A5103223022- Bioinformatics and Genomic Networks
- Microbial Metabolic Engineering and Bioproduction
- Computational Drug Discovery Methods
- RNA modifications and cancer
- RNA Research and Splicing
- Advanced Proteomics Techniques and Applications
- Biomedical Text Mining and Ontologies
- Exercise and Physiological Responses
- International Development and Aid
- Machine Learning in Bioinformatics
- Underground infrastructure and sustainability
- Genomics and Phylogenetic Studies
- Cancer-related molecular mechanisms research
- Sinusitis and nasal conditions
- Cerebrovascular and Carotid Artery Diseases
- Knee injuries and reconstruction techniques
- Facial Nerve Paralysis Treatment and Research
- Infrastructure Maintenance and Monitoring
- Sports injuries and prevention
- Wine Industry and Tourism
- Acute Ischemic Stroke Management
- Plant Disease Resistance and Genetics
- Pharmaceutical Economics and Policy
- Urban Stormwater Management Solutions
- Global Health and Surgery
Université de Sherbrooke
2020-2023
University of Central Lancashire
2015
University of Dundee
2007-2010
Western General Hospital
2010
McGill University
2005
The PIPs database (http://www.compbio.dundee.ac.uk/www-pips) is a resource for studying protein-protein interactions in human. It contains predictions of >37,000 high probability which >34,000 are not reported the interaction databases HPRD, BIND, DIP or OPHID. were calculated by Bayesian method that combines information from expression, orthology, domain co-occurrence, post-translational modifications and sub-cellular location. also take account topology predicted network. web interface to...
Although the prediction of protein-protein interactions has been extensively investigated for yeast, few such datasets exist far larger proteome in human. Furthermore, it recently estimated that overall average false positive rate available computational and high-throughput experimental interaction is as high 90%. The human was by combining orthogonal protein features within a probabilistic framework. include co-expression, orthology to known interacting proteins full-Bayesian combination...
High throughput genomic/proteomic strategies, such as microarray studies, drug screens, and genetic often produce a list of genes that are believed to be important for one or more reasons. Unfortunately it is difficult discern meaningful biological relationships from lists. This study presents new bioinformatic approach can used identify regulatory subnetworks lists significant proteins. We demonstrate the utility this using an interaction network yeast constructed BIND, TRANSFAC, SCPD,...
Small nucleolar RNAs (snoRNAs), a group of noncoding present amongst all eukaryotes, are most extensively characterized for their regulation ribosome biogenesis and splicing. Despite central roles, current snoRNA annotations remain incomplete. Several eukaryote genome contain few or no snoRNAs, none distinguish expressed snoRNAs from pseudogenes, recently subclass with distinct features expression levels. To address this, we developed SnoBIRD, BERT-based C/D box predictor trained on spanning...
Abstract Background High-grade adult-type diffuse gliomas (HGGs) constitute a heterogeneous group of aggressive tumors that are mostly incurable. Recent advances highlighting the contribution ribosomes to cancer development have offered new clinical perspectives. Here, we uncovered isocitrate dehydrogenase (IDH)wt and IDHmut HGGs display distinct alterations ribosome biology, in terms rRNA epitranscriptomics biogenesis, which could novel hallmarks can be exploited for management these...
Patients with transient ischaemic attack or stroke benefit from early diagnosis, specialist assessment, and treatment thrombolysis, unit care secondary prevention. The challenge such patients is to minimise delays ensure that appropriate, provide this the available resources.An ongoing prospective audit of a clinic (1 January 2005 30 September 2009), as part Scottish Stroke Care Audit, three month targeted immediate telephone access consultant February 2009 April 2009).Stroke services in...
Results The PIPs framework [1] uses a naive Bayesian method that combines the predictive capabilities of numerous features to calculate likelihood interaction between two proteins. Features considered by predictor include co-expression, orthology, domain co-occurrence, post translational modification and new feature analysing semantic similarity Gene Ontology terms. now includes modules make predictions based on topology predicted protein-protein network. We predict 318800 which 310732...
Abstract Background Alternative splicing can increase the diversity of gene functions by generating multiple isoforms with different sequences and functions. However, extent to which events have functional consequences remains unclear predicting impact on protein activity is limited gene-specific analysis. Results To accelerate identification functionally relevant alternative we created SAPFIR, a predictor features associated events. This webserver tool uses InterProScan predict such as...
Abstract Recent proteogenomic approaches have led to the discovery that regions of transcriptome previously annotated as non-coding (i.e. UTRs, open reading frames overlapping coding sequences in a different frame, and RNAs) frequently encode proteins (termed alternative proteins). This suggests identified protein-protein interaction networks are partially incomplete since not present conventional protein databases. Here we used resource OpenProt combined spectrum- peptide-centric analysis...
Background Protein-protein interactions carry out and regulate many fundamental cellular activities. The comprehensive study of such on a global scale leads to better understanding diverse processes the molecular mechanisms diseases when these are deregulated. Large experimental datasets human interactome becoming available [1] but their coverage is still very low. Bioinformatic predictors can fill this gap provide high quality interaction datasets.