Peer Reviewed Articles and Book Chapters


ePlant
Jamie Waese, Jim Fan, Asher Pasha, Hans Yu, Geoffrey Fucile, Ruian Shi, Matthew Cumming, Lawrence A. Kelley, Michael J. Sternberg, Vivek Krishnakumar, Erik Ferlanti, Jason Miller, Chris Town, Wolfgang Stuerzlinger, Nicholas J. Provart. ePlant: Visualizing and Exploring Multiple Levels of Data for Hypothesis Generation in Plant Biology. Plant Cell. 2017 Aug; 29(8): 1806–1821.
https://doi.org/10.1105/tpc.17.00073



Topo-phylogeny
Jamie Waese, Nicholas J. Provart, David S. Guttman. Topo-phylogeny: Visualizing evolutionary relationships on a topographic landscape. PLOS ONE. Published: May 1, 2017
https://doi.org/10.1371/journal.pone.0175895



RSVP Visual Search Study
Jamie Waese, Wolfgang Stuerzlinger, Nicholas J. Provart (2016) An Evaluation of Interaction Methods for Controlling RSVP Displays in Visual Search Tasks. IEEE Proceedings of the International Symposium on Big Data Visual Analytics, November 22, 2016, Sydney, Australia.
http://ieeexplore.ieee.org/document/7787041/



Gene Slider
Jamie Waese, Asher Pasha, Tingting Wang, Anna van Weringh, David Guttman, Nicholas J. Provart. Gene Slider: sequence logo interactive data-visualization for education and research. Bioinformatics, Volume 32, Issue 23, 1 December 2016, Pages 3670–3672.
https://doi.org/10.1093/bioinformatics/btw525



Expression Angler
Ryan S. Austin, Shu Hiu, Jamie Waese, Asher Pasha, Nina Wang, Jim Fan, Curtis Foong, Robert Breit, Alan Moses, Nicholas J. Provart (2016), New BAR Tools for Mining Expression Data and Exploring Cis-Elements in Arabidopsis thaliana. Bioinformatics. The Plant Journal, 2016 Nov;88(3):490-504. Epub 2016 Oct 5. https://www.ncbi.nlm.nih.gov/pubmed/27401965



The Bio-Analytic Resource for Plant Biology
Jamie Waese and Nicholas J. Provart. The Bio-Analytic Resource for Plant Biology. Book chapter in: Methods in Molecular Biology - Plant Genomics Databases, Aalt-Jan van Dijk ed., Springer, 2017. ISBN 978-1-4939-6658-5
http://www.springer.com/gp/book/9781493966561



The Bio-Analytic Resource: Data visualization and analytic tools for multiple levels of plant biology
Jamie Waese and Nicholas J. Provart. The Bio-Analytic Resource: Data visualization and analytic tools for multiple levels of plant biology. Current Plant Biology Volumes 7–8, November 2016, Pages 2-5.
https://doi.org/10.1016/j.cpb.2016.12.001



50 Years of Arabidopsis Research - Citation Network
Nicholas Provart, Jose Alonso, Sarah Assmann, Dominique Bergmann, Siobhan Brady, Jelena Brkljacic, John Browse, Clint Chapple, Vincent Colot, Sean Cutler, Jeff Dangl, David Ehrhardt, Joanna Friesner, Wolf Frommer, Erich Grotewold, Elliot Meyerowitz, Jennifer Nemhauser, Magnus Nordborg, Craig Pikaard, John Shanklin, Chris Somerville, Shauna Somerville, Mark Stitt, Keiko Torii, Jamie Waese, Doris Wagner, and Peter McCourt. 50 Years of Arabidopsis Research: Highlights and Future Directions. New Phytologist, Octoboer 2015. Tansley Review. DOI: 10.1111/nph.13687
http://onlinelibrary.wiley.com/doi/10.1111/nph.13687/abstract



Light Stage
Paul E. Debevec, Andreas Wenger, Chris Tchou, Andrew Gardner, Jamie Waese, Tim Hawkins (2002). A lighting reproduction approach to live-action compositing. Proceeding SIGGRAPH '02 Proceedings of the 29th annual conference on Computer graphics and interactive techniques. Pages 547-556
https://dl.acm.org/citation.cfm?id=566614



High Dynamic Range Light Probe
Jamie Waese, Paul Debevec (2001) A Real Time High Dynamic Range Light Probe. SIGGRAPH 2001 Technical Sketches
http://vgl.ict.usc.edu/Research/rtlp/RealTimeLightProbe-sketch-2001.pdf




Conference Presentations


Designing & Building Data Visualization Tools for Large Biological Data Sets. SORA-TABA Workshop & DLSPH Biostatistics Research Day. Hospital for Sick Children (SickKids), Peter Gilgan Centre for Research and Learning Auditorium, May 5, 2017
http://sorataba.org/sorataba-workshop-2017/
Download Slides Here



ePlant: An agile approach to visualizing multiple levels of biological data. Jamie Waese, Asher Pasha, Nicholas Provart, International Conference of Arabidopsis Researchers at Paris, July 9, 2015.


Gene Slider: A new visualization tool for the AIP. Jamie Waese, Asher Pasha, Nicholas Provart. Arabidopsis Information Portal Developer Workshop at the Texas Advanced Computing Center, University of Texas at Austin, November 5, 2014.


ePlant: A user friendly data visualization tool for integrating and exploring multiple levels of biological data. Jamie Waese, Asher Pasha, Nicholas Provart, International Conference of Arabidopsis Researchers at Vancouver, June 29, 2014.


Data Sets, Webservices and Visualization Apps from the Bio-Analytic Resource for use in the AIP and other Cyberinfrastructure Assets. Nicholas Provart, Jamie Waese, Zhenming Yu, Asher Pasha, Rohan V. Patel, Sylva Donaldson, Adrian Platts, Mathieu Blanchette and Stephen I. Wright. International Arabidopsis Informatics Consortium session at the XXII Plant and Animal Genome conference in San Diego, January 13, 2014.


Building Data Visualization Tools For Large Biological Datasets, Toronto Bioinformatics Users Group (TorBUG), March 27, 2013





Refereed Posters


ePlant: A user friendly data visualization tool for integrating and exploring multiple levels of biological data. Jamie Waese, Asher Pasha, Nicholas Provart, International Conference of Arabidopsis Researchers 2014.


Gene Slider: A Sequence Logo Interactive data visualization tool for Education and Research, Jamie Waese, Asher Pasha, Nicholas Provart, BioVis 2013.




Publications & Conference Presentations

Here is a list of academic publications and conference presentations.


Category Research