Search Page

1

Cite

Share

The importance of identifying alternative splicing in vertebrate genome annotation.

Frankish A, Mudge JM, Thomas M, Harrow J. Frankish A, et al. Among authors: mudge jm. Database (Oxford). 2012 Mar 20;2012:bas014. doi: 10.1093/database/bas014. Print 2012. Database (Oxford). 2012. PMID: 22434846 Free PMC article.

Cite

Share

2

Cite

Share

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, Nicholson C, Robertson DH, Wilming LG, Harrow JL. Mudge JM, et al. Genome Biol. 2008;9(5):R91. doi: 10.1186/gb-2008-9-5-r91. Epub 2008 May 28. Genome Biol. 2008. PMID: 18507838 Free PMC article.

Cite

Share

3

Cite

Share

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

Mudge JM, Frankish A, Fernandez-Banet J, Alioto T, Derrien T, Howald C, Reymond A, Guigó R, Hubbard T, Harrow J. Mudge JM, et al. Mol Biol Evol. 2011 Oct;28(10):2949-59. doi: 10.1093/molbev/msr127. Epub 2011 May 6. Mol Biol Evol. 2011. PMID: 21551269 Free PMC article.

Cite

Share

4

Cite

Share

Functional transcriptomics in the post-ENCODE era.

Mudge JM, Frankish A, Harrow J. Mudge JM, et al. Genome Res. 2013 Dec;23(12):1961-73. doi: 10.1101/gr.161315.113. Epub 2013 Oct 30. Genome Res. 2013. PMID: 24172201 Free PMC article.

Cite

Share

5

Cite

Share

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

Farrell CM, O'Leary NA, Harte RA, Loveland JE, Wilming LG, Wallin C, Diekhans M, Barrell D, Searle SM, Aken B, Hiatt SM, Frankish A, Suner MM, Rajput B, Steward CA, Brown GR, Bennett R, Murphy M, Wu W, Kay MP, Hart J, Rajan J, Weber J, Snow C, Riddick LD, Hunt T, Webb D, Thomas M, Tamez P, Rangwala SH, McGarvey KM, Pujar S, Shkeda A, Mudge JM, Gonzalez JM, Gilbert JG, Trevanion SJ, Baertsch R, Harrow JL, Hubbard T, Ostell JM, Haussler D, Pruitt KD. Farrell CM, et al. Among authors: mudge jm. Nucleic Acids Res. 2014 Jan;42(Database issue):D865-72. doi: 10.1093/nar/gkt1059. Epub 2013 Nov 11. Nucleic Acids Res. 2014. PMID: 24217909 Free PMC article.

Cite

Share

6

Cite

Share

The Vertebrate Genome Annotation browser 10 years on.

Harrow JL, Steward CA, Frankish A, Gilbert JG, Gonzalez JM, Loveland JE, Mudge J, Sheppard D, Thomas M, Trevanion S, Wilming LG. Harrow JL, et al. Among authors: mudge j. Nucleic Acids Res. 2014 Jan;42(Database issue):D771-9. doi: 10.1093/nar/gkt1241. Epub 2013 Dec 6. Nucleic Acids Res. 2014. PMID: 24316575 Free PMC article.

Cite

Share

7

Cite

Share

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, Petryszak R, Mudge JM, Fonseca N, Brazma A, Guigo R, Harrow J. Frankish A, et al. Among authors: mudge jm. BMC Genomics. 2015;16 Suppl 8(Suppl 8):S2. doi: 10.1186/1471-2164-16-S8-S2. Epub 2015 Jun 18. BMC Genomics. 2015. PMID: 26110515 Free PMC article.

Cite

Share

8

Cite

Share

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

Mudge JM, Harrow J. Mudge JM, et al. Mamm Genome. 2015 Oct;26(9-10):366-78. doi: 10.1007/s00335-015-9583-x. Epub 2015 Jul 18. Mamm Genome. 2015. PMID: 26187010 Free PMC article.

Cite

Share

9

Cite

Share

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

Wright JC, Mudge J, Weisser H, Barzine MP, Gonzalez JM, Brazma A, Choudhary JS, Harrow J. Wright JC, et al. Among authors: mudge j. Nat Commun. 2016 Jun 2;7:11778. doi: 10.1038/ncomms11778. Nat Commun. 2016. PMID: 27250503 Free PMC article.

Cite

Share

10

Cite

Share

Extension of human lncRNA transcripts by RACE coupled with long-read high-throughput sequencing (RACE-Seq).

Lagarde J, Uszczynska-Ratajczak B, Santoyo-Lopez J, Gonzalez JM, Tapanari E, Mudge JM, Steward CA, Wilming L, Tanzer A, Howald C, Chrast J, Vela-Boza A, Rueda A, Lopez-Domingo FJ, Dopazo J, Reymond A, Guigó R, Harrow J. Lagarde J, et al. Among authors: mudge jm. Nat Commun. 2016 Aug 17;7:12339. doi: 10.1038/ncomms12339. Nat Commun. 2016. PMID: 27531712 Free PMC article.

Cite

Share