Simon Potter
A5075070129- Genetic Associations and Epidemiology
- Genomics and Phylogenetic Studies
- RNA and protein synthesis mechanisms
- Advanced Proteomics Techniques and Applications
- Epigenetics and DNA Methylation
- Bioinformatics and Genomic Networks
- Parkinson's Disease Mechanisms and Treatments
- Genomic variations and chromosomal abnormalities
- Helicobacter pylori-related gastroenterology studies
- RNA modifications and cancer
- Microbial Community Ecology and Physiology
- Neurological diseases and metabolism
- Chromosomal and Genetic Variations
- Systemic Lupus Erythematosus Research
- Cytokine Signaling Pathways and Interactions
- Enzyme Structure and Function
- Autism Spectrum Disorder Research
- Genetics, Bioinformatics, and Biomedical Research
- Hemoglobin structure and function
- Diet, Metabolism, and Disease
- Protein Structure and Dynamics
- Aortic aneurysm repair treatments
- Spondyloarthritis Studies and Treatments
- Connective tissue disorders research
- Genetic Mapping and Diversity in Plants and Animals
Wellcome Sanger Institute
2010-2022
Wellcome Trust
2015-2019
European Bioinformatics Institute
2015-2019
University of Duisburg-Essen
2016
Potters Bar Community Hospital
2013-2016
Royal Brisbane and Women's Hospital
2016
Institut du Cerveau
2013
Pitié-Salpêtrière Hospital
2013
Sorbonne Université
2013
St Thomas' Hospital
2010
In the last two years Pfam database (http://pfam.xfam.org) has undergone a substantial reorganisation to reduce effort involved in making release, thereby permitting more frequent releases. Arguably most significant of these changes is that now primarily based on UniProtKB reference proteomes, with counts matched sequences and species reported website restricted this smaller set. Building families proteomes brings greater stability, which decreases amount manual curation required maintain...
The last few years have witnessed significant changes in Pfam (https://pfam.xfam.org). number of families has grown substantially to a total 17,929 release 32.0. New additions been coupled with efforts improve existing families, including refinement domain boundaries, their classification into clans, as well functional annotation. We recently began collaborate the RepeatsDB resource definition tandem repeat within Pfam. carried out comparison structural database, namely Evolutionary...
The EMBL-EBI provides free access to popular bioinformatics sequence analysis applications as well a full-featured text search engine with powerful cross-referencing and data retrieval capabilities. Access these services is provided via user-friendly web interfaces established RESTful SOAP Web Services APIs (https://www.ebi.ac.uk/seqdb/confluence/display/JDSAT/EMBL-EBI+Web+Services+APIs+-+Data+Retrieval). Both systems have been developed the same core principles that allow them integrate an...
The HMMER webserver [http://www.ebi.ac.uk/Tools/hmmer] is a free-to-use service which provides fast searches against widely used sequence databases and profile hidden Markov model (HMM) libraries using the software suite (http://hmmer.org). results of search may be summarized in number ways, allowing users to view filter significant hits by domain architecture or taxonomy. For large scale usage, we provide an application programmatic interface (API) has been expanded scope, such that all...
The Ensembl (http://www.ensembl.org/) database project provides a bioinformatics framework to organise biology around the sequences of large genomes. It is comprehensive source stable automatic annotation human genome sequence, with confirmed gene predictions that have been integrated external data sources, and available as either an interactive web site or flat files. also open software engineering develop portable system able handle very genomes associated requirements from sequence...
InterPro (http://www.ebi.ac.uk/interpro/) is a freely available database used to classify protein sequences into families and predict the presence of important domains sites. InterProScan underlying software that allows both nucleic acid be searched against InterPro's predictive models, which are provided by its member databases. Here, we report recent developments with associated software, including addition two new databases (SFLD CDD), functionality include residue-level annotation...
The InterPro database (http://www.ebi.ac.uk/interpro/) classifies protein sequences into families and predicts the presence of functionally important domains sites. Here, we report recent developments with (version 70.0) its associated software, including an 18% growth in size terms on new entries, updates to content, inclusion additional entry type, refined modelling discontinuous domains, development a programmatic interface website. These extend enrich information provided by InterPro,...
MGnify (http://www.ebi.ac.uk/metagenomics) provides a free to use platform for the assembly, analysis and archiving of microbiome data derived from sequencing microbial populations that are present in particular environments. Over past 2 years, (formerly EBI Metagenomics) has more than doubled number publicly available analysed datasets held within resource. Recently, an updated approach been unveiled (version 5.0), replacing previous single pipeline with multiple pipelines tailored...
Genome-wide association studies have identified hundreds of loci for type 2 diabetes, coronary artery disease and myocardial infarction, as well related traits such body mass index, glucose insulin levels, lipid blood pressure. These also pointed to thousands with promising but not yet compelling evidence. To establish at additional characterize the genome-wide significant by fine-mapping, we designed "Metabochip," a custom genotyping array that assays nearly 200,000 SNP markers. Here,...
Ensembl Genomes (http://www.ensemblgenomes.org) is an integrating resource for genome-scale data from non-vertebrate species, complementing the resources vertebrate genomics developed in project (http://www.ensembl.org). Together, two provide a consistent set of programmatic and interactive interfaces to rich range including genome sequence, gene models, transcript genetic variation, comparative analysis. This paper provides update previous publications about resource, with focus on recent...
While there have been studies exploring regulatory variation in one or more tissues, the complexity of tissue-specificity multiple primary tissues is not yet well understood. We explore depth role cis-regulatory three human tissues: lymphoblastoid cell lines (LCL), skin, and fat. The samples (156 LCL, 160 166 fat) were derived simultaneously from a subset well-phenotyped healthy female twins MuTHER resource. discover an abundance cis-eQTLs each tissue similar to previous estimates (858 4.7%...
Mutations in the glucocerebrosidase gene (GBA), which cause Gaucher disease, are also potent risk factors for Parkinson's disease. We examined whether a genetic burden of variants other lysosomal storage disorder genes is more broadly associated with disease susceptibility. The sequence kernel association test was used to interrogate variant among 54 genes, leveraging whole exome sequencing data from 1156 cases and 1679 control subjects. discovered significant rare, likely damaging risk....
Epigenetic modifications such as DNA methylation play a key role in gene regulation and disease susceptibility. However, little is known about the genome-wide frequency, localization, function of variation how it regulated by genetic environmental factors. We utilized Multiple Tissue Human Expression Resource (MuTHER) generated Illumina 450K adipose methylome data from 648 twins. found that individual CpGs had low variance variability was suppressed promoters. noted highly heritable...