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Dr. Jonathan M. Mudge

project leader, European Bioinformatics Institute, European Molecular Biology Laboratory


Dr Jonathan M. Mudge has 20 years of experience in human and mouse gene annotation, formerly based at the Wellcome Trust Sanger Institute and now the EMBL-EBI at the Hinxton Genome Campus, UK. He is a project leader in Ensembl-GENCODE, specialising in the discovery and annotation of protein-coding genes as part of the general ‘untangling’ of genomic, transcriptional and translational complexity.


In particular, he has in recent years been pioneering the integration of evolutionary methods and experimental analyses in gene annotation workflows. His collaborative work has found great success in identifying potential ‘missing’ proteins via the coordinated analysis of PhyloCSF signatures of protein sequence evolution, transcriptomics libraries, Ribo-seq / Ribosome profiling data, and MS peptide datasets. This has led into a deeper consideration of the role of translation in vertebrate genomes: not just to make ‘normal’ proteins, but also to act in gene regulation (e.g. via the translation of uORFs or via non-sense mediated decay), and with the potential to mark disease states via the aberrant expression of ‘non-normal’ proteins. Each of these roles or presentations are now seen as targets for GENCODE annotation.


Dr Mudge has recently published work investigating the genomic basis of epilepsy, including on the potential relevance of newly identified transcriptional features in key epilepsy genes and non-coding regions of the genome."

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