Jonathan Mudge Email & Phone Number

I am a genome scientist, specifically a Principle Computer Biologist and manager at the Wellcome Trust Sanger Institute. My field of work concerns the study of the human transcriptome, and I have made significant contributions to the GENCODE and ENCODE projects. My particular interest is the function and evolution of transcriptional complexity, and I am now developing these ideas in the field of variation analysis. Specifically, I wish to understand how variation interpretation can be confounded by the existence of transcriptional complexity. I am also working on the development of proteogenomics methodologies to aid gene discovery, as well as the integration of novel datasets such as RNAseq and Hi-C into annotation workflows.

Listed skills include Molecular Biology, Transcriptomics, Variation Analysis, Phylogenetics, and 27 others.

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  Principle Computer Biologist

  Wellcome Trust Sanger Institute

  Jul 2005 - Present - Cambridge

  The HAVANA team carry out the manual analysis and annotation of vertebrate genome sequences, and generate the GENCODE geneset for the human ENCODE project. I play a key role in both the planning and implementation of our scientific strategy, and manage 7 members of staff. My recent achievements include:- Developing pipelines for the integration of next generation datasets into gene annotation, including RNAseq, CAGE, ribosome profiling, mass spectrometry. - Working to improve… Show more The HAVANA team carry out the manual analysis and annotation of vertebrate genome sequences, and generate the GENCODE geneset for the human ENCODE project. I play a key role in both the planning and implementation of our scientific strategy, and manage 7 members of staff. My recent achievements include:- Developing pipelines for the integration of next generation datasets into gene annotation, including RNAseq, CAGE, ribosome profiling, mass spectrometry. - Working to improve the usablity of our resources, in particular to help distinguish and understand functional transcription events. - Promoting our resources at international meetings, presenting at conferences including ASHG, Genome Informatics, HGM, SMBE and AGBT. - Detailing our work in several high-impact publications, listed below. - Coordinating our annotation with the ongoing efforts of the Genome Reference Consortium. - Reaching out to other communities to show how we can aid them. In particular, I am now working with disease biologists and clinicians on the interpretation of variation linked to specific diseases. - Organising and running workshops, for example a 2 day meeting focusing on protegenomics. Publications as first author: Improving GENCODE reference gene annotation using a high-stringency proteogenomics workflow. Nat Commun. (2016)Creating reference gene annotation for the mouse C57BL6/J genome assembly. Mamm Genome. (2015)Functional transcriptomics in the post-ENCODE era. Genome Res. (2013)The origins, evolution, and functional potential of alternative splicing in vertebrates. Mol Biol Evol. (2011)Dynamic instability of the major urinary protein gene family revealed by genomic and phenotypic comparisons between C57 and 129 strain mice. Genome Biol. (2008)Evolutionary implications of pericentromeric gene expression in humans. Cytogenet Genome Res. (2005)Neocentromeres in 15q24-26 map to duplicons which flanked an ancestral centromere in 15q25. Genome Res. (2003) Show less