Publications

• Michael L Sierk, Michael E Smoot, Ellen J Bass and William R Pearson. 2010 Improving pairwise sequence alignment accuracy using near-optimal protein sequence alignments. BMC Bioinformatcs 11(146).


• Robert K. Bradley, Adam Roberts, Michael Smoot, Sudeep Juvekar, Jaeyoung Do, Colin Dewey, Ian Holmes, Lior Pachter 2009 Fast Statistical Alignment. PLoS Computational Biology 5(5).


• Natalie Yeung, Melissa S. Cline, Allan Kuchinsky, Michael E. Smoot, and Gary D. Bader. 2008 UNIT 8.13 Exploring Biological Networks with Cytoscape Software, Current Protocols in Bioinformatics, John Wiley and Sons, Inc.


• Kalaev, M., Smoot, M., Ideker, T., Sharan, R. 2008 NetworkBLAST: comparative analysis of protein networks. Bioinformatics 24, 594-6


• Cline MS, Smoot M, Cerami E, Kuchinsky A, Landys N, Workman C, Christmas R, Avila-Campilo I, Creech M, Gross B, Hanspers K, Isserlin R, Kelley R, Killcoyne S, Lotia S, Maere S, Morris J, Ono K, Pavlovic V, Pico AR, Vailaya A, Wang PL, Adler A, Conklin BR, Hood L, Kuiper M, Sander C, Schmulevich I, Schwikowski B, Warner GJ, Ideker T, Bader GD. 2007 Integration of biological networks and gene expression data using Cytoscape. Nature Protocols. 2(10) 2366-82.


• Michael E. Smoot, Ellen J. Bass, Stephanie A. Guerlain, William R. Pearson. 2005. A System for Visualizing and Analyzing Near-optimal Protein Sequence Alignments. Information Visualization. 4, 224-237.


• Michael E. Smoot. 2005. Analyzing, Exploring, and Visualizing Near-optimal Protein Sequence Alignments. Dissertation. University of Virginia.


• Michael E. Smoot, Stephanie A. Guerlain, William R. Pearson. 2004. Visualization of near-optimal sequence alignments. Bioinformatics. 20(6),953-958.


• Stefan Kurtz, Adam Phillippy, Arthur L Delcher, Michael Smoot, Martin Shumway, Corina Antonescu, Steven L Salzberg. 2004 Versatile and open software for comparing large genomes. Genome Biology, 5:R12.


• Smoot, M.E.; Pearson, W.R.; Guerlain, S.A.; 2002 Near optimal solutions navigator 2002 IEEE International Conference on Systems, Man and Cybernetics, 6-9 Oct. 2002, vol.5.