitation. MeJa induced accumulation triterpene beta-amyrin, a precursor saponins, LC-MS analysis confirmed...
The human genome-scale metabolic reconstruction details all known reactions occurring in humans, and thereby holds substantial promise for studying complex diseases phenotypes. Capturing the whole is an on-going task since last community effort generated a consensus reconstruction, several updates have been developed. We report new version, Recon 2.2, which integrates various alternative versions with significant additional updates. In addition to re-establishing further key objectives...
Abstract Motivation: Large-scale gene expression profiling generates data sets that are rich in observed features but poor numbers of observations. The analysis such is a challenge has been object vigorous research. algorithms use for this purpose have poorly documented and rarely compared objectively, posing problem uncertainty about the outcomes analyses. One way to objectively test apply them on computational network models which mechanisms completely know. Results: We present system...