2016
Current biomarkers of renal disease in systemic vasculitis lack predictive value and are insensitive to early damage. To identify novel biomarkers of renal vasculitis flare, we analysed the longitudinal urinary metabolomic profile of a rat model of anti-neutrophil cytoplasmic antibody (ANCA) vasculitis. Wistar-Kyoto (WKY) rats were immunised with human myeloperoxidase …
2015
Metabolomics studies have been reported for virtually all of the main rheumatologic diseases, although notably none yet for SSc. Our own group has demonstrated the use of urinary metabolic fingerprint analysis to predict responses to anti-TNF, and we have suggested that metabolites resulting from TNF-driven cachexia are among the useful …
2014
Background Metabolomics is a systems approach to the analysis of cellular processes through small-molecule metabolite profiling. Standardisation of sample handling and acquisition approaches has contributed to reproducibility. However, the development of robust methods for the analysis of metabolomic data is a work-in-progress. The tools that do exist are often not …
Pathomx is a workflow-based data analysis tool built on IPython. It began as a metabolomic-analysis toolkit, but has extended to support general data analysis workflows. It aims to be simple to use for non-experts while powerful enough for complex analysis tasks. Key to both of these goals is the ability …
MetaboHunter is a Python module for accessing the MetaboHunter web service web service for automated assignment of 1D raw, bucketed or peak picked NMR spectra.
More information about the algorithm is available in the published paper:
Tulpan, D., Leger, S., Belliveau, L., Culf, A., Cuperlovic-Culf, M. (2011). MetaboHunter: semi-automatic identification …
BioCyc is a Python interface to the BioCyc. Acting as a wrapper it queries the database and then presents the XML returned in a pythonic object-based interface. Support for IPython views is included offering nice summary tables of object attributes.
BioCyc are approaching the renewal period for their NIH grant …
This short demo shows analysis of a publically available GEO dataset using Pathomx, with a workflow build using the new visual editor (available in the next release).
You can download the example dataset from here.
Pathomx is an open-source workflow-based scientific analysis application. Source code is available here with packaged …
2013
Short demo of an experimental analysis of metabolomic (NMR) data using Pathomx. Metabolomic test dataset produced from THP-1 cells grown under normal and hypoxic conditions. Spectra (2D 1H JRES) have been pre-processed and quantified using the BML-NMR service.
The video shows an example analysis from processed data through to metabolic …
A Python implementation of the Icoshift algorithm, a versatile tool for the rapid alignment of 1D NMR spectra
Icoshift is a Matlab-based algorithm for the alignment of NMR spectra developed by Francesco Savorani and Giorgio Tomasi. It performs correlation shifting of spectral intervals using an FFT engine that aligns …
Background: Macrophages are abundant in the synovium of RA and are the major source of many inflammatory cytokines, including TNFα. Disease severity correlates strongly with both synovial macrophage abundance and activation status but inversely with oxygen levels. Given the importance of oxygen to cell metabolism, differentiation and function, we hypothesized …
OBJECTIVE: Anti-tumor necrosis factor (anti-TNF) therapies are highly effective in rheumatoid arthritis (RA) and psoriatic arthritis (PsA), but a significant number of patients exhibit only a partial or no therapeutic response. Inflammation alters local and systemic metabolism, and TNF plays a role in this. We undertook this study to determine …
Inflammation is an important component of normal responses to infection and injury. However, chronic activation of the immune system, due to aberrant responses to normal stimuli, can lead to the establishment of a persistent inflammatory state. Such inflammatory conditions are often debilitating, and are associated with a number of important …
2012
Metabolomics in the Analysis of Inflammatory Diseases is chapter 11 in the open-access book Metabolomics edited by Ute Roessner.
Metabolomics is a rapidly emerging field in life sciences, which aims to identify and quantify metabolites in a biological system. Analytical chemistry is combined with sophisticated informatics and statistics tools to …
2011
Background: Macrophages have a wide range of immunological and non-immunological functions, ranging from clearance of apoptotic cells, tissue remodelling, and release of pro and anti-inflammatory mediators at sites of tissue damage or infection. Subsets of phenoty- pically distinct macrophages may be uniquely adapted to perform these roles. Phenotypically and functionally …
Macrophages have a wide range of immunological and non-immunological functions in the host, ranging from clearance of apoptotic cells, tissue remodelling, and release of pro and anti-inflammatory mediators at site of tissue damage or infection. Within these wide-ranging functions however, subsets of macrophages show unique phenotypic adaptations to their role …
Established 1980