Joanna Jakubowska

Genome Visualisation and User Studies in Biologist-Computer Interaction

Joanna Jakubowska

o refereed publications:

VisGenome and Ensembl: Usability of Integrated Genome Maps – J. Jakubowska, E. Hunt, J. McClure, M. Chalmers, M. McBride, and A. F. Dominiczak – DILS’08 proceedings – the paper is nominated for the Best Paper award.

CartoonPlus: A New Scaling Algorithm for Genomics Data – J. Jakubowska, E. Hunt, and M. Chalmers – ICCS 2008 proceedings – LNCS, Springer.

VisGenome: visualization of single and comparative genome representations – J. Jakubowska, E. Hunt, M. Chalmers, M. McBride, and A. F. Dominiczak – 2007 – Bioinformatics – vol. 23, no. 19.

Defining Mapping Mashups with BioXMash – E. Hunt, J. Jakubowska, C. Boesinger, and M. Norrie – 2007 – Journal of Integrative Bioinformatics – 4(3):64.

Genome Visualisation – J. Jakubowska – 2006 – HCI Engage, Doctoral Consortium.

o other publications:

VisGenome with CartoonPlus: a New Scaling Algorithm for Genomics Data – Jakubowska, E. Hunt, and M. Chalmers – DILS’08, poster/demo.

CartoonPlus: A new Scaling Algorithm for Genomics Data – J. Jakubowska, E. Hunt, and M. Chalmers – Department of Computing Science at the University of Glasgow – 2007 – Tech. Report: TR-2007-259.

Usability of VisGenome and Ensembl – A User Study – J. Jakubowska, E. Hunt, and M. Chalmers – Department of Computing Science at the University of Glasgow – 2007 – Tech. Report: TR-2007-244.

Granularity of genomics data in genome visualisation – J. Jakubowska, E. Hunt, and M. Chalmers – Department of Computing Science at the University of Glasgow – 2006 – Tech. Report: TR-2006-221.

VisGenome – genome visualisation at different levels of detail – J. Jakubowska, E. Hunt, M. Chalmers, and A. F. Dominiczak – 3^rd International Workshop on Data Integration in the Life Sciences 2006 (DILS’06).

System level visualization of eQTLs and pQTLs – J. Jakubowska, E. Hunt, M. Chalmers, D. Leader, M. McBride, and A. F. Dominiczak – BioSysBio: Bioinformatics and Systems Biology Conference in Edinburgh 14-15 July 2005 – BMC Bioinformatics.

Migrating data integration agents for genomics – E. Hunt, K. Renaud, R. Sinnott, and J. Jakubowska – 2005 – Workshop on Ubiquitous Computing and e-Research in Edinburgh.

o presentations:

DILS’08 on 26^th June 2008 –

ICCS’08 on 24^th June 2008 –

SET meeting on 14^th of January 2008 –

GIST meeting on 31^st of May 2007 –

Napier University on 4^th of May 2007 –

BRC on 3^rd of November 2006 –

HCI Engage on 11^th of September 2006 –

GIST meeting on 1^st of June 2006 –

ETH Zürich on 3^rd of May 2006 –

SET meeting on 25^th of November 2005 –

o posters

o eQtls & pQTLs examples from the article:

Norbert Hubner, Caroline A. Wallace, Heike Zimdahl, Enrico Petretto, Herbert Schultz, Fiona Maciver, Michael Mueller, Oliver Hummel, Jan Monti, Vaclav Zidek, Alena Musilova, Vladimir Kren, Helen Causton, Laurence Game, Gabriele Born, Sabine Schmidt, Anita Müller, Stuart A. Cook, Theodore W. Kutz, John Whittaker, Michal Pravenec & Timothy J. Aitman,

“Integrated transcriptional profiling and linkage analysis for identification of genes underlying disease”,

Nature Genetics 37, 243 – 253 (2005)

presented in Der Browser in 4 versions:

1^st version (eQTLs and pQTLs are in different columns)

2^nd version (eQTLs and pQTLs are coloured and located in the same column)

3^rd version (video - with CGI script)

4^th version (video - with fisheye effect)

o previous work