Dr Jonathan M. Mudge | Former Senior Computer Biologist at the Sanger Institute

This person is a member of Sanger Institute Alumni.

Mudge, Jonathan M.

My work concerns the description of gene and transcript structures, chiefly as part of the human GENCODE project. My particular focus is on furthering our understanding of transcriptional complexity and how this relates to human biology, especially through the intergation of next generation technology datasets.

I am a Team Leader within the HAVANA group.

My work seeks to address one of the most profound questions in modern genomics: which transcripts are functional, and how do they function? I use a wide variety of experimental datasets to provide insights into transcript functionality for the human and mouse GENCODE projects, from RNAseq to mass spectrometry. Furthermore, I am particuarly interested in the evolution of transcriptional complexity (having an educational background in evolutionary biology), and use comparative analysis as a powerful tool for the annotation of functionality. More recently I have become focused on medical genetics, asking how an understanding of this complexity can be used to gain insights into the nature and consequences of human variation. To this end, an important part of my work is to explore ways to increase the sophistication of our GENCODE genesets while simultaneously improving their usability. I am also committed to scientific communication, regularly presenting our work at international conferences, and helping to organise workshops and outreach events within the community.

Ultimately, my goal is to help bridge the information gap between our in silico geneset and the actual transcriptome as it exists in nature.


  • Functional transcriptomics in the post-ENCODE era.

    Mudge JM, Frankish A and Harrow J

    Genome research 2013;23;12;1961-73

  • Creating reference gene annotation for the mouse C57BL6/J genome assembly.

    Mudge JM and Harrow J

    Mammalian genome : official journal of the International Mammalian Genome Society 2015;26;9-10;366-78

  • The origins, evolution, and functional potential of alternative splicing in vertebrates.

    Mudge JM, Frankish A, Fernandez-Banet J, Alioto T, Derrien T et al.

    Molecular biology and evolution 2011;28;10;2949-59

  • Dynamic instability of the major urinary protein gene family revealed by genomic and phenotypic comparisons between C57 and 129 strain mice.

    Mudge JM, Armstrong SD, McLaren K, Beynon RJ, Hurst JL et al.

    Genome biology 2008;9;5;R91

  • Evolutionary implications of pericentromeric gene expression in humans.

    Mudge JM and Jackson MS

    Cytogenetic and genome research 2005;108;1-3;47-57

  • Neocentromeres in 15q24-26 map to duplicons which flanked an ancestral centromere in 15q25.

    Ventura M, Mudge JM, Palumbo V, Burn S, Blennow E et al.

    Genome research 2003;13;9;2059-68

  • Comparison of GENCODE and RefSeq gene annotation and the impact of reference geneset on variant effect prediction.

    Frankish A, Uszczynska B, Ritchie GR, Gonzalez JM, Pervouchine D et al.

    BMC genomics 2015;16 Suppl 8;S2

  • The importance of identifying alternative splicing in vertebrate genome annotation.

    Frankish A, Mudge JM, Thomas M and Harrow J

    Database : the journal of biological databases and curation 2012;2012;bas014

Mudge, Jonathan M.