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Article
Open AccessBlood pro-resolving mediators are linked with synovial pathology and are predictive of DMARD responsiveness in rheumatoid arthritis
Biomarkers are needed for predicting the effectiveness of disease modifying antirheumatic drugs (DMARDs). Here, using functional lipid mediator profiling and deeply phenotyped patients with early rheumatoid ar...
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Article
Open AccessCharacterization of four subtypes in morphologically normal tissue excised proximal and distal to breast cancer
Widespread mammographic screening programs and improved self-monitoring allow for breast cancer to be detected earlier than ever before. Breast-conserving surgery is a successful treatment for select women. Ho...
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Article
Reconstructing kinase network topologies from phosphoproteomics data reveals cancer-associated rewiring
Understanding how oncogenic mutations rewire regulatory-protein networks is important for rationalizing the mechanisms of oncogenesis and for individualizing anticancer treatments. We report a chemical phospho...
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Article
Open AccessProteomics informed by transcriptomics for characterising active transposable elements and genome annotation in Aedes aegypti
Aedes aegypti is a vector for the (re-)emerging human pathogens dengue, chikungunya, yellow fever and Zika viruses. Almost half of the Ae. aegypti genome is comprised of transposable e...
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Article
Open AccessNovel application of heuristic optimisation enables the creation and thorough evaluation of robust support vector machine ensembles for machine learning applications
Today’s researchers have access to an unprecedented range of powerful machine learning tools with which to build models for classifying samples according to their metabolomic profile (e.g. separating diseased ...
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Article
Application of gas chromatography mass spectrometry (GC–MS) in conjunction with multivariate classification for the diagnosis of gastrointestinal diseases
Gastrointestinal diseases such as irritable bowel syndrome, Crohn’s disease (CD) and ulcerative colitis are a growing concern in the developed world. Current techniques for diagnosis are often costly, time con...
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Protocol
Computational Approaches to Selected Reaction Monitoring Assay Design
Selected reaction monitoring (SRM) is becoming the tool of choice for targeted quantitative proteomics, with applications as diverse as clinical diagnostics and systems biology. Assay design is critical to the...
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Article
De novo derivation of proteomes from transcriptomes for transcript and protein identification
Integration of transcriptomic and proteomic data allows more detailed annotation of proteomes of model and non-model species.
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Article
The quantification of pollutants in drinking water by use of artificial neural networks
Drinking water attained from aquifers (ground water) is susceptible to contamination from a wide variety of sources. The importance of ensuring that the water is of high quality is paramount. Multivariate cali...
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Protocol
Mining Proteomic MS/MS Data for MRM Transitions
Multiple reaction monitoring (MRM) of peptides is a popular proteomics technique that employs tandem mass spectrometry to quantify selected proteins of interest, such as those previously identified in differen...
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Chapter and Conference Paper
Development of a Workflow for Protein Sequence Analysis Based on the Taverna Workbench® Software
A workflow based on the Taverna Workbench® software and tentatively named WPSA was developed to perform a generic protein sequence analysis eliminating the need to cut and paste data throughout web application...
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Article
Protein-folding location can regulate manganese-binding versus copper- or zinc-binding
Metal ions are needed by at least a quarter of proteins — although metallochaperones insert the 'correct' metal ion into some metal-containing proteins, metallochaperones have not been found for a large propor...
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Article
Open AccessOSPACS: Ultrasound image management system
Ultrasound scanning uses the medical imaging format, DICOM, for electronically storing the images and data associated with a particular scan. Large health care facilities typically use a picture archiving and ...
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Article
Proposed minimum reporting standards for data analysis in metabolomics
The goal of this group is to define the reporting requirements associated with the statistical analysis (including univariate, multivariate, informatics, machine learning etc.) of metabolite data with respect ...
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Article
Open AccessGene regulatory network of human adipocyte differentiation
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Chapter and Conference Paper
A Novel Graph Optimisation Algorithm for the Extraction of Gene Regulatory Networks from Temporal Microarray Data
A gene regulatory network (GRN) extracted from microarray data has the potential to give us a concise and precise way of understanding how genes interact under the experimental conditions studied [1, 2]. Learn...
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Article
Quantitative proteomic approach to study subcellular localization of membrane proteins
As proteins within cells are spatially organized according to their role, knowledge about protein localization gives insight into protein function. Here, we describe the LOPIT technique (localization of organe...
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Chapter and Conference Paper
An Overview of Soft Computing Techniques Used in the Drug Discovery Process
Drug discovery (DD) research has evolved to the point of critical dependence on computerized systems, databases and newer disciplines. Such disciplines include but are not limited to bioinformatics, chemoinfor...
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Article
Open Accessi-Tracker: For quantitative proteomics using iTRAQ™
iTRAQ™ technology for protein quantitation using mass spectrometry is a recent, powerful means of determining relative protein levels in up to four samples simultaneously. Although protein identification of sa...
