Publications by authors named "Jonathan Mudge"

34Publications

Ensembl 2021.

Nucleic Acids Res 2020 Nov 2. Epub 2020 Nov 2.

European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

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http://dx.doi.org/10.1093/nar/gkaa942DOI Listing
November 2020

Functional signatures of evolutionarily young CTCF binding sites.

BMC Biol 2020 09 23;18(1):132. Epub 2020 Sep 23.

European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.

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http://dx.doi.org/10.1186/s12915-020-00863-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7520972PMC
September 2020

Evidence for a novel overlapping coding sequence in POLG initiated at a CUG start codon.

BMC Genet 2020 03 6;21(1):25. Epub 2020 Mar 6.

Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.

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http://dx.doi.org/10.1186/s12863-020-0828-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7059407PMC
March 2020

Few SINEs of life: Alu elements have little evidence for biological relevance despite elevated translation.

NAR Genom Bioinform 2020 Mar 19;2(1):lqz023. Epub 2019 Dec 19.

Bioinformatics Unit, Spanish National Cancer Research Centre, 28029 Madrid, Spain.

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http://dx.doi.org/10.1093/nargab/lqz023DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6924539PMC
March 2020

Ensembl 2020.

Nucleic Acids Res 2020 01;48(D1):D682-D688

European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

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http://dx.doi.org/10.1093/nar/gkz966DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7145704PMC
January 2020

Molecular complexity of the major urinary protein system of the Norway rat, Rattus norvegicus.

Sci Rep 2019 07 24;9(1):10757. Epub 2019 Jul 24.

Centre for Proteome Research, Institute of Integrative Biology, University of Liverpool, Crown Street, L697ZB, Liverpool, United Kingdom.

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http://dx.doi.org/10.1038/s41598-019-46950-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6656916PMC
July 2019

The state of play in higher eukaryote gene annotation.

Nat Rev Genet 2016 12 24;17(12):758-772. Epub 2016 Oct 24.

Department of Computational Genomics, Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK.

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http://dx.doi.org/10.1038/nrg.2016.119DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5876476PMC
December 2016

Flexible Data Analysis Pipeline for High-Confidence Proteogenomics.

J Proteome Res 2016 12 10;15(12):4686-4695. Epub 2016 Nov 10.

School of Informatics, Communications, and Media, University of Applied Sciences Upper Austria , Hagenberg 4232, Austria.

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http://dx.doi.org/10.1021/acs.jproteome.6b00765DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5703597PMC
December 2016

Improving GENCODE reference gene annotation using a high-stringency proteogenomics workflow.

Nat Commun 2016 06 2;7:11778. Epub 2016 Jun 2.

Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK.

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http://dx.doi.org/10.1038/ncomms11778DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4895710PMC
June 2016

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

Mamm Genome 2015 Oct 18;26(9-10):366-78. Epub 2015 Jul 18.

Wellcome Trust Sanger Institute, Cambridge, UK.

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http://dx.doi.org/10.1007/s00335-015-9583-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4602055PMC
October 2015

The Vertebrate Genome Annotation browser 10 years on.

Nucleic Acids Res 2014 Jan 6;42(Database issue):D771-9. Epub 2013 Dec 6.

Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1HH, UK.

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http://dx.doi.org/10.1093/nar/gkt1241DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3964964PMC
January 2014

Current status and new features of the Consensus Coding Sequence database.

Nucleic Acids Res 2014 Jan 11;42(Database issue):D865-72. Epub 2013 Nov 11.

National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA, Center for Biomolecular Science and Engineering, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK and Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA.

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http://dx.doi.org/10.1093/nar/gkt1059DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3965069PMC
January 2014

Functional transcriptomics in the post-ENCODE era.

Genome Res 2013 Dec 30;23(12):1961-73. Epub 2013 Oct 30.

Department of Informatics, Wellcome Trust Sanger Institute, Hinxton CB10 1SA, United Kingdom.

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http://dx.doi.org/10.1101/gr.161315.113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3847767PMC
December 2013

The importance of identifying alternative splicing in vertebrate genome annotation.

Database (Oxford) 2012 20;2012:bas014. Epub 2012 Mar 20.

Human and Vertebrate Analysis and Annotation Team, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK.

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http://dx.doi.org/10.1093/database/bas014DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3308168PMC
June 2012