A5089978830- Gene Regulatory Network Analysis
- Bioinformatics and Genomic Networks
- Microbial Metabolic Engineering and Bioproduction
- Genomics and Phylogenetic Studies
- Bacterial Genetics and Biotechnology
- Scientific Computing and Data Management
- Bacteriophages and microbial interactions
- Biomedical Text Mining and Ontologies
- RNA and protein synthesis mechanisms
- Computational Drug Discovery Methods
- Genetics, Bioinformatics, and Biomedical Research
- Gene expression and cancer classification
- Distributed and Parallel Computing Systems
- Monoclonal and Polyclonal Antibodies Research
- Bacterial biofilms and quorum sensing
- Fungal and yeast genetics research
- Glycosylation and Glycoproteins Research
- Genetics, Aging, and Longevity in Model Organisms
- Cell Image Analysis Techniques
- CRISPR and Genetic Engineering
- Machine Learning in Bioinformatics
- Protein purification and stability
- T-cell and B-cell Immunology
- Evolutionary Algorithms and Applications
- Telomeres, Telomerase, and Senescence
Newcastle University
2015-2024
Northumbria University
2022
Newcastle University Singapore
2020
University of Newcastle Australia
2003-2019
University of Toronto
2012
Newcastle Hospitals - Campus for Ageing and Vitality
2008-2011
University of Auckland
2010-2011
European Bioinformatics Institute
2003-2011
Imperial College London
2010
Centre for Life
2008
Abstract Motivation: In silico experiments in bioinformatics involve the co-ordinated use of computational tools and information repositories. A growing number these resources are being made available with programmatic access form Web services. Bioinformatics scientists will need to orchestrate services workflows as part their analyses. Results: The Taverna project has developed a tool for composition enactment life sciences community. includes workbench application which provides graphical...
To estimate the minimal gene set required to sustain bacterial life in nutritious conditions, we carried out a systematic inactivation of Bacillus subtilis genes. Among ≈4,100 genes organism, only 192 were shown be indispensable by this or previous work. Another 79 predicted essential. The vast majority essential categorized relatively few domains cell metabolism, with about half involved information processing, one-fifth synthesis envelope and determination shape division, one-tenth related...
Abstract Life sciences research is based on individuals, often with diverse skills, assembled into groups. These groups use their specialist expertise to address scientific problems. The in silico experiments undertaken by these can be represented as workflows involving the co‐ordinated of analysis programs and information repositories that may globally distributed. With regards Grid computing, requirements relate sharing resources rather than computational power. my project has developed...
Data Resource Profile: Accessible for Integrated Epigenomic Studies (ARIES) Caroline L Relton, Tom Gaunt, Wendy McArdle, Karen Ho, Aparna Duggirala, Hashem Shihab, Geoff Woodward, Oliver Lyttleton, David M Evans, Wolf Reik, Yu-Lee Paul, Gabriella Ficz, Susan E Ozanne, Anil Wipat, Keith Flanagan, Allyson Lister, Bastiaan T Heijmans, Ring and George Davey Smith MRC Integrative Epidemiology Unit, School of Social Community Medicine, University Bristol, UK, Institute Genetic Newcastle...
Abstract Synthetic biology builds upon genetics, molecular biology, and metabolic engineering by applying principles to the design of biological systems. When designing a synthetic system, biologists need exchange information about multiple types molecules, intended behavior actual experimental measurements. The Biology Open Language (SBOL) has been developed as standard support specification in following an open community process involving both bench scientists scientific modelers software...
Background Fatigue is a debilitating condition with significant impact on patients' quality of life. frequently reported by patients suffering from primary Sjögren's Syndrome (pSS), chronic autoimmune characterised dryness the eyes and mouth. However, although fatigue common in pSS, it does not manifest all sufferers, providing an excellent model which to explore potential underpinning biological mechanisms. Methods Whole blood samples 133 fully-phenotyped pSS stratified for presence...
The SynBioHub repository (https://synbiohub.org) is an open-source software project that facilitates the sharing of information about engineered biological systems. provides computational access for and data integration, a graphical user interface enables users to search share designs in Web browser. By connecting relevant repositories (e.g., iGEM repository, JBEI ICE, other instances SynBioHub), allows browse, upload, download various standard formats, regardless their location or...
The mucosal microbiota is recognised as an important factor for our health, with many disease states linked to imbalances in the normal community structure. Hence, there considerable interest identifying molecular basis of human-microbe interactions. In this work we investigated capacity microbes thrive on surfaces, either mutualists, commensals or pathogens, using comparative genomics identify co-occurring traits. We identified a novel domain named M60-like/PF13402 (new Pfam entry PF13402),...
Abstract Traditional drug discovery faces a severe efficacy crisis. Repurposing of registered drugs provides an alternative with lower costs and faster development timelines. However, the data necessary for identification disease modules, i.e. pathways sub-networks describing mechanisms complex diseases which contain potential targets, are scattered across independent databases. Moreover, existing studies limited to predictions specific or non-translational algorithmic approaches. There is...
Abstract Background The king scallop, Pecten maximus, is distributed in shallow waters along the Atlantic coast of Europe. It forms basis a valuable commercial fishery and plays key role coastal ecosystems food webs. Like other filter feeding bivalves it can accumulate potent phytotoxins, to which has evolved some immunity. molecular origins this immunity are interest evolutionary biologists, pharmaceutical companies, fisheries management. Findings Here we report genome assembly species,...
Abstract Motivation: New developments in post-genomic technology now provide researchers with the data necessary to study regulatory processes a holistic fashion at multiple levels of biological organization. One major challenges for biologist is integrate and interpret these vast resources gain greater understanding structure function molecular that mediate adaptive cell cycle driven changes gene expression. In order achieve this biologists require new tools techniques allow pathway related...
Psoriasis is a common chronic skin disorder, but the mechanisms involved in resolution and clearance of plaques remain poorly defined. We investigated mechanism action UVB, which highly effective clearing psoriasis inducing remission, tested hypothesis that apoptosis key mechanism. To distinguish bystander effects, equal erythemal doses two UVB wavelengths were compared following vivo irradiation psoriatic plaques; one clinically (311 nm) has no therapeutic effect on (290 nm). Only 311 nm...
Abstract Motivation: Fabrication of synthetic biological systems is greatly enhanced by incorporating engineering design principles and techniques such as computer-aided design. To this end, the ongoing standardization parts presents an opportunity to develop libraries standard virtual in form mathematical models that can be combined inform system Results: We present online Repository, populated with a collection standardized readily recombined model different using inherent modularity...
Synthetic Biology Open Language (SBOL) Visual is a graphical standard for genetic engineering. It consists of symbols representing DNA subsequences, including regulatory elements and assembly features. These can be used to draw illustrations communication instruction, as image assets computer-aided design. SBOL community standard, freely available personal, academic, commercial use (Creative Commons CC0 license). We provide prototypical symbol images that have been in scientific publications...
The Synthetic Biology Open Language (SBOL) is a standard that enables collaborative engineering of biological systems across different institutions and tools. SBOL developed through careful consideration recent synthetic biology trends, real use cases, consensus among leading researchers in the field members commercial biotechnology enterprises. We demonstrate discuss how set SBOL-enabled software tools can form an integrated, cross-organizational workflow to recapitulate design one largest...
Abstract People who are engineering biological organisms often find it useful to communicate in diagrams, both about the structure of nucleic acid sequences that they and functional relationships between sequence features other molecular species. Some typical practices conventions have begun emerge for such diagrams. The Synthetic Biology Open Language Visual (SBOL Visual) has been developed as a standard organizing systematizing order produce coherent language expressing function genetic...
Bacterial biofilms in natural and artificial environments perform a wide array of beneficial or detrimental functions exhibit resistance to physical as well chemical perturbations. In dynamic environments, where periodic aperiodic flows over surfaces are involved, can be subjected large shear forces. The ability withstand these forces, which is often attributed the resilience extracellular matrix. This attribute matrix referred viscoelasticity result self-assembly cross-linking multiple...
The Synthetic Biology Open Language (SBOL) is a community-developed data standard that allows knowledge about biological designs to be captured using machine-tractable, ontology-backed representation built Semantic Web technologies. While early versions of SBOL focused only on the description DNA-based components and their sub-components, can now used represent across multiple scales throughout entire synthetic biology workflow, from specification single molecule or DNA fragment through...
Abstract In Saccharomyces cerevisiae, Cdc13 binds telomeric DNA to recruit telomerase and “cap” chromosome ends. temperature-sensitive cdc13-1 mutants is degraded cell-cycle progression inhibited. To identify novel proteins pathways that cap telomeres, or respond uncapped we combined with the yeast gene deletion collection used high-throughput spot-test assays measure growth. We identified 369 deletions, in eight different phenotypic classes, reproducibly demonstrated subtle genetic...
To better understand telomere biology in budding yeast, we have performed systematic suppressor/enhancer analyses on yeast strains containing a point mutation the essential capping gene CDC13 (cdc13-1) or null DNA damage response and YKU70 (yku70Δ). We Quantitative Fitness Analysis (QFA) thousands of mutations affecting telomere-capping proteins combination with library deletion mutations. perform QFA, typically inoculate 384 separate cultures onto solid agar plates monitor growth each...