Gremlin: An interactive visualization model for analyzing genomic rearrangements

IEEE Transactions on Visualization and Computer Graphics

Volumn 16, Issue 6, 2010, Pages 918-926

  O'Brien, Trevor ^a   Ritz, Anna ^a   Raphael, Benjamin ^a   Laidlaw, David ^a  

^a BROWN UNIVERSITY   (United States)

Author keywords

bioinformatics; Information visualization; insight based evaluation

Indexed keywords

CANCER GENOME; COMPARATIVE ANALYSIS; COMPLETE GENOMES; DATA INTEGRATION; DATA SETS; EVALUATION METHODOLOGIES; GENOME REARRANGEMENTS; GLOBAL CONTEXT; GLOBAL TRENDS; HUMAN CANCER; INFORMATION VISUALIZATION; INSIGHT-BASED EVALUATION; INTERACTIVE VISUALIZATIONS; LOCAL FEATURE; MULTISCALES; STRUCTURAL REARRANGEMENT; UNCERTAINTY VISUALIZATION; USER STUDY; USER STUDY EVALUATION; VISUAL ANALYSIS; VISUALIZATION MODELS;

BIOINFORMATICS; GENES; INFORMATION ANALYSIS; INFORMATION SYSTEMS; UNCERTAINTY ANALYSIS; VISUALIZATION;

DATA VISUALIZATION;

ARTICLE; BIOLOGICAL MODEL; COMPUTER GRAPHICS; COMPUTER INTERFACE; COMPUTER SIMULATION; GENE REARRANGEMENT; GENETIC DATABASE; HUMAN; HUMAN GENOME;

COMPUTER GRAPHICS; COMPUTER SIMULATION; DATABASES, GENETIC; GENE REARRANGEMENT; GENOME, HUMAN; HUMANS; MODELS, GENETIC; USER-COMPUTER INTERFACE;

EID: 78149247551     PISSN: 10772626     EISSN: None     Source Type: Journal    
DOI: 10.1109/TVCG.2010.163     Document Type: Article

References (14)

1. M. Bostock and J. Heer. Protovis: A graphical toolkit for visualization. IEEE Transactions on Visualization and Computer Graphics, 15(6):1121-1128, 2009.
2. K. Chen, J. W. Wallis, M. D. McLellan, D. E. Larson, J. M. Kalicki, C. S. Pohl, S. D. McGrath, M. C. Wendl, Q. Zhang, D. P. Locke, X. Shi, R. S. Fulton, T. J. Ley, R. K. Wilson, L. Ding, and E. R. Mardis. BreakDancer: an algorithm for high-resolution mapping of genomic structural variation. Nature Methods, 6(9):677-681, August 2009.
3. A. Esteban-Marcos, A. E. Darling, and M. A. Ragan. Seevolution. Bioinformatics, 25(7):960-961, 2009.
4. D. Karolchik, G. Bejerano, A. S. Hinrichs, R. M. Kuhn, W. Miller, K. R. Rosenbloom, A. S. Zweig, D. Haussler, and W. J. Kent. Comparative genomic analysis using the UCSC genome browser. 395, November 2007.
5. M. Krzywinski, J. Schein, A. a. Birol, J. Connors, R. Gascoyne, D. Horsman, S. J. Jones, and M. A. Marra. Circos: An information aesthetic for comparative genomics. Genome Research, 19(9):1639-1645, September 2009.
6. M. Meyer, T. Munzner, and H. Pfister. MizBee: A multiscale synteny browser. IEEE Transactions on Visualization and Computer Graphics, 15(6):897-904, 2009.
7. C. B. Nielsen, M. Cantor, I. Dubchak, D. Gordon, and T. Wang. Visualizing genomes: Techniques and challenges. Nature Methods, 7 (3 Suppl), March 2010.
8. C. North. Toward measuring visualization insight. IEEE Comput. Graph. Appl., 26(3):6-9, 2006.
9. E. D. Pleasance, R. K. Cheetham, P. J. Stephens, D. J. McBride, S. J. Humphray, C. D. Greenman, I. Varela, M.-L. Lin, G. R. OrdÃ?Ãez, G. R. Bignell, K. Ye, J. Alipaz, M. J. Bauer, D. Beare, A. Butler, R. J. Carter, L. Chen, A. J. Cox, S. Edkins, P. I. Kokko-Gonzales, N. A. Gormley, R. J. Grocock, C. D. Haudenschild, M. M. Hims, T. James, M. Jia, Z. Kingsbury, C. Leroy, J. Marshall, A. Menzies, L. J. Mudie, Z. Ning, T. Royce, O. B. Schulz-Trieglaff, A. Spiridou, L. A. Stebbings, L. Szajkowski, J. Teague, D. Williamson, L. Chin, M. T. Ross, P. J. Campbell, D. R. Bentley, P. A. Futreal, and M. R. Stratton. A comprehensive catalogue of somatic mutations from a human cancer genome. Nature, advance online publication, December 2009.
10. P. Saraiya, C. North, and K. Duca. An insight-based methodology for evaluating bioinformatics visualizations. IEEE Transactions on Visualization and Computer Graphics, 11(4):443-456, 2005.
11. S. Sindi, E. Helman, A. Bashir, and B. J. Raphael. A geometric approach for classification and comparison of structural variants. Bioinformatics (Oxford, England), 25(12):i222-230, June 2009.
12. A. Sinha and J. Meller. Cinteny: Flexible analysis and visualization of synteny and genome rearrangements in multiple organisms. BMC Bioinformatics, 8(1):82, 2007.
13. E. R. Tufte. The Visual Display of Quantitative Information. Graphics Press, Cheshire, Connecticut, 2001.
14. J. Yang, J. Wang, Z.-J. Yao, Q. Jin, Y. Shen, and R. Chen. Genome-Comp: A visualization tool for microbial genome comparison. Journal of Microbiological Methods, 54(3):423-426, 2003.