Dr Jane Loveland | Principal Computer Biologist

Loveland, Jane

I am part of the HAVANA management team and work on the manual annotation of human, mouse and zebrafish genomes, and latterly the swine and rat genomes.

I have a background in virus research, plant biochemisty and molecular biology.  Whilst working in the photosynthesis group at IACR Rothamsted I completed my PhD (Lancaster University), investigating the biochemistry and molecular biological aspects of inhibitors of Rubisco (CA1Pase). After leaving bench science I moved into bioinformatics, working as a computational molecular biology specialist for the BBSRC, providing teaching and support for molecular biology software packages for 8 BBSRC Institutes.

I joined the Sanger Institute in 2002 as part of the HAVANA group. As part of the HAVANA management team I have been involved in a number of major international collaborations, including generating the GENCODE annotation for the ENCODE project, collaborating with NCBI/UCSC/Ensembl/HGNC and MGI to produce the CCDS annotation and as a co-ordinator for the Immune Response Annotation Group for the swine community. Recently I have been leading a community annotation initiative with the rat genome database ( RGD). I have been the co-ordinator of the Open Door Workshops since 2002, and present human, mouse and zebrafish workshops around the world.

Publications

  • The pig X and Y Chromosomes: structure, sequence, and evolution.

    Skinner BM, Sargent CA, Churcher C, Hunt T, Herrero J et al.

    Genome research 2016;26;1;130-9

  • A 2.5-kilobase deletion containing a cluster of nine microRNAs in the latency-associated-transcript locus of the pseudorabies virus affects the host response of porcine trigeminal ganglia during established latency.

    Mahjoub N, Dhorne-Pollet S, Fuchs W, Endale Ahanda ML, Lange E et al.

    Journal of virology 2015;89;1;428-42

  • The Vertebrate Genome Annotation browser 10 years on.

    Harrow JL, Steward CA, Frankish A, Gilbert JG, Gonzalez JM et al.

    Nucleic acids research 2014;42;Database issue;D771-9

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

    Farrell CM, O'Leary NA, Harte RA, Loveland JE, Wilming LG et al.

    Nucleic acids research 2014;42;Database issue;D865-72

  • Structural and functional annotation of the porcine immunome.

    Dawson HD, Loveland JE, Pascal G, Gilbert JG, Uenishi H et al.

    BMC genomics 2013;14;332

  • Analyses of pig genomes provide insight into porcine demography and evolution.

    Groenen MA, Archibald AL, Uenishi H, Tuggle CK, Takeuchi Y et al.

    Nature 2012;491;7424;393-8

  • Community gene annotation in practice.

    Loveland JE, Gilbert JG, Griffiths E and Harrow JL

    Database : the journal of biological databases and curation 2012;2012;bas009

  • A 2.5-kilobase deletion containing a cluster of nine microRNAs in the latency-associated-transcript locus of the pseudorabies virus affects the host response of porcine trigeminal ganglia during established latency.

    Mahjoub N, Dhorne-Pollet S, Fuchs W, Endale Ahanda ML, Lange E et al.

    Journal of virology 2015;89;1;428-42

  • The Vertebrate Genome Annotation browser 10 years on.

    Harrow JL, Steward CA, Frankish A, Gilbert JG, Gonzalez JM et al.

    Nucleic acids research 2014;42;Database issue;D771-9

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

    Farrell CM, O'Leary NA, Harte RA, Loveland JE, Wilming LG et al.

    Nucleic acids research 2014;42;Database issue;D865-72

  • Best practices in bioinformatics training for life scientists.

    Via A, Blicher T, Bongcam-Rudloff E, Brazas MD, Brooksbank C et al.

    Briefings in bioinformatics 2013;14;5;528-37

  • iAnn: an event sharing platform for the life sciences.

    Jimenez RC, Albar JP, Bhak J, Blatter MC, Blicher T et al.

    Bioinformatics (Oxford, England) 2013;29;15;1919-21

  • Structural and functional annotation of the porcine immunome.

    Dawson HD, Loveland JE, Pascal G, Gilbert JG, Uenishi H et al.

    BMC genomics 2013;14;332

  • The zebrafish reference genome sequence and its relationship to the human genome.

    Howe K, Clark MD, Torroja CF, Torrance J, Berthelot C et al.

    Nature 2013;496;7446;498-503

  • Analyses of pig genomes provide insight into porcine demography and evolution.

    Groenen MA, Archibald AL, Uenishi H, Tuggle CK, Takeuchi Y et al.

    Nature 2012;491;7424;393-8

  • An integrated encyclopedia of DNA elements in the human genome.

    ENCODE Project Consortium

    Nature 2012;489;7414;57-74

  • Bioinformatics Training Network (BTN): a community resource for bioinformatics trainers.

    Schneider MV, Walter P, Blatter MC, Watson J, Brazas MD et al.

    Briefings in bioinformatics 2012;13;3;383-9

  • 2-Carboxy-D-arabinitol 1-phosphate (CA1P) phosphatase: evidence for a wider role in plant Rubisco regulation.

    Andralojc PJ, Madgwick PJ, Tao Y, Keys A, Ward JL et al.

    The Biochemical journal 2012;442;3;733-42

  • Community gene annotation in practice.

    Loveland JE, Gilbert JG, Griffiths E and Harrow JL

    Database : the journal of biological databases and curation 2012;2012;bas009

  • The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes.

    Pruitt KD, Harrow J, Harte RA, Wallin C, Diekhans M et al.

    Genome research 2009;19;7;1316-23

  • DNA sequence of human chromosome 17 and analysis of rearrangement in the human lineage.

    Zody MC, Garber M, Adams DJ, Sharpe T, Harrow J et al.

    Nature 2006;440;7087;1045-9

  • Genomic anatomy of the Tyrp1 (brown) deletion complex.

    Smyth IM, Wilming L, Lee AW, Taylor MS, Gautier P et al.

    Proceedings of the National Academy of Sciences of the United States of America 2006;103;10;3704-9

  • Evidence for widespread reticulate evolution within human duplicons.

    Jackson MS, Oliver K, Loveland J, Humphray S, Dunham I et al.

    American journal of human genetics 2005;77;5;824-40

  • VEGA, the genome browser with a difference.

    Loveland J

    Briefings in bioinformatics 2005;6;2;189-93

  • The DNA sequence of the human X chromosome.

    Ross MT, Grafham DV, Coffey AJ, Scherer S, McLay K et al.

    Nature 2005;434;7031;325-37

  • The DNA sequence and comparative analysis of human chromosome 10.

    Deloukas P, Earthrowl ME, Grafham DV, Rubenfield M, French L et al.

    Nature 2004;429;6990;375-81

  • DNA sequence and analysis of human chromosome 9.

    Humphray SJ, Oliver K, Hunt AR, Plumb RW, Loveland JE et al.

    Nature 2004;429;6990;369-74

  • The DNA sequence and analysis of human chromosome 13.

    Dunham A, Matthews LH, Burton J, Ashurst JL, Howe KL et al.

    Nature 2004;428;6982;522-8

  • The DNA sequence and analysis of human chromosome 6.

    Mungall AJ, Palmer SA, Sims SK, Edwards CA, Ashurst JL et al.

    Nature 2003;425;6960;805-11

Loveland, Jane